From 01c027b51209ffd59653c632b1aeefa002eca73c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andreas=20S=C3=B8gaard?= Date: Mon, 13 May 2024 06:01:45 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20Aske-Ros?= =?UTF-8?q?ted/graphnet@6c8878667d833ad386ca756ebd4a9d5b12987e57=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .buildinfo | 2 +- _images/dataconverter.svg | 74 + _images/datarepresentation.svg | 280 ++++ _images/favicon.svg | 118 ++ _images/model.svg | 38 + _images/standardmodel.svg | 148 ++ _modules/graphnet/data/constants.html | 53 +- .../graphnet/data/curated_datamodule.html | 684 ++++++++ _modules/graphnet/data/dataclasses.html | 37 +- _modules/graphnet/data/dataconverter.html | 96 +- _modules/graphnet/data/dataloader.html | 39 +- _modules/graphnet/data/datamodule.html | 151 +- _modules/graphnet/data/dataset/dataset.html | 124 +- .../data/dataset/parquet/parquet_dataset.html | 512 ++++-- .../data/dataset/sqlite/sqlite_dataset.html | 59 +- .../data/extractors/combine_extractors.html | 428 +++++ .../graphnet/data/extractors/extractor.html | 42 +- .../data/extractors/icecube/i3extractor.html | 37 +- .../icecube/i3featureextractor.html | 37 +- .../icecube/i3genericextractor.html | 37 +- .../icecube/i3hybridrecoextractor.html | 37 +- .../icecube/i3ntmuonlabelsextractor.html | 37 +- .../icecube/i3particleextractor.html | 37 +- .../extractors/icecube/i3pisaextractor.html | 37 +- .../extractors/icecube/i3quesoextractor.html | 37 +- .../extractors/icecube/i3retroextractor.html | 37 +- .../icecube/i3splinempeextractor.html | 37 +- .../extractors/icecube/i3truthextractor.html | 37 +- .../extractors/icecube/i3tumextractor.html | 37 +- .../icecube/utilities/collections.html | 37 +- .../extractors/icecube/utilities/frames.html | 37 +- .../icecube/utilities/i3_filters.html | 37 +- .../extractors/icecube/utilities/types.html | 37 +- .../internal/parquet_extractor.html | 424 +++++ .../data/extractors/liquido/h5_extractor.html | 488 ++++++ .../prometheus/prometheus_extractor.html | 488 ++++++ .../data/parquet/deprecated_methods.html | 37 +- _modules/graphnet/data/pipeline.html | 595 ------- .../data/pre_configured/dataconverters.html | 79 +- .../data/readers/graphnet_file_reader.html | 79 +- _modules/graphnet/data/readers/i3reader.html | 51 +- .../data/readers/internal_parquet_reader.html | 448 ++++++ .../graphnet/data/readers/liquido_reader.html | 442 ++++++ .../data/readers/prometheus_reader.html | 456 ++++++ .../data/sqlite/deprecated_methods.html | 37 +- .../data/utilities/parquet_to_sqlite.html | 549 ------- _modules/graphnet/data/utilities/random.html | 37 +- .../data/utilities/sqlite_utilities.html | 45 +- .../utilities/string_selection_resolver.html | 37 +- .../data/writers/graphnet_writer.html | 37 +- .../graphnet/data/writers/parquet_writer.html | 265 +++- .../graphnet/data/writers/sqlite_writer.html | 50 +- .../datasets/prometheus_datasets.html | 543 +++++++ _modules/graphnet/datasets/test_dataset.html | 454 ++++++ _modules/graphnet/deployment/deployer.html | 37 +- .../deployment/deployment_module.html | 37 +- .../deployment/icecube/cleaning_module.html | 37 +- .../deployment/icecube/inference_module.html | 37 +- _modules/graphnet/exceptions/exceptions.html | 395 +++++ _modules/graphnet/models/coarsening.html | 37 +- .../graphnet/models/components/embedding.html | 107 +- .../graphnet/models/components/layers.html | 37 +- _modules/graphnet/models/components/pool.html | 37 +- .../graphnet/models/detector/detector.html | 37 +- .../graphnet/models/detector/icecube.html | 44 +- .../graphnet/models/detector/liquido.html | 428 +++++ .../graphnet/models/detector/prometheus.html | 437 ++++- _modules/graphnet/models/gnn/RNN_tito.html | 37 +- _modules/graphnet/models/gnn/convnet.html | 37 +- _modules/graphnet/models/gnn/dynedge.html | 47 +- .../graphnet/models/gnn/dynedge_jinst.html | 37 +- .../models/gnn/dynedge_kaggle_tito.html | 37 +- _modules/graphnet/models/gnn/gnn.html | 37 +- _modules/graphnet/models/gnn/icemix.html | 55 +- .../graphnet/models/graphs/edges/edges.html | 37 +- .../models/graphs/edges/minkowski.html | 37 +- .../models/graphs/graph_definition.html | 37 +- _modules/graphnet/models/graphs/graphs.html | 37 +- .../graphnet/models/graphs/nodes/nodes.html | 136 +- _modules/graphnet/models/graphs/utils.html | 54 +- _modules/graphnet/models/model.html | 37 +- _modules/graphnet/models/rnn/node_rnn.html | 37 +- .../models/standard_averaged_model.html | 37 +- _modules/graphnet/models/standard_model.html | 37 +- .../graphnet/models/task/classification.html | 37 +- .../graphnet/models/task/reconstruction.html | 37 +- _modules/graphnet/models/task/task.html | 37 +- .../graphnet/models/transformer/iseecube.html | 495 ++++++ _modules/graphnet/models/utils.html | 37 +- _modules/graphnet/pisa/fitting.html | 1183 -------------- _modules/graphnet/pisa/plotting.html | 542 ------- _modules/graphnet/training/callbacks.html | 37 +- _modules/graphnet/training/labels.html | 76 +- .../graphnet/training/loss_functions.html | 37 +- _modules/graphnet/training/utils.html | 43 +- .../graphnet/training/weight_fitting.html | 37 +- _modules/graphnet/utilities/argparse.html | 37 +- .../utilities/config/base_config.html | 37 +- .../utilities/config/configurable.html | 37 +- .../utilities/config/dataset_config.html | 37 +- .../utilities/config/model_config.html | 37 +- .../graphnet/utilities/config/parsing.html | 37 +- .../utilities/config/training_config.html | 37 +- .../graphnet/utilities/deprecation_tools.html | 37 +- _modules/graphnet/utilities/filesys.html | 40 +- _modules/graphnet/utilities/imports.html | 53 +- _modules/graphnet/utilities/logging.html | 37 +- _modules/graphnet/utilities/maths.html | 37 +- _modules/index.html | 54 +- _sources/about.md.txt | 48 - _sources/about/about.rst.txt | 35 + .../graphnet.data.curated_datamodule.rst.txt | 8 + ...data.extractors.combine_extractors.rst.txt | 8 + ...ractors.internal.parquet_extractor.rst.txt | 8 + .../graphnet.data.extractors.internal.rst.txt | 36 + ...ta.extractors.liquido.h5_extractor.rst.txt | 8 + .../graphnet.data.extractors.liquido.rst.txt | 36 + ...rs.prometheus.prometheus_extractor.rst.txt | 8 + ...raphnet.data.extractors.prometheus.rst.txt | 36 + _sources/api/graphnet.data.extractors.rst.txt | 4 + ...ta.readers.internal_parquet_reader.rst.txt | 8 + ...aphnet.data.readers.liquido_reader.rst.txt | 8 + ...net.data.readers.prometheus_reader.rst.txt | 8 + _sources/api/graphnet.data.readers.rst.txt | 3 + _sources/api/graphnet.data.rst.txt | 2 +- ...phnet.datasets.prometheus_datasets.rst.txt | 8 + _sources/api/graphnet.datasets.rst.txt | 37 + .../graphnet.datasets.test_dataset.rst.txt | 8 + .../graphnet.exceptions.exceptions.rst.txt | 8 + ...sa.rst.txt => graphnet.exceptions.rst.txt} | 9 +- ... graphnet.models.detector.liquido.rst.txt} | 4 +- _sources/api/graphnet.models.detector.rst.txt | 1 + _sources/api/graphnet.models.rst.txt | 1 + ...phnet.models.transformer.iseecube.rst.txt} | 4 +- .../api/graphnet.models.transformer.rst.txt | 36 + _sources/api/graphnet.pisa.plotting.rst.txt | 8 - _sources/api/graphnet.rst.txt | 3 +- _sources/contribute.md.txt | 37 - _sources/contribute/contribute.rst.txt | 54 + .../data_conversion/data_conversion.rst.txt | 278 ++++ _sources/datasets/datasets.rst.txt | 368 +++++ .../getting_started/getting_started.md.txt | 695 ++++++++ _sources/index.rst.txt | 20 +- _sources/install.md.txt | 82 - _sources/installation/install.rst.txt | 46 + _sources/integration/integration.rst.txt | 261 +++ _sources/intro/intro.rst.txt | 40 + _sources/models/models.rst.txt | 515 ++++++ _sources/substitutions.rst.txt | 15 + _static/basic.css | 2 +- _static/doctools.js | 2 +- _static/language_data.js | 4 +- _static/searchtools.js | 165 +- about/about.html | 414 +++++ api/graphnet.constants.html | 48 +- api/graphnet.data.constants.html | 96 +- api/graphnet.data.curated_datamodule.html | 947 +++++++++++ api/graphnet.data.dataclasses.html | 72 +- api/graphnet.data.dataconverter.html | 71 +- api/graphnet.data.dataloader.html | 78 +- api/graphnet.data.datamodule.html | 77 +- api/graphnet.data.dataset.dataset.html | 91 +- api/graphnet.data.dataset.html | 55 +- api/graphnet.data.dataset.parquet.html | 54 +- ....data.dataset.parquet.parquet_dataset.html | 114 +- api/graphnet.data.dataset.sqlite.html | 54 +- ...et.data.dataset.sqlite.sqlite_dataset.html | 66 +- ...t.data.extractors.combine_extractors.html} | 202 ++- api/graphnet.data.extractors.extractor.html | 88 +- api/graphnet.data.extractors.html | 98 +- api/graphnet.data.extractors.icecube.html | 82 +- ...t.data.extractors.icecube.i3extractor.html | 82 +- ...extractors.icecube.i3featureextractor.html | 82 +- ...extractors.icecube.i3genericextractor.html | 84 +- ...ractors.icecube.i3hybridrecoextractor.html | 84 +- ...ctors.icecube.i3ntmuonlabelsextractor.html | 86 +- ...xtractors.icecube.i3particleextractor.html | 84 +- ...ta.extractors.icecube.i3pisaextractor.html | 84 +- ...a.extractors.icecube.i3quesoextractor.html | 86 +- ...a.extractors.icecube.i3retroextractor.html | 84 +- ...tractors.icecube.i3splinempeextractor.html | 84 +- ...a.extractors.icecube.i3truthextractor.html | 82 +- ...ata.extractors.icecube.i3tumextractor.html | 90 +- ...ractors.icecube.utilities.collections.html | 86 +- ...a.extractors.icecube.utilities.frames.html | 94 +- ...net.data.extractors.icecube.utilities.html | 82 +- ...tractors.icecube.utilities.i3_filters.html | 106 +- ...ta.extractors.icecube.utilities.types.html | 104 +- api/graphnet.data.extractors.internal.html | 640 ++++++++ ...extractors.internal.parquet_extractor.html | 673 ++++++++ ....data.extractors.liquido.h5_extractor.html | 713 +++++++++ api/graphnet.data.extractors.liquido.html | 642 ++++++++ api/graphnet.data.extractors.prometheus.html | 642 ++++++++ ...ctors.prometheus.prometheus_extractor.html | 724 +++++++++ api/graphnet.data.html | 70 +- ...phnet.data.parquet.deprecated_methods.html | 54 +- api/graphnet.data.parquet.html | 54 +- ...et.data.pre_configured.dataconverters.html | 88 +- api/graphnet.data.pre_configured.html | 55 +- ...net.data.readers.graphnet_file_reader.html | 87 +- api/graphnet.data.readers.html | 87 +- api/graphnet.data.readers.i3reader.html | 81 +- ...data.readers.internal_parquet_reader.html} | 310 ++-- api/graphnet.data.readers.liquido_reader.html | 687 ++++++++ ...aphnet.data.readers.prometheus_reader.html | 687 ++++++++ ...aphnet.data.sqlite.deprecated_methods.html | 54 +- api/graphnet.data.sqlite.html | 60 +- api/graphnet.data.utilities.html | 59 +- ...hnet.data.utilities.parquet_to_sqlite.html | 125 +- api/graphnet.data.utilities.random.html | 56 +- ...phnet.data.utilities.sqlite_utilities.html | 78 +- ...a.utilities.string_selection_resolver.html | 64 +- ...graphnet.data.writers.graphnet_writer.html | 64 +- api/graphnet.data.writers.html | 54 +- api/graphnet.data.writers.parquet_writer.html | 91 +- api/graphnet.data.writers.sqlite_writer.html | 62 +- api/graphnet.datasets.html | 512 ++++++ ...graphnet.datasets.prometheus_datasets.html | 666 ++++++++ api/graphnet.datasets.test_dataset.html | 547 +++++++ api/graphnet.deployment.deployer.html | 48 +- ...graphnet.deployment.deployment_module.html | 54 +- api/graphnet.deployment.html | 54 +- ...ployment.i3modules.deprecated_methods.html | 48 +- api/graphnet.deployment.i3modules.html | 48 +- ...et.deployment.icecube.cleaning_module.html | 48 +- api/graphnet.deployment.icecube.html | 48 +- ...raphnet.deployment.icecube.i3deployer.html | 48 +- ...t.deployment.icecube.inference_module.html | 48 +- api/graphnet.exceptions.exceptions.html | 517 ++++++ ...net.pisa.html => graphnet.exceptions.html} | 89 +- api/graphnet.html | 72 +- api/graphnet.models.coarsening.html | 93 +- api/graphnet.models.components.embedding.html | 86 +- api/graphnet.models.components.html | 66 +- api/graphnet.models.components.layers.html | 115 +- api/graphnet.models.components.pool.html | 93 +- api/graphnet.models.detector.detector.html | 80 +- api/graphnet.models.detector.html | 87 +- api/graphnet.models.detector.icecube.html | 154 +- api/graphnet.models.detector.liquido.html | 720 +++++++++ api/graphnet.models.detector.prometheus.html | 1412 ++++++++++++++++- api/graphnet.models.gnn.RNN_tito.html | 71 +- api/graphnet.models.gnn.convnet.html | 71 +- api/graphnet.models.gnn.dynedge.html | 73 +- api/graphnet.models.gnn.dynedge_jinst.html | 71 +- ...aphnet.models.gnn.dynedge_kaggle_tito.html | 71 +- api/graphnet.models.gnn.gnn.html | 71 +- api/graphnet.models.gnn.html | 65 +- api/graphnet.models.gnn.icemix.html | 75 +- api/graphnet.models.graphs.edges.edges.html | 93 +- api/graphnet.models.graphs.edges.html | 65 +- ...raphnet.models.graphs.edges.minkowski.html | 69 +- ...aphnet.models.graphs.graph_definition.html | 69 +- api/graphnet.models.graphs.graphs.html | 75 +- api/graphnet.models.graphs.html | 65 +- api/graphnet.models.graphs.nodes.html | 65 +- api/graphnet.models.graphs.nodes.nodes.html | 97 +- api/graphnet.models.graphs.utils.html | 87 +- api/graphnet.models.html | 77 +- api/graphnet.models.model.html | 87 +- api/graphnet.models.rnn.html | 65 +- api/graphnet.models.rnn.node_rnn.html | 71 +- ...aphnet.models.standard_averaged_model.html | 89 +- api/graphnet.models.standard_model.html | 131 +- api/graphnet.models.task.classification.html | 77 +- api/graphnet.models.task.html | 65 +- api/graphnet.models.task.reconstruction.html | 117 +- api/graphnet.models.task.task.html | 105 +- api/graphnet.models.transformer.html | 583 +++++++ api/graphnet.models.transformer.iseecube.html | 654 ++++++++ api/graphnet.models.utils.html | 79 +- api/graphnet.pisa.fitting.html | 673 -------- api/graphnet.training.callbacks.html | 64 +- api/graphnet.training.html | 55 +- api/graphnet.training.labels.html | 81 +- api/graphnet.training.loss_functions.html | 114 +- api/graphnet.training.utils.html | 150 +- api/graphnet.training.weight_fitting.html | 66 +- api/graphnet.utilities.argparse.html | 60 +- ...graphnet.utilities.config.base_config.html | 58 +- ...raphnet.utilities.config.configurable.html | 52 +- ...phnet.utilities.config.dataset_config.html | 84 +- api/graphnet.utilities.config.html | 48 +- ...raphnet.utilities.config.model_config.html | 54 +- api/graphnet.utilities.config.parsing.html | 64 +- ...hnet.utilities.config.training_config.html | 56 +- api/graphnet.utilities.decorators.html | 48 +- api/graphnet.utilities.deprecation_tools.html | 48 +- api/graphnet.utilities.filesys.html | 56 +- api/graphnet.utilities.html | 49 +- api/graphnet.utilities.imports.html | 71 +- api/graphnet.utilities.logging.html | 94 +- api/graphnet.utilities.maths.html | 50 +- api/modules.html | 41 +- contribute.html => contribute/contribute.html | 148 +- data_conversion/data_conversion.html | 690 ++++++++ datasets/datasets.html | 826 ++++++++++ genindex.html | 534 ++++++- getting_started/getting_started.html | 1091 +++++++++++++ index.html | 107 +- install.html | 518 ------ installation/install.html | 625 ++++++++ integration/integration.html | 705 ++++++++ intro/intro.html | 406 +++++ models/models.html | 1018 ++++++++++++ objects.inv | Bin 7789 -> 8955 bytes py-modindex.html | 134 +- search.html | 42 +- searchindex.js | 2 +- sitemap.xml | 2 +- about.html => substitutions.html | 92 +- 311 files changed, 39665 insertions(+), 7557 deletions(-) create mode 100644 _images/dataconverter.svg create mode 100644 _images/datarepresentation.svg create mode 100644 _images/favicon.svg create mode 100644 _images/model.svg create mode 100644 _images/standardmodel.svg create mode 100644 _modules/graphnet/data/curated_datamodule.html create mode 100644 _modules/graphnet/data/extractors/combine_extractors.html create mode 100644 _modules/graphnet/data/extractors/internal/parquet_extractor.html create mode 100644 _modules/graphnet/data/extractors/liquido/h5_extractor.html create mode 100644 _modules/graphnet/data/extractors/prometheus/prometheus_extractor.html delete mode 100644 _modules/graphnet/data/pipeline.html create mode 100644 _modules/graphnet/data/readers/internal_parquet_reader.html create mode 100644 _modules/graphnet/data/readers/liquido_reader.html create mode 100644 _modules/graphnet/data/readers/prometheus_reader.html delete mode 100644 _modules/graphnet/data/utilities/parquet_to_sqlite.html create mode 100644 _modules/graphnet/datasets/prometheus_datasets.html create mode 100644 _modules/graphnet/datasets/test_dataset.html create mode 100644 _modules/graphnet/exceptions/exceptions.html create mode 100644 _modules/graphnet/models/detector/liquido.html create mode 100644 _modules/graphnet/models/transformer/iseecube.html delete mode 100644 _modules/graphnet/pisa/fitting.html delete mode 100644 _modules/graphnet/pisa/plotting.html delete mode 100644 _sources/about.md.txt create mode 100644 _sources/about/about.rst.txt create mode 100644 _sources/api/graphnet.data.curated_datamodule.rst.txt create mode 100644 _sources/api/graphnet.data.extractors.combine_extractors.rst.txt create mode 100644 _sources/api/graphnet.data.extractors.internal.parquet_extractor.rst.txt create mode 100644 _sources/api/graphnet.data.extractors.internal.rst.txt create mode 100644 _sources/api/graphnet.data.extractors.liquido.h5_extractor.rst.txt create mode 100644 _sources/api/graphnet.data.extractors.liquido.rst.txt create mode 100644 _sources/api/graphnet.data.extractors.prometheus.prometheus_extractor.rst.txt create mode 100644 _sources/api/graphnet.data.extractors.prometheus.rst.txt create mode 100644 _sources/api/graphnet.data.readers.internal_parquet_reader.rst.txt create mode 100644 _sources/api/graphnet.data.readers.liquido_reader.rst.txt create mode 100644 _sources/api/graphnet.data.readers.prometheus_reader.rst.txt create mode 100644 _sources/api/graphnet.datasets.prometheus_datasets.rst.txt create mode 100644 _sources/api/graphnet.datasets.rst.txt create mode 100644 _sources/api/graphnet.datasets.test_dataset.rst.txt create mode 100644 _sources/api/graphnet.exceptions.exceptions.rst.txt rename _sources/api/{graphnet.pisa.rst.txt => graphnet.exceptions.rst.txt} (74%) rename _sources/api/{graphnet.pisa.fitting.rst.txt => graphnet.models.detector.liquido.rst.txt} (52%) rename _sources/api/{graphnet.data.pipeline.rst.txt => graphnet.models.transformer.iseecube.rst.txt} (51%) create mode 100644 _sources/api/graphnet.models.transformer.rst.txt delete mode 100644 _sources/api/graphnet.pisa.plotting.rst.txt delete mode 100644 _sources/contribute.md.txt create mode 100644 _sources/contribute/contribute.rst.txt create mode 100644 _sources/data_conversion/data_conversion.rst.txt create mode 100644 _sources/datasets/datasets.rst.txt create mode 100644 _sources/getting_started/getting_started.md.txt delete mode 100644 _sources/install.md.txt create mode 100644 _sources/installation/install.rst.txt create mode 100644 _sources/integration/integration.rst.txt create mode 100644 _sources/intro/intro.rst.txt create mode 100644 _sources/models/models.rst.txt create mode 100644 _sources/substitutions.rst.txt create mode 100644 about/about.html create mode 100644 api/graphnet.data.curated_datamodule.html rename api/{graphnet.data.pipeline.html => graphnet.data.extractors.combine_extractors.html} (70%) create mode 100644 api/graphnet.data.extractors.internal.html create mode 100644 api/graphnet.data.extractors.internal.parquet_extractor.html create mode 100644 api/graphnet.data.extractors.liquido.h5_extractor.html create mode 100644 api/graphnet.data.extractors.liquido.html create mode 100644 api/graphnet.data.extractors.prometheus.html create mode 100644 api/graphnet.data.extractors.prometheus.prometheus_extractor.html rename api/{graphnet.pisa.plotting.html => graphnet.data.readers.internal_parquet_reader.html} (54%) create mode 100644 api/graphnet.data.readers.liquido_reader.html create mode 100644 api/graphnet.data.readers.prometheus_reader.html create mode 100644 api/graphnet.datasets.html create mode 100644 api/graphnet.datasets.prometheus_datasets.html create mode 100644 api/graphnet.datasets.test_dataset.html create mode 100644 api/graphnet.exceptions.exceptions.html rename api/{graphnet.pisa.html => graphnet.exceptions.html} (83%) create mode 100644 api/graphnet.models.detector.liquido.html create mode 100644 api/graphnet.models.transformer.html create mode 100644 api/graphnet.models.transformer.iseecube.html delete mode 100644 api/graphnet.pisa.fitting.html rename contribute.html => contribute/contribute.html (68%) create mode 100644 data_conversion/data_conversion.html create mode 100644 datasets/datasets.html create mode 100644 getting_started/getting_started.html delete mode 100644 install.html create mode 100644 installation/install.html create mode 100644 integration/integration.html create mode 100644 intro/intro.html create mode 100644 models/models.html rename about.html => substitutions.html (56%) diff --git a/.buildinfo b/.buildinfo index 67510ee00..e8e38a82f 100644 --- a/.buildinfo +++ b/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 38e647a1ad5b910b669ed012bb05995f +config: 93489d55c3e099bd65b6f8c23347c61a tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/_images/dataconverter.svg b/_images/dataconverter.svg new file mode 100644 index 000000000..b30246132 --- /dev/null +++ b/_images/dataconverter.svg @@ -0,0 +1,74 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/_images/datarepresentation.svg b/_images/datarepresentation.svg new file mode 100644 index 000000000..775afef71 --- /dev/null +++ b/_images/datarepresentation.svg @@ -0,0 +1,280 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/_images/favicon.svg b/_images/favicon.svg new file mode 100644 index 000000000..f384f90af --- /dev/null +++ b/_images/favicon.svg @@ -0,0 +1,118 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/_images/model.svg b/_images/model.svg new file mode 100644 index 000000000..8d09ede64 --- /dev/null +++ b/_images/model.svg @@ -0,0 +1,38 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/_images/standardmodel.svg b/_images/standardmodel.svg new file mode 100644 index 000000000..571ac438d --- /dev/null +++ b/_images/standardmodel.svg @@ -0,0 +1,148 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/_modules/graphnet/data/constants.html b/_modules/graphnet/data/constants.html index 9b2cbe685..c276bb049 100644 --- a/_modules/graphnet/data/constants.html +++ b/_modules/graphnet/data/constants.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -355,7 +382,8 @@

    Source code for graphnet.dat "sensor_pos_z", "t", ] - KAGGLE = ["x", "y", "z", "time", "charge", "auxiliary"] + KAGGLE = ["x", "y", "z", "time", "charge", "auxiliary"] + LIQUIDO = ["sipm_x", "sipm_y", "sipm_z", "t"] @@ -375,7 +403,6 @@

    Source code for graphnet.dat "zenith", "pid", "elasticity", - "sim_type", "interaction_type", "interaction_time", # Added for vertex reconstruction "inelasticity", @@ -411,7 +438,17 @@

    Source code for graphnet.dat "primary_hadron_1_energy", "total_energy", ] - KAGGLE = ["zenith", "azimuth"] + KAGGLE = ["zenith", "azimuth"] + LIQUIDO = [ + "vertex_x", + "vertex_y", + "vertex_z", + "zenith", + "azimuth", + "interaction_time", + "energy", + "pid", + ] @@ -437,7 +474,7 @@

    Source code for graphnet.dat Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/data/curated_datamodule.html b/_modules/graphnet/data/curated_datamodule.html new file mode 100644 index 000000000..c336e86b7 --- /dev/null +++ b/_modules/graphnet/data/curated_datamodule.html @@ -0,0 +1,684 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + graphnet.data.curated_datamodule — graphnet documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
    + +
    + + +
    + + + + +
    +
    + +
    +
    +
    + +
    +
    +
    +
    +
    +
    + + +
    +
    +
    + +
    +
    + +

    Source code for graphnet.data.curated_datamodule

    +"""Contains a Generic class for curated DataModules/Datasets.
+
+Inheriting subclasses are data-specific implementations that allow the user to
+import and download pre-converteddatasets for training of deep learning based
+methods in GraphNeT.
+"""
+
+from typing import Dict, Any, Optional, List, Tuple, Union
+from abc import abstractmethod
+import os
+
+from .datamodule import GraphNeTDataModule
+from graphnet.models.graphs import GraphDefinition
+from graphnet.data.dataset import ParquetDataset, SQLiteDataset
+
+
+
    
+[docs]
+class CuratedDataset(GraphNeTDataModule):
+    """Generic base class for curated datasets.
+
+    Curated Datasets in GraphNeT are pre-converted datasets that have been
+    prepared for training and evaluation of deep learning models. On these
+    Datasets, graphnet users can train and benchmark their models against SOTA
+    methods.
+    """
+
+    def __init__(
+        self,
+        graph_definition: GraphDefinition,
+        download_dir: str,
+        truth: Optional[List[str]] = None,
+        features: Optional[List[str]] = None,
+        backend: str = "parquet",
+        train_dataloader_kwargs: Optional[Dict[str, Any]] = None,
+        validation_dataloader_kwargs: Dict[str, Any] = None,
+        test_dataloader_kwargs: Dict[str, Any] = None,
+    ) -> None:
+        """Construct CuratedDataset.
+
+        Args:
+            graph_definition: Method that defines the data representation.
+            download_dir: Directory to download dataset to.
+            truth (Optional): List of event-level truth to include. Will
+                            include all available information if not given.
+            features (Optional): List of input features from pulsemap to use.
+                                If not given, all available features will be
+                                used.
+            backend (Optional): data backend to use. Either "parquet" or
+                            "sqlite". Defaults to "parquet".
+            train_dataloader_kwargs (Optional): Arguments for the training
+                                        DataLoader. Default None.
+            validation_dataloader_kwargs (Optional): Arguments for the
+                                        validation DataLoader, Default None.
+            test_dataloader_kwargs (Optional): Arguments for the test
+                                    DataLoader. Default None.
+        """
+        # From user
+        self._download_dir = download_dir
+        self._graph_definition = graph_definition
+        self._backend = backend.lower()
+
+        # Checks
+        assert backend.lower() in self.available_backends
+        assert backend.lower() in ["sqlite", "parquet"]  # Double-check
+        if backend.lower() == "parquet":
+            dataset_ref = ParquetDataset  # type: ignore
+        elif backend.lower() == "sqlite":
+            dataset_ref = SQLiteDataset  # type: ignore
+
+        # Methods:
+        features, truth = self._verify_args(features=features, truth=truth)
+        self.prepare_data()
+        self._check_properties()
+        dataset_args, selec, test_selec = self._prepare_args(
+            backend=backend, features=features, truth=truth
+        )
+        # Instantiate
+        super().__init__(
+            dataset_reference=dataset_ref,
+            dataset_args=dataset_args,
+            train_dataloader_kwargs=train_dataloader_kwargs,
+            validation_dataloader_kwargs=validation_dataloader_kwargs,
+            test_dataloader_kwargs=test_dataloader_kwargs,
+            selection=selec,
+            test_selection=test_selec,
+        )
+
+
    
+[docs]
+    @abstractmethod
+    def prepare_data(self) -> None:
+        """Download and prepare data."""
    
+
+
+    @abstractmethod
+    def _prepare_args(
+        self, backend: str, features: List[str], truth: List[str]
+    ) -> Tuple[Dict[str, Any], Union[List[int], None], Union[List[int], None]]:
+        """Prepare arguments to DataModule.
+
+        Args:
+            backend: backend of dataset. Either "parquet" or "sqlite"
+            features: List of features from user to use as input.
+            truth: List of event-level truth form user.
+
+            This method should return three outputs in the following order:
+
+            A) `dataset_args`
+            B) `selection` if wanted, else None
+            C) ``test_selection` if wanted, else None.
+
+            See documentation on GraphNeTDataModule for details on these
+            arguments:
+            https://graphnet-team.github.io/graphnet/api/graphnet.data.datamodule.html
+        """
+
+    def _verify_args(
+        self, features: Union[List[str], None], truth: Union[List[str], None]
+    ) -> Tuple[List[str], List[str]]:
+        """Check arguments for truth and features from the user.
+
+        Will check to make sure that the given args are available. If not
+        available, and AssertError is thrown.
+        """
+        if features is None:
+            features = self._features
+        else:
+            self._assert_isin(given=features, available=self._features)
+        if truth is None:
+            truth = self._event_truth
+        else:
+            self._assert_isin(given=truth, available=self._event_truth)
+
+        return features, truth
+
+    def _assert_isin(self, given: List[str], available: List[str]) -> None:
+        for key in given:
+            assert key in available
+
+
    
+[docs]
+    def description(self) -> None:
+        """Print details on the Dataset."""
+        event_counts = self.events
+        print(
+            "\n",
+            f"{self.__class__.__name__} contains data from",
+            f"{self.experiment} and was added to GraphNeT by",
+            f"{self.creator}.",
+            "\n\n",
+            "COMMENTS ON USAGE: \n",
+            f"{self.creator}: {self.comments} \n",
+            "\n",
+            "DATASET DETAILS: \n",
+            f"pulsemaps: {self.pulsemaps} \n",
+            f"truth table: {self.truth_table} \n",
+            f"input features: {self.features}\n",
+            f"pulse truth: {self.pulse_truth} \n",
+            f"event truth: {self.event_truth} \n",
+            f"Number of training events: {event_counts['train']} \n",
+            f"Number of validation events: {event_counts['val']} \n",
+            f"Number of test events: {event_counts['test']} \n",
+            "\n",
+            "CITATION:\n",
+            f"{self.citation}",
+        )
    
+
+
+    def _check_properties(self) -> None:
+        """Check that fields have been filled out."""
+        attr = [
+            "pulsemaps",
+            "truth_table",
+            "event_truth",
+            "pulse_truth",
+            "features",
+            "experiment",
+            "citation",
+            "creator",
+            "available_backends",
+        ]
+        for attribute in attr:
+            assert hasattr(self, "_" + attribute), f"missing {attribute}"
+
+    @property
+    def pulsemaps(self) -> List[str]:
+        """Produce a list of available pulsemaps in Dataset."""
+        return self._pulsemaps
+
+    @property
+    def truth_table(self) -> List[str]:
+        """Produce name of table containing event-level truth in Dataset."""
+        return self._truth_table
+
+    @property
+    def event_truth(self) -> List[str]:
+        """Produce a list of available event-level truth in Dataset."""
+        return self._event_truth
+
+    @property
+    def pulse_truth(self) -> Union[List[str], None]:
+        """Produce a list of available pulse-level truth in Dataset."""
+        return self._pulse_truth
+
+    @property
+    def features(self) -> List[str]:
+        """Produce a list of available input features in Dataset."""
+        return self._features
+
+    @property
+    def experiment(self) -> str:
+        """Produce the name of the experiment that the data comes from."""
+        return self._experiment
+
+    @property
+    def citation(self) -> str:
+        """Produce a string that describes how to cite this Dataset."""
+        return self._citation
+
+    @property
+    def comments(self) -> str:
+        """Produce comments on the dataset from the creator."""
+        return self._comments
+
+    @property
+    def creator(self) -> str:
+        """Produce name of person who created the Dataset."""
+        return self._creator
+
+    @property
+    def events(self) -> Dict[str, int]:
+        """Produce a dict that contains number events in each selection."""
+        n_train = len(self._train_dataset)
+        if hasattr(self, "_val_dataset"):
+            n_val = len(self._val_dataset)
+        else:
+            n_val = 0
+        if hasattr(self, "_test_dataset"):
+            n_test = len(self._test_dataset)
+        else:
+            n_test = 0
+
+        return {"train": n_train, "val": n_val, "test": n_test}
+
+    @property
+    def available_backends(self) -> List[str]:
+        """Produce a list of available data formats that the data comes in."""
+        return self._available_backends
+
+    @property
+    def dataset_dir(self) -> str:
+        """Produce path directory that contains dataset files."""
+        dataset_dir = os.path.join(
+            self._download_dir, self.__class__.__name__, self._backend
+        )
+        return dataset_dir
    
+
+
+
+
    
+[docs]
+class ERDAHostedDataset(CuratedDataset):
+    """A base class for dataset/datamodule hosted at ERDA.
+
+    Inheriting subclasses will just need to fill out the `_file_hashes`
+    attribute, which points to the file-id of a ERDA-hosted sharelink. It
+    is assumed that sharelinks point to a single compressed file that has
+    been compressed using `tar` with extension ".tar.gz".
+
+    E.g. suppose that the sharelink below
+    https://sid.erda.dk/share_redirect/FbEEzAbg5A
+    points to a compressed sqlite database. Then:
+    _file_hashes = {'sqlite' : "FbEEzAbg5A"}
+    """
+
+    # Member variables
+    _mirror = "https://sid.erda.dk/share_redirect"
+    _file_hashes: Dict[str, str] = {}  # Must be filled out by you!
+
+
    
+[docs]
+    def prepare_data(self) -> None:
+        """Prepare the dataset for training."""
+        assert self._file_hashes is not None  # mypy
+        file_hash = self._file_hashes[self._backend]
+        if os.path.exists(self.dataset_dir):
+            return
+        else:
+            # Download, unzip and delete zipped file
+            os.makedirs(self.dataset_dir)
+            file_path = os.path.join(self.dataset_dir, file_hash + ".tar.gz")
+            os.system(f"wget -O {file_path} {self._mirror}/{file_hash}")
+            os.system(f"tar -xf {file_path} -C {self.dataset_dir}")
+            os.system(f"rm {file_path}")
    
+
    
+
+
    + +
    +
    +
    +
    +
    +
    +
    + +
    +
    +
    +
    +
    + © Copyright 2021-2024, GraphNeT team. + +
    + Created using + Sphinx 7.3.7. + and + Material for + Sphinx +
    +
    +
    +
    + + + + \ No newline at end of file diff --git a/_modules/graphnet/data/dataclasses.html b/_modules/graphnet/data/dataclasses.html index a93a3e455..c4ed82038 100644 --- a/_modules/graphnet/data/dataclasses.html +++ b/_modules/graphnet/data/dataclasses.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -372,7 +399,7 @@

    Source code for graphnet.d Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/data/dataconverter.html b/_modules/graphnet/data/dataconverter.html index 5ccbe3ea5..f2911d05e 100644 --- a/_modules/graphnet/data/dataconverter.html +++ b/_modules/graphnet/data/dataconverter.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -333,7 +360,6 @@

    Source code for graphnet from multiprocessing.sharedctypes import Synchronized import pandas as pd import os -from glob import glob from graphnet.utilities.decorators import final @@ -342,6 +368,10 @@

    Source code for graphnet from .writers.graphnet_writer import GraphNeTWriter from .extractors import Extractor from .extractors.icecube import I3Extractor +from .extractors.liquido import H5Extractor +from .extractors.internal import ParquetExtractor +from .extractors.prometheus import PrometheusExtractor + from .dataclasses import I3FileSet @@ -369,7 +399,13 @@

    Source code for graphnet file_reader: GraphNeTFileReader, save_method: GraphNeTWriter, outdir: str, - extractors: Union[List[Extractor], List[I3Extractor]], + extractors: Union[ + List[Extractor], + List[I3Extractor], + List[ParquetExtractor], + List[H5Extractor], + List[PrometheusExtractor], + ], index_column: str = "event_no", num_workers: int = 1, ) -> None: @@ -387,6 +423,9 @@

    Source code for graphnet num_workers: The number of CPUs used for parallel processing. Defaults to 1 (no multiprocessing). """ + # Base class constructor + super().__init__(name=__name__, class_name=self.__class__.__name__) + # Member Variable Assignment self._file_reader = file_reader self._save_method = save_method @@ -400,10 +439,8 @@

    Source code for graphnet # with reader. if not isinstance(extractors, list): extractors = [extractors] - self._file_reader.set_extractors(extractors=extractors) - # Base class constructor - super().__init__(name=__name__, class_name=self.__class__.__name__) + self._file_reader.set_extractors(extractors=extractors) @final def __call__(self, input_dir: Union[str, List[str]]) -> None: @@ -447,10 +484,9 @@

    Source code for graphnet # Iterate over files for _ in map_fn( self._process_file, - tqdm(input_files, unit="file(s)", colour="green"), + tqdm(input_files, unit=" file(s)", colour="green"), ): self.debug("processing file.") - self._update_shared_variables(pool) @final @@ -463,13 +499,27 @@

    Source code for graphnet This function is called in parallel. """ # Read and apply extractors - data: List[OrderedDict] = self._file_reader(file_path=file_path) - - # Count number of events - n_events = len(data) - - # Assign event_no's to each event in data and transform to pd.DataFrame - dataframes = self._assign_event_no(data=data) + data = self._file_reader(file_path=file_path) + + # + if isinstance(data, list): + # Assign event_no's to each event in data + # and transform to pd.DataFrame + n_events = len(data) + dataframes = self._assign_event_no(data=data) + elif isinstance(data, dict): + keys = [key for key in data.keys()] + counter = [] + for key in keys: + assert isinstance(data[key], pd.DataFrame) + assert self._index_column in data[key].columns + counter.append(len(data[key][self._index_column])) + dataframes = data + n_events = len( + pd.unique(data[keys[np.argmin(counter)]][self._index_column]) + ) + else: + assert 1 == 2, "should not reach here." # Delete `data` to save memory del data @@ -539,7 +589,6 @@

    Source code for graphnet ) -> int: """Count number of rows that features from `extractor_name` have.""" extractor_dict = event_dict[extractor_name] - try: # If all features in extractor_name have the same length # this line of code will execute without error and result @@ -632,7 +681,9 @@

    Source code for graphnet
    [docs] @final - def merge_files(self, files: Optional[List[str]] = None) -> None: + def merge_files( + self, files: Optional[List[str]] = None, **kwargs: Any + ) -> None: """Merge converted files. `DataConverter` will call the `.merge_files` method in the @@ -660,8 +711,7 @@

    Source code for graphnet merge_path = os.path.join(self._output_dir, "merged") self.info(f"Merging files to {merge_path}") self._save_method.merge_files( - files=files_to_merge, - output_dir=merge_path, + files=files_to_merge, output_dir=merge_path, **kwargs )

    @@ -689,7 +739,7 @@

    Source code for graphnet Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/data/dataloader.html b/_modules/graphnet/data/dataloader.html index 6aa911562..c39bee23e 100644 --- a/_modules/graphnet/data/dataloader.html +++ b/_modules/graphnet/data/dataloader.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -363,7 +390,7 @@

    Source code for graphnet.da dataset: Dataset, batch_size: int = 1, shuffle: bool = False, - num_workers: int = 10, + num_workers: int = 1, persistent_workers: bool = True, collate_fn: Callable = collate_fn, prefetch_factor: int = 2, @@ -443,7 +470,7 @@

    Source code for graphnet.da Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/data/datamodule.html b/_modules/graphnet/data/datamodule.html index 9813c0db0..b8e4f9c09 100644 --- a/_modules/graphnet/data/datamodule.html +++ b/_modules/graphnet/data/datamodule.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -323,9 +350,8 @@

    Source code for graphnet.data.datamodule

     """Base `Dataloader` class(es) used in `graphnet`."""
-from typing import Dict, Any, Optional, List, Tuple, Union
+from typing import Dict, Any, Optional, List, Tuple, Union, Type
 import pytorch_lightning as pl
-from torch.utils.data import DataLoader
 from copy import deepcopy
 from sklearn.model_selection import train_test_split
 import pandas as pd
@@ -337,6 +363,7 @@ 
    Source code for graphnet.da
     ParquetDataset,
 )
 from graphnet.utilities.logging import Logger
+from graphnet.data.dataloader import DataLoader
 
 
 
    
@@ -346,13 +373,15 @@ 
    Source code for graphnet.da
 
     def __init__(
         self,
-        dataset_reference: Union[SQLiteDataset, ParquetDataset, Dataset],
+        dataset_reference: Union[
+            Type[SQLiteDataset], Type[ParquetDataset], Type[Dataset]
+        ],
         dataset_args: Dict[str, Any],
         selection: Optional[Union[List[int], List[List[int]]]] = None,
         test_selection: Optional[Union[List[int], List[List[int]]]] = None,
-        train_dataloader_kwargs: Optional[Dict[str, Any]] = None,
-        validation_dataloader_kwargs: Optional[Dict[str, Any]] = None,
-        test_dataloader_kwargs: Optional[Dict[str, Any]] = None,
+        train_dataloader_kwargs: Dict[str, Any] = None,
+        validation_dataloader_kwargs: Dict[str, Any] = None,
+        test_dataloader_kwargs: Dict[str, Any] = None,
         train_val_split: Optional[List[float]] = [0.9, 0.10],
         split_seed: int = 42,
     ) -> None:
@@ -366,13 +395,14 @@ 
    Source code for graphnet.da
             selection: (Optional) a list of event id's used for training
                     and validation, Default None.
             test_selection: (Optional) a list of event id's used for testing,
-                            Default None.
+                            Defaults to None.
             train_dataloader_kwargs: Arguments for the training DataLoader,
-                                    Default None.
+                                 Defaults{"batch_size": 2, "num_workers": 1}.
             validation_dataloader_kwargs: Arguments for the validation
-                                        DataLoader, Default None.
+                                        DataLoader. Defaults to
+                                        `train_dataloader_kwargs`.
             test_dataloader_kwargs: Arguments for the test DataLoader,
-                                    Default None.
+                                    Defaults to `train_dataloader_kwargs`.
             train_val_split (Optional): Split ratio for training and
                                 validation sets. Default is [0.9, 0.10].
             split_seed: seed used for shuffling and splitting selections into
@@ -387,17 +417,101 @@ 
    Source code for graphnet.da
         self._train_val_split = train_val_split or [0.0]
         self._rng = split_seed
 
-        self._train_dataloader_kwargs = train_dataloader_kwargs or {}
-        self._validation_dataloader_kwargs = validation_dataloader_kwargs or {}
-        self._test_dataloader_kwargs = test_dataloader_kwargs or {}
+        if train_dataloader_kwargs is None:
+            train_dataloader_kwargs = {"batch_size": 2, "num_workers": 1}
+
+        self._set_dataloader_kwargs(
+            train_dataloader_kwargs,
+            validation_dataloader_kwargs,
+            test_dataloader_kwargs,
+        )
 
         # If multiple dataset paths are given, we should use EnsembleDataset
         self._use_ensemble_dataset = isinstance(
             self._dataset_args["path"], list
         )
 
+        # Create Dataloaders
         self.setup("fit")
 
+    def _set_dataloader_kwargs(
+        self,
+        train_dl_args: Dict[str, Any],
+        val_dl_args: Union[Dict[str, Any], None],
+        test_dl_args: Union[Dict[str, Any], None],
+    ) -> None:
+        """Copy train dataloader args to other dataloaders if not given.
+
+        Also checks that ParquetDataset dataloaders have multiprocessing
+        context set to "spawn" as this is strictly required.
+
+        See: https://docs.pola.rs/user-guide/misc/multiprocessing/
+        """
+        if val_dl_args is None:
+            self.info(
+                "No `val_dataloader_kwargs` given. This arg has "
+                "been set to `train_dataloader_kwargs` with `shuffle` = False."
+            )
+            val_dl_args = deepcopy(train_dl_args)
+            val_dl_args["shuffle"] = False  # Important for inference
+        if (test_dl_args is None) & (self._test_selection is not None):
+            test_dl_args = deepcopy(train_dl_args)
+            test_dl_args["shuffle"] = False  # Important for inference
+            self.info(
+                "No `test_dataloader_kwargs` given. This arg has "
+                "been set to `train_dataloader_kwargs` with `shuffle` = False."
+            )
+
+        if self._dataset == ParquetDataset:
+            train_dl_args = self._add_context(train_dl_args, "training")
+            val_dl_args = self._add_context(val_dl_args, "validation")
+            if self._test_selection is not None:
+                assert test_dl_args is not None
+                test_dl_args = self._add_context(test_dl_args, "test")
+
+        self._train_dataloader_kwargs = train_dl_args
+        self._validation_dataloader_kwargs = val_dl_args
+        self._test_dataloader_kwargs = test_dl_args or {}
+
+    def _add_context(
+        self, dataloader_args: Dict[str, Any], dataloader_type: str
+    ) -> Dict[str, Any]:
+        """Handle assignment of `multiprocessing_context` arg to loaders.
+
+        Datasets relying on threaded libraries often require the
+        multiprocessing context to be set to "spawn" if "num_workers" > 0. This
+        method will check the arguments for this entry and throw an error if
+        the field is already assigned to a wrong value. If the value is not
+        specified, it is added automatically with a log entry.
+        """
+        arg = "multiprocessing_context"
+        if dataloader_args["num_workers"] != 0:
+            # If using multiprocessing
+            if arg in dataloader_args:
+                if dataloader_args[arg] != "spawn":
+                    # Wrongly assigned by user
+                    self.error(
+                        "DataLoaders using `ParquetDataset` must have "
+                        "multiprocessing_context = 'spawn'. "
+                        f" Found '{dataloader_args[arg]}' in ",
+                        f"{dataloader_type} dataloader.",
+                    )
+                    raise ValueError("multiprocessing_context must be 'spawn'")
+                else:
+                    # Correctly assigned by user
+                    return dataloader_args
+            else:
+                # Forgotten assignment by user
+                dataloader_args[arg] = "spawn"
+                self.warning_once(
+                    f"{self.__class__.__name__} has automatically "
+                    "set multiprocessing_context = 'spawn' in "
+                    f"{dataloader_type} dataloader."
+                )
+                return dataloader_args
+        else:
+            return dataloader_args
+
 
    
 [docs]
     def prepare_data(self) -> None:
@@ -654,6 +768,7 @@ 
    Source code for graphnet.da
         assert isinstance(selection, (int, list))
         if isinstance(selection, int):
             flat_selection = [selection]
+
         elif isinstance(selection[0], list):
             flat_selection = [
                 item
@@ -814,7 +929,7 @@ 
    Source code for graphnet.da
               
           
    
             Created using
-            Sphinx 7.2.6.
+            Sphinx 7.3.7.
              and
             Material for
               Sphinx
diff --git a/_modules/graphnet/data/dataset/dataset.html b/_modules/graphnet/data/dataset/dataset.html
index 84a3f8d92..d93f07d8f 100644
--- a/_modules/graphnet/data/dataset/dataset.html
+++ b/_modules/graphnet/data/dataset/dataset.html
@@ -122,10 +122,9 @@
     
     
     
-    
+    
     
     
-    
     
     
   
@@ -281,14 +280,42 @@
     
  • 
     
     
-      Install
+      Installation
       
     
     
    • 
     
  • 
     
     
-      Contribute
+      Models In GraphNeT
+      
+    
+    
    • 
+    
  • 
+    
+    
+      Datasets In GraphNeT
+      
+    
+    
    • 
+    
  • 
+    
+    
+      Data Conversion in GraphNeT
+      
+    
+    
    • 
+    
  • 
+    
+    
+      Integrating New Experiments into GraphNeT
+      
+    
+    
    • 
+    
  • 
+    
+    
+      Contributing To GraphNeT
       
     
     
    • 
@@ -353,7 +380,7 @@ 
    Source code for graphn
     DatasetConfig,
     DatasetConfigSaverABCMeta,
 )
-from graphnet.utilities.config.parsing import traverse_and_apply
+from graphnet.exceptions.exceptions import ColumnMissingException
 from graphnet.utilities.logging import Logger
 from graphnet.models.graphs import GraphDefinition
 
@@ -362,13 +389,6 @@ 
    Source code for graphn
 )
 
 
-
    
-[docs]
-class ColumnMissingException(Exception):
-    """Exception to indicate a missing column in a dataset."""
    
-
-
-
 
    
 [docs]
 def load_module(class_name: str) -> Type:
@@ -637,13 +657,14 @@ 
    Source code for graphn
         self._path = path
         self._selection = None
         self._pulsemaps = pulsemaps
-        self._features = [index_column] + features
+        self._features = features
         self._truth = [index_column] + truth
         self._index_column = index_column
         self._truth_table = truth_table
         self._loss_weight_default_value = loss_weight_default_value
         self._graph_definition = deepcopy(graph_definition)
         self._labels = labels
+        self._string_column = graph_definition._detector.string_index_name
 
         if node_truth is not None:
             assert isinstance(node_truth_table, str)
@@ -668,7 +689,10 @@ 
    Source code for graphn
 
         self._selection = None
         if self._string_selection:
-            self._selection = f"string in {str(tuple(self._string_selection))}"
+            # Broken into multple lines lines for length
+            col = self._string_column
+            condition = str(tuple(self._string_selection))
+            self._selection = f"{col} in {condition}"
 
         self._loss_weight_column = loss_weight_column
         self._loss_weight_table = loss_weight_table
@@ -711,10 +735,6 @@ 
    Source code for graphn
         else:
             self._indices = selection
 
-        # Purely internal member variables
-        self._missing_variables: Dict[str, List[str]] = {}
-        self._remove_missing_columns()
-
         # Implementation-specific post-init code.
         self._post_init()
 
@@ -742,9 +762,7 @@ 
    Source code for graphn
         """Return a list of all unique values in `self._index_column`."""
 
     @abstractmethod
-    def _get_event_index(
-        self, sequential_index: Optional[int]
-    ) -> Optional[int]:
+    def _get_event_index(self, sequential_index: int) -> int:
         """Return the event index corresponding to a `sequential_index`."""
 
 
    
@@ -756,7 +774,7 @@ 
    Source code for graphn
         columns: Union[List[str], str],
         sequential_index: Optional[int] = None,
         selection: Optional[str] = None,
-    ) -> List[Tuple[Any, ...]]:
+    ) -> np.ndarray:
         """Query a table at a specific index, optionally with some selection.
 
         Args:
@@ -878,7 +896,9 @@ 
    Source code for graphn
         """Return a list missing columns in `table`."""
         for column in columns:
             try:
-                self.query_table(table, [column], 0)
+                self.query_table(
+                    table=table, columns=[column], sequential_index=0
+                )
             except ColumnMissingException:
                 if table not in self._missing_variables:
                     self._missing_variables[table] = []
@@ -890,12 +910,7 @@ 
    Source code for graphn
 
     def _query(
         self, sequential_index: int
-    ) -> Tuple[
-        List[Tuple[float, ...]],
-        Tuple[Any, ...],
-        Optional[List[Tuple[Any, ...]]],
-        Optional[float],
-    ]:
+    ) -> Tuple[np.ndarray, np.ndarray, Optional[np.ndarray], Optional[float]]:
         """Query file for event features and truth information.
 
         The returned lists have lengths corresponding to the number of pulses
@@ -917,11 +932,14 @@ 
    Source code for graphn
             features_pulsemap = self.query_table(
                 pulsemap, self._features, sequential_index, self._selection
             )
-            features.extend(features_pulsemap)
+            features.append(features_pulsemap)
+
+        if len(self._pulsemaps) > 0:
+            features = np.concatenate(features, axis=0)
 
-        truth: Tuple[Any, ...] = self.query_table(
+        truth = self.query_table(
             self._truth_table, self._truth, sequential_index
-        )[0]
+        )
         if self._node_truth:
             assert self._node_truth_table is not None
             node_truth = self.query_table(
@@ -933,26 +951,22 @@ 
    Source code for graphn
         else:
             node_truth = None
 
-        loss_weight: Optional[float] = None  # Default
         if self._loss_weight_column is not None:
             assert self._loss_weight_table is not None
-            loss_weight_list = self.query_table(
+            loss_weight = self.query_table(
                 self._loss_weight_table,
                 self._loss_weight_column,
                 sequential_index,
             )
-            if len(loss_weight_list):
-                loss_weight = loss_weight_list[0][0]
-            else:
-                loss_weight = -1.0
-
+        else:
+            loss_weight = None
         return features, truth, node_truth, loss_weight
 
     def _create_graph(
         self,
-        features: List[Tuple[float, ...]],
-        truth: Tuple[Any, ...],
-        node_truth: Optional[List[Tuple[Any, ...]]] = None,
+        features: np.ndarray,
+        truth: np.ndarray,
+        node_truth: Optional[np.ndarray] = None,
         loss_weight: Optional[float] = None,
     ) -> Data:
         """Create Pytorch Data (i.e. graph) object.
@@ -967,9 +981,11 @@ 
    Source code for graphn
         Returns:
             Graph object.
         """
-        # Convert nested list to simple dict
+        # Convert truth to dict
+        if len(truth.shape) == 1:
+            truth = truth.reshape(1, -1)
         truth_dict = {
-            key: truth[index] for index, key in enumerate(self._truth)
+            key: truth[:, index] for index, key in enumerate(self._truth)
         }
 
         # Define custom labels
@@ -977,10 +993,9 @@ 
    Source code for graphn
 
         # Convert nested list to simple dict
         if node_truth is not None:
-            node_truth_array = np.asarray(node_truth)
             assert self._node_truth is not None
             node_truth_dict = {
-                key: node_truth_array[:, index]
+                key: node_truth[:, index]
                 for index, key in enumerate(self._node_truth)
             }
 
@@ -991,19 +1006,16 @@ 
    Source code for graphn
 
         # Catch cases with no reconstructed pulses
         if len(features):
-            node_features = np.asarray(features)[
-                :, 1:
-            ]  # first entry is index column
+            node_features = features
         else:
-            node_features = np.array([]).reshape((0, len(self._features) - 1))
+            node_features = np.array([]).reshape((0, len(self._features)))
 
+        assert isinstance(features, np.ndarray)
         # Construct graph data object
         assert self._graph_definition is not None
         graph = self._graph_definition(
             input_features=node_features,
-            input_feature_names=self._features[
-                1:
-            ],  # first entry is index column
+            input_feature_names=self._features,
             truth_dicts=truth_dicts,
             custom_label_functions=self._label_fns,
             loss_weight_column=self._loss_weight_column,
@@ -1017,13 +1029,11 @@ 
    Source code for graphn
         """Return dictionary of  labels, to be added as graph attributes."""
         if "pid" in truth_dict.keys():
             abs_pid = abs(truth_dict["pid"])
-            sim_type = truth_dict["sim_type"]
 
             labels_dict = {
                 self._index_column: truth_dict[self._index_column],
                 "muon": int(abs_pid == 13),
                 "muon_stopped": int(truth_dict.get("stopped_muon") == 1),
-                "noise": int((abs_pid == 1) & (sim_type != "data")),
                 "neutrino": int(
                     (abs_pid != 13) & (abs_pid != 1)
                 ),  # @TODO: `abs_pid in [12,14,16]`?
@@ -1031,7 +1041,7 @@ 
    Source code for graphn
                 "v_u": int(abs_pid == 14),
                 "v_t": int(abs_pid == 16),
                 "track": int(
-                    (abs_pid == 14) & (truth_dict["interaction_type"] == 1)
+                    (abs_pid == 14) & (truth_dict.get("interaction_type") == 1)
                 ),
                 "dbang": self._get_dbang_label(truth_dict),
                 "corsika": int(abs_pid > 20),
@@ -1099,7 +1109,7 @@ 
    Source code for graphn
               
           
    
             Created using
-            Sphinx 7.2.6.
+            Sphinx 7.3.7.
              and
             Material for
               Sphinx
diff --git a/_modules/graphnet/data/dataset/parquet/parquet_dataset.html b/_modules/graphnet/data/dataset/parquet/parquet_dataset.html
index 10827b1ba..057bdf4bf 100644
--- a/_modules/graphnet/data/dataset/parquet/parquet_dataset.html
+++ b/_modules/graphnet/data/dataset/parquet/parquet_dataset.html
@@ -122,10 +122,9 @@
     
     
     
-    
+    
     
     
-    
     
     
   
@@ -281,14 +280,42 @@
     
  • 
     
     
-      Install
+      Installation
       
     
     
    • 
     
  • 
     
     
-      Contribute
+      Models In GraphNeT
+      
+    
+    
    • 
+    
  • 
+    
+    
+      Datasets In GraphNeT
+      
+    
+    
    • 
+    
  • 
+    
+    
+      Data Conversion in GraphNeT
+      
+    
+    
    • 
+    
  • 
+    
+    
+      Integrating New Experiments into GraphNeT
+      
+    
+    
    • 
+    
  • 
+    
+    
+      Contributing To GraphNeT
       
     
     
    • 
@@ -322,145 +349,396 @@
           
    
             
   
    Source code for graphnet.data.dataset.parquet.parquet_dataset
    -"""`Dataset` class(es) for reading from Parquet files."""
-
-from typing import Any, Dict, List, Optional, Tuple, Union, cast
+"""Base :py:class:`Dataset` class(es) used in GraphNeT."""
+
+from copy import deepcopy
+from abc import ABC, abstractmethod
+from typing import (
+    cast,
+    Any,
+    Callable,
+    Dict,
+    List,
+    Optional,
+    Tuple,
+    Union,
+    Iterable,
+    Type,
+)
 
 import numpy as np
-import awkward as ak
+import torch
+import os
+from torch_geometric.data import Data
+import polars as pol
+from polars.series.series import Series
+from polars.exceptions import InvalidOperationError
+from glob import glob
+from bisect import bisect_right
+from collections import OrderedDict
 
-from graphnet.data.dataset.dataset import Dataset, ColumnMissingException
+from graphnet.models.graphs import GraphDefinition
+from graphnet.data.dataset import Dataset
+from graphnet.exceptions.exceptions import ColumnMissingException
 
 
 
    
 [docs]
 class ParquetDataset(Dataset):
-    """Pytorch dataset for reading from Parquet files."""
+    """Dataset class for Parquet-files converted with `ParquetWriter`."""
 
-    # Implementing abstract method(s)
-    def _init(self) -> None:
-        # Check(s)
-        if not isinstance(self._path, list):
-
-            assert isinstance(self._path, str)
-
-            assert self._path.endswith(
-                ".parquet"
-            ), f"Format of input file `{self._path}` is not supported"
-
-        assert (
-            self._node_truth is None
-        ), "Argument `node_truth` is currently not supported."
-        assert (
-            self._node_truth_table is None
-        ), "Argument `node_truth_table` is currently not supported."
-        assert (
-            self._string_selection is None
-        ), "Argument `string_selection` is currently not supported"
-
-        # Set custom member variable(s)
-        if not isinstance(self._path, list):
-            self._parquet_hook = ak.from_parquet(self._path, lazy=False)
-        else:
-            self._parquet_hook = ak.concatenate(
-                ak.from_parquet(file) for file in self._path
-            )
+    def __init__(
+        self,
+        path: str,
+        graph_definition: GraphDefinition,
+        pulsemaps: Union[str, List[str]],
+        features: List[str],
+        truth: List[str],
+        *,
+        node_truth: Optional[List[str]] = None,
+        index_column: str = "event_no",
+        truth_table: str = "truth",
+        node_truth_table: Optional[str] = None,
+        string_selection: Optional[List[int]] = None,
+        selection: Optional[Union[str, List[int], List[List[int]]]] = None,
+        dtype: torch.dtype = torch.float32,
+        loss_weight_table: Optional[str] = None,
+        loss_weight_column: Optional[str] = None,
+        loss_weight_default_value: Optional[float] = None,
+        seed: Optional[int] = None,
+        cache_size: int = 1,
+    ):
+        """Construct Dataset.
+
+            NOTE: DataLoaders using this Dataset should have
+            "multiprocessing_context = 'spawn'" set to avoid thread locking.
+
+        Args:
+            path: Path to the file(s) from which this `Dataset` should read.
+            pulsemaps: Name(s) of the pulse map series that should be used to
+                construct the nodes on the individual graph objects, and their
+                features. Multiple pulse series maps can be used, e.g., when
+                different DOM types are stored in different maps.
+            features: List of columns in the input files that should be used as
+                node features on the graph objects.
+            truth: List of event-level columns in the input files that should
+                be used added as attributes on the  graph objects.
+            node_truth: List of node-level columns in the input files that
+                should be used added as attributes on the graph objects.
+            index_column: Name of the column in the input files that contains
+                unique indicies to identify and map events across tables.
+            truth_table: Name of the table containing event-level truth
+                information.
+            node_truth_table: Name of the table containing node-level truth
+                information.
+            string_selection: Subset of strings for which data should be read
+                and used to construct graph objects. Defaults to None, meaning
+                all strings for which data exists are used.
+            selection: The batch ids to include in the dataset.
+                        Defaults to None, meaning that batches are read.
+            dtype: Type of the feature tensor on the graph objects returned.
+            loss_weight_table: Name of the table containing per-event loss
+                weights.
+            loss_weight_column: Name of the column in `loss_weight_table`
+                containing per-event loss weights. This is also the name of the
+                corresponding attribute assigned to the graph object.
+            loss_weight_default_value: Default per-event loss weight.
+                NOTE: This default value is only applied when
+                `loss_weight_table` and `loss_weight_column` are specified, and
+                in this case to events with no value in the corresponding
+                table/column. That is, if no per-event loss weight table/column
+                is provided, this value is ignored. Defaults to None.
+            seed: Random number generator seed, used for selecting a random
+                subset of events when resolving a string-based selection (e.g.,
+                `"10000 random events ~ event_no % 5 > 0"` or `"20% random
+                events ~ event_no % 5 > 0"`).
+            graph_definition: Method that defines the graph representation.
+            cache_size: Number of batches to cache in memory.
+                        Must be at least 1. Defaults to 1.
+        """
+        self._validate_selection(selection)
+        # Base class constructor
+        super().__init__(
+            path=path,
+            pulsemaps=pulsemaps,
+            features=features,
+            truth=truth,
+            node_truth=node_truth,
+            index_column=index_column,
+            truth_table=truth_table,
+            node_truth_table=node_truth_table,
+            string_selection=string_selection,
+            selection=selection,
+            dtype=dtype,
+            loss_weight_table=loss_weight_table,
+            loss_weight_column=loss_weight_column,
+            loss_weight_default_value=loss_weight_default_value,
+            seed=seed,
+            graph_definition=graph_definition,
+        )
 
-    def _get_all_indices(self) -> List[int]:
-        return np.arange(
-            len(
-                ak.to_numpy(
-                    self._parquet_hook[self._truth_table][self._index_column]
-                ).tolist()
-            )
-        ).tolist()
+        # mypy..
+        assert isinstance(self._path, str)
+        self._path: str = self._path
+        # Member Variables
+        self._cache_size = cache_size
+        self._batch_sizes = self._calculate_sizes()
+        self._batch_cumsum = np.cumsum(self._batch_sizes)
+        self._file_cache = self._initialize_file_cache(
+            truth_table=truth_table,
+            node_truth_table=node_truth_table,
+            pulsemaps=pulsemaps,
+        )
+        self._string_selection = string_selection
+        # Purely internal member variables
+        self._missing_variables: Dict[str, List[str]] = {}
+        self._remove_missing_columns()
 
-    def _get_event_index(
-        self, sequential_index: Optional[int]
-    ) -> Optional[int]:
-        index: Optional[int]
-        if sequential_index is None:
-            index = None
-        else:
-            index = cast(List[int], self._indices)[sequential_index]
-
-        return index
-
-    def _format_dictionary_result(
-        self, dictionary: Dict
-    ) -> List[Tuple[Any, ...]]:
-        """Convert the output of `ak.to_list()` into a list of tuples."""
-        # All scalar values
-        if all(map(np.isscalar, dictionary.values())):
-            return [tuple(dictionary.values())]
-
-        # All arrays should have same length
-        array_lengths = [
-            len(values)
-            for values in dictionary.values()
-            if not np.isscalar(values)
-        ]
-        assert len(set(array_lengths)) == 1, (
-            f"Arrays in {dictionary} have differing lengths "
-            f"({set(array_lengths)})."
+    def _initialize_file_cache(
+        self,
+        truth_table: str,
+        node_truth_table: Optional[str],
+        pulsemaps: Union[str, List[str]],
+    ) -> Dict[str, OrderedDict]:
+        tables = [truth_table]
+        if node_truth_table is not None:
+            tables.append(node_truth_table)
+        if isinstance(pulsemaps, str):
+            tables.append(pulsemaps)
+        elif isinstance(pulsemaps, list):
+            tables.extend(pulsemaps)
+
+        cache: Dict[str, OrderedDict] = {}
+        for table in tables:
+            cache[table] = OrderedDict()
+        return cache
+
+    def _validate_selection(
+        self,
+        selection: Optional[Union[str, List[int], List[List[int]]]] = None,
+    ) -> None:
+        if selection is not None:
+            try:
+                assert not isinstance(selection, str)
+            except AssertionError:
+                e = AssertionError(
+                    f"{self.__class__.__name__} does not support "
+                    "str-selections."
+                )
+                raise e
+
+    def _init(self) -> None:
+        return
+
+    def _get_event_index(self, sequential_index: int) -> int:
+        event_index = self.query_table(
+            table=self._truth_table,
+            sequential_index=sequential_index,
+            columns=[self._index_column],
         )
-        nb_elements = array_lengths[0]
+        return event_index
 
-        # Broadcast scalars
-        for key in dictionary:
-            value = dictionary[key]
-            if np.isscalar(value):
-                dictionary[key] = np.repeat(
-                    value, repeats=nb_elements
-                ).tolist()
+    def __len__(self) -> int:
+        """Return length of dataset, i.e. number of training examples."""
+        return sum(self._batch_sizes)
 
-        return list(map(tuple, list(zip(*dictionary.values()))))
+    def _get_all_indices(self) -> List[int]:
+        """Return a list of all unique values in `self._index_column`."""
+        files = glob(os.path.join(self._path, self._truth_table, "*.parquet"))
+        return np.arange(0, len(files), 1)
+
+    def _calculate_sizes(self) -> List[int]:
+        """Calculate the number of events in each batch."""
+        sizes = []
+        for batch_id in self._indices:
+            path = os.path.join(
+                self._path,
+                self._truth_table,
+                f"{self.truth_table}_{batch_id}.parquet",
+            )
+            sizes.append(len(pol.read_parquet(path)))
+        return sizes
+
+    def _get_row_idx(self, sequential_index: int) -> int:
+        """Return the row index corresponding to a `sequential_index`."""
+        file_idx = bisect_right(self._batch_cumsum, sequential_index)
+        if file_idx > 0:
+            idx = int(sequential_index - self._batch_cumsum[file_idx - 1])
+        else:
+            idx = sequential_index
+        return idx
 
 
    
 [docs]
-    def query_table(
+    def query_table(  # type: ignore
         self,
         table: str,
         columns: Union[List[str], str],
         sequential_index: Optional[int] = None,
         selection: Optional[str] = None,
-    ) -> List[Tuple[Any, ...]]:
-        """Query table at a specific index, optionally with some selection."""
-        # Check(s)
-        assert (
-            selection is None
-        ), "Argument `selection` is currently not supported"
-
-        index = self._get_event_index(sequential_index)
-
-        try:
-            if index is None:
-                ak_array = self._parquet_hook[table][columns][:]
-            else:
-                ak_array = self._parquet_hook[table][columns][index]
-        except ValueError as e:
-            if "does not exist (not in record)" in str(e):
-                raise ColumnMissingException(str(e))
-            else:
-                raise e
+    ) -> np.ndarray:
+        """Query a table at a specific index, optionally with some selection.
+
+        Args:
+            table: Table to be queried.
+            columns: Columns to read out.
+            sequential_index: Sequentially numbered index
+                (i.e. in [0,len(self))) of the event to query. This _may_
+                differ from the indexation used in `self._indices`. If no value
+                is provided, the entire column is returned.
+            selection: Selection to be imposed before reading out data.
+                Defaults to None.
+
+        Returns:
+            List of tuples containing the values in `columns`. If the `table`
+                contains only scalar data for `columns`, a list of length 1 is
+                returned
+
+        Raises:
+            ColumnMissingException: If one or more element in `columns` is not
+                present in `table`.
+        """
+        if isinstance(columns, str):
+            columns = [columns]
 
-        output = ak_array.to_list()
+        if sequential_index is None:
+            file_idx = np.arange(0, len(self._batch_cumsum), 1)
+        else:
+            file_idx = [bisect_right(self._batch_cumsum, sequential_index)]
+
+        file_indices = [self._indices[idx] for idx in file_idx]
+
+        arrays = []
+        for file_idx in file_indices:
+            array = self._query_table(
+                table=table,
+                columns=columns,
+                file_idx=file_idx,
+                sequential_index=sequential_index,
+                selection=selection,
+            )
+            arrays.append(array)
+        return np.concatenate(arrays, axis=0)
    
 
-        result: List[Tuple[Any, ...]] = []
 
-        # Querying single index
-        if isinstance(output, dict):
-            assert list(output.keys()) == columns
-            result = self._format_dictionary_result(output)
+    def _query_table(
+        self,
+        table: str,
+        columns: Union[List[str], str],
+        file_idx: int,
+        sequential_index: Optional[int] = None,
+        selection: Optional[str] = None,
+    ) -> np.ndarray:
 
-        # Querying entire columm
-        elif isinstance(output, list):
-            for dictionary in output:
-                assert list(dictionary.keys()) == columns
-                result.extend(self._format_dictionary_result(dictionary))
+        self._load_table(table_name=table, file_idx=file_idx)
+        df = self._file_cache[table][file_idx]
+        if sequential_index is not None:
+            row_id = self._get_row_idx(sequential_index)
+        else:
+            row_id = np.arange(0, len(df), 1)
+        df = df[row_id]
+        if len(df) > 0:
+            self._raise_column_exception(
+                df_columns=df.columns, columns=columns, table=table
+            )
+            data = df.select(columns)
+            if isinstance(data[columns[0]][0], Series):
+                x = [data[col][0].to_numpy().reshape(-1, 1) for col in columns]
+                array = np.concatenate(x, axis=1)
+            else:
+                array = data.to_numpy()
+        else:
+            array = np.array()
+        return array
+
+    def _load_table(self, table_name: str, file_idx: int) -> None:
+        """Load and possibly cache a parquet table."""
+        if file_idx not in self._file_cache[table_name].keys():
+            file_path = os.path.join(
+                self._path, table_name, f"{table_name}_{file_idx}.parquet"
+            )
+            df = pol.read_parquet(file_path).sort(self._index_column)
+            if (table_name in self._pulsemaps) or (
+                table_name == self._node_truth_table
+            ):
+                if table_name == self._node_truth_table:
+                    pol_columns = [pol.col(self._node_truth)]
+                else:
+                    pol_columns = [pol.col(feat) for feat in self._features]
+
+                if self._string_selection:
+                    pol_columns.append(pol.col(self._string_column))
+
+                df = df.group_by(self._index_column).agg(pol_columns)
+
+            self._file_cache[table_name][file_idx] = df.sort(
+                self._index_column
+            )
+            n_files_cached: int = len(self._file_cache[table_name])
+            if n_files_cached > self._cache_size:
+                del self._file_cache[table_name][
+                    list(self._file_cache[table_name].keys())[0]
+                ]
+
+    def _raise_column_exception(
+        self, df_columns: List[str], columns: Union[List[str], str], table: str
+    ) -> None:
+        if isinstance(columns, str):
+            columns = [columns]
+        for column in columns:
+            if column not in df_columns:
+                raise ColumnMissingException(f"{column} not in {table}")
+
+    def __getitem__(self, sequential_index: int) -> Data:
+        """Return graph `Data` object at `index`."""
+        if not (0 <= sequential_index < len(self)):
+            raise IndexError(
+                f"Index {sequential_index} not in range [0, {len(self) - 1}]"
+            )
+        if self._node_truth_table is not None:
+            assert isinstance(self._node_truth, (list, str))  # mypy..
+            node_truth = self.query_table(
+                table=self._node_truth_table,
+                columns=self._node_truth,
+                sequential_index=sequential_index,
+            )
+        else:
+            node_truth = None
+
+        if self._loss_weight_table is not None:
+            assert isinstance(self._loss_weight_column, str)
+            loss_weight = self.query_table(
+                table=self._loss_weight_table,
+                columns=self._loss_weight_column,
+                sequential_index=sequential_index,
+            )
+        else:
+            loss_weight = None
+
+        features = []
+        for pulsemap in self._pulsemaps:
+            features.append(
+                self.query_table(
+                    table=pulsemap,
+                    columns=self._features,
+                    sequential_index=sequential_index,
+                )
+            )
+        features = np.concatenate(features, axis=0)
 
-        return result
    
-
    
+        truth = self.query_table(
+            table=self._truth_table,
+            columns=self._truth,
+            sequential_index=sequential_index,
+        )
+
+        graph = self._create_graph(
+            features=features,
+            truth=truth,
+            node_truth=node_truth,
+            loss_weight=loss_weight,
+        )
+        return graph
    @@ -486,7 +764,7 @@

    Source Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/data/dataset/sqlite/sqlite_dataset.html b/_modules/graphnet/data/dataset/sqlite/sqlite_dataset.html index ef174366f..7cbda8a17 100644 --- a/_modules/graphnet/data/dataset/sqlite/sqlite_dataset.html +++ b/_modules/graphnet/data/dataset/sqlite/sqlite_dataset.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -324,9 +351,10 @@

    Source code for graphnet.data.dataset.sqlite.sqlite_dataset

     """`Dataset` class(es) for reading data from SQLite databases."""
 
-from typing import Any, List, Optional, Tuple, Union
+from typing import Any, List, Optional, Tuple, Union, Dict
 import pandas as pd
 import sqlite3
+import numpy as np
 
 from graphnet.data.dataset.dataset import Dataset, ColumnMissingException
 
@@ -363,6 +391,9 @@ 
    Source c
         self._conn: Optional[sqlite3.Connection] = None
 
     def _post_init(self) -> None:
+        # Purely internal member variables
+        self._missing_variables: Dict[str, List[str]] = {}
+        self._remove_missing_columns()
         self._close_connection()
 
 
    
@@ -405,7 +436,7 @@ 
    Source c
                 raise ColumnMissingException(str(e))
             else:
                 raise e
-        return result
    
+        return np.asarray(result)
    def _get_all_indices(self) -> List[int]: @@ -416,18 +447,18 @@

    Source c self._close_connection() return indices.values.ravel().tolist() - def _get_event_index( - self, sequential_index: Optional[int] - ) -> Optional[int]: + def _get_event_index(self, sequential_index: Optional[int]) -> int: index: int = 0 if sequential_index is not None: index_ = self._indices[sequential_index] if self._database_list is None: - assert isinstance(index_, int) - index = index_ + if not isinstance(index_, int): + index_ = int(index_) # type: ignore else: - assert isinstance(index_, list) - index = index_[0] + if not isinstance(index_, int): + index_ = int(index_[0]) + assert isinstance(index_, int) + index = index_ return index # Custom, internal method(s) @@ -501,7 +532,7 @@

    Source c Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/data/extractors/combine_extractors.html b/_modules/graphnet/data/extractors/combine_extractors.html new file mode 100644 index 000000000..76854d3e1 --- /dev/null +++ b/_modules/graphnet/data/extractors/combine_extractors.html @@ -0,0 +1,428 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + graphnet.data.extractors.combine_extractors — graphnet documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
    + +
    + + +
    + + + + +
    +
    + +
    +
    +
    + +
    +
    +
    +
    +
    +
    + + +
    +
    +
    + +
    +
    + +

    Source code for graphnet.data.extractors.combine_extractors

    +"""Module for combining multiple extractors into a single extractor."""
+from typing import TYPE_CHECKING
+
+from graphnet.utilities.imports import has_icecube_package
+from graphnet.data.extractors.icecube.i3extractor import I3Extractor
+from typing import List, Dict
+
+if has_icecube_package() or TYPE_CHECKING:
+    from icecube import icetray  # pyright: reportMissingImports=false
+
+
+
    
+[docs]
+class CombinedExtractor(I3Extractor):
+    """Class for combining multiple extractors.
+
+    This class is used to combine multiple extractors into a single extractor
+    with a new name.
+    """
+
+    def __init__(self, extractors: List[I3Extractor], extractor_name: str):
+        """Construct CombinedExtractor.
+
+        Args:
+        extractors: List of extractors to combine. The extractors must all return data on the same level; e.g. all event-level data or pulse-level data. Mixing tables that contain event-level and pulse-level information will fail.
+        extractor_name: Name of the new extractor.
+        """
+        super().__init__(extractor_name=extractor_name)
+        self._extractors = extractors
+
+    def __call__(self, frame: "icetray.I3Frame") -> Dict[str, float]:
+        """Extract data from frame using all extractors.
+
+        Args:
+        frame: I3Frame to extract data from.
+        """
+        output = {}
+        for extractor in self._extractors:
+            output.update(extractor(frame))
+        return output
    
+
+
    + +
    +
    +
    +
    +
    +
    +
    + +
    +
    +
    +
    +
    + © Copyright 2021-2024, GraphNeT team. + +
    + Created using + Sphinx 7.3.7. + and + Material for + Sphinx +
    +
    +
    +
    + + + + \ No newline at end of file diff --git a/_modules/graphnet/data/extractors/extractor.html b/_modules/graphnet/data/extractors/extractor.html index 3d5037a63..22f43696f 100644 --- a/_modules/graphnet/data/extractors/extractor.html +++ b/_modules/graphnet/data/extractors/extractor.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -323,8 +350,9 @@

    Source code for graphnet.data.extractors.extractor

     """Base I3Extractor class(es)."""
-from typing import Any
+from typing import Any, Union
 from abc import ABC, abstractmethod
+import pandas as pd
 
 from graphnet.utilities.logging import Logger
 
@@ -362,7 +390,7 @@ 
    Source code for g
         super().__init__(name=__name__, class_name=self.__class__.__name__)
 
     @abstractmethod
-    def __call__(self, data: Any) -> dict:
+    def __call__(self, data: Any) -> Union[dict, pd.DataFrame]:
         """Extract information from data."""
         pass
 
@@ -395,7 +423,7 @@ 
    Source code for g
    Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/data/extractors/icecube/i3extractor.html b/_modules/graphnet/data/extractors/icecube/i3extractor.html index 4715a0a3c..92e23878c 100644 --- a/_modules/graphnet/data/extractors/icecube/i3extractor.html +++ b/_modules/graphnet/data/extractors/icecube/i3extractor.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -444,7 +471,7 @@

    Source Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/data/extractors/icecube/i3featureextractor.html b/_modules/graphnet/data/extractors/icecube/i3featureextractor.html index df6ff594f..e527f6b29 100644 --- a/_modules/graphnet/data/extractors/icecube/i3featureextractor.html +++ b/_modules/graphnet/data/extractors/icecube/i3featureextractor.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -663,7 +690,7 @@

    Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/data/extractors/icecube/i3genericextractor.html b/_modules/graphnet/data/extractors/icecube/i3genericextractor.html index 9c046b41a..284e1d308 100644 --- a/_modules/graphnet/data/extractors/icecube/i3genericextractor.html +++ b/_modules/graphnet/data/extractors/icecube/i3genericextractor.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -643,7 +670,7 @@

    Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/data/extractors/icecube/i3hybridrecoextractor.html b/_modules/graphnet/data/extractors/icecube/i3hybridrecoextractor.html index d40fde3f4..d35e08408 100644 --- a/_modules/graphnet/data/extractors/icecube/i3hybridrecoextractor.html +++ b/_modules/graphnet/data/extractors/icecube/i3hybridrecoextractor.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -400,7 +427,7 @@

    Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/data/extractors/icecube/i3ntmuonlabelsextractor.html b/_modules/graphnet/data/extractors/icecube/i3ntmuonlabelsextractor.html index 53a306b78..99c65d232 100644 --- a/_modules/graphnet/data/extractors/icecube/i3ntmuonlabelsextractor.html +++ b/_modules/graphnet/data/extractors/icecube/i3ntmuonlabelsextractor.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -407,7 +434,7 @@

    Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/data/extractors/icecube/i3particleextractor.html b/_modules/graphnet/data/extractors/icecube/i3particleextractor.html index 59ba1c7c4..511fcb466 100644 --- a/_modules/graphnet/data/extractors/icecube/i3particleextractor.html +++ b/_modules/graphnet/data/extractors/icecube/i3particleextractor.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -393,7 +420,7 @@

    Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/data/extractors/icecube/i3pisaextractor.html b/_modules/graphnet/data/extractors/icecube/i3pisaextractor.html index 9134c216c..01b12285e 100644 --- a/_modules/graphnet/data/extractors/icecube/i3pisaextractor.html +++ b/_modules/graphnet/data/extractors/icecube/i3pisaextractor.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -385,7 +412,7 @@

    Sou Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/data/extractors/icecube/i3quesoextractor.html b/_modules/graphnet/data/extractors/icecube/i3quesoextractor.html index a0d16868c..5231089b1 100644 --- a/_modules/graphnet/data/extractors/icecube/i3quesoextractor.html +++ b/_modules/graphnet/data/extractors/icecube/i3quesoextractor.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -395,7 +422,7 @@

    So Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/data/extractors/icecube/i3retroextractor.html b/_modules/graphnet/data/extractors/icecube/i3retroextractor.html index 5299392c8..ccfdfa786 100644 --- a/_modules/graphnet/data/extractors/icecube/i3retroextractor.html +++ b/_modules/graphnet/data/extractors/icecube/i3retroextractor.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -467,7 +494,7 @@

    So Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/data/extractors/icecube/i3splinempeextractor.html b/_modules/graphnet/data/extractors/icecube/i3splinempeextractor.html index d2c33d7d9..d794fc6b0 100644 --- a/_modules/graphnet/data/extractors/icecube/i3splinempeextractor.html +++ b/_modules/graphnet/data/extractors/icecube/i3splinempeextractor.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -379,7 +406,7 @@

    Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/data/extractors/icecube/i3truthextractor.html b/_modules/graphnet/data/extractors/icecube/i3truthextractor.html index 386bed579..ce42482c5 100644 --- a/_modules/graphnet/data/extractors/icecube/i3truthextractor.html +++ b/_modules/graphnet/data/extractors/icecube/i3truthextractor.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -789,7 +816,7 @@

    So Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/data/extractors/icecube/i3tumextractor.html b/_modules/graphnet/data/extractors/icecube/i3tumextractor.html index 2bfb35fdd..ebafcaef6 100644 --- a/_modules/graphnet/data/extractors/icecube/i3tumextractor.html +++ b/_modules/graphnet/data/extractors/icecube/i3tumextractor.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -382,7 +409,7 @@

    Sour Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/data/extractors/icecube/utilities/collections.html b/_modules/graphnet/data/extractors/icecube/utilities/collections.html index 680b630b3..60354a156 100644 --- a/_modules/graphnet/data/extractors/icecube/utilities/collections.html +++ b/_modules/graphnet/data/extractors/icecube/utilities/collections.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -436,7 +463,7 @@

    Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/data/extractors/icecube/utilities/frames.html b/_modules/graphnet/data/extractors/icecube/utilities/frames.html index 559d122c9..1cfc52261 100644 --- a/_modules/graphnet/data/extractors/icecube/utilities/frames.html +++ b/_modules/graphnet/data/extractors/icecube/utilities/frames.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -439,7 +466,7 @@

    So Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/data/extractors/icecube/utilities/i3_filters.html b/_modules/graphnet/data/extractors/icecube/utilities/i3_filters.html index e02d4474e..7237fa78b 100644 --- a/_modules/graphnet/data/extractors/icecube/utilities/i3_filters.html +++ b/_modules/graphnet/data/extractors/icecube/utilities/i3_filters.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -483,7 +510,7 @@

    Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/data/extractors/icecube/utilities/types.html b/_modules/graphnet/data/extractors/icecube/utilities/types.html index 8cda573aa..347bdc75f 100644 --- a/_modules/graphnet/data/extractors/icecube/utilities/types.html +++ b/_modules/graphnet/data/extractors/icecube/utilities/types.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -660,7 +687,7 @@

    Sou Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/data/extractors/internal/parquet_extractor.html b/_modules/graphnet/data/extractors/internal/parquet_extractor.html new file mode 100644 index 000000000..6554d80d0 --- /dev/null +++ b/_modules/graphnet/data/extractors/internal/parquet_extractor.html @@ -0,0 +1,424 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + graphnet.data.extractors.internal.parquet_extractor — graphnet documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
    + +
    + + +
    + + + + +
    +
    + +
    +
    +
    + +
    +
    +
    +
    +
    +
    + + +
    +
    +
    + +
    +
    + +

    Source code for graphnet.data.extractors.internal.parquet_extractor

    +"""Parquet Extractor for conversion from internal parquet format."""
+import polars as pol
+import pandas as pd
+
+from graphnet.data.extractors import Extractor
+
+
+
    
+[docs]
+class ParquetExtractor(Extractor):
+    """Class for extracting information from internal GraphNeT parquet files.
+
+    Contains functionality required to extract data from internal parquet
+    files, i.e files saved using the ParquetWriter. This allows for conversion
+    between internal data formats.
+    """
+
+    def __init__(self, extractor_name: str):
+        """Construct ParquetExtractor.
+
+        Args:
+            extractor_name: Name of the `ParquetExtractor` instance.
+            Used to keep track of the provenance of different data,
+            and to name tables to which this data is saved.
+        """
+        # Member variable(s)
+        self._table = extractor_name
+        # Base class constructor
+        super().__init__(extractor_name=extractor_name)
+
+    def __call__(self, file_path: str) -> pd.DataFrame:
+        """Extract information from parquet file."""
+        if self._table in file_path:
+            return pol.read_parquet(file_path).to_pandas()
+        else:
+            return None
    
+
+
    + +
    +
    +
    +
    +
    +
    +
    + +
    +
    +
    +
    +
    + © Copyright 2021-2024, GraphNeT team. + +
    + Created using + Sphinx 7.3.7. + and + Material for + Sphinx +
    +
    +
    +
    + + + + \ No newline at end of file diff --git a/_modules/graphnet/data/extractors/liquido/h5_extractor.html b/_modules/graphnet/data/extractors/liquido/h5_extractor.html new file mode 100644 index 000000000..d3e267f2f --- /dev/null +++ b/_modules/graphnet/data/extractors/liquido/h5_extractor.html @@ -0,0 +1,488 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + graphnet.data.extractors.liquido.h5_extractor — graphnet documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
    + +
    + + +
    + + + + +
    +
    + +
    +
    +
    + +
    +
    +
    +
    +
    +
    + + +
    +
    +
    + +
    +
    + +

    Source code for graphnet.data.extractors.liquido.h5_extractor

    +"""H5 Extractor for LiquidO data files."""
+from typing import List
+import numpy as np
+import pandas as pd
+import h5py
+
+from graphnet.data.extractors import Extractor
+
+
+
    
+[docs]
+class H5Extractor(Extractor):
+    """Class for extracting information from LiquidO h5 files."""
+
+    def __init__(self, extractor_name: str, column_names: List[str]):
+        """Construct H5Extractor.
+
+        Args:
+            extractor_name: Name of the `ParquetExtractor` instance.
+            Used to keep track of the provenance of different data,
+            and to name tables to which this data is saved.
+            column_names: Name of the columns in `extractor_name`.
+        """
+        # Member variable(s)
+        self._table = extractor_name
+        self._column_names = column_names
+        # Base class constructor
+        super().__init__(extractor_name=extractor_name)
+
+    def __call__(self, file_path: str) -> pd.DataFrame:
+        """Extract information from h5 file."""
+        with h5py.File(file_path, "r") as f:
+            available_tables = [f for f in f.keys()]
+            if self._table in available_tables:
+                array = f[self._table][:]
+                # Will throw error if the number of columns don't match
+                self._verify_columns(array)
+                df = pd.DataFrame(array, columns=self._column_names)
+                return df
+            else:
+                return None
+
+    def _verify_columns(self, array: np.ndarray) -> None:
+        try:
+            assert array.shape[1] == len(self._column_names)
+        except AssertionError as e:
+            self.error(
+                f"Got {len(self._column_names)} column names but "
+                f"{self._table} has {array.shape[1]}. Please make sure "
+                f"that the column names match. ({self._column_names})"
+            )
+            raise e
    
+
+
+
+
    
+[docs]
+class H5HitExtractor(H5Extractor):
+    """Extractor for `HitData` in LiquidO H5 files."""
+
+    def __init__(self) -> None:
+        """Extractor for `HitData` in LiquidO H5 files."""
+        # Base class constructor
+        super().__init__(
+            extractor_name="HitData",
+            column_names=[
+                "event_no",
+                "sipmID",
+                "sipm_x",
+                "sipm_y",
+                "sipm_z",
+                "t",
+                "var",
+            ],
+        )
    
+
+
+
+
    
+[docs]
+class H5TruthExtractor(H5Extractor):
+    """Extractor for `TruthData` in LiquidO H5 files."""
+
+    def __init__(self) -> None:
+        """Extractor for `TruthData` in LiquidO H5 files."""
+        # Base class constructor
+        super().__init__(
+            extractor_name="TruthData",
+            column_names=[
+                "event_no",
+                "vertex_x",
+                "vertex_y",
+                "vertex_z",
+                "zenith",
+                "azimuth",
+                "interaction_time",
+                "energy",
+                "pid",
+            ],
+        )
    
+
+
    + +
    +
    +
    +
    +
    +
    +
    + +
    +
    +
    +
    +
    + © Copyright 2021-2024, GraphNeT team. + +
    + Created using + Sphinx 7.3.7. + and + Material for + Sphinx +
    +
    +
    +
    + + + + \ No newline at end of file diff --git a/_modules/graphnet/data/extractors/prometheus/prometheus_extractor.html b/_modules/graphnet/data/extractors/prometheus/prometheus_extractor.html new file mode 100644 index 000000000..c31911ff8 --- /dev/null +++ b/_modules/graphnet/data/extractors/prometheus/prometheus_extractor.html @@ -0,0 +1,488 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + graphnet.data.extractors.prometheus.prometheus_extractor — graphnet documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
    + +
    + + +
    + + + + +
    +
    + +
    +
    +
    + +
    +
    +
    +
    +
    +
    + + +
    +
    +
    + +
    +
    + +

    Source code for graphnet.data.extractors.prometheus.prometheus_extractor

    +"""Parquet Extractor for conversion of simulation files from PROMETHEUS."""
+from typing import List
+import pandas as pd
+import numpy as np
+
+from graphnet.data.extractors import Extractor
+
+
+
    
+[docs]
+class PrometheusExtractor(Extractor):
+    """Class for extracting information from PROMETHEUS parquet files.
+
+    Contains functionality required to extract data from PROMETHEUS parquet
+    files.
+    """
+
+    def __init__(self, extractor_name: str, columns: List[str]):
+        """Construct PrometheusExtractor.
+
+        Args:
+            extractor_name: Name of the `PrometheusExtractor` instance.
+            Used to keep track of the provenance of different data,
+            and to name tables to which this data is saved.
+            columns: List of column names to extract from the table.
+        """
+        # Member variable(s)
+        self._table = extractor_name
+        self._columns = columns
+        # Base class constructor
+        super().__init__(extractor_name=extractor_name)
+
+    def __call__(self, event: pd.DataFrame) -> pd.DataFrame:
+        """Extract information from parquet file."""
+        output = {key: [] for key in self._columns}  # type: ignore
+        for key in self._columns:
+            if key in event.keys():
+                data = event[key]
+                if isinstance(data, np.ndarray):
+                    data = data.tolist()
+                if isinstance(data, list):
+                    output[key].extend(data)
+                else:
+                    output[key].append(data)
+            else:
+                self.warning_once(f"{key} not found in {self._table}!")
+        return output
    
+
+
+
+
    
+[docs]
+class PrometheusTruthExtractor(PrometheusExtractor):
+    """Class for extracting event level truth from Prometheus parquet files.
+
+    This Extractor will "initial_state" i.e. neutrino truth.
+    """
+
+    def __init__(self, table_name: str = "mc_truth") -> None:
+        """Construct PrometheusTruthExtractor.
+
+        Args:
+            table_name: Name of the table in the parquet files that contain
+                event-level truth. Defaults to "mc_truth".
+        """
+        columns = [
+            "interaction",
+            "initial_state_energy",
+            "initial_state_type",
+            "initial_state_zenith",
+            "initial_state_azimuth",
+            "initial_state_x",
+            "initial_state_y",
+            "initial_state_z",
+        ]
+        super().__init__(extractor_name=table_name, columns=columns)
    
+
+
+
+
    
+[docs]
+class PrometheusFeatureExtractor(PrometheusExtractor):
+    """Class for extracting pulses/photons from Prometheus parquet files."""
+
+    def __init__(self, table_name: str = "photons"):
+        """Construct PrometheusFeatureExtractor.
+
+        Args:
+            table_name: Name of table in parquet files that contain the
+                photons/pulses. Defaults to "photons".
+        """
+        columns = [
+            "sensor_pos_x",
+            "sensor_pos_y",
+            "sensor_pos_z",
+            "string_id",
+            "sensor_id",
+            "t",
+        ]
+        super().__init__(extractor_name=table_name, columns=columns)
    
+
+
    + +
    +
    +
    +
    +
    +
    +
    + +
    +
    +
    +
    +
    + © Copyright 2021-2024, GraphNeT team. + +
    + Created using + Sphinx 7.3.7. + and + Material for + Sphinx +
    +
    +
    +
    + + + + \ No newline at end of file diff --git a/_modules/graphnet/data/parquet/deprecated_methods.html b/_modules/graphnet/data/parquet/deprecated_methods.html index 238ca2429..ca1425ee8 100644 --- a/_modules/graphnet/data/parquet/deprecated_methods.html +++ b/_modules/graphnet/data/parquet/deprecated_methods.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -409,7 +436,7 @@

    Source code Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/data/pipeline.html b/_modules/graphnet/data/pipeline.html deleted file mode 100644 index d969001ce..000000000 --- a/_modules/graphnet/data/pipeline.html +++ /dev/null @@ -1,595 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - graphnet.data.pipeline — graphnet documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Skip to content -
    - -
    - - -
    - - - - -
    -
    - -
    -
    -
    - -
    -
    -
    -
    -
    -
    - - -
    -
    -
    - -
    -
    - -

    Source code for graphnet.data.pipeline

    -"""Class(es) used for analysis in PISA."""
-
-from abc import ABC
-import dill
-from functools import reduce
-import os
-from typing import Dict, List, Optional, Tuple
-
-import numpy as np
-import pandas as pd
-from pytorch_lightning import Trainer
-import sqlite3
-import torch
-from torch.utils.data import DataLoader
-
-from graphnet.data.utilities.sqlite_utilities import (
-    create_table_and_save_to_sql,
-)
-from graphnet.training.utils import get_predictions, make_dataloader
-from graphnet.models.graphs import GraphDefinition
-
-from graphnet.utilities.logging import Logger
-
-
-
    
-[docs]
-class InSQLitePipeline(ABC, Logger):
-    """Create a SQLite database for PISA analysis.
-
-    The database will contain truth and GNN predictions and, if available,
-    RETRO reconstructions.
-    """
-
-    def __init__(
-        self,
-        module_dict: Dict,
-        features: List[str],
-        truth: List[str],
-        device: torch.device,
-        retro_table_name: str = "retro",
-        outdir: Optional[str] = None,
-        batch_size: int = 100,
-        n_workers: int = 10,
-        pipeline_name: str = "pipeline",
-    ):
-        """Initialise the pipeline.
-
-        Args:
-            module_dict: A dictionary with GNN modules from GraphNet. E.g.
-                {'energy': gnn_module_for_energy_regression}
-            features: List of input features for the GNN modules.
-            truth: List of truth for the GNN ModuleList.
-            device: The device used for computation.
-            retro_table_name: Name of the retro table for.
-            outdir: the directory in which the pipeline database will be
-                stored.
-            batch_size: Batch size for inference.
-            n_workers: Number of workers used in dataloading.
-            pipeline_name: Name of the pipeline. If such a pipeline already
-                exists, an error will be prompted to avoid overwriting.
-        """
-        self._pipeline_name = pipeline_name
-        self._device = device
-        self.n_workers = n_workers
-        self._features = features
-        self._truth = truth
-        self._batch_size = batch_size
-        self._outdir = outdir
-        self._module_dict = module_dict
-        self._retro_table_name = retro_table_name
-
-        # Base class constructor
-        super().__init__(name=__name__, class_name=self.__class__.__name__)
-
-    def __call__(
-        self,
-        database: str,
-        pulsemap: str,
-        graph_definition: GraphDefinition,
-        chunk_size: int = 1000000,
-    ) -> None:
-        """Run inference of each field in self._module_dict[target][''].
-
-        Args:
-            database: Path to database with pulsemap and truth.
-            pulsemap: Name of pulsemaps.
-            graph_definition: GraphDefinition for Dataset
-            chunk_size: database will be sliced in chunks of size `chunk_size`.
-                Use this parameter to control memory usage.
-        """
-        outdir = self._get_outdir(database)
-        if isinstance(
-            self._device, str
-        ):  # Because pytorch lightning insists on breaking pytorch cuda device naming scheme
-            device = int(self._device[-1])
-        if not os.path.isdir(outdir):
-            dataloaders, event_batches = self._setup_dataloaders(
-                graph_definition=graph_definition,
-                chunk_size=chunk_size,
-                db=database,
-                pulsemap=pulsemap,
-                selection=None,
-                persistent_workers=False,
-            )
-            i = 0
-            for dataloader in dataloaders:
-                self.info("CHUNK %s / %s" % (i, len(dataloaders)))
-                df = self._inference(device, dataloader)
-                truth = self._get_truth(database, event_batches[i].tolist())
-                retro = self._get_retro(database, event_batches[i].tolist())
-                self._append_to_pipeline(outdir, truth, retro, df)
-                i += 1
-        else:
-            self.info(outdir)
-            self.info(
-                "WARNING - Pipeline named %s already exists! \n Please rename pipeline!"
-                % self._pipeline_name
-            )
-
-    def _setup_dataloaders(
-        self,
-        chunk_size: int,
-        db: str,
-        pulsemap: str,
-        graph_definition: GraphDefinition,
-        selection: Optional[List[int]] = None,
-        persistent_workers: bool = False,
-    ) -> Tuple[List[DataLoader], List[np.ndarray]]:
-        if selection is None:
-            selection = self._get_all_event_nos(db)
-        n_chunks = np.ceil(len(selection) / chunk_size)
-        event_batches = np.array_split(selection, n_chunks)
-        dataloaders = []
-        for batch in event_batches:
-            dataloaders.append(
-                make_dataloader(
-                    db=db,
-                    graph_definition=graph_definition,
-                    pulsemaps=pulsemap,
-                    features=self._features,
-                    truth=self._truth,
-                    batch_size=self._batch_size,
-                    shuffle=False,
-                    selection=batch.tolist(),
-                    num_workers=self.n_workers,
-                    persistent_workers=persistent_workers,
-                )
-            )
-        return dataloaders, event_batches
-
-    def _get_all_event_nos(self, db: str) -> List[int]:
-        with sqlite3.connect(db) as con:
-            query = "SELECT event_no FROM truth"
-            selection = pd.read_sql(query, con).values.ravel().tolist()
-        return selection
-
-    def _combine_outputs(self, dataframes: List[pd.DataFrame]) -> pd.DataFrame:
-        return reduce(lambda x, y: pd.merge(x, y, on="event_no"), dataframes)
-
-    def _inference(
-        self, device: torch.device, dataloader: DataLoader
-    ) -> pd.DataFrame:
-        dataframes = []
-        for target in self._module_dict.keys():
-            # dataloader = iter(dataloader)
-            trainer = Trainer(devices=[device], accelerator="gpu")
-            model = torch.load(
-                self._module_dict[target]["path"],
-                map_location="cpu",
-                pickle_module=dill,
-            )
-            model.eval()
-            model.inference()
-            results = get_predictions(
-                trainer,
-                model,
-                dataloader,
-                self._module_dict[target]["output_column_names"],
-                additional_attributes=["event_no"],
-            )
-            dataframes.append(
-                results.sort_values("event_no").reset_index(drop=True)
-            )
-            df = self._combine_outputs(dataframes)
-        return df
-
-    def _get_outdir(self, database: str) -> str:
-        if self._outdir is None:
-            database_name = database.split("/")[-3]
-            outdir = (
-                database.split(database_name)[0]
-                + database_name
-                + "/pipelines/"
-                + self._pipeline_name
-            )
-        else:
-            outdir = self._outdir
-        return outdir
-
-    def _get_truth(self, database: str, selection: List[int]) -> pd.DataFrame:
-        with sqlite3.connect(database) as con:
-            query = "SELECT * FROM truth WHERE event_no in %s" % str(
-                tuple(selection)
-            )
-            truth = pd.read_sql(query, con)
-        return truth
-
-    def _get_retro(self, database: str, selection: List[int]) -> pd.DataFrame:
-        try:
-            with sqlite3.connect(database) as con:
-                query = "SELECT * FROM %s WHERE event_no in %s" % (
-                    self._retro_table_name,
-                    str(tuple(selection)),
-                )
-                retro = pd.read_sql(query, con)
-            return retro
-        except:  # noqa: E722
-            self.info("%s table does not exist" % self._retro_table_name)
-
-    def _append_to_pipeline(
-        self,
-        outdir: str,
-        truth: pd.DataFrame,
-        retro: pd.DataFrame,
-        df: pd.DataFrame,
-    ) -> None:
-        os.makedirs(outdir, exist_ok=True)
-        pipeline_database = outdir + "/%s.db" % self._pipeline_name
-        create_table_and_save_to_sql(df, "reconstruction", pipeline_database)
-        create_table_and_save_to_sql(truth, "truth", pipeline_database)
-        if isinstance(retro, pd.DataFrame):
-            create_table_and_save_to_sql(
-                retro, self._retro_table_name, pipeline_database
-            )
    
-
-
    - -
    -
    -
    -
    -
    -
    -
    - -
    -
    -
    -
    -
    - © Copyright 2021-2024, GraphNeT team. - -
    - Created using - Sphinx 7.2.6. - and - Material for - Sphinx -
    -
    -
    -
    - - - - \ No newline at end of file diff --git a/_modules/graphnet/data/pre_configured/dataconverters.html b/_modules/graphnet/data/pre_configured/dataconverters.html index 23e0e57ae..8eb56946a 100644 --- a/_modules/graphnet/data/pre_configured/dataconverters.html +++ b/_modules/graphnet/data/pre_configured/dataconverters.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -327,9 +354,10 @@

    Source c from typing import List, Union, Type from graphnet.data import DataConverter -from graphnet.data.readers import I3Reader +from graphnet.data.readers import I3Reader, ParquetReader from graphnet.data.writers import ParquetWriter, SQLiteWriter from graphnet.data.extractors.icecube import I3Extractor +from graphnet.data.extractors.internal import ParquetExtractor from graphnet.data.extractors.icecube.utilities.i3_filters import I3Filter @@ -427,6 +455,45 @@

    Source c outdir=outdir, ) + + +
    +[docs] +class ParquetToSQLiteConverter(DataConverter): + """Preconfigured DataConverter for converting Parquet to SQLite files. + + This class converts Parquet files written by ParquetWriter to SQLite. + """ + + def __init__( + self, + extractors: List[ParquetExtractor], + outdir: str, + index_column: str = "event_no", + num_workers: int = 1, + ): + """Convert internal Parquet files to SQLite. + + Args: + extractors: The `Extractor`(s) that will be applied to the input + files. + outdir: The directory to save the files in. + icetray_verbose: Set the level of verbosity of icetray. + Defaults to 0. + index_column: Name of the event id column added to the events. + Defaults to "event_no". + num_workers: The number of CPUs used for parallel processing. + Defaults to 1 (no multiprocessing). + """ + super().__init__( + file_reader=ParquetReader(), + save_method=SQLiteWriter(), + extractors=extractors, + num_workers=num_workers, + index_column=index_column, + outdir=outdir, + )
    + @@ -451,7 +518,7 @@

    Source c Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/data/readers/graphnet_file_reader.html b/_modules/graphnet/data/readers/graphnet_file_reader.html index b14cda367..f7706ba94 100644 --- a/_modules/graphnet/data/readers/graphnet_file_reader.html +++ b/_modules/graphnet/data/readers/graphnet_file_reader.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -328,16 +355,20 @@

    Source co file formats. """ -from typing import List, Union, OrderedDict, Any +from typing import List, Union, OrderedDict, Any, Dict from abc import abstractmethod, ABC import glob import os +import pandas as pd from graphnet.utilities.decorators import final from graphnet.utilities.logging import Logger from graphnet.data.dataclasses import I3FileSet from graphnet.data.extractors.extractor import Extractor from graphnet.data.extractors.icecube import I3Extractor +from graphnet.data.extractors.internal import ParquetExtractor +from graphnet.data.extractors.liquido import H5Extractor +from graphnet.data.extractors.prometheus import PrometheusExtractor
    @@ -357,13 +388,21 @@

    Source co _accepted_extractors: List[Any] = [] @abstractmethod - def __call__(self, file_path: Union[str, I3FileSet]) -> List[OrderedDict]: + def __call__( + self, file_path: Any + ) -> Union[List[OrderedDict[str, pd.DataFrame]], Dict[str, pd.DataFrame]]: """Open and apply extractors to a single file. - The `output` must be a list of dictionaries, where the number of events - in the file `n_events` satisfies `len(output) = n_events`. I.e each - element in the list is a dictionary, and each field in the dictionary - is the output of a single extractor. + The `output` must be either + A) list of dictionaries, where the number of events + in the file `n_events` satisfies `len(output) = n_events`. + I.e each element in the list is a dictionary, and each field in + the dictionary is the output of a single extractor. If this is + provided, the `DataConverter` will automatically assign event ids. + B) A single dictionary where each field contains a single dataframe, + which holds the data from the `Extractor` for the entire file. In + this case, the `Reader` must itself assign event ids. This method + is faster if your files are not storing events serially. """ @property @@ -412,7 +451,14 @@

    Source co [docs] @final def set_extractors( - self, extractors: Union[List[Extractor], List[I3Extractor]] + self, + extractors: Union[ + List[Extractor], + List[I3Extractor], + List[ParquetExtractor], + List[H5Extractor], + List[PrometheusExtractor], + ], ) -> None: """Set `Extractor`(s) as member variable. @@ -427,7 +473,14 @@

    Source co @final def _validate_extractors( - self, extractors: Union[List[Extractor], List[I3Extractor]] + self, + extractors: Union[ + List[Extractor], + List[I3Extractor], + List[ParquetExtractor], + List[H5Extractor], + List[PrometheusExtractor], + ], ) -> None: for extractor in extractors: try: @@ -500,7 +553,7 @@

    Source co

    Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/data/readers/i3reader.html b/_modules/graphnet/data/readers/i3reader.html index c0135b94a..b370044d7 100644 --- a/_modules/graphnet/data/readers/i3reader.html +++ b/_modules/graphnet/data/readers/i3reader.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -372,6 +399,8 @@

    Source code for graph icetray_verbose: Set the level of verbosity of icetray. Defaults to 0. """ + # checks + assert isinstance(gcd_rescue, str) # Set verbosity if icetray_verbose == 0: icetray.I3Logger.global_logger = icetray.I3NullLogger() @@ -442,12 +471,16 @@

    Source code for graph path, self._gcd_rescue, ) + # checks + assert len(i3_files) == len(gcd_files) # Pack as I3FileSets - filesets = [ - I3FileSet(i3_file, gcd_file) - for i3_file, gcd_file in zip(i3_files, gcd_files) - ] + filesets = [] + for i3_file, gcd_file in zip(i3_files, gcd_files): + assert isinstance(i3_file, str) + assert isinstance(gcd_file, str), print(gcd_file, self._gcd_rescue) + filesets.append(I3FileSet(i3_file, gcd_file)) + return filesets @@ -489,7 +522,7 @@

    Source code for graph Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/data/readers/internal_parquet_reader.html b/_modules/graphnet/data/readers/internal_parquet_reader.html new file mode 100644 index 000000000..a595fc887 --- /dev/null +++ b/_modules/graphnet/data/readers/internal_parquet_reader.html @@ -0,0 +1,448 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + graphnet.data.readers.internal_parquet_reader — graphnet documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
    + +
    + + +
    + + + + +
    +
    + +
    +
    +
    + +
    +
    +
    +
    +
    +
    + + +
    +
    +
    + +
    +
    + +

    Source code for graphnet.data.readers.internal_parquet_reader

    +"""Module containing different reader for GraphNeT internal parquet format."""
+
+from typing import List, Union, Dict
+from glob import glob
+import os
+import pandas as pd
+
+from graphnet.data.extractors.internal import ParquetExtractor
+from .graphnet_file_reader import GraphNeTFileReader
+
+
+
    
+[docs]
+class ParquetReader(GraphNeTFileReader):
+    """A class for reading the internal GraphNeT parquet format."""
+
+    _accepted_file_extensions = [".parquet"]
+    _accepted_extractors = [ParquetExtractor]
+
+    def __call__(self, file_path: str) -> Dict[str, pd.DataFrame]:
+        """Extract data from single parquet file.
+
+        Args:
+            file_path: Path to parquet file.
+
+        Returns:
+            Extracted data.
+        """
+        # Open file
+        outputs = {}
+        for extractor in self._extractors:
+            output = extractor(file_path)
+            if output is not None:
+                outputs[extractor._extractor_name] = output
+        return outputs
+
+
    
+[docs]
+    def find_files(self, path: Union[str, List[str]]) -> List[str]:
+        """Search parquet folders for files.
+
+        Args:
+            path: directory containing the parquet folders.
+
+        Returns:
+            List of parquet files in the folders.
+        """
+        # Find all I3 and GCD files in the specified directories.
+        files = []
+        if isinstance(path, str):
+            path = [path]
+        for p in path:
+            for extractor in self._extractors:
+                files.extend(
+                    glob(
+                        os.path.join(p, extractor._extractor_name, "*.parquet")
+                    )
+                )
+        return files
    
+
    
+
+
    + +
    +
    +
    +
    +
    +
    +
    + +
    +
    +
    +
    +
    + © Copyright 2021-2024, GraphNeT team. + +
    + Created using + Sphinx 7.3.7. + and + Material for + Sphinx +
    +
    +
    +
    + + + + \ No newline at end of file diff --git a/_modules/graphnet/data/readers/liquido_reader.html b/_modules/graphnet/data/readers/liquido_reader.html new file mode 100644 index 000000000..7286950ab --- /dev/null +++ b/_modules/graphnet/data/readers/liquido_reader.html @@ -0,0 +1,442 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + graphnet.data.readers.liquido_reader — graphnet documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
    + +
    + + +
    + + + + +
    +
    + +
    +
    +
    + +
    +
    +
    +
    +
    +
    + + +
    +
    +
    + +
    +
    + +

    Source code for graphnet.data.readers.liquido_reader

    +"""Modules for reading data files from LiquidO."""
+
+from typing import List, Union, Dict
+from glob import glob
+import os
+import pandas as pd
+
+from graphnet.data.extractors.liquido import H5Extractor
+from .graphnet_file_reader import GraphNeTFileReader
+
+
+
    
+[docs]
+class LiquidOReader(GraphNeTFileReader):
+    """A class for reading h5 files from LiquidO."""
+
+    _accepted_file_extensions = [".h5"]
+    _accepted_extractors = [H5Extractor]
+
+    def __call__(self, file_path: str) -> Dict[str, pd.DataFrame]:
+        """Extract data from single parquet file.
+
+        Args:
+            file_path: Path to h5 file.
+
+        Returns:
+            Extracted data.
+        """
+        # Open file
+        outputs = {}
+        for extractor in self._extractors:
+            output = extractor(file_path)
+            if output is not None:
+                outputs[extractor._extractor_name] = output
+        return outputs
+
+
    
+[docs]
+    def find_files(self, path: Union[str, List[str]]) -> List[str]:
+        """Search folder(s) for h5 files.
+
+        Args:
+            path: directory to search for h5 files.
+
+        Returns:
+            List of h5 files in the folders.
+        """
+        files = []
+        if isinstance(path, str):
+            path = [path]
+        for p in path:
+            files.extend(glob(os.path.join(p, "*.h5")))
+        return files
    
+
    
+
+
    + +
    +
    +
    +
    +
    +
    +
    + +
    +
    +
    +
    +
    + © Copyright 2021-2024, GraphNeT team. + +
    + Created using + Sphinx 7.3.7. + and + Material for + Sphinx +
    +
    +
    +
    + + + + \ No newline at end of file diff --git a/_modules/graphnet/data/readers/prometheus_reader.html b/_modules/graphnet/data/readers/prometheus_reader.html new file mode 100644 index 000000000..728856905 --- /dev/null +++ b/_modules/graphnet/data/readers/prometheus_reader.html @@ -0,0 +1,456 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + graphnet.data.readers.prometheus_reader — graphnet documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
    + +
    + + +
    + + + + +
    +
    + +
    +
    +
    + +
    +
    +
    +
    +
    +
    + + +
    +
    +
    + +
    +
    + +

    Source code for graphnet.data.readers.prometheus_reader

    +"""Modules for reading data files from the Prometheus project."""
+
+from typing import List, Union, OrderedDict
+import pandas as pd
+from pathlib import Path
+
+from graphnet.data.extractors.prometheus import PrometheusExtractor
+from .graphnet_file_reader import GraphNeTFileReader
+
+
+
    
+[docs]
+class PrometheusReader(GraphNeTFileReader):
+    """A class for reading parquet files from Prometheus simulation."""
+
+    _accepted_file_extensions = [".parquet"]
+    _accepted_extractors = [PrometheusExtractor]
+
+    def __call__(self, file_path: str) -> List[OrderedDict]:
+        """Extract data from single parquet file.
+
+        Args:
+            file_path: Path to parquet file.
+
+        Returns:
+            Extracted data.
+        """
+        # Open file
+        outputs = []
+        file = pd.read_parquet(file_path)
+        for k in range(len(file)):  # Loop over events in file
+            extracted_event = OrderedDict()
+            for extractor in self._extractors:
+                assert isinstance(extractor, PrometheusExtractor)
+                if extractor._table in file.columns:
+                    output = extractor(file[extractor._table][k])
+                    extracted_event[extractor._extractor_name] = output
+            outputs.append(extracted_event)
+        return outputs
+
+
    
+[docs]
+    def find_files(self, path: Union[str, List[str]]) -> List[str]:
+        """Search folder(s) for parquet files.
+
+        Args:
+            path: directory to search for parquet files.
+
+        Returns:
+            List of parquet files in the folders.
+        """
+        files = []
+        if isinstance(path, str):
+            path = [path]
+
+        # List of files as Path objects
+        for p in path:
+            files.extend(
+                list(Path(p).rglob(f"*{self.accepted_file_extensions}"))
+            )
+
+        # List of files as str's
+        paths_as_str: List[str] = []
+        for f in files:
+            paths_as_str.append(f.absolute().as_posix())
+
+        return paths_as_str
    
+
    
+
+
    + +
    +
    +
    +
    +
    +
    +
    + +
    +
    +
    +
    +
    + © Copyright 2021-2024, GraphNeT team. + +
    + Created using + Sphinx 7.3.7. + and + Material for + Sphinx +
    +
    +
    +
    + + + + \ No newline at end of file diff --git a/_modules/graphnet/data/sqlite/deprecated_methods.html b/_modules/graphnet/data/sqlite/deprecated_methods.html index d97e492fc..d431d8126 100644 --- a/_modules/graphnet/data/sqlite/deprecated_methods.html +++ b/_modules/graphnet/data/sqlite/deprecated_methods.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -411,7 +438,7 @@

    Source code Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/data/utilities/parquet_to_sqlite.html b/_modules/graphnet/data/utilities/parquet_to_sqlite.html deleted file mode 100644 index 63a97a6eb..000000000 --- a/_modules/graphnet/data/utilities/parquet_to_sqlite.html +++ /dev/null @@ -1,549 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - graphnet.data.utilities.parquet_to_sqlite — graphnet documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Skip to content -
    - -
    - - -
    - - - - -
    -
    - -
    -
    -
    - -
    -
    -
    -
    -
    -
    - - -
    -
    -
    - -
    -
    - -

    Source code for graphnet.data.utilities.parquet_to_sqlite

    -"""Utilities for converting files from Parquet to SQLite."""
-
-import glob
-import os
-from typing import List, Optional, Union
-
-import awkward as ak
-import numpy as np
-import pandas as pd
-from tqdm.auto import trange
-
-from graphnet.data.utilities.sqlite_utilities import (
-    create_table_and_save_to_sql,
-)
-from graphnet.utilities.logging import Logger
-
-
-
    
-[docs]
-class ParquetToSQLiteConverter(Logger):
-    """Convert Parquet files to a SQLite database.
-
-    Each event in the parquet file(s) are assigned a unique event id. By
-    default, every field in the parquet file(s) are extracted. One can choose
-    to exclude certain fields by using the argument exclude_fields.
-    """
-
-    def __init__(
-        self,
-        parquet_path: Union[str, List[str]],
-        mc_truth_table: str = "mc_truth",
-        excluded_fields: Optional[Union[str, List[str]]] = None,
-    ):
-        """Construct `ParquetToSQLiteConverter`."""
-        # checks
-        if isinstance(parquet_path, str):
-            pass
-        elif isinstance(parquet_path, list):
-            assert isinstance(
-                parquet_path[0], str
-            ), "Argument `parquet_path` must be a string or list of strings"
-        else:
-            assert isinstance(
-                parquet_path, str
-            ), "Argument `parquet_path` must be a string or list of strings"
-
-        assert isinstance(
-            mc_truth_table, str
-        ), "Argument `mc_truth_table` must be a string"
-        self._parquet_files = self._find_parquet_files(parquet_path)
-        if excluded_fields is not None:
-            self._excluded_fields = excluded_fields
-        else:
-            self._excluded_fields = []
-        self._mc_truth_table = mc_truth_table
-        self._event_counter = 0
-
-        # Base class constructor
-        super().__init__(name=__name__, class_name=self.__class__.__name__)
-
-    def _find_parquet_files(self, paths: Union[str, List[str]]) -> List[str]:
-        if isinstance(paths, str):
-            if paths.endswith(".parquet"):
-                files = [paths]
-            else:
-                files = glob.glob(f"{paths}/*.parquet")
-        elif isinstance(paths, list):
-            files = []
-            for path in paths:
-                files.extend(self._find_parquet_files(path))
-        assert len(files) > 0, f"No files found in {paths}"
-        return files
-
-
    
-[docs]
-    def run(self, outdir: str, database_name: str) -> None:
-        """Run Parquet to SQLite conversion.
-
-        Args:
-            outdir: Output directory for SQLite database.
-            database_name: Name of output SQLite database.
-        """
-        self._create_output_directories(outdir, database_name)
-        database_path = os.path.join(
-            outdir, database_name, "data", database_name + ".db"
-        )
-        self.info(f"Processing {len(self._parquet_files)} Parquet file(s)")
-        for i in trange(
-            len(self._parquet_files),
-            unit="file(s)",
-            colour="green",
-            position=0,
-        ):
-            parquet_file = ak.from_parquet(self._parquet_files[i])
-            n_events_in_file = self._count_events(parquet_file)
-            for j in trange(
-                len(parquet_file.fields),
-                desc="%s" % (self._parquet_files[i].split("/")[-1]),
-                colour="#ffa500",
-                position=1,
-                leave=False,
-            ):
-                if parquet_file.fields[j] not in self._excluded_fields:
-                    self._save_to_sql(
-                        database_path,
-                        parquet_file,
-                        parquet_file.fields[j],
-                        n_events_in_file,
-                    )
-            self._event_counter += n_events_in_file
-        self._save_config(outdir, database_name)
-        self.info(
-            "Database saved at: \n"
-            f"{outdir}/{database_name}/data/{database_name}.db"
-        )
    
-
-
-    def _count_events(self, open_parquet_file: ak.Array) -> int:
-        return len(open_parquet_file[self._mc_truth_table])
-
-    def _save_to_sql(
-        self,
-        database_path: str,
-        ak_array: ak.Array,
-        field_name: str,
-        n_events_in_file: int,
-    ) -> None:
-        df = self._convert_to_dataframe(ak_array, field_name, n_events_in_file)
-
-        if len(df) > n_events_in_file:
-            is_pulse_map = True
-        else:
-            is_pulse_map = False
-
-        create_table_and_save_to_sql(
-            df,
-            field_name,
-            database_path,
-            integer_primary_key=not is_pulse_map,
-        )
-
-    def _convert_to_dataframe(
-        self,
-        ak_array: ak.Array,
-        field_name: str,
-        n_events_in_file: int,
-    ) -> pd.DataFrame:
-        df = pd.DataFrame(ak.to_pandas(ak_array[field_name]))
-        if len(df.columns) == 1:
-            if df.columns == ["values"]:
-                df.columns = [field_name]
-
-        if "event_no" in df.columns:
-            return df
-
-        # If true, the dataframe contains more than 1 row pr. event (i.e.,
-        # pulsemap).
-        if len(df) != n_events_in_file:
-            event_nos = []
-            c = 0
-            for event_no in range(
-                self._event_counter, self._event_counter + n_events_in_file, 1
-            ):
-                try:
-                    event_nos.extend(
-                        np.repeat(event_no, len(df[df.columns[0]][c])).tolist()
-                    )
-
-                # KeyError indicates that this df has no entry for event_no
-                # (e.g., an event with no detector response).
-                except KeyError:
-                    pass
-                c += 1
-        else:
-            event_nos = np.arange(0, n_events_in_file, 1) + self._event_counter
-        df["event_no"] = event_nos
-        return df
-
-    def _create_output_directories(
-        self, outdir: str, database_name: str
-    ) -> None:
-        os.makedirs(outdir + "/" + database_name + "/data", exist_ok=True)
-        os.makedirs(outdir + "/" + database_name + "/config", exist_ok=True)
-
-    def _save_config(self, outdir: str, database_name: str) -> None:
-        """Save the list of converted Parquet files to a CSV file."""
-        df = pd.DataFrame(data=self._parquet_files, columns=["files"])
-        df.to_csv(outdir + "/" + database_name + "/config/files.csv")
    
-
-
    - -
    -
    -
    -
    -
    -
    -
    - -
    -
    -
    -
    -
    - © Copyright 2021-2024, GraphNeT team. - -
    - Created using - Sphinx 7.2.6. - and - Material for - Sphinx -
    -
    -
    -
    - - - - \ No newline at end of file diff --git a/_modules/graphnet/data/utilities/random.html b/_modules/graphnet/data/utilities/random.html index 3ccca08ca..800f43590 100644 --- a/_modules/graphnet/data/utilities/random.html +++ b/_modules/graphnet/data/utilities/random.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -375,7 +402,7 @@

    Source code for graph Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/data/utilities/sqlite_utilities.html b/_modules/graphnet/data/utilities/sqlite_utilities.html index a3137f96f..d597c655a 100644 --- a/_modules/graphnet/data/utilities/sqlite_utilities.html +++ b/_modules/graphnet/data/utilities/sqlite_utilities.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -397,9 +424,13 @@

    Source code primary_key_candidates.append(val) # There should only be one primary key: - assert len(primary_key_candidates) == 1 + if len(primary_key_candidates) > 0: + assert len(primary_key_candidates) == 1 + primary_key_name = primary_key_candidates[0] + else: + primary_key_name = None - return integer_primary_key, primary_key_candidates[0] + return integer_primary_key, primary_key_name @@ -575,7 +606,7 @@

    Source code Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/data/utilities/string_selection_resolver.html b/_modules/graphnet/data/utilities/string_selection_resolver.html index 8b7938f75..4d6d2a40c 100644 --- a/_modules/graphnet/data/utilities/string_selection_resolver.html +++ b/_modules/graphnet/data/utilities/string_selection_resolver.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -676,7 +703,7 @@

    So Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/data/writers/graphnet_writer.html b/_modules/graphnet/data/writers/graphnet_writer.html index 872aa88c1..81aeb36eb 100644 --- a/_modules/graphnet/data/writers/graphnet_writer.html +++ b/_modules/graphnet/data/writers/graphnet_writer.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -446,7 +473,7 @@

    Source code fo Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/data/writers/parquet_writer.html b/_modules/graphnet/data/writers/parquet_writer.html index f854d3e96..f2663fadb 100644 --- a/_modules/graphnet/data/writers/parquet_writer.html +++ b/_modules/graphnet/data/writers/parquet_writer.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -325,10 +352,14 @@

    Source code for """DataConverter for the Parquet backend.""" import os -from typing import List, Optional, Dict +from typing import List, Optional, Dict, Any -import awkward import pandas as pd +import polars as pol +from glob import glob +from tqdm import tqdm +import numpy as np +from multiprocessing import Pool from .graphnet_writer import GraphNeTWriter @@ -338,14 +369,30 @@

    Source code for class ParquetWriter(GraphNeTWriter): """Class for writing interim data format to Parquet.""" - # Class variables - _file_extension = ".parquet" - _merge_dataframes = False + def __init__( + self, + truth_table: str = "truth", + index_column: str = "event_no", + ) -> None: + """Construct `ParquetWriter`. + + Args: + truth_table: Name of the tables containing event-level truth data. + defaults to "truth". + index_column: The column used for indexation. + Defaults to "event_no". + """ + super().__init__(name=__name__, class_name=self.__class__.__name__) + # Class variables + self._file_extension = ".parquet" + self._merge_dataframes = True + self._index_column = index_column + self._truth_table = truth_table # Abstract method implementation(s) def _save_file( self, - data: Dict[str, List[pd.DataFrame]], + data: Dict[str, pd.DataFrame], output_file_path: str, n_events: int, ) -> None: @@ -353,31 +400,189 @@

    Source code for # Check(s) if n_events > 0: - events = [] - for k in range(n_events): - event = {} - for table in data.keys(): - event[table] = data[table][k].to_dict(orient="list") - - events.append(event) - - awkward.to_parquet(awkward.from_iter(events), output_file_path) + for table in data.keys(): + save_path = os.path.dirname(output_file_path) + file_name = os.path.splitext( + os.path.basename(output_file_path) + )[0] + + table_dir = os.path.join(save_path, f"{table}") + os.makedirs(table_dir, exist_ok=True) + df = data[table].set_index(self._index_column) + df.to_parquet( + os.path.join(table_dir, file_name + f"_{table}.parquet") + )
    [docs] - def merge_files(self, files: List[str], output_dir: str) -> None: - """Merge parquet files. + def merge_files( + self, + files: List[str], + output_dir: str, + events_per_batch: int = 200000, + num_workers: int = 1, + ) -> None: + """Convert files into shuffled batches. - Args: - files: input files for merging. - output_dir: directory to store merged file(s) in. + Events will be shuffled, and the resulting batches will constitute + random subsamples of the full dataset. - Raises: - NotImplementedError + Args: + files: Files converted to parquet. Note this argument is ignored + by this method, as these files are automatically found + using the `output_dir`. + output_dir: The directory to store the batched data. + events_per_batch: Number of events in each batch. + Defaults to 200000. + num_workers: Number of workers to use for merging. Defaults to 1. """ - self.error(f"{self.__class__.__name__} does not have a merge method.") - raise NotImplementedError
    - + # Handle inputs + input_dir = output_dir.replace("merged", "") + truth_dir = os.path.join(input_dir, self._truth_table) + tables = os.listdir(input_dir) + self._validate_inputs( + tables=tables, input_dir=input_dir, truth_dir=truth_dir + ) + + truth_files = glob(os.path.join(truth_dir, "*.parquet")) + + # Exit if no files found + if len(truth_files) == 0: + self.warning(f"No files found in {truth_dir}. Exiting.") + return + + # Produce a shuffled master-list of event_no's + truth_meta = self._identify_events( + index_column=self._index_column, + truth_table=self._truth_table, + truth_files=truth_files, + ) + + # Split event_nos into smaller batches "shards" + shards = self._split_dataframe( + df=truth_meta, chunk_size=events_per_batch + ) + + # Construct list of arguments for processing function + arguments = [] + for i in range(len(shards)): + arguments.append( + [ + tables, + shards[i], + input_dir, + i, + self._index_column, + output_dir, + ] + ) + + # Setup map function + if num_workers > 1: + self.info( + f"Processing {len(arguments)} batches using " + f"{num_workers} cores." + ) + pool = Pool(num_workers) + map_func = pool.imap + else: + self.info(f"Processing {len(arguments)} batches in main thread.") + map_func = map # type: ignore + + # Process files + for _ in map_func( + self._process_shard, + tqdm(arguments, unit="shard(s)", colour="green"), + ): + pass + + + def _identify_events( + self, index_column: str, truth_files: List[str], truth_table: str + ) -> pd.DataFrame: + res = pol.DataFrame() + for truth_file in truth_files: + df = pol.read_parquet(truth_file) + df2 = pol.concat( + [ + df.select([index_column]), + pol.DataFrame( + { + "file_name": np.repeat( + truth_file.replace( + f"_{truth_table}.parquet", "" + ).split("/")[-1], + len(df), + ) + } + ).select(["file_name"]), + ], + how="horizontal", + ) + res = pol.concat([res, df2]) + return res.to_pandas().sample(frac=1.0) + + def _split_dataframe( + self, df: pd.DataFrame, chunk_size: int + ) -> List[pd.DataFrame]: + chunks = list() + num_chunks = int(np.ceil(len(df) // chunk_size) + 1) + for i in range(num_chunks): + chunks.append(df[i * chunk_size : (i + 1) * chunk_size]) + return chunks + + def _process_shard(self, settings: List[Any]) -> None: + tables, splits, input_dir, batch_ids, index_column, outdir = settings + if outdir is None: + outdir = os.path.join(input_dir, "merged") + if not isinstance(splits, list): + splits = [splits] + + if not isinstance(batch_ids, list): + batch_ids = [batch_ids] + + for batch_id, split in zip(batch_ids, splits): + unique_files = pd.unique(split["file_name"]) + for table in tables: + table_shards = [] + for unique_file in unique_files: + path = ( + os.path.join(input_dir, table, unique_file) + + f"_{table}.parquet" + ) + df = pd.read_parquet(path) + + id = split[index_column][split["file_name"] == unique_file] + + # Filter out indices that point to empty events + idx = [i for i in id if i in df.index] + table_shards.append(df.loc[idx, :]) + + os.makedirs(os.path.join(outdir, table), exist_ok=True) + if len(table_shards) > 0: + combined_df = pd.concat(table_shards, axis=0) + combined_df.to_parquet( + os.path.join( + outdir, table, f"{table}_{batch_id}.parquet" + ) + ) + + def _validate_inputs( + self, tables: List[str], input_dir: str, truth_dir: str + ) -> None: + try: + assert "merged" not in tables + except AssertionError as e: + self.error( + f"Directory appears to already contain merged files" + f" under {os.path.join(input_dir, 'merged')}" + ) + raise e + try: + assert os.path.isdir(truth_dir) + except AssertionError as e: + self.error(f"Directory for truth {truth_dir} does not exist.") + raise e @@ -403,7 +608,7 @@

    Source code for Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/data/writers/sqlite_writer.html b/_modules/graphnet/data/writers/sqlite_writer.html index 6a16d4171..1703f796c 100644 --- a/_modules/graphnet/data/writers/sqlite_writer.html +++ b/_modules/graphnet/data/writers/sqlite_writer.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -350,6 +377,7 @@

    Source code for self, merged_database_name: str = "merged.db", max_table_size: Optional[int] = None, + index_column: str = "event_no", ) -> None: """Initialize `SQLiteWriter`. @@ -363,12 +391,14 @@

    Source code for you have many events, as tables exceeding 400 million rows tend to be noticably slower to query. Defaults to None (All events are put into a single database). + index_column: Name of column that contains event id. """ # Member Variables self._file_extension = ".db" self._merge_dataframes = True self._max_table_size = max_table_size self._database_name = merged_database_name + self._index_column = index_column # Add file extension to database name if forgotten if not self._database_name.endswith(self._file_extension): @@ -409,6 +439,7 @@

    Source code for output_file_path, default_type="FLOAT", integer_primary_key=len(df) <= n_events, + index_column=self._index_column, ) saved_any = True @@ -423,6 +454,7 @@

    Source code for self, files: List[str], output_dir: str, + primary_key_rescue: str = "event_no", ) -> None: """SQLite-specific method for merging output files/databases. @@ -437,6 +469,9 @@

    Source code for you have many events, as tables exceeding 400 million rows tend to be noticably slower to query. Defaults to None (All events are put into a single database.) + primary_key_rescue: The name of the columns on which the primary + key is constructed. This will only be used if it is not + possible to infer the primary key name. """ # Warnings if self._max_table_size: @@ -448,10 +483,10 @@

    Source code for # Set variables self._partition_count = 1 + self._primary_key_rescue = primary_key_rescue # Construct full database path database_path = os.path.join(output_dir, self._database_name) - print(database_path) # Start merging if files are given if len(files) > 0: os.makedirs(output_dir, exist_ok=True) @@ -487,10 +522,11 @@

    Source code for # Merge temporary databases into newly created one for file_count, input_file in tqdm(enumerate(files), colour="green"): - # Extract table names and index column name in database try: tables, primary_key = get_primary_keys(database=input_file) + if primary_key is None: + primary_key = self._primary_key_rescue except AssertionError as e: if "No tables found in database." in str(e): self.warning(f"Database {input_file} is empty. Skipping.") @@ -585,7 +621,7 @@

    Source code for Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/datasets/prometheus_datasets.html b/_modules/graphnet/datasets/prometheus_datasets.html new file mode 100644 index 000000000..fb26e78fa --- /dev/null +++ b/_modules/graphnet/datasets/prometheus_datasets.html @@ -0,0 +1,543 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + graphnet.datasets.prometheus_datasets — graphnet documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
    + +
    + + +
    + + + + +
    +
    + +
    +
    +
    + +
    +
    +
    +
    +
    +
    + + +
    +
    +
    + +
    +
    + +

    Source code for graphnet.datasets.prometheus_datasets

    +"""Public datasets from Prometheus Simulation."""
+from typing import Dict, Any, List, Tuple, Union
+import os
+from sklearn.model_selection import train_test_split
+from glob import glob
+import numpy as np
+
+from graphnet.training.labels import Direction, Track
+from graphnet.data import ERDAHostedDataset
+from graphnet.data.constants import FEATURES
+from graphnet.data.utilities import query_database
+
+
+
    
+[docs]
+class PublicPrometheusDataset(ERDAHostedDataset):
+    """A generic class for public Prometheus Datasets hosted using ERDA."""
+
+    # Static Member Variables:
+    _pulsemaps = ["photons"]
+    _truth_table = "mc_truth"
+    _event_truth = [
+        "interaction",
+        "initial_state_energy",
+        "initial_state_type",
+        "initial_state_zenith",
+        "initial_state_azimuth",
+        "initial_state_x",
+        "initial_state_y",
+        "initial_state_z",
+    ]
+    _pulse_truth = None
+    _features = FEATURES.PROMETHEUS
+
+    def _prepare_args(
+        self, backend: str, features: List[str], truth: List[str]
+    ) -> Tuple[Dict[str, Any], Union[List[int], None], Union[List[int], None]]:
+        """Prepare arguments for dataset.
+
+        Args:
+            backend: backend of dataset. Either "parquet" or "sqlite".
+            features: List of features from user to use as input.
+            truth: List of event-level truth variables from user.
+
+        Returns: Dataset arguments, train/val selection, test selection
+        """
+        if backend == "sqlite":
+            dataset_paths = glob(os.path.join(self.dataset_dir, "*.db"))
+            assert len(dataset_paths) == 1
+            dataset_path = dataset_paths[0]
+            event_nos = query_database(
+                database=dataset_path,
+                query=f"SELECT event_no FROM {self._truth_table}",
+            )
+            train_val, test = train_test_split(
+                event_nos["event_no"].tolist(),
+                test_size=0.10,
+                random_state=42,
+                shuffle=True,
+            )
+        elif backend == "parquet":
+            dataset_path = self.dataset_dir
+            n_batches = len(
+                glob(
+                    os.path.join(dataset_path, self._truth_table, "*.parquet")
+                )
+            )
+            train_val, test = train_test_split(
+                np.arange(0, n_batches),
+                test_size=0.10,
+                random_state=42,
+                shuffle=True,
+            )
+        dataset_args = {
+            "truth_table": self._truth_table,
+            "pulsemaps": self._pulsemaps,
+            "path": dataset_path,
+            "graph_definition": self._graph_definition,
+            "features": features,
+            "truth": truth,
+            "labels": {
+                "direction": Direction(
+                    azimuth_key="initial_state_azimuth",
+                    zenith_key="initial_state_zenith",
+                ),
+                "track": Track(
+                    pid_key="initial_state_type", interaction_key="interaction"
+                ),
+            },
+        }
+
+        return dataset_args, train_val, test
    
+
+
+
+
    
+[docs]
+class TRIDENTSmall(PublicPrometheusDataset):
+    """Public Dataset for Prometheus simulation of a TRIDENT geometry.
+
+    Contains ~ 1 million track events between 10 GeV - 10 TeV.
+    """
+
+    _experiment = "TRIDENT Prometheus Simulation"
+    _creator = "Rasmus F. Ørsøe"
+    _comments = (
+        "Contains ~1 million track events."
+        " Simulation produced by Stephan Meighen-Berger, "
+        "U. Melbourne."
+    )
+    _available_backends = ["sqlite"]
+    _file_hashes = {"sqlite": "aooZEpVsAM"}
+    _citation = None
    
+
+
+
+
    
+[docs]
+class PONESmall(PublicPrometheusDataset):
+    """Public Dataset for Prometheus simulation of a P-ONE geometry.
+
+    Contains ~ 1 million track events between 10 GeV - 10 TeV.
+    """
+
+    _experiment = "P-ONE Prometheus Simulation"
+    _creator = "Rasmus F. Ørsøe"
+    _comments = (
+        "Contains ~1 million track events."
+        " Simulation produced by Stephan Meighen-Berger, "
+        "U. Melbourne."
+    )
+    _available_backends = ["sqlite"]
+    _file_hashes = {"sqlite": "GIt0hlG9qI"}
+    _citation = None
    
+
+
+
+
    
+[docs]
+class BaikalGVDSmall(PublicPrometheusDataset):
+    """Public Dataset for Prometheus simulation of a Baikal-GVD geometry.
+
+    Contains ~ 1 million track events between 10 GeV - 10 TeV.
+    """
+
+    _experiment = "Baikal-GVD Prometheus Simulation"
+    _creator = "Rasmus F. Ørsøe"
+    _comments = (
+        "Contains ~1 million track events."
+        " Simulation produced by Stephan Meighen-Berger, "
+        "U. Melbourne."
+    )
+    _available_backends = ["sqlite"]
+    _file_hashes = {"sqlite": "FtFs5fxXB7"}
+    _citation = None
    
+
+
    + +
    +
    +
    +
    +
    +
    +
    + +
    +
    +
    +
    +
    + © Copyright 2021-2024, GraphNeT team. + +
    + Created using + Sphinx 7.3.7. + and + Material for + Sphinx +
    +
    +
    +
    + + + + \ No newline at end of file diff --git a/_modules/graphnet/datasets/test_dataset.html b/_modules/graphnet/datasets/test_dataset.html new file mode 100644 index 000000000..42ae61be0 --- /dev/null +++ b/_modules/graphnet/datasets/test_dataset.html @@ -0,0 +1,454 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + graphnet.datasets.test_dataset — graphnet documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
    + +
    + + +
    + + + + +
    +
    + +
    +
    +
    + +
    +
    +
    +
    +
    +
    + + +
    +
    +
    + +
    +
    + +

    Source code for graphnet.datasets.test_dataset

    +"""A CuratedDataset for unit tests."""
+from typing import Dict, Any, List, Tuple, Union
+import os
+
+from graphnet.data import ERDAHostedDataset
+from graphnet.data.constants import FEATURES
+
+
+
    
+[docs]
+class TestDataset(ERDAHostedDataset):
+    """A CuratedDataset class for unit tests of ERDAHosted Datasets.
+
+    This dataset should not be used outside the context of unit tests.
+    """
+
+    # Static Member Variables:
+    _pulsemaps = ["photons"]
+    _truth_table = "mc_truth"
+    _event_truth = [
+        "interaction",
+        "initial_state_energy",
+        "initial_state_type",
+        "initial_state_zenith",
+        "initial_state_azimuth",
+        "initial_state_x",
+        "initial_state_y",
+        "initial_state_z",
+    ]
+    _pulse_truth = None
+    _features = FEATURES.PROMETHEUS
+    _experiment = "ARCA Prometheus Simulation"
+    _creator = "Rasmus F. Ørsøe"
+    _comments = (
+        "This Dataset should be used for unit tests only."
+        " Simulation produced by Stephan Meighen-Berger, "
+        "U. Melbourne."
+    )
+    _available_backends = ["sqlite"]
+    _file_hashes = {"sqlite": "EK3hSNgYr5"}
+    _citation = None
+
+    def _prepare_args(
+        self, backend: str, features: List[str], truth: List[str]
+    ) -> Tuple[Dict[str, Any], Union[List[int], None], Union[List[int], None]]:
+        """Prepare arguments for dataset.
+
+        Args:
+            backend: backend of dataset. Either "parquet" or "sqlite"
+            features: List of features from user to use as input.
+            truth: List of event-level truth form user.
+
+        Returns: Dataset arguments and selections
+        """
+        dataset_path = os.path.join(self.dataset_dir, "merged.db")
+
+        dataset_args = {
+            "truth_table": self._truth_table,
+            "pulsemaps": self._pulsemaps,
+            "path": dataset_path,
+            "graph_definition": self._graph_definition,
+            "features": features,
+            "truth": truth,
+        }
+        selection = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9]  # event 5 is empty
+        return dataset_args, selection, None
    
+
+
    + +
    +
    +
    +
    +
    +
    +
    + +
    +
    +
    +
    +
    + © Copyright 2021-2024, GraphNeT team. + +
    + Created using + Sphinx 7.3.7. + and + Material for + Sphinx +
    +
    +
    +
    + + + + \ No newline at end of file diff --git a/_modules/graphnet/deployment/deployer.html b/_modules/graphnet/deployment/deployer.html index ea737ce89..a861b606f 100644 --- a/_modules/graphnet/deployment/deployer.html +++ b/_modules/graphnet/deployment/deployer.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -483,7 +510,7 @@

    Source code for graphne Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/deployment/deployment_module.html b/_modules/graphnet/deployment/deployment_module.html index d035ff90b..64cc88236 100644 --- a/_modules/graphnet/deployment/deployment_module.html +++ b/_modules/graphnet/deployment/deployment_module.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -449,7 +476,7 @@

    Source code fo Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/deployment/icecube/cleaning_module.html b/_modules/graphnet/deployment/icecube/cleaning_module.html index 90cb9682f..01270e793 100644 --- a/_modules/graphnet/deployment/icecube/cleaning_module.html +++ b/_modules/graphnet/deployment/icecube/cleaning_module.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -577,7 +604,7 @@

    Source c Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/deployment/icecube/inference_module.html b/_modules/graphnet/deployment/icecube/inference_module.html index a43c935a0..62afac462 100644 --- a/_modules/graphnet/deployment/icecube/inference_module.html +++ b/_modules/graphnet/deployment/icecube/inference_module.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -554,7 +581,7 @@

    Source Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/exceptions/exceptions.html b/_modules/graphnet/exceptions/exceptions.html new file mode 100644 index 000000000..ba18b5143 --- /dev/null +++ b/_modules/graphnet/exceptions/exceptions.html @@ -0,0 +1,395 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + graphnet.exceptions.exceptions — graphnet documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
    + +
    + + +
    + + + + +
    +
    + +
    +
    +
    + +
    +
    +
    +
    +
    +
    + + +
    +
    +
    + +
    +
    + +

    Source code for graphnet.exceptions.exceptions

    +"""Module containing GraphNeT-specific Exceptions."""
+
+
+
    
+[docs]
+class ColumnMissingException(Exception):
+    """Exception to indicate a missing column in a dataset."""
    
+
+
    + +
    +
    +
    +
    +
    +
    +
    + +
    +
    +
    +
    +
    + © Copyright 2021-2024, GraphNeT team. + +
    + Created using + Sphinx 7.3.7. + and + Material for + Sphinx +
    +
    +
    +
    + + + + \ No newline at end of file diff --git a/_modules/graphnet/models/coarsening.html b/_modules/graphnet/models/coarsening.html index 301d35d73..ee7357e9b 100644 --- a/_modules/graphnet/models/coarsening.html +++ b/_modules/graphnet/models/coarsening.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -694,7 +721,7 @@

    Source code for graphnet. Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/models/components/embedding.html b/_modules/graphnet/models/components/embedding.html index 9e280dde3..f73cb60b1 100644 --- a/_modules/graphnet/models/components/embedding.html +++ b/_modules/graphnet/models/components/embedding.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -327,6 +354,8 @@

    Source code for import torch.nn as nn from torch.functional import Tensor +from typing import Optional + from pytorch_lightning import LightningModule @@ -385,34 +414,60 @@

    Source code for This module incorporates sinusoidal positional embeddings and auxiliary embeddings to process input sequences and produce meaningful - representations. + representations. The module assumes that the input data is in the format of + (x, y, z, time, charge, auxiliary), being the first four features + mandatory. """ def __init__( self, seq_length: int = 128, + mlp_dim: Optional[int] = None, output_dim: int = 384, scaled: bool = False, + n_features: int = 6, ): """Construct `FourierEncoder`. Args: seq_length: Dimensionality of the base sinusoidal positional embeddings. - output_dim: Output dimensionality of the final projection. + mlp_dim (Optional): Size of hidden, latent space of MLP. If not + given, `mlp_dim` is set automatically as multiples of + `seq_length` (in consistent with the 2nd place solution), + depending on `n_features`. + output_dim: Dimension of the output (I.e. number of columns). scaled: Whether or not to scale the embeddings. + n_features: The number of features in the input data. """ super().__init__() + self.sin_emb = SinusoidalPosEmb(dim=seq_length, scaled=scaled) self.aux_emb = nn.Embedding(2, seq_length // 2) self.sin_emb2 = SinusoidalPosEmb(dim=seq_length // 2, scaled=scaled) - self.projection = nn.Sequential( - nn.Linear(6 * seq_length, 6 * seq_length), - nn.LayerNorm(6 * seq_length), + + if n_features < 4: + raise ValueError( + f"At least x, y, z and time of the DOM are required. Got only " + f"{n_features} features." + ) + elif n_features >= 6: + hidden_dim = 6 * seq_length + else: + hidden_dim = int((n_features + 0.5) * seq_length) + + if mlp_dim is None: + mlp_dim = hidden_dim + + self.mlp = nn.Sequential( + nn.Linear(hidden_dim, mlp_dim), + nn.LayerNorm(mlp_dim), nn.GELU(), - nn.Linear(6 * seq_length, output_dim), + nn.Linear(mlp_dim, output_dim), ) + self.n_features = n_features +
    [docs] def forward( @@ -422,19 +477,23 @@

    Source code for ) -> Tensor: """Forward pass.""" length = torch.log10(seq_length.to(dtype=x.dtype)) - x = torch.cat( - [ - self.sin_emb(4096 * x[:, :, :3]).flatten(-2), # pos - self.sin_emb(1024 * x[:, :, 4]), # charge - self.sin_emb(4096 * x[:, :, 3]), # time - self.aux_emb(x[:, :, 5].long()), # auxiliary - self.sin_emb2(length) - .unsqueeze(1) - .expand(-1, max(seq_length), -1), - ], - -1, - ) - x = self.projection(x) + embeddings = [self.sin_emb(4096 * x[:, :, :3]).flatten(-2)] # Position + + if self.n_features >= 5: + embeddings.append(self.sin_emb(1024 * x[:, :, 4])) # Charge + + embeddings.append(self.sin_emb(4096 * x[:, :, 3])) # Time + + if self.n_features >= 6: + embeddings.append(self.aux_emb(x[:, :, 5].long())) # Auxiliary + + embeddings.append( + self.sin_emb2(length).unsqueeze(1).expand(-1, max(seq_length), -1) + ) # Length + + x = torch.cat(embeddings, -1) + x = self.mlp(x) + return x

    @@ -507,7 +566,7 @@

    Source code for Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/models/components/layers.html b/_modules/graphnet/models/components/layers.html index 02ee5c87f..8a42cce29 100644 --- a/_modules/graphnet/models/components/layers.html +++ b/_modules/graphnet/models/components/layers.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -999,7 +1026,7 @@

    Source code for gr Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/models/components/pool.html b/_modules/graphnet/models/components/pool.html index 11ce78f3d..ce921b2ce 100644 --- a/_modules/graphnet/models/components/pool.html +++ b/_modules/graphnet/models/components/pool.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -642,7 +669,7 @@

    Source code for grap Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/models/detector/detector.html b/_modules/graphnet/models/detector/detector.html index be4d6bf1d..2cc389fd0 100644 --- a/_modules/graphnet/models/detector/detector.html +++ b/_modules/graphnet/models/detector/detector.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -436,7 +463,7 @@

    Source code for gr Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/models/detector/icecube.html b/_modules/graphnet/models/detector/icecube.html index 67974ea57..b43da6a7e 100644 --- a/_modules/graphnet/models/detector/icecube.html +++ b/_modules/graphnet/models/detector/icecube.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -383,6 +410,13 @@

    Source code for gra class IceCubeKaggle(Detector): """`Detector` class for Kaggle Competition.""" + geometry_table_path = os.path.join( + ICECUBE_GEOMETRY_TABLE_DIR, "icecube86.parquet" + ) + xyz = ["x", "y", "z"] + string_id_column = "string" + sensor_id_column = "sensor_id" +
    [docs] def feature_map(self) -> Dict[str, Callable]: @@ -533,7 +567,7 @@

    Source code for gra

    Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/models/detector/liquido.html b/_modules/graphnet/models/detector/liquido.html new file mode 100644 index 000000000..2688671f0 --- /dev/null +++ b/_modules/graphnet/models/detector/liquido.html @@ -0,0 +1,428 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + graphnet.models.detector.liquido — graphnet documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
    + +
    + + +
    + + + + +
    +
    + +
    +
    +
    + +
    +
    +
    +
    +
    +
    + + +
    +
    +
    + +
    +
    + +

    Source code for graphnet.models.detector.liquido

    +"""LiquidO-specific `Detector` class(es)."""
+
+from typing import Dict, Callable
+import torch
+import os
+
+from graphnet.models.detector.detector import Detector
+from graphnet.constants import LIQUIDO_GEOMETRY_TABLE_DIR
+
+
+
    
+[docs]
+class LiquidO_v1(Detector):
+    """`Detector` class for LiquidO prototype."""
+
+    geometry_table_path = os.path.join(
+        LIQUIDO_GEOMETRY_TABLE_DIR, "liquido_v1.parquet"
+    )
+    xyz = ["sipm_x", "sipm_y", "sipm_z"]
+    string_id_column = "fiber_id"
+    sensor_id_column = "sipm_id"
+
+
    
+[docs]
+    def feature_map(self) -> Dict[str, Callable]:
+        """Map standardization functions to each dimension."""
+        feature_map = {
+            "sipm_x": self._sipm_xyz,
+            "sipm_y": self._sipm_xyz,
+            "sipm_z": self._sipm_xyz,
+            "t": self._t,
+        }
+        return feature_map
    
+
+
+    def _sipm_xyz(self, x: torch.tensor) -> torch.tensor:
+        return x / 1000
+
+    def _t(self, x: torch.tensor) -> torch.tensor:
+        return x / 500
    
+
+
    + +
    +
    +
    +
    +
    +
    +
    + +
    +
    +
    +
    +
    + © Copyright 2021-2024, GraphNeT team. + +
    + Created using + Sphinx 7.3.7. + and + Material for + Sphinx +
    +
    +
    +
    + + + + \ No newline at end of file diff --git a/_modules/graphnet/models/detector/prometheus.html b/_modules/graphnet/models/detector/prometheus.html index 3674c8065..3903aa155 100644 --- a/_modules/graphnet/models/detector/prometheus.html +++ b/_modules/graphnet/models/detector/prometheus.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -332,13 +359,265 @@

    Source code for from graphnet.constants import PROMETHEUS_GEOMETRY_TABLE_DIR +
    +[docs] +class ORCA150SuperDense(Detector): + """`Detector` class for Prometheus ORCA150SuperDense.""" + + geometry_table_path = os.path.join( + PROMETHEUS_GEOMETRY_TABLE_DIR, "orca_150.parquet" + ) + xyz = ["sensor_pos_x", "sensor_pos_y", "sensor_pos_z"] + string_id_column = "sensor_string_id" + sensor_id_column = "sensor_id" + +
    +[docs] + def feature_map(self) -> Dict[str, Callable]: + """Map standardization functions to each dimension.""" + feature_map = { + "sensor_pos_x": self._sensor_pos_xy, + "sensor_pos_y": self._sensor_pos_xy, + "sensor_pos_z": self._sensor_pos_z, + "t": self._t, + } + return feature_map
    + + + def _sensor_pos_xy(self, x: torch.tensor) -> torch.tensor: + return x / 100 + + def _sensor_pos_z(self, x: torch.tensor) -> torch.tensor: + return (x + 350) / 100 + + def _t(self, x: torch.tensor) -> torch.tensor: + return x / 1.05e04
    + + + +
    +[docs] +class TRIDENT1211(Detector): + """`Detector` class for Prometheus TRIDENT1211.""" + + geometry_table_path = os.path.join( + PROMETHEUS_GEOMETRY_TABLE_DIR, "trident.parquet" + ) + xyz = ["sensor_pos_x", "sensor_pos_y", "sensor_pos_z"] + string_id_column = "sensor_string_id" + sensor_id_column = "sensor_id" + +
    +[docs] + def feature_map(self) -> Dict[str, Callable]: + """Map standardization functions to each dimension.""" + feature_map = { + "sensor_pos_x": self._sensor_pos_xy, + "sensor_pos_y": self._sensor_pos_xy, + "sensor_pos_z": self._sensor_pos_z, + "t": self._t, + } + return feature_map
    + + + def _sensor_pos_xy(self, x: torch.tensor) -> torch.tensor: + return x / 1900 + + def _sensor_pos_z(self, x: torch.tensor) -> torch.tensor: + return x / 3000 + + def _t(self, x: torch.tensor) -> torch.tensor: + return x / 1.05e04
    + + + +
    +[docs] +class IceCubeUpgrade7(Detector): + """`Detector` class for Prometheus IceCubeUpgrade7.""" + + geometry_table_path = os.path.join( + PROMETHEUS_GEOMETRY_TABLE_DIR, "icecube_upgrade.parquet" + ) + xyz = ["sensor_pos_x", "sensor_pos_y", "sensor_pos_z"] + string_id_column = "sensor_string_id" + sensor_id_column = "sensor_id" + +
    +[docs] + def feature_map(self) -> Dict[str, Callable]: + """Map standardization functions to each dimension.""" + feature_map = { + "sensor_pos_x": self._sensor_pos_xy, + "sensor_pos_y": self._sensor_pos_xy, + "sensor_pos_z": self._sensor_pos_z, + "t": self._t, + } + return feature_map
    + + + def _sensor_pos_xy(self, x: torch.tensor) -> torch.tensor: + return x / 10 + + def _sensor_pos_z(self, x: torch.tensor) -> torch.tensor: + return x / 2000 + + def _t(self, x: torch.tensor) -> torch.tensor: + return x / 1.05e04
    + + + +
    +[docs] +class WaterDemo81(Detector): + """`Detector` class for Prometheus WaterDemo81.""" + + geometry_table_path = os.path.join( + PROMETHEUS_GEOMETRY_TABLE_DIR, "demo_water.parquet" + ) + xyz = ["sensor_pos_x", "sensor_pos_y", "sensor_pos_z"] + string_id_column = "sensor_string_id" + sensor_id_column = "sensor_id" + +
    +[docs] + def feature_map(self) -> Dict[str, Callable]: + """Map standardization functions to each dimension.""" + feature_map = { + "sensor_pos_x": self._sensor_pos_xy, + "sensor_pos_y": self._sensor_pos_xy, + "sensor_pos_z": self._sensor_pos_z, + "t": self._t, + } + return feature_map
    + + + def _sensor_pos_xy(self, x: torch.tensor) -> torch.tensor: + return x / 500 + + def _sensor_pos_z(self, x: torch.tensor) -> torch.tensor: + return x / 2000 + + def _t(self, x: torch.tensor) -> torch.tensor: + return x / 1.05e04
    + + + +
    +[docs] +class BaikalGVD8(Detector): + """`Detector` class for Prometheus BaikalGVD8.""" + + geometry_table_path = os.path.join( + PROMETHEUS_GEOMETRY_TABLE_DIR, "gvd.parquet" + ) + xyz = ["sensor_pos_x", "sensor_pos_y", "sensor_pos_z"] + string_id_column = "sensor_string_id" + sensor_id_column = "sensor_id" + +
    +[docs] + def feature_map(self) -> Dict[str, Callable]: + """Map standardization functions to each dimension.""" + feature_map = { + "sensor_pos_x": self._sensor_pos_xy, + "sensor_pos_y": self._sensor_pos_xy, + "sensor_pos_z": self._sensor_pos_z, + "t": self._t, + } + return feature_map
    + + + def _sensor_pos_xy(self, x: torch.tensor) -> torch.tensor: + return x / 10 + + def _sensor_pos_z(self, x: torch.tensor) -> torch.tensor: + return x / 1000 + + def _t(self, x: torch.tensor) -> torch.tensor: + return x / 1.05e04
    + + + +
    +[docs] +class IceDemo81(Detector): + """`Detector` class for Prometheus IceDemo81.""" + + geometry_table_path = os.path.join( + PROMETHEUS_GEOMETRY_TABLE_DIR, "demo_ice.parquet" + ) + xyz = ["sensor_pos_x", "sensor_pos_y", "sensor_pos_z"] + string_id_column = "sensor_string_id" + sensor_id_column = "sensor_id" + +
    +[docs] + def feature_map(self) -> Dict[str, Callable]: + """Map standardization functions to each dimension.""" + feature_map = { + "sensor_pos_x": self._sensor_pos_xy, + "sensor_pos_y": self._sensor_pos_xy, + "sensor_pos_z": self._sensor_pos_z, + "t": self._t, + } + return feature_map
    + + + def _sensor_pos_xy(self, x: torch.tensor) -> torch.tensor: + return x / 500 + + def _sensor_pos_z(self, x: torch.tensor) -> torch.tensor: + return x / 3000 + + def _t(self, x: torch.tensor) -> torch.tensor: + return x / 1.05e04
    + + + +
    +[docs] +class ARCA115(Detector): + """`Detector` class for Prometheus ARCA115.""" + + geometry_table_path = os.path.join( + PROMETHEUS_GEOMETRY_TABLE_DIR, "arca.parquet" + ) + xyz = ["sensor_pos_x", "sensor_pos_y", "sensor_pos_z"] + string_id_column = "sensor_string_id" + sensor_id_column = "sensor_id" + +
    +[docs] + def feature_map(self) -> Dict[str, Callable]: + """Map standardization functions to each dimension.""" + feature_map = { + "sensor_pos_x": self._sensor_pos_xy, + "sensor_pos_y": self._sensor_pos_xy, + "sensor_pos_z": self._sensor_pos_z, + "t": self._t, + } + return feature_map
    + + + def _sensor_pos_xy(self, x: torch.tensor) -> torch.tensor: + return x / 100 + + def _sensor_pos_z(self, x: torch.tensor) -> torch.tensor: + return x / 1000 + + def _t(self, x: torch.tensor) -> torch.tensor: + return x / 1.05e04
    + + +
    [docs] class ORCA150(Detector): - """`Detector` class for Prometheus prototype.""" + """`Detector` class for Prometheus ORCA150.""" geometry_table_path = os.path.join( - PROMETHEUS_GEOMETRY_TABLE_DIR, "orca_150.parquet" + PROMETHEUS_GEOMETRY_TABLE_DIR, "orca.parquet" ) xyz = ["sensor_pos_x", "sensor_pos_y", "sensor_pos_z"] string_id_column = "sensor_string_id" @@ -357,11 +636,149 @@

    Source code for return feature_map

    + def _sensor_pos_xy(self, x: torch.tensor) -> torch.tensor: + return x / 10 + + def _sensor_pos_z(self, x: torch.tensor) -> torch.tensor: + return x / 100 + + def _t(self, x: torch.tensor) -> torch.tensor: + return x / 1.05e04 + + + +
    +[docs] +class IceCube86Prometheus(Detector): + """`Detector` class for Prometheus IceCube86.""" + + geometry_table_path = os.path.join( + PROMETHEUS_GEOMETRY_TABLE_DIR, "icecube86.parquet" + ) + xyz = ["sensor_pos_x", "sensor_pos_y", "sensor_pos_z"] + string_id_column = "sensor_string_id" + sensor_id_column = "sensor_id" + +
    +[docs] + def feature_map(self) -> Dict[str, Callable]: + """Map standardization functions to each dimension.""" + feature_map = { + "sensor_pos_x": self._sensor_pos_xy, + "sensor_pos_y": self._sensor_pos_xy, + "sensor_pos_z": self._sensor_pos_z, + "t": self._t, + } + return feature_map
    + + def _sensor_pos_xy(self, x: torch.tensor) -> torch.tensor: return x / 100 def _sensor_pos_z(self, x: torch.tensor) -> torch.tensor: - return (x + 350) / 100 + return x / 1000 + + def _t(self, x: torch.tensor) -> torch.tensor: + return x / 1.05e04
    + + + +
    +[docs] +class IceCubeDeepCore8(Detector): + """`Detector` class for Prometheus IceCubeDeepCore8.""" + + geometry_table_path = os.path.join( + PROMETHEUS_GEOMETRY_TABLE_DIR, "icecube_deepcore.parquet" + ) + xyz = ["sensor_pos_x", "sensor_pos_y", "sensor_pos_z"] + string_id_column = "sensor_string_id" + sensor_id_column = "sensor_id" + +
    +[docs] + def feature_map(self) -> Dict[str, Callable]: + """Map standardization functions to each dimension.""" + feature_map = { + "sensor_pos_x": self._sensor_pos_xy, + "sensor_pos_y": self._sensor_pos_xy, + "sensor_pos_z": self._sensor_pos_z, + "t": self._t, + } + return feature_map
    + + + def _sensor_pos_xy(self, x: torch.tensor) -> torch.tensor: + return x / 100 + + def _sensor_pos_z(self, x: torch.tensor) -> torch.tensor: + return x / 1000 + + def _t(self, x: torch.tensor) -> torch.tensor: + return x / 1.05e04
    + + + +
    +[docs] +class IceCubeGen2(Detector): + """`Detector` class for Prometheus IceCubeGen2.""" + + geometry_table_path = os.path.join( + PROMETHEUS_GEOMETRY_TABLE_DIR, "icecube_gen2.parquet" + ) + xyz = ["sensor_pos_x", "sensor_pos_y", "sensor_pos_z"] + string_id_column = "sensor_string_id" + sensor_id_column = "sensor_id" + +
    +[docs] + def feature_map(self) -> Dict[str, Callable]: + """Map standardization functions to each dimension.""" + feature_map = { + "sensor_pos_x": self._sensor_pos_xyz, + "sensor_pos_y": self._sensor_pos_xyz, + "sensor_pos_z": self._sensor_pos_xyz, + "t": self._t, + } + return feature_map
    + + + def _sensor_pos_xyz(self, x: torch.tensor) -> torch.tensor: + return x / 1000 + + def _t(self, x: torch.tensor) -> torch.tensor: + return x / 1.05e04
    + + + +
    +[docs] +class PONETriangle(Detector): + """`Detector` class for Prometheus PONE Triangle.""" + + geometry_table_path = os.path.join( + PROMETHEUS_GEOMETRY_TABLE_DIR, "pone_triangle.parquet" + ) + xyz = ["sensor_pos_x", "sensor_pos_y", "sensor_pos_z"] + string_id_column = "sensor_string_id" + sensor_id_column = "sensor_id" + +
    +[docs] + def feature_map(self) -> Dict[str, Callable]: + """Map standardization functions to each dimension.""" + feature_map = { + "sensor_pos_x": self._sensor_pos_xyz, + "sensor_pos_y": self._sensor_pos_xyz, + "sensor_pos_z": self._sensor_pos_xyz, + "t": self._t, + } + return feature_map
    + + + def _sensor_pos_xyz(self, x: torch.tensor) -> torch.tensor: + return x / 100 def _t(self, x: torch.tensor) -> torch.tensor: return x / 1.05e04
    @@ -370,8 +787,8 @@

    Source code for
    [docs] -class Prometheus(ORCA150): - """Reference to ORCA150."""
    +class Prometheus(ORCA150SuperDense): + """Reference to ORCA150SuperDense.""" @@ -397,7 +814,7 @@

    Source code for Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/models/gnn/RNN_tito.html b/_modules/graphnet/models/gnn/RNN_tito.html index 155e0f2e8..31dd6c280 100644 --- a/_modules/graphnet/models/gnn/RNN_tito.html +++ b/_modules/graphnet/models/gnn/RNN_tito.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -482,7 +509,7 @@

    Source code for graphne Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/models/gnn/convnet.html b/_modules/graphnet/models/gnn/convnet.html index 9c1b3f2f7..ed02b94df 100644 --- a/_modules/graphnet/models/gnn/convnet.html +++ b/_modules/graphnet/models/gnn/convnet.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -470,7 +497,7 @@

    Source code for graphnet Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/models/gnn/dynedge.html b/_modules/graphnet/models/gnn/dynedge.html index d939a00c7..deacc6246 100644 --- a/_modules/graphnet/models/gnn/dynedge.html +++ b/_modules/graphnet/models/gnn/dynedge.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -358,7 +385,7 @@

    Source code for graphnet readout_layer_sizes: Optional[List[int]] = None, global_pooling_schemes: Optional[Union[str, List[str]]] = None, add_global_variables_after_pooling: bool = False, - activation_layer: Callable = None, + activation_layer: Optional[str] = None, add_norm_layer: bool = False, skip_readout: bool = False, ): @@ -483,8 +510,14 @@

    Source code for graphnet add_global_variables_after_pooling ) - if activation_layer is None: + if activation_layer is None or activation_layer.lower() == "relu": activation_layer = torch.nn.ReLU() + elif activation_layer.lower() == "gelu": + activation_layer = torch.nn.GELU() + else: + raise ValueError( + f"Activation layer {activation_layer} not supported." + ) # Base class constructor super().__init__(nb_inputs, self._readout_layer_sizes[-1]) @@ -695,7 +728,7 @@

    Source code for graphnet Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/models/gnn/dynedge_jinst.html b/_modules/graphnet/models/gnn/dynedge_jinst.html index 54e3e08fc..3e4beece3 100644 --- a/_modules/graphnet/models/gnn/dynedge_jinst.html +++ b/_modules/graphnet/models/gnn/dynedge_jinst.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -505,7 +532,7 @@

    Source code for gr Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/models/gnn/dynedge_kaggle_tito.html b/_modules/graphnet/models/gnn/dynedge_kaggle_tito.html index 61998b585..29744d2af 100644 --- a/_modules/graphnet/models/gnn/dynedge_kaggle_tito.html +++ b/_modules/graphnet/models/gnn/dynedge_kaggle_tito.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -630,7 +657,7 @@

    Source code Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/models/gnn/gnn.html b/_modules/graphnet/models/gnn/gnn.html index 4f0a11b6d..11acff46b 100644 --- a/_modules/graphnet/models/gnn/gnn.html +++ b/_modules/graphnet/models/gnn/gnn.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -387,7 +414,7 @@

    Source code for graphnet.mod Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/models/gnn/icemix.html b/_modules/graphnet/models/gnn/icemix.html index d59d697b9..d65297300 100644 --- a/_modules/graphnet/models/gnn/icemix.html +++ b/_modules/graphnet/models/gnn/icemix.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -333,7 +360,7 @@

    Source code for graphnet. """ import torch import torch.nn as nn -from typing import Set, Dict, Any, List +from typing import Set, Dict, Any from graphnet.models.components.layers import ( Block_rel, @@ -360,7 +387,8 @@

    Source code for graphnet. def __init__( self, hidden_dim: int = 384, - seq_length: int = 128, + mlp_ratio: int = 4, + seq_length: int = 192, depth: int = 12, head_size: int = 32, depth_rel: int = 4, @@ -368,11 +396,13 @@

    Source code for graphnet. scaled_emb: bool = False, include_dynedge: bool = False, dynedge_args: Dict[str, Any] = None, + n_features: int = 6, ): """Construct `DeepIce`. Args: hidden_dim: The latent feature dimension. + mlp_ratio: Mlp expansion ratio of FourierEncoder and Transformer. seq_length: The base feature dimension. depth: The depth of the transformer. head_size: The size of the attention heads. @@ -385,11 +415,16 @@

    Source code for graphnet. provided, DynEdge will be initialized with the original Kaggle Competition settings. If `include_dynedge` is False, this argument have no impact. + n_features: The number of features in the input data. """ super().__init__(seq_length, hidden_dim) fourier_out_dim = hidden_dim // 2 if include_dynedge else hidden_dim self.fourier_ext = FourierEncoder( - seq_length, fourier_out_dim, scaled=scaled_emb + seq_length=seq_length, + mlp_dim=None, + output_dim=fourier_out_dim, + scaled=scaled_emb, + n_features=n_features, ) self.rel_pos = SpacetimeEncoder(head_size) self.sandwich = nn.ModuleList( @@ -406,7 +441,7 @@

    Source code for graphnet. Block( input_dim=hidden_dim, num_heads=hidden_dim // head_size, - mlp_ratio=4, + mlp_ratio=mlp_ratio, drop_path=0.0 * (i / (depth - 1)), init_values=1, ) @@ -428,7 +463,7 @@

    Source code for graphnet. (336, 256), ], global_pooling_schemes=None, - activation_layer=nn.GELU(), + activation_layer="gelu", add_norm_layer=True, skip_readout=True, ) @@ -514,7 +549,7 @@

    Source code for graphnet. Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/models/graphs/edges/edges.html b/_modules/graphnet/models/graphs/edges/edges.html index c8778c6a0..cb3d3fbe5 100644 --- a/_modules/graphnet/models/graphs/edges/edges.html +++ b/_modules/graphnet/models/graphs/edges/edges.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -545,7 +572,7 @@

    Source code for g Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/models/graphs/edges/minkowski.html b/_modules/graphnet/models/graphs/edges/minkowski.html index eb0721ff9..1c218cda2 100644 --- a/_modules/graphnet/models/graphs/edges/minkowski.html +++ b/_modules/graphnet/models/graphs/edges/minkowski.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -451,7 +478,7 @@

    Source code f Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/models/graphs/graph_definition.html b/_modules/graphnet/models/graphs/graph_definition.html index 141e4a4e4..5b13ae1db 100644 --- a/_modules/graphnet/models/graphs/graph_definition.html +++ b/_modules/graphnet/models/graphs/graph_definition.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -801,7 +828,7 @@

    Source code Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/models/graphs/graphs.html b/_modules/graphnet/models/graphs/graphs.html index 7e77b2ccc..55767ca84 100644 --- a/_modules/graphnet/models/graphs/graphs.html +++ b/_modules/graphnet/models/graphs/graphs.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -405,7 +432,7 @@

    Source code for graphn Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/models/graphs/nodes/nodes.html b/_modules/graphnet/models/graphs/nodes/nodes.html index e11b5d06f..139545acf 100644 --- a/_modules/graphnet/models/graphs/nodes/nodes.html +++ b/_modules/graphnet/models/graphs/nodes/nodes.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -324,7 +351,7 @@

    Source code for graphnet.models.graphs.nodes.nodes

     """Class(es) for building/connecting graphs."""
 
-from typing import List, Tuple, Optional, Union
+from typing import List, Tuple, Optional, Dict
 from abc import abstractmethod
 
 import torch
@@ -666,7 +693,12 @@ 
    Source code for g
         input_feature_names: Optional[List[str]] = None,
         max_pulses: int = 768,
         z_name: str = "dom_z",
-        hlc_name: str = "hlc",
+        hlc_name: Optional[str] = "hlc",
+        add_ice_properties: bool = True,
+        ice_args: Dict[str, Optional[float]] = {
+            "z_offset": None,
+            "z_scaling": None,
+        },
     ) -> None:
         """Construct `IceMixNodes`.
 
@@ -676,9 +708,11 @@ 
    Source code for g
             max_pulses: Maximum number of pulses to keep in the event.
             z_name: Name of the z-coordinate column.
             hlc_name: Name of the `Hard Local Coincidence Check` column.
+            add_ice_properties: If True, scattering and absoption length of
+            ice in IceCube are added to the feature set based on z coordinate.
+            ice_args: Offset and scaling of the z coordinate in the Detector,
+            to be able to make similar conversion in the ice data.
         """
-        super().__init__(input_feature_names=input_feature_names)
-
         if input_feature_names is None:
             input_feature_names = [
                 "dom_x",
@@ -690,33 +724,39 @@ 
    Source code for g
                 "rde",
             ]
 
-        if z_name not in input_feature_names:
-            raise ValueError(
-                f"z name {z_name} not found in "
-                f"input_feature_names {input_feature_names}"
-            )
+        if add_ice_properties:
+            if z_name not in input_feature_names:
+                raise ValueError(
+                    f"z name '{z_name}' not found in "
+                    f"input_feature_names {input_feature_names}"
+                )
+            self.all_features = input_feature_names + [
+                "scatt_lenght",
+                "abs_lenght",
+            ]
+            self.f_scattering, self.f_absoprtion = ice_transparency(**ice_args)
+        else:
+            self.all_features = input_feature_names
+
+        super().__init__(input_feature_names=input_feature_names)
+
         if hlc_name not in input_feature_names:
-            raise ValueError(
-                f"hlc name {hlc_name} not found in "
-                f"input_feature_names {input_feature_names}"
+            self.warning(
+                f"hlc name '{hlc_name}' not found in input_feature_names"
+                f" '{input_feature_names}', subsampling will be random."
             )
-
-        self.all_features = input_feature_names + [
-            "scatt_lenght",
-            "abs_lenght",
-        ]
+            hlc_name = None
 
         self.feature_indexes = {
             feat: self.all_features.index(feat) for feat in input_feature_names
         }
 
-        self.f_scattering, self.f_absoprtion = ice_transparency()
-
         self.input_feature_names = input_feature_names
         self.n_features = len(self.all_features)
         self.max_length = max_pulses
         self.z_name = z_name
         self.hlc_name = hlc_name
+        self.add_ice_properties = add_ice_properties
 
     def _define_output_feature_names(
         self, input_feature_names: List[str]
@@ -743,35 +783,47 @@ 
    Source code for g
             ids = torch.arange(event_length)
         else:
             ids = torch.randperm(event_length)
-            auxiliary_n = torch.nonzero(
-                x[:, self.feature_indexes[self.hlc_name]] == 0
-            ).squeeze(1)
-            auxiliary_p = torch.nonzero(
-                x[:, self.feature_indexes[self.hlc_name]] == 1
-            ).squeeze(1)
-            ids_n = ids[auxiliary_n][: min(self.max_length, len(auxiliary_n))]
-            ids_p = ids[auxiliary_p][
-                : min(self.max_length - len(ids_n), len(auxiliary_p))
-            ]
-            ids = torch.cat([ids_n, ids_p]).sort().values
+            if self.hlc_name is not None:
+                auxiliary_n = torch.nonzero(
+                    x[:, self.feature_indexes[self.hlc_name]] == 0
+                ).squeeze(1)
+                auxiliary_p = torch.nonzero(
+                    x[:, self.feature_indexes[self.hlc_name]] == 1
+                ).squeeze(1)
+                ids_n = ids[auxiliary_n][
+                    : min(self.max_length, len(auxiliary_n))
+                ]
+                ids_p = ids[auxiliary_p][
+                    : min(self.max_length - len(ids_n), len(auxiliary_p))
+                ]
+
+                ids = torch.cat([ids_n, ids_p]).sort().values
+            else:
+                ids = ids[: self.max_length]
+
         return ids
 
     def _construct_nodes(self, x: torch.Tensor) -> Tuple[Data, List[str]]:
 
         event_length = x.shape[0]
-        x[:, self.feature_indexes[self.hlc_name]] = torch.logical_not(
-            x[:, self.feature_indexes[self.hlc_name]]
-        )  # hlc in kaggle was flipped
+        if self.hlc_name is not None:
+            x[:, self.feature_indexes[self.hlc_name]] = torch.logical_not(
+                x[:, self.feature_indexes[self.hlc_name]]
+            )  # hlc in kaggle was flipped
         ids = self._pulse_sampler(x, event_length)
         event_length = min(self.max_length, event_length)
 
         graph = torch.zeros([event_length, self.n_features])
-        for idx, feature in enumerate(
-            self.all_features[: self.n_features - 2]
-        ):
+
+        if self.add_ice_properties:
+            graph = self._add_ice_properties(graph, x, ids)
+            non_ice_features = self.all_features[: self.n_features - 2]
+        else:
+            non_ice_features = self.all_features
+
+        for idx, feature in enumerate(non_ice_features):
             graph[:event_length, idx] = x[ids, self.feature_indexes[feature]]
 
-        graph = self._add_ice_properties(graph, x, ids)  # ice properties
         return Data(x=graph)
    @@ -798,7 +850,7 @@

    Source code for g Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/models/graphs/utils.html b/_modules/graphnet/models/graphs/utils.html index 18ba17add..99d9f1c47 100644 --- a/_modules/graphnet/models/graphs/utils.html +++ b/_modules/graphnet/models/graphs/utils.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -324,7 +351,7 @@

    Source code for graphnet.models.graphs.utils

     """Utility functions for construction of graphs."""
 
-from typing import List, Tuple
+from typing import List, Tuple, Optional, Dict, Union
 import os
 import numpy as np
 import pandas as pd
@@ -503,13 +530,19 @@ 
    Source code for graphne
 
 
    
 [docs]
-def ice_transparency() -> Tuple[interp1d, interp1d]:
+def ice_transparency(
+    z_offset: float = None, z_scaling: float = None
+) -> Tuple[interp1d, interp1d]:
     """Return interpolation functions for optical properties of IceCube.
 
         NOTE: The resulting interpolation functions assumes that the
         Z-coordinate of pulse are scaled as `z = z/500`.
         Any deviation from this scaling method results in inaccurate results.
 
+    Args:
+        z_offset: Offset to be added to the depth of the DOM.
+        z_scaling: Scaling factor to be applied to the depth of the DOM.
+
     Returns:
         f_scattering: Function that takes a normalized depth and returns the
                       corresponding normalized scattering length.
@@ -520,8 +553,11 @@ 
    Source code for graphne
     df = pd.read_parquet(
         os.path.join(DATA_DIR, "ice_properties/ice_transparency.parquet"),
     )
-    df["z"] = df["depth"] - 1950
-    df["z_norm"] = df["z"] / 500
+
+    z_offset = z_offset or -1950.0
+    z_scaling = z_scaling or 500.0
+
+    df["z_norm"] = (df["depth"] + z_offset) / z_scaling
     df[
         ["scattering_len_norm", "absorption_len_norm"]
     ] = RobustScaler().fit_transform(df[["scattering_len", "absorption_len"]])
@@ -554,7 +590,7 @@ 
    Source code for graphne
               
           
    
             Created using
-            Sphinx 7.2.6.
+            Sphinx 7.3.7.
              and
             Material for
               Sphinx
diff --git a/_modules/graphnet/models/model.html b/_modules/graphnet/models/model.html
index 4449c04fe..15bde9cce 100644
--- a/_modules/graphnet/models/model.html
+++ b/_modules/graphnet/models/model.html
@@ -122,10 +122,9 @@
     
     
     
-    
+    
     
     
-    
     
     
   
@@ -281,14 +280,42 @@
     
  • 
     
     
-      Install
+      Installation
       
     
     
    • 
     
  • 
     
     
-      Contribute
+      Models In GraphNeT
+      
+    
+    
    • 
+    
  • 
+    
+    
+      Datasets In GraphNeT
+      
+    
+    
    • 
+    
  • 
+    
+    
+      Data Conversion in GraphNeT
+      
+    
+    
    • 
+    
  • 
+    
+    
+      Integrating New Experiments into GraphNeT
+      
+    
+    
    • 
+    
  • 
+    
+    
+      Contributing To GraphNeT
       
     
     
    • 
@@ -519,7 +546,7 @@ 
    Source code for graphnet.model
    Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/models/rnn/node_rnn.html b/_modules/graphnet/models/rnn/node_rnn.html index e508b91e5..09ef6b1c0 100644 --- a/_modules/graphnet/models/rnn/node_rnn.html +++ b/_modules/graphnet/models/rnn/node_rnn.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -491,7 +518,7 @@

    Source code for graphne Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/models/standard_averaged_model.html b/_modules/graphnet/models/standard_averaged_model.html index b6bf471e3..56b377034 100644 --- a/_modules/graphnet/models/standard_averaged_model.html +++ b/_modules/graphnet/models/standard_averaged_model.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -518,7 +545,7 @@

    Source code Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/models/standard_model.html b/_modules/graphnet/models/standard_model.html index badd936c1..bcf11812f 100644 --- a/_modules/graphnet/models/standard_model.html +++ b/_modules/graphnet/models/standard_model.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -918,7 +945,7 @@

    Source code for graph Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/models/task/classification.html b/_modules/graphnet/models/task/classification.html index cc251f57b..0ca049558 100644 --- a/_modules/graphnet/models/task/classification.html +++ b/_modules/graphnet/models/task/classification.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -397,7 +424,7 @@

    Source code for Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/models/task/reconstruction.html b/_modules/graphnet/models/task/reconstruction.html index 381966505..11dcdfe1a 100644 --- a/_modules/graphnet/models/task/reconstruction.html +++ b/_modules/graphnet/models/task/reconstruction.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -618,7 +645,7 @@

    Source code for Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/models/task/task.html b/_modules/graphnet/models/task/task.html index 97f4dce52..526a12357 100644 --- a/_modules/graphnet/models/task/task.html +++ b/_modules/graphnet/models/task/task.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -830,7 +857,7 @@

    Source code for graphnet.m Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/models/transformer/iseecube.html b/_modules/graphnet/models/transformer/iseecube.html new file mode 100644 index 000000000..f7373af7e --- /dev/null +++ b/_modules/graphnet/models/transformer/iseecube.html @@ -0,0 +1,495 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + graphnet.models.transformer.iseecube — graphnet documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
    + +
    + + +
    + + + + +
    +
    + +
    +
    +
    + +
    +
    +
    +
    +
    +
    + + +
    +
    +
    + +
    +
    + +

    Source code for graphnet.models.transformer.iseecube

    +"""Implementation of ISeeCube Transformer architecture used in.
+
+https://github.com/ChenLi2049/ISeeCube/
+"""
+
+import torch
+import torch.nn as nn
+
+from graphnet.models.components.embedding import FourierEncoder
+from graphnet.models.gnn.gnn import GNN
+from graphnet.models.utils import array_to_sequence
+
+from torchscale.architecture.config import EncoderConfig
+from torchscale.architecture.encoder import Encoder
+
+from torch_geometric.data import Data
+from torch import Tensor
+
+
+
    
+[docs]
+class ISeeCube(GNN):
+    """ISeeCube model."""
+
+    def __init__(
+        self,
+        hidden_dim: int = 384,
+        seq_length: int = 196,
+        num_layers: int = 16,
+        num_heads: int = 12,
+        mlp_dim: int = 1536,
+        rel_pos_buckets: int = 32,
+        max_rel_pos: int = 256,
+        num_register_tokens: int = 3,
+        scaled_emb: bool = False,
+        n_features: int = 6,
+    ):
+        """Construct `ISeeCube`.
+
+        Args:
+            hidden_dim: The latent feature dimension.
+            seq_length: The number of pulses in a neutrino event.
+            num_layers: The depth of the transformer.
+            num_heads: The number of the attention heads.
+            mlp_dim: The mlp dimension of FourierEncoder and Transformer.
+            rel_pos_buckets: Relative position buckets for relative position
+                bias.
+            max_rel_pos: Maximum relative position for relative position bias.
+            num_register_tokens: The number of register tokens.
+            scaled_emb: Whether to scale the sinusoidal positional embeddings.
+            n_features: The number of features in the input data.
+        """
+        super().__init__(seq_length, hidden_dim)
+        self.fourier_ext = FourierEncoder(
+            seq_length=seq_length,
+            mlp_dim=mlp_dim,
+            output_dim=hidden_dim,
+            scaled=scaled_emb,
+            n_features=n_features,
+        )
+        self.pos_embedding = nn.Parameter(
+            torch.empty(1, seq_length, hidden_dim).normal_(std=0.02),
+            requires_grad=True,
+        )
+
+        self.class_token = nn.Parameter(
+            torch.empty(1, 1, hidden_dim),
+            requires_grad=True,
+        )
+        self.register_tokens = nn.Parameter(
+            torch.empty(1, num_register_tokens, hidden_dim),
+            requires_grad=True,
+        )
+
+        encoder_config = EncoderConfig(
+            encoder_attention_heads=num_heads,
+            encoder_embed_dim=hidden_dim,
+            encoder_ffn_embed_dim=mlp_dim,
+            encoder_layers=num_layers,
+            rel_pos_buckets=rel_pos_buckets,
+            max_rel_pos=max_rel_pos,
+        )
+        self.encoder = Encoder(encoder_config)
+
+        self.layer_norm = nn.LayerNorm(hidden_dim)
+
+
    
+[docs]
+    def forward(self, data: Data) -> Tensor:
+        """Apply learnable forward pass."""
+        x, _, _ = array_to_sequence(data.x, data.batch, padding_value=0)
+        x = self.fourier_ext(x)
+        batch_size = x.shape[0]
+
+        x += self.pos_embedding
+
+        batch_class_token = self.class_token.expand(batch_size, -1, -1)
+        batch_register_tokens = self.register_tokens.expand(batch_size, -1, -1)
+        x = torch.cat([batch_class_token, batch_register_tokens, x], dim=1)
+
+        x = self.encoder(src_tokens=None, token_embeddings=x)
+        x = x["encoder_out"]
+
+        x = self.layer_norm(x)
+
+        return x[:, 0]
    
+
    
+
+
    + +
    +
    +
    +
    +
    +
    +
    + +
    +
    +
    +
    +
    + © Copyright 2021-2024, GraphNeT team. + +
    + Created using + Sphinx 7.3.7. + and + Material for + Sphinx +
    +
    +
    +
    + + + + \ No newline at end of file diff --git a/_modules/graphnet/models/utils.html b/_modules/graphnet/models/utils.html index 2640186a4..edf92c21b 100644 --- a/_modules/graphnet/models/utils.html +++ b/_modules/graphnet/models/utils.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -463,7 +490,7 @@

    Source code for graphnet.model Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/pisa/fitting.html b/_modules/graphnet/pisa/fitting.html deleted file mode 100644 index cb80d18d0..000000000 --- a/_modules/graphnet/pisa/fitting.html +++ /dev/null @@ -1,1183 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - graphnet.pisa.fitting — graphnet documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Skip to content -
    - -
    - - -
    - - - - -
    -
    - -
    -
    -
    - -
    -
    -
    -
    -
    -
    - - -
    -
    -
    - -
    -
    - -

    Source code for graphnet.pisa.fitting

    -"""Functions and classes for fitting contours using PISA."""
-
-import configparser
-from contextlib import contextmanager
-import io
-import multiprocessing
-import os
-import random
-from typing import Any, Dict, List, Optional, Tuple, TYPE_CHECKING
-
-from configupdater import ConfigUpdater
-import matplotlib as mpl
-import matplotlib.pyplot as plt
-import numpy as np
-import pandas as pd
-
-from graphnet.utilities.imports import has_pisa_package
-
-if has_pisa_package() or TYPE_CHECKING:
-    import pisa  # pyright: reportMissingImports=false
-    from pisa.core.distribution_maker import DistributionMaker
-    from pisa.core.pipeline import Pipeline
-    from pisa.analysis.analysis import Analysis
-    from pisa import ureg
-
-from graphnet.data.utilities import create_table_and_save_to_sql
-
-mpl.use("pdf")
-plt.rc("font", family="serif")
-
-
-
    
-[docs]
-@contextmanager
-def config_updater(
-    config_path: str,
-    new_config_path: Optional[str] = None,
-    dummy_section: str = "temp",
-) -> ConfigUpdater:
-    """Update config files and saves them to file.
-
-    Args:
-        config_path: Path to original config file.
-        new_config_path: Path to save updated config file.
-        dummy_section: Dummy section name to use for config files without
-            section headers.
-
-    Yields:
-        ConfigUpdater instance for programatically updating config file.
-    """
-    # Modify original config file is no new config path is provided.
-    if new_config_path is None:
-        new_config_path = config_path
-
-    # Load config file
-    updater = ConfigUpdater()
-    has_dummy_section = False
-    try:
-        updater.read(config_path)
-
-    # If it is missing section headers (e.g., binning.cfg), add a dummy section
-    # header before reading file contents.
-    except configparser.MissingSectionHeaderError:
-        with open(config_path, "r") as configfile:
-            updater.read_string(f"[{dummy_section}]\n" + configfile.read())
-        has_dummy_section = True
-
-    # Expose updater instance in contest (i.e.,
-    # `with config_updater(...) as updater:``).
-    try:
-        yield updater
-
-    # Write new config to file
-    finally:
-        with open(new_config_path, "w") as configfile:
-            if has_dummy_section:
-                # Removing dummy section header if necessary
-                with io.StringIO() as buffer:
-                    updater.write(buffer)
-                    buffer.seek(0)
-                    lines = buffer.readlines()[1:]
-                configfile.writelines(lines)
-            else:
-                updater.write(configfile)
    
-
-
-
-
    
-[docs]
-class WeightFitter:
-    """Class for fitting weights using PISA."""
-
-    def __init__(
-        self,
-        database_path: str,
-        truth_table: str = "truth",
-        index_column: str = "event_no",
-        statistical_fit: bool = False,
-    ) -> None:
-        """Construct `WeightFitter`."""
-        self._database_path = database_path
-        self._truth_table = truth_table
-        self._index_column = index_column
-        self._statistical_fit = statistical_fit
-
-
    
-[docs]
-    def fit_weights(
-        self,
-        config_outdir: str,
-        weight_name: str = "",
-        pisa_config_dict: Optional[Dict] = None,
-        add_to_database: bool = False,
-    ) -> pd.DataFrame:
-        """Fit flux weights to each neutrino event in `self._database_path`.
-
-        If `statistical_fit=True`, only statistical effects are accounted for.
-        If `True`, certain systematic effects are included, but not
-        hypersurfaces.
-
-        Args:
-            config_outdir: The output directory in which to store the
-                configuration.
-            weight_name: The name of the weight. If `add_to_database=True`,
-                this will be the name of the table.
-            pisa_config_dict: The dictionary of PISA configurations. Can be
-                used to change assumptions regarding the fit.
-            add_to_database: If `True`, a table will be added to the database
-                called `weight_name` with two columns:
-                `[index_column, weight_name]`
-
-        Returns:
-            A dataframe with columns `[index_column, weight_name]`.
-        """
-        # If its a standard weight
-        if pisa_config_dict is None:
-            if not weight_name:
-                print(weight_name)
-                weight_name = "pisa_weight_graphnet_standard"
-
-        # If it is a custom weight without name
-        elif pisa_config_dict is not None:
-            if not weight_name:
-                weight_name = "pisa_custom_weight"
-
-        pisa_config_path = self._make_config(
-            config_outdir, weight_name, pisa_config_dict
-        )
-
-        model = Pipeline(pisa_config_path)
-
-        if self._statistical_fit == "True":
-            # Only free parameters will be [aeff_scale] - corresponding to a statistical fit
-            free_params = model.params.free.names
-            for free_param in free_params:
-                if free_param not in ["aeff_scale"]:
-                    model.params[free_param].is_fixed = True
-
-        # for stage in range(len(model.stages)):
-        model.stages[-1].apply_mode = "events"
-        model.stages[-1].calc_mode = "events"
-        model.run()
-
-        all_data = []
-        for container in model.data:
-            data = pd.DataFrame(container["event_no"], columns=["event_no"])
-            data[weight_name] = container["weights"]
-            all_data.append(data)
-        results = pd.concat(all_data)
-
-        if add_to_database:
-            create_table_and_save_to_sql(
-                results.columns, weight_name, self._database_path
-            )
-        return results.sort_values("event_no").reset_index(drop=True)
    
-
-
-    def _make_config(
-        self,
-        config_outdir: str,
-        weight_name: str,
-        pisa_config_dict: Optional[Dict] = None,
-    ) -> str:
-        os.makedirs(config_outdir + "/" + weight_name, exist_ok=True)
-        if pisa_config_dict is None:
-            # Run on standard settings
-            pisa_config_dict = {
-                "reco_energy": {"num_bins": 8},
-                "reco_coszen": {"num_bins": 8},
-                "pid": {"bin_edges": [0, 0.5, 1]},
-                "true_energy": {"num_bins": 200},
-                "true_coszen": {"num_bins": 200},
-                "livetime": 10
-                * 0.01,  # set to 1% of 10 years - correspond to the size of the oscNext burn sample
-            }
-
-        pisa_config_dict["pipeline"] = self._database_path
-        pisa_config_dict["post_fix"] = None
-        pipeline_cfg_path = self._create_configs(
-            pisa_config_dict, config_outdir + "/" + weight_name
-        )
-        return pipeline_cfg_path
-
-    def _create_configs(self, config_dict: Dict, path: str) -> str:
-        # Update binning config
-        root = os.path.realpath(
-            os.path.join(os.getcwd(), os.path.dirname(__file__))
-        )
-        if config_dict["post_fix"] is not None:
-            config_name = "config%s" % config_dict["post_fix"]
-        else:
-            # config_dict["post_fix"] = '_pred'
-            config_name = "config"
-
-        with config_updater(
-            root
-            + "/resources/configuration_templates/binning_config_template.cfg",
-            "%s/binning_%s.cfg" % (path, config_name),
-            dummy_section="binning",
-        ) as updater:
-            updater["binning"][
-                "graphnet_dynamic_binning.reco_energy"
-            ].value = (
-                "{'num_bins':%s, 'is_log':True, 'domain':[0.5,55] * units.GeV, 'tex': r'E_{\\rm reco}'}"
-                % config_dict["reco_energy"]["num_bins"]
-            )  # noqa: W605
-            updater["binning"][
-                "graphnet_dynamic_binning.reco_coszen"
-            ].value = (
-                "{'num_bins':%s, 'is_lin':True, 'domain':[-1,1], 'tex':r'\\cos{\\theta}_{\\rm reco}'}"
-                % config_dict["reco_coszen"]["num_bins"]
-            )  # noqa: W605
-            updater["binning"]["graphnet_dynamic_binning.pid"].value = (
-                "{'bin_edges': %s, 'tex':r'{\\rm PID}'}"
-                % config_dict["pid"]["bin_edges"]
-            )  # noqa: W605
-            updater["binning"]["true_allsky_fine.true_energy"].value = (
-                "{'num_bins':%s, 'is_log':True, 'domain':[1,1000] * units.GeV, 'tex': r'E_{\\rm true}'}"
-                % config_dict["true_energy"]["num_bins"]
-            )  # noqa: W605
-            updater["binning"]["true_allsky_fine.true_coszen"].value = (
-                "{'num_bins':%s, 'is_lin':True, 'domain':[-1,1], 'tex':r'\\cos\,\\theta_{Z,{\\rm true}}'}"  # noqa: W605
-                % config_dict["true_coszen"]["num_bins"]
-            )  # noqa: W605
-
-        # Update pipeline config
-        with config_updater(
-            root
-            + "/resources/configuration_templates/pipeline_config_weight_template.cfg",
-            "%s/pipeline_%s.cfg" % (path, config_name),
-        ) as updater:
-            updater["pipeline"].add_before.comment(
-                "#include %s/binning_%s.cfg as binning" % (path, config_name)
-            )
-            updater["data.sqlite_loader"]["post_fix"].value = config_dict[
-                "post_fix"
-            ]
-            updater["data.sqlite_loader"]["database"].value = config_dict[
-                "pipeline"
-            ]
-            if "livetime" in config_dict.keys():
-                updater["aeff.aeff"]["param.livetime"].value = (
-                    "%s * units.common_year" % config_dict["livetime"]
-                )
-        return "%s/pipeline_%s.cfg" % (path, config_name)
    
-
-
-
-
    
-[docs]
-class ContourFitter:
-    """Class for fitting contours using PISA."""
-
-    def __init__(
-        self,
-        outdir: str,
-        pipeline_path: str,
-        post_fix: str = "_pred",
-        model_name: str = "gnn",
-        include_retro: bool = True,
-        statistical_fit: bool = False,
-    ):
-        """Construct `ContourFitter`."""
-        self._outdir = outdir
-        self._pipeline_path = pipeline_path
-        self._post_fix = post_fix
-        self._model_name = model_name
-        self._include_retro = include_retro
-        self._statistical_fit = str(statistical_fit)
-        self._allowed_contour_types = ["1d", "2d"]
-
-
    
-[docs]
-    def fit_1d_contour(
-        self,
-        run_name: str,
-        config_dict: Dict,
-        grid_size: int = 30,
-        n_workers: int = 1,
-        theta23_minmax: Tuple[float, float] = (36.0, 54.0),
-        dm31_minmax: Tuple[float, float] = (2.3, 2.7),
-    ) -> None:
-        """Fit 1D contours."""
-        self._fit_contours(
-            config_dict=config_dict,
-            run_name=run_name,
-            grid_size=grid_size,
-            n_workers=n_workers,
-            theta23_minmax=theta23_minmax,
-            dm31_minmax=dm31_minmax,
-            contour_type="1d",
-        )
    
-
-
-
    
-[docs]
-    def fit_2d_contour(
-        self,
-        run_name: str,
-        config_dict: Dict,
-        grid_size: int = 30,
-        n_workers: int = 1,
-        theta23_minmax: Tuple[float, float] = (36.0, 54.0),
-        dm31_minmax: Tuple[float, float] = (2.3, 2.7),
-    ) -> None:
-        """Fit 2D contours."""
-        self._fit_contours(
-            config_dict=config_dict,
-            run_name=run_name,
-            grid_size=grid_size,
-            n_workers=n_workers,
-            theta23_minmax=theta23_minmax,
-            dm31_minmax=dm31_minmax,
-            contour_type="2d",
-        )
    
-
-
-    def _check_inputs(
-        self,
-        contour_type: str,
-        dm31_minmax: Tuple[float, float],
-        theta23_minmax: Tuple[float, float],
-        n_workers: int,
-    ) -> bool:
-        """Check whether inputs are as expected."""
-        if contour_type.lower() not in self._allowed_contour_types:
-            print(
-                "%s not recognized as valid contour type. Only %s is recognized"
-                % (contour_type, self._allowed_contour_types)
-            )
-            return False
-        if (
-            (len(theta23_minmax) != 2)
-            or (len(dm31_minmax) != 2)
-            or (dm31_minmax[0] > dm31_minmax[1])
-            or (theta23_minmax[0] > theta23_minmax[1])
-        ):
-            print(
-                "theta23 or dm31 min max values are not understood. Please provide a list on the form [min, max] for both variables"
-            )
-            return False
-        if n_workers < 1:
-            print("found n_workers < 1. n_workers must be positive integers.")
-            return False
-        return True
-
-    def _fit_contours(
-        self,
-        run_name: str,
-        config_dict: Dict,
-        grid_size: int,
-        n_workers: int,
-        contour_type: str,
-        theta23_minmax: Tuple[float, float],
-        dm31_minmax: Tuple[float, float],
-    ) -> None:
-        """Fit contours."""
-        inputs_ok = self._check_inputs(
-            contour_type=contour_type,
-            dm31_minmax=dm31_minmax,
-            theta23_minmax=theta23_minmax,
-            n_workers=n_workers,
-        )
-        if not inputs_ok:
-            return
-
-        minimizer_cfg = self._get_minimizer_path(config_dict)
-        cfgs = self._setup_config_files(run_name, config_dict)
-        theta23_range = np.linspace(
-            theta23_minmax[0], theta23_minmax[1], grid_size
-        )
-        dm31_range = (
-            np.linspace(dm31_minmax[0], dm31_minmax[1], grid_size) * 1e-3
-        )
-        if contour_type.lower() == "1d":
-            settings = self._make_1d_settings(
-                cfgs=cfgs,
-                grid_size=grid_size,
-                run_name=run_name,
-                minimizer_cfg=minimizer_cfg,
-                theta23_range=theta23_range,
-                dm31_range=dm31_range,
-                n_workers=n_workers,
-            )
-            p = multiprocessing.Pool(processes=len(settings))
-            _ = p.map_async(self._parallel_fit_1d_contour, settings)
-            p.close()
-            p.join()
-            # self._parallel_fit_1d_contour(settings[0])
-        elif contour_type.lower() == "2d":
-            settings = self._make_2d_settings(
-                cfgs=cfgs,
-                grid_size=grid_size,
-                run_name=run_name,
-                minimizer_cfg=minimizer_cfg,
-                theta23_range=theta23_range,
-                dm31_range=dm31_range,
-                n_workers=n_workers,
-            )
-            p = multiprocessing.Pool(processes=len(settings))
-            _ = p.map_async(self._parallel_fit_2d_contour, settings)
-            p.close()
-            p.join()
-            # self._parallel_fit_2d_contour(settings[0])
-        df = self._merge_temporary_files(run_name)
-        df.to_csv(self._outdir + "/" + run_name + "/merged_results.csv")
-
-    def _merge_temporary_files(self, run_name: str) -> pd.DataFrame:
-        files = os.listdir(self._outdir + "/" + run_name + "/tmp")
-        df = pd.concat(
-            [
-                pd.read_csv(f"{self._outdir}/{run_name}/tmp/{file}")
-                for file in files
-            ],
-            ignore_index=True,
-        )
-        return df
-
-    def _parallel_fit_2d_contour(self, settings: List[List[Any]]) -> None:
-        """Fit 2D contours in parallel.
-
-        Length of settings determines the amount of jobs this worker gets.
-        Results are saved to temporary .csv-files that are later merged.
-
-        Args:
-            settings: A list of fitting settings.
-        """
-        results = []
-        for i in range(len(settings)):
-            (
-                cfg_path,
-                model_name,
-                outdir,
-                theta23_value,
-                deltam31_value,
-                id,
-                run_name,
-                fix_all,
-                minimizer_cfg,
-            ) = settings[i]
-            minimizer_cfg = pisa.utils.fileio.from_file(minimizer_cfg)
-            model = DistributionMaker([cfg_path])
-            data = model.get_outputs(return_sum=True)
-            ana = Analysis()
-            if fix_all == "True":
-                # Only free parameters will be [parameter, aeff_scale] - corresponding to a statistical fit
-                free_params = model.params.free.names
-                for free_param in free_params:
-                    if free_param != "aeff_scale":
-                        if free_param == "theta23":
-                            model.params.theta23.is_fixed = True
-                            model.params.theta23.nominal_value = (
-                                float(theta23_value) * ureg.degree
-                            )
-                        elif free_param == "deltam31":
-                            model.params.deltam31.is_fixed = True
-                            model.params.deltam31.nominal_value = (
-                                float(deltam31_value) * ureg.electron_volt**2
-                            )
-                        else:
-                            model.params[free_param].is_fixed = True
-            else:
-                # Only fixed parameters will be [parameter]
-                model.params.theta23.is_fixed = True
-                model.params.deltam31.is_fixed = True
-                model.params.theta23.nominal_value = (
-                    float(theta23_value) * ureg.degree
-                )
-                model.params.deltam31.nominal_value = (
-                    float(deltam31_value) * ureg.electron_volt**2
-                )
-            model.reset_all()
-            result = ana.fit_hypo(
-                data,
-                model,
-                metric="mod_chi2",
-                minimizer_settings=minimizer_cfg,
-                fit_octants_separately=True,
-            )
-            results.append(
-                [
-                    theta23_value,
-                    deltam31_value,
-                    result[0]["params"].theta23.value,
-                    result[0]["params"].deltam31.value,
-                    result[0]["metric_val"],
-                    model_name,
-                    id,
-                    result[0]["minimizer_metadata"]["success"],
-                ]
-            )
-        self._save_temporary_results(
-            outdir=outdir, run_name=run_name, results=results, id=id
-        )
-
-    def _parallel_fit_1d_contour(self, settings: List[List[Any]]) -> None:
-        """Fit 1D contours in parallel.
-
-        Length of settings determines the amount of jobs this worker gets.
-        Results are saved to temporary .csv-files that are later merged.
-
-        Args:
-            settings: A list of fitting settings.
-        """
-        results = []
-        for i in range(len(settings)):
-            (
-                cfg_path,
-                model_name,
-                outdir,
-                theta23_value,
-                deltam31_value,
-                id,
-                run_name,
-                parameter,
-                fix_all,
-                minimizer_cfg,
-            ) = settings[i]
-            minimizer_cfg = pisa.utils.fileio.from_file(minimizer_cfg)
-            ana = Analysis()
-            model = DistributionMaker([cfg_path])
-            data = model.get_outputs(return_sum=True)
-            if fix_all == "True":
-                # Only free parameters will be [parameter, aeff_scale] - corresponding to a statistical fit
-                free_params = model.params.free.names
-                for free_param in free_params:
-                    if free_param not in ["aeff_scale", "theta23", "deltam31"]:
-                        model.params[free_param].is_fixed = True
-                if parameter == "theta23":
-                    model.params.theta23.is_fixed = True
-                    model.params.theta23.nominal_value = (
-                        float(theta23_value) * ureg.degree
-                    )
-                elif parameter == "deltam31":
-                    model.params.deltam31.is_fixed = True
-                    model.params.deltam31.nominal_value = (
-                        float(deltam31_value) * ureg.electron_volt**2
-                    )
-            else:
-                # Only fixed parameters will be [parameter]
-                if parameter == "theta23":
-                    model.params.theta23.is_fixed = True
-                    model.params.theta23.nominal_value = (
-                        float(theta23_value) * ureg.degree
-                    )
-                elif parameter == "deltam31":
-                    model.params.deltam31.is_fixed = True
-                    model.params.deltam31.nominal_value = (
-                        float(deltam31_value) * ureg.electron_volt**2
-                    )
-                else:
-                    print("parameter not supported: %s" % parameter)
-            model.reset_all()
-            result = ana.fit_hypo(
-                data,
-                model,
-                metric="mod_chi2",
-                minimizer_settings=minimizer_cfg,
-                fit_octants_separately=True,
-            )
-            results.append(
-                [
-                    theta23_value,
-                    deltam31_value,
-                    result[0]["params"].theta23.value,
-                    result[0]["params"].deltam31.value,
-                    result[0]["metric_val"],
-                    model_name,
-                    id,
-                    result[0]["minimizer_metadata"]["success"],
-                ]
-            )
-        self._save_temporary_results(
-            outdir=outdir, run_name=run_name, results=results, id=id
-        )
-
-    def _save_temporary_results(
-        self, outdir: str, run_name: str, results: List[List[Any]], id: int
-    ) -> None:
-        os.makedirs(outdir + "/" + run_name + "/tmp", exist_ok=True)
-        results_df = pd.DataFrame(
-            data=results,
-            columns=[
-                "theta23_fixed",
-                "dm31_fixed",
-                "theta23_best_fit",
-                "dm31_best_fit",
-                "mod_chi2",
-                "model",
-                "id",
-                "converged",
-            ],
-        )
-        results_df.to_csv(
-            outdir + "/" + run_name + "/tmp" + "/tmp_%s.csv" % id
-        )
-
-    def _make_2d_settings(
-        self,
-        cfgs: Dict,
-        grid_size: int,
-        run_name: str,
-        minimizer_cfg: str,
-        theta23_range: Tuple[float, float],
-        dm31_range: Tuple[float, float],
-        n_workers: int,
-    ) -> List[np.ndarray]:
-        settings = []
-        count = 0
-        for model_name in cfgs.keys():
-            for i in range(0, grid_size):
-                for k in range(0, grid_size):
-                    settings.append(
-                        [
-                            cfgs[model_name],
-                            model_name,
-                            self._outdir,
-                            theta23_range[i],
-                            dm31_range[k],
-                            count,
-                            run_name,
-                            self._statistical_fit,
-                            minimizer_cfg,
-                        ]
-                    )
-                    count += 1
-        random.shuffle(settings)
-        return np.array_split(settings, n_workers)
-
-    def _make_1d_settings(
-        self,
-        cfgs: Dict,
-        grid_size: int,
-        run_name: str,
-        minimizer_cfg: str,
-        theta23_range: Tuple[float, float],
-        dm31_range: Tuple[float, float],
-        n_workers: int,
-    ) -> List[np.ndarray]:
-        settings = []
-        count = 0
-        for model_name in cfgs.keys():
-            for i in range(0, grid_size):
-                settings.append(
-                    [
-                        cfgs[model_name],
-                        model_name,
-                        self._outdir,
-                        theta23_range[i],
-                        -1,
-                        count,
-                        run_name,
-                        "theta23",
-                        self._statistical_fit,
-                        minimizer_cfg,
-                    ]
-                )
-                count += 1
-            for i in range(0, grid_size):
-                settings.append(
-                    [
-                        cfgs[model_name],
-                        model_name,
-                        self._outdir,
-                        -1,
-                        dm31_range[i],
-                        count,
-                        run_name,
-                        "deltam31",
-                        self._statistical_fit,
-                        minimizer_cfg,
-                    ]
-                )
-                count += 1
-        random.shuffle(settings)
-        return np.array_split(settings, n_workers)
-
-    def _setup_config_files(self, run_name: str, config_dict: Dict) -> Dict:
-        cfgs = {}
-        cfgs[self._model_name] = self._make_configs(
-            outdir=self._outdir,
-            post_fix=self._post_fix,
-            run_name=run_name,
-            is_retro=False,
-            pipeline_path=self._pipeline_path,
-            config_dict=config_dict,
-        )
-        if self._include_retro:
-            cfgs["retro"] = self._make_configs(
-                outdir=self._outdir,
-                post_fix=self._post_fix,
-                run_name=run_name,
-                is_retro=True,
-                pipeline_path=self._pipeline_path,
-                config_dict=config_dict,
-            )
-        return cfgs
-
-    def _get_minimizer_path(self, config_dict: Optional[Dict]) -> str:
-        if config_dict is not None and "minimizer_cfg" in config_dict.keys():
-            minimizer_cfg = config_dict["minimizer_cfg"]
-        else:
-            root = os.path.realpath(
-                os.path.join(os.getcwd(), os.path.dirname(__file__))
-            )
-            minimizer_cfg = (
-                root + "/resources/minimizer/graphnet_standard.json"
-            )
-        return minimizer_cfg
-
-    def _create_configs(self, config_dict: Dict, path: str) -> str:
-        # Update binning config
-        root = os.path.realpath(
-            os.path.join(os.getcwd(), os.path.dirname(__file__))
-        )
-        if config_dict["post_fix"] is not None:
-            config_name = "config%s" % config_dict["post_fix"]
-        else:
-            config_name = "config"
-
-        with config_updater(
-            root
-            + "/resources/configuration_templates/binning_config_template.cfg",
-            "%s/binning_%s.cfg" % (path, config_name),
-            dummy_section="binning",
-        ) as updater:
-            updater["binning"][
-                "graphnet_dynamic_binning.reco_energy"
-            ].value = (
-                "{'num_bins':%s, 'is_log':True, 'domain':[0.5,55] * units.GeV, 'tex': r'E_{\\rm reco}'}"
-                % config_dict["reco_energy"]["num_bins"]
-            )  # noqa: W605
-            updater["binning"][
-                "graphnet_dynamic_binning.reco_coszen"
-            ].value = (
-                "{'num_bins':%s, 'is_lin':True, 'domain':[-1,1], 'tex':r'\\cos{\\theta}_{\\rm reco}'}"
-                % config_dict["reco_coszen"]["num_bins"]
-            )  # noqa: W605
-            updater["binning"]["graphnet_dynamic_binning.pid"].value = (
-                "{'bin_edges': %s, 'tex':r'{\\rm PID}'}"
-                % config_dict["pid"]["bin_edges"]
-            )  # noqa: W605
-            updater["binning"]["true_allsky_fine.true_energy"].value = (
-                "{'num_bins':%s, 'is_log':True, 'domain':[1,1000] * units.GeV, 'tex': r'E_{\\rm true}'}"
-                % config_dict["true_energy"]["num_bins"]
-            )  # noqa: W605
-            updater["binning"]["true_allsky_fine.true_coszen"].value = (
-                "{'num_bins':%s, 'is_lin':True, 'domain':[-1,1], 'tex':r'\\cos\,\\theta_{Z,{\\rm true}}'}"  # noqa: W605
-                % config_dict["true_coszen"]["num_bins"]
-            )  # noqa: W605
-
-        # Update pipeline config
-        with config_updater(
-            root
-            + "/resources/configuration_templates/pipeline_config_template.cfg",
-            "%s/pipeline_%s.cfg" % (path, config_name),
-        ) as updater:
-            updater["pipeline"].add_before.comment(
-                "#include %s/binning_%s.cfg as binning" % (path, config_name)
-            )
-            updater["data.sqlite_loader"]["post_fix"].value = config_dict[
-                "post_fix"
-            ]
-            updater["data.sqlite_loader"]["database"].value = config_dict[
-                "pipeline"
-            ]
-            if "livetime" in config_dict.keys():
-                updater["aeff.aeff"]["param.livetime"].value = (
-                    "%s * units.common_year" % config_dict["livetime"]
-                )
-        return "%s/pipeline_%s.cfg" % (path, config_name)
-
-    def _make_configs(
-        self,
-        outdir: str,
-        run_name: str,
-        is_retro: bool,
-        pipeline_path: str,
-        post_fix: str = "_pred",
-        config_dict: Optional[Dict] = None,
-    ) -> str:
-        os.makedirs(outdir + "/" + run_name, exist_ok=True)
-        if config_dict is None:
-            # Run on standard settings
-            config_dict = {
-                "reco_energy": {"num_bins": 8},
-                "reco_coszen": {"num_bins": 8},
-                "pid": {"bin_edges": [0, 0.5, 1]},
-                "true_energy": {"num_bins": 200},
-                "true_coszen": {"num_bins": 200},
-                "livetime": 10,
-            }
-
-        config_dict["pipeline"] = pipeline_path
-        if is_retro:
-            config_dict["post_fix"] = "_retro"
-        else:
-            config_dict["post_fix"] = post_fix
-        pipeline_cfg_path = self._create_configs(
-            config_dict, outdir + "/" + run_name
-        )
-        return pipeline_cfg_path
    
-
-
    - -
    -
    -
    -
    -
    -
    -
    - -
    -
    -
    -
    -
    - © Copyright 2021-2024, GraphNeT team. - -
    - Created using - Sphinx 7.2.6. - and - Material for - Sphinx -
    -
    -
    -
    - - - - \ No newline at end of file diff --git a/_modules/graphnet/pisa/plotting.html b/_modules/graphnet/pisa/plotting.html deleted file mode 100644 index 530683a56..000000000 --- a/_modules/graphnet/pisa/plotting.html +++ /dev/null @@ -1,542 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - graphnet.pisa.plotting — graphnet documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Skip to content -
    - -
    - - -
    - - - - -
    -
    - -
    -
    -
    - -
    -
    -
    -
    -
    -
    - - -
    -
    -
    - -
    -
    - -

    Source code for graphnet.pisa.plotting

    -"""Functions for plotting contours from PISA fits."""
-
-from typing import Any, Dict, List, Tuple
-
-import matplotlib.pyplot as plt
-from matplotlib.figure import Figure
-import numpy as np
-import pandas as pd
-
-
-
    
-[docs]
-def read_entry(entry: Dict) -> Tuple[Any, ...]:
-    """Parse the contents of `entry`."""
-    path = entry["path"]
-    model_name = entry["model"]
-    try:
-        label = entry["label"]
-    except KeyError:
-        label = path.split("/")[-2]
-    try:
-        ls = entry["linestyle"]
-    except KeyError:
-        ls = "-"
-    try:
-        color = entry["color"]
-    except KeyError:
-        color = None
-    entry_data = pd.read_csv(path)
-
-    return entry_data, model_name, label, ls, color
    
-
-
-
-
    
-[docs]
-def plot_2D_contour(
-    contour_data: List[Dict],
-    xlim: Tuple[float, float] = (0.4, 0.6),
-    ylim: Tuple[float, float] = (2.38 * 1e-3, 2.55 * 1e-3),
-    chi2_critical_value: float = 4.605,
-    width: float = 3.176,
-    height: float = 2.388,
-) -> Figure:
-    """Plot 2D contours from GraphNeT PISA fits.
-
-    Args:
-        contour_data: List of dictionaries with plotting information. Format is
-            for each dictionary is:
-                {'path': path_to_pisa_fit_result,
-                 'model': 'name_of_my_model_in_fit'}.
-            One can specify optional fields in the dictionary: "label" - the
-            legend label, "color" - the color of the contour, "linestyle" - the
-            style of the contour line.
-        xlim: Lower and upper bound of x-axis.
-        ylim: Lower and upper bound of y-axis.
-        chi2_critical_value: The critical value of the chi2 fits. Defaults to
-            4.605 (90% CL). @NOTE: This, and the below, can't both be right.
-        width: width of figure in inches.
-        height: height of figure in inches.
-
-    Returns:
-        The figure with contours.
-    """
-    fig, ax = plt.subplots(figsize=(width, height), constrained_layout=True)
-    proxy = []
-    labels = []
-    for entry in contour_data:
-        entry_data, model_name, label, ls, color = read_entry(entry)
-        model_idx = entry_data["model"] == model_name
-        model_data = entry_data.loc[model_idx]
-        x = pd.unique(model_data.sort_values("theta23_fixed")["theta23_fixed"])
-        y = pd.unique(model_data.sort_values("dm31_fixed")["dm31_fixed"])
-        z = np.zeros((len(y), len(x)))
-        for i in range(len(x)):
-            for k in range(len(y)):
-                idx = (model_data["theta23_fixed"] == x[i]) & (
-                    model_data["dm31_fixed"] == y[k]
-                )
-                match = model_data["mod_chi2"][idx]
-                if len(match) > 0:
-                    if model_data["converged"][idx].values is True:
-                        match = float(match)
-                    else:
-                        match = 10000  # Sets the z value very high to exclude it from contour
-                else:
-                    match = 10000  # Sets the z value very high to exclude it from contour
-                z[k, i] = match
-
-        CS = ax.contour(
-            np.sin(np.deg2rad(x)) ** 2,
-            y,
-            z,
-            levels=[chi2_critical_value],
-            colors=color,
-            label=label,
-            linestyles=ls,
-            linewidths=2,
-        )
-        # ax.clabel(CS, inline=1, fontsize=10)
-        proxy.extend(
-            [plt.Rectangle((0, 0), 1, 1, fc=color) for pc in CS.collections]
-        )
-        if chi2_critical_value == 4.605:
-            label = label + " 90 $\\%$ CL"
-        labels.append(label)
-    plt.legend(proxy, labels, frameon=False, loc="upper right")
-    plt.xlim(xlim[0], xlim[1])
-    plt.ylim(ylim[0], ylim[1])
-    plt.xlabel("$\\sin^2(\\theta_{23})$", fontsize=12)
-    plt.ylabel("$\\Delta m_{31}^2 [eV^2]$", fontsize=12)
-    plt.ticklabel_format(axis="y", style="sci", scilimits=(0, 0))
-    plt.title("Sensitivity (Simplified Analysis)")
-    return fig
    
-
-
-
-
    
-[docs]
-def plot_1D_contour(
-    contour_data: List[Dict],
-    chi2_critical_value: float = 2.706,
-    width: float = 2 * 3.176,
-    height: float = 2.388,
-) -> Figure:
-    """Plot 1D contours from GraphNeT PISA fits.
-
-    Args:
-        contour_data: List of dictionaries with plotting information. Format is
-            for each dictionary is:
-                {'path': path_to_pisa_fit_result,
-                 'model': 'name_of_my_model_in_fit'}.
-            One can specify optional fields in the dictionary: "label" - the
-            legend label, "color" - the color of the contour, "linestyle" - the
-            style of the contour line.
-        chi2_critical_value: The critical value of the chi2 fits. Defaults to
-            2.706 (90% CL). @NOTE: This, and the above, can't both be right.
-        width: width of figure in inches.
-        height: height of figure in inches.
-
-    Returns:
-        The figure with contours.
-    """
-    variables = ["theta23_fixed", "dm31_fixed"]
-    fig, ax = plt.subplots(
-        1, 2, figsize=(width, height), constrained_layout=True
-    )
-    ls = 0
-    for entry in contour_data:
-        entry_data, model_name, label, ls, color = read_entry(entry)
-        for variable in variables:
-            model_idx = entry_data["model"] == model_name
-            padding_idx = entry_data[variable] != -1
-            chi2_idx = entry_data["mod_chi2"] < chi2_critical_value
-            model_data = entry_data.loc[
-                (model_idx) & (padding_idx) & (chi2_idx), :
-            ]
-            x = model_data.sort_values(variable)
-            if variable == "theta23_fixed":
-                ax[0].set_ylabel("$\\chi^2$", fontsize=12)
-                ax[0].plot(
-                    np.sin(np.deg2rad(x[variable])) ** 2,
-                    x["mod_chi2"],
-                    color=color,
-                    label=label,
-                    ls=ls,
-                )
-                ax[0].set_xlabel("$\\sin(\\theta_{23})^2$", fontsize=12)
-            elif variable == "dm31_fixed":
-                ax[1].plot(
-                    x[variable], x["mod_chi2"], color=color, label=label, ls=ls
-                )
-                ax[1].ticklabel_format(axis="x", style="sci", scilimits=(0, 0))
-                ax[1].set_xlabel("$\\Delta m_{31}^2 [eV^2]$", fontsize=12)
-    h = [item.get_text() for item in ax[1].get_yticklabels()]
-    empty_string_labels = [""] * len(h)
-    ax[1].set_yticklabels(empty_string_labels)
-    ax[0].set_ylim(0, chi2_critical_value)
-    ax[1].set_ylim(0, chi2_critical_value)
-    ax[0].legend()
-    return fig
    
-
-
    - -
    -
    -
    -
    -
    -
    -
    - -
    -
    -
    -
    -
    - © Copyright 2021-2024, GraphNeT team. - -
    - Created using - Sphinx 7.2.6. - and - Material for - Sphinx -
    -
    -
    -
    - - - - \ No newline at end of file diff --git a/_modules/graphnet/training/callbacks.html b/_modules/graphnet/training/callbacks.html index 7bea62b10..223ead861 100644 --- a/_modules/graphnet/training/callbacks.html +++ b/_modules/graphnet/training/callbacks.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -640,7 +667,7 @@

    Source code for graphnet Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/training/labels.html b/_modules/graphnet/training/labels.html index 0da6b1526..5440be6b8 100644 --- a/_modules/graphnet/training/labels.html +++ b/_modules/graphnet/training/labels.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -398,6 +425,45 @@

    Source code for graphnet.tr z = torch.cos(graph[self._zenith_key]).reshape(-1, 1) return torch.cat((x, y, z), dim=1) + + +
    +[docs] +class Track(Label): + """Class for producing NuMuCC label. + + Label is set to `1` if the event is a NuMu CC event, else `0`. + """ + + def __init__( + self, + key: str = "track", + pid_key: str = "pid", + interaction_key: str = "interaction_type", + ): + """Construct `Track` label. + + Args: + key: The name of the field in `Data` where the label will be + stored. That is, `graph[key] = label`. + pid_key: The name of the pre-existing key in `graph` that will + be used to access the pdg encoding, used when calculating + the direction. + interaction_key: The name of the pre-existing key in `graph` that + will be used to access the interaction type (1 denoting CC), + used when calculating the direction. + """ + self._pid_key = pid_key + self._int_key = interaction_key + + # Base class constructor + super().__init__(key=key) + + def __call__(self, graph: Data) -> torch.tensor: + """Compute label for `graph`.""" + label = (graph[self._pid_key] == 14) & (graph[self._int_key] == 1) + return label.type(torch.int)
    + @@ -422,7 +488,7 @@

    Source code for graphnet.tr Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/training/loss_functions.html b/_modules/graphnet/training/loss_functions.html index a5dab2a8f..2b907c806 100644 --- a/_modules/graphnet/training/loss_functions.html +++ b/_modules/graphnet/training/loss_functions.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -842,7 +869,7 @@

    Source code for gra Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/training/utils.html b/_modules/graphnet/training/utils.html index b2e9890bd..249ad1eb7 100644 --- a/_modules/graphnet/training/utils.html +++ b/_modules/graphnet/training/utils.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -506,7 +533,7 @@

    Source code for graphnet.tra truth_table=truth_table, index_column=index_column, ) - elif db.endswith(".parquet"): + else: dataset = ParquetDataset( path=db, graph_definition=graph_definition, @@ -516,10 +543,6 @@

    Source code for graphnet.tra truth_table=truth_table, index_column=index_column, ) - else: - raise RuntimeError( - f"File {db} with format {db.split('.'[-1])} not supported." - ) selection = dataset._get_all_indices() # Perform train/validation split @@ -701,7 +724,7 @@

    Source code for graphnet.tra Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/training/weight_fitting.html b/_modules/graphnet/training/weight_fitting.html index 5c42395a7..6d39cf0a4 100644 --- a/_modules/graphnet/training/weight_fitting.html +++ b/_modules/graphnet/training/weight_fitting.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -564,7 +591,7 @@

    Source code for gra Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/utilities/argparse.html b/_modules/graphnet/utilities/argparse.html index f46e09075..05cfe51ff 100644 --- a/_modules/graphnet/utilities/argparse.html +++ b/_modules/graphnet/utilities/argparse.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -515,7 +542,7 @@

    Source code for graphnet Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/utilities/config/base_config.html b/_modules/graphnet/utilities/config/base_config.html index 32d6f50c1..94622f99a 100644 --- a/_modules/graphnet/utilities/config/base_config.html +++ b/_modules/graphnet/utilities/config/base_config.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -435,7 +462,7 @@

    Source code fo Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/utilities/config/configurable.html b/_modules/graphnet/utilities/config/configurable.html index eb58aed73..eb5b50ae7 100644 --- a/_modules/graphnet/utilities/config/configurable.html +++ b/_modules/graphnet/utilities/config/configurable.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -394,7 +421,7 @@

    Source code f Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/utilities/config/dataset_config.html b/_modules/graphnet/utilities/config/dataset_config.html index 743743b2e..654f2c796 100644 --- a/_modules/graphnet/utilities/config/dataset_config.html +++ b/_modules/graphnet/utilities/config/dataset_config.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -623,7 +650,7 @@

    Source code Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/utilities/config/model_config.html b/_modules/graphnet/utilities/config/model_config.html index e990ed616..f70455f80 100644 --- a/_modules/graphnet/utilities/config/model_config.html +++ b/_modules/graphnet/utilities/config/model_config.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -713,7 +740,7 @@

    Source code f Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/utilities/config/parsing.html b/_modules/graphnet/utilities/config/parsing.html index 0bdfbcebc..a900ee833 100644 --- a/_modules/graphnet/utilities/config/parsing.html +++ b/_modules/graphnet/utilities/config/parsing.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -461,7 +488,7 @@

    Source code for gr Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/utilities/config/training_config.html b/_modules/graphnet/utilities/config/training_config.html index dda012503..0677ef70d 100644 --- a/_modules/graphnet/utilities/config/training_config.html +++ b/_modules/graphnet/utilities/config/training_config.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -364,7 +391,7 @@

    Source cod Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/utilities/deprecation_tools.html b/_modules/graphnet/utilities/deprecation_tools.html index df8e2670d..d455ba74a 100644 --- a/_modules/graphnet/utilities/deprecation_tools.html +++ b/_modules/graphnet/utilities/deprecation_tools.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -382,7 +409,7 @@

    Source code for Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/utilities/filesys.html b/_modules/graphnet/utilities/filesys.html index 5a4640792..1cd7374ba 100644 --- a/_modules/graphnet/utilities/filesys.html +++ b/_modules/graphnet/utilities/filesys.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -415,7 +442,8 @@

    Source code for graphnet. folder_i3_files = list(filter(is_i3_file, folder_files)) folder_gcd_files = list(filter(is_gcd_file, folder_files)) - # Make sure that no more than one GCD file is found; and use rescue file of none is found. + # Make sure that no more than one GCD file is found; + # and use rescue file if none is found. assert len(folder_gcd_files) <= 1 if len(folder_gcd_files) == 0: assert gcd_rescue is not None @@ -453,7 +481,7 @@

    Source code for graphnet. Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/utilities/imports.html b/_modules/graphnet/utilities/imports.html index 67929efcd..6726c5d70 100644 --- a/_modules/graphnet/utilities/imports.html +++ b/_modules/graphnet/utilities/imports.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -363,22 +390,6 @@

    Source code for graphnet. -
    -[docs] -def has_pisa_package() -> bool: - """Check whether the `pisa` package is available.""" - try: - import pisa # pyright: reportMissingImports=false - - return True - except ImportError: - Logger(log_folder=None).warning_once( - "`pisa` not available. Some functionality may be missing.", - ) - return False
    - - -
    [docs] def requires_icecube(test_function: Callable) -> Callable: @@ -420,7 +431,7 @@

    Source code for graphnet.

    Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/utilities/logging.html b/_modules/graphnet/utilities/logging.html index f4b14db28..271fbfd42 100644 --- a/_modules/graphnet/utilities/logging.html +++ b/_modules/graphnet/utilities/logging.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -630,7 +657,7 @@

    Source code for graphnet. Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/graphnet/utilities/maths.html b/_modules/graphnet/utilities/maths.html index cff801128..61a5fae36 100644 --- a/_modules/graphnet/utilities/maths.html +++ b/_modules/graphnet/utilities/maths.html @@ -122,10 +122,9 @@ - + - @@ -281,14 +280,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -357,7 +384,7 @@

    Source code for graphnet.ut Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/_modules/index.html b/_modules/index.html index b9ec07420..f33d5ba19 100644 --- a/_modules/index.html +++ b/_modules/index.html @@ -122,10 +122,9 @@ - + - @@ -280,14 +279,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -322,6 +349,7 @@

    All modules for which code is available

    @@ -401,6 +430,8 @@
  • PROMETHEUS
  • KAGGLE +
    • +
  • LIQUIDO
    • @@ -448,6 +479,13 @@ KAGGLE + +
  • + + + LIQUIDO + +
    • @@ -490,10 +528,24 @@ KAGGLE + +
  • + + + LIQUIDO + +
    • + +
  • + + + curated_datamodule + +
  • @@ -522,15 +574,15 @@ datamodule +
    • +
  • - pipeline + datasets -
    • -
  • @@ -542,14 +594,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -603,6 +655,8 @@
  • PROMETHEUS
  • KAGGLE +
    • +
  • LIQUIDO
    • @@ -617,6 +671,8 @@
  • PROMETHEUS
  • KAGGLE +
    • +
  • LIQUIDO
    • @@ -659,6 +715,10 @@
    KAGGLE = ['x', 'y', 'z', 'time', 'charge', 'auxiliary']
    +
    +
    +LIQUIDO = ['sipm_x', 'sipm_y', 'sipm_z', 't']
    +
    @@ -667,15 +727,15 @@

    Namespace for standard names working with I3TruthExtractor.

    -ICECUBE86 = ['energy', 'energy_track', 'energy_cascade', 'position_x', 'position_y', 'position_z', 'azimuth', 'zenith', 'pid', 'elasticity', 'sim_type', 'interaction_type', 'interaction_time', 'inelasticity', 'stopped_muon']
    +ICECUBE86 = ['energy', 'energy_track', 'energy_cascade', 'position_x', 'position_y', 'position_z', 'azimuth', 'zenith', 'pid', 'elasticity', 'interaction_type', 'interaction_time', 'inelasticity', 'stopped_muon']
    -DEEPCORE = ['energy', 'energy_track', 'energy_cascade', 'position_x', 'position_y', 'position_z', 'azimuth', 'zenith', 'pid', 'elasticity', 'sim_type', 'interaction_type', 'interaction_time', 'inelasticity', 'stopped_muon']
    +DEEPCORE = ['energy', 'energy_track', 'energy_cascade', 'position_x', 'position_y', 'position_z', 'azimuth', 'zenith', 'pid', 'elasticity', 'interaction_type', 'interaction_time', 'inelasticity', 'stopped_muon']
    -UPGRADE = ['energy', 'energy_track', 'energy_cascade', 'position_x', 'position_y', 'position_z', 'azimuth', 'zenith', 'pid', 'elasticity', 'sim_type', 'interaction_type', 'interaction_time', 'inelasticity', 'stopped_muon']
    +UPGRADE = ['energy', 'energy_track', 'energy_cascade', 'position_x', 'position_y', 'position_z', 'azimuth', 'zenith', 'pid', 'elasticity', 'interaction_type', 'interaction_time', 'inelasticity', 'stopped_muon']
    @@ -685,6 +745,10 @@
    KAGGLE = ['zenith', 'azimuth']
    +
    +
    +LIQUIDO = ['vertex_x', 'vertex_y', 'vertex_z', 'zenith', 'azimuth', 'interaction_time', 'energy', 'pid']
    +
    @@ -712,12 +776,12 @@ - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.data.curated_datamodule.html b/api/graphnet.data.curated_datamodule.html new file mode 100644 index 000000000..fa2532030 --- /dev/null +++ b/api/graphnet.data.curated_datamodule.html @@ -0,0 +1,947 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + curated_datamodule — graphnet documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
    + +
    + + +
    + + + + +
    +
    + +
    +
    +
    + +
    +
    +
    +
    +
    +
    + + +
    +
    +
    + +
    +
    + +
    +

    curated_datamodule

    +

    Contains a Generic class for curated DataModules/Datasets.

    +

    Inheriting subclasses are data-specific implementations that allow the user to +import and download pre-converteddatasets for training of deep learning based +methods in GraphNeT.

    +
    +
    +class graphnet.data.curated_datamodule.CuratedDataset(graph_definition, download_dir, truth, features, backend, train_dataloader_kwargs, validation_dataloader_kwargs, test_dataloader_kwargs)[source]
    +

    Bases: GraphNeTDataModule

    +

    Generic base class for curated datasets.

    +

    Curated Datasets in GraphNeT are pre-converted datasets that have been +prepared for training and evaluation of deep learning models. On these +Datasets, graphnet users can train and benchmark their models against SOTA +methods.

    +

    Construct CuratedDataset.

    +
    +
    Parameters:
    +
      +

    • graph_definition (GraphDefinition) – Method that defines the data representation.

      • +

    • download_dir (str) – Directory to download dataset to.

      • +

    • truth (Optional) – List of event-level truth to include. Will +include all available information if not given.

      • +

    • features (Optional) – List of input features from pulsemap to use. +If not given, all available features will be +used.

      • +

    • backend (Optional) – data backend to use. Either “parquet” or +“sqlite”. Defaults to “parquet”.

      • +

    • train_dataloader_kwargs (Optional) – Arguments for the training +DataLoader. Default None.

      • +

    • validation_dataloader_kwargs (Optional) – Arguments for the +validation DataLoader, Default None.

      • +

    • test_dataloader_kwargs (Optional) – Arguments for the test +DataLoader. Default None.

      • +
    +
    +
    +
    +
    +abstract prepare_data()[source]
    +

    Download and prepare data.

    +
    +
    Return type:
    +

    None

    +
    +
    +
    +
    +
    +description()[source]
    +

    Print details on the Dataset.

    +
    +
    Return type:
    +

    None

    +
    +
    +
    +
    +
    +property pulsemaps: List[str]
    +

    Produce a list of available pulsemaps in Dataset.

    +
    +
    +
    +property truth_table: List[str]
    +

    Produce name of table containing event-level truth in Dataset.

    +
    +
    +
    +property event_truth: List[str]
    +

    Produce a list of available event-level truth in Dataset.

    +
    +
    +
    +property pulse_truth: List[str] | None
    +

    Produce a list of available pulse-level truth in Dataset.

    +
    +
    +
    +property features: List[str]
    +

    Produce a list of available input features in Dataset.

    +
    +
    +
    +property experiment: str
    +

    Produce the name of the experiment that the data comes from.

    +
    +
    +
    +property citation: str
    +

    Produce a string that describes how to cite this Dataset.

    +
    +
    +
    +property comments: str
    +

    Produce comments on the dataset from the creator.

    +
    +
    +
    +property creator: str
    +

    Produce name of person who created the Dataset.

    +
    +
    +
    +property events: Dict[str, int]
    +

    Produce a dict that contains number events in each selection.

    +
    +
    +
    +property available_backends: List[str]
    +

    Produce a list of available data formats that the data comes in.

    +
    +
    +
    +property dataset_dir: str
    +

    Produce path directory that contains dataset files.

    +
    +
    +
    +
    +class graphnet.data.curated_datamodule.ERDAHostedDataset(graph_definition, download_dir, truth, features, backend, train_dataloader_kwargs, validation_dataloader_kwargs, test_dataloader_kwargs)[source]
    +

    Bases: CuratedDataset

    +

    A base class for dataset/datamodule hosted at ERDA.

    +

    Inheriting subclasses will just need to fill out the _file_hashes +attribute, which points to the file-id of a ERDA-hosted sharelink. It +is assumed that sharelinks point to a single compressed file that has +been compressed using tar with extension “.tar.gz”.

    +

    E.g. suppose that the sharelink below +https://sid.erda.dk/share_redirect/FbEEzAbg5A +points to a compressed sqlite database. Then: +_file_hashes = {‘sqlite’ : “FbEEzAbg5A”}

    +

    Construct CuratedDataset.

    +
    +
    Parameters:
    +
      +

    • graph_definition (GraphDefinition) – Method that defines the data representation.

      • +

    • download_dir (str) – Directory to download dataset to.

      • +

    • truth (Optional) – List of event-level truth to include. Will +include all available information if not given.

      • +

    • features (Optional) – List of input features from pulsemap to use. +If not given, all available features will be +used.

      • +

    • backend (Optional) – data backend to use. Either “parquet” or +“sqlite”. Defaults to “parquet”.

      • +

    • train_dataloader_kwargs (Optional) – Arguments for the training +DataLoader. Default None.

      • +

    • validation_dataloader_kwargs (Optional) – Arguments for the +validation DataLoader, Default None.

      • +

    • test_dataloader_kwargs (Optional) – Arguments for the test +DataLoader. Default None.

      • +
    +
    +
    +
    +
    +prepare_data()[source]
    +

    Prepare the dataset for training.

    +
    +
    Return type:
    +

    None

    +
    +
    +
    +
    +
    + + +
    +
    +
    +
    +
    + + + + + \ No newline at end of file diff --git a/api/graphnet.data.dataclasses.html b/api/graphnet.data.dataclasses.html index 9a0ff4708..2c6708832 100644 --- a/api/graphnet.data.dataclasses.html +++ b/api/graphnet.data.dataclasses.html @@ -123,14 +123,13 @@ - + - - + @@ -285,14 +284,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -368,6 +395,13 @@ constants + +
  • + + + curated_datamodule + +
  • @@ -486,15 +520,15 @@ datamodule +
    • +
  • - pipeline + datasets -
    • -
  • @@ -506,14 +540,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -597,8 +631,8 @@
    Parameters:
      -

    • i3_file (str) –

      • -

    • gcd_file (str) –

      • +

    • i3_file (str)

      • +

    • gcd_file (str)

    @@ -619,10 +653,10 @@
    Parameters:
      -

    • i3_files (List[str]) –

      • -

    • gcd_file (str) –

      • -

    • output_folder (str) –

      • -

    • modules (List[Any]) –

      • +

    • i3_files (List[str])

      • +

    • gcd_file (str)

      • +

    • output_folder (str)

      • +

    • modules (List[Any])

    @@ -655,7 +689,7 @@
    Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.data.dataloader.html b/api/graphnet.data.dataloader.html index a292c039d..e86d352ef 100644 --- a/api/graphnet.data.dataloader.html +++ b/api/graphnet.data.dataloader.html @@ -123,10 +123,9 @@ - + - @@ -285,14 +284,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -368,6 +395,13 @@ constants + +
  • + + + curated_datamodule + +
  • @@ -448,15 +482,15 @@ datamodule +
    • +
  • - pipeline + datasets -
    • -
  • @@ -468,14 +502,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -552,7 +586,7 @@

    Batch

    Parameters:
    -

    graphs (List[Data]) –

    +

    graphs (List[Data])

    @@ -565,7 +599,7 @@

    bool

    Parameters:
    -

    selection_name (str) –

    +

    selection_name (str)

    @@ -578,14 +612,14 @@
    Parameters:
      -

    • dataset (Dataset[T_co]) –

      • -

    • batch_size (int | None) –

      • -

    • shuffle (bool) –

      • -

    • num_workers (int) –

      • -

    • persistent_workers (bool) –

      • -

    • collate_fn (Callable) –

      • -

    • prefetch_factor (int | None) –

      • -

    • kwargs (Any) –

      • +

    • dataset (Dataset[T_co])

      • +

    • batch_size (int | None)

      • +

    • shuffle (bool)

      • +

    • num_workers (int)

      • +

    • persistent_workers (bool)

      • +

    • collate_fn (Callable)

      • +

    • prefetch_factor (int | None)

      • +

    • kwargs (Any)

    @@ -599,8 +633,8 @@
    Parameters:
    @@ -655,7 +689,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.data.datamodule.html b/api/graphnet.data.datamodule.html index 4c98ffe66..bd8465a7f 100644 --- a/api/graphnet.data.datamodule.html +++ b/api/graphnet.data.datamodule.html @@ -123,13 +123,12 @@ - + - - + @@ -285,14 +284,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -368,6 +395,13 @@ constants + +
  • + + + curated_datamodule + +
  • @@ -475,15 +509,15 @@
    • + +
  • - pipeline + datasets -
    • -
  • @@ -495,14 +529,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -584,20 +618,21 @@
    Parameters:
      -

    • dataset_reference (Union[SQLiteDataset, ParquetDataset, Dataset]) – A non-instantiated reference +

    • dataset_reference (Union[Type[SQLiteDataset], Type[ParquetDataset], Type[Dataset]]) – A non-instantiated reference to the dataset class.

    • dataset_args (Dict[str, Any]) – Arguments to instantiate graphnet.data.dataset.Dataset with.

    • selection (Union[List[int], List[List[int]], None], default: None) – (Optional) a list of event id’s used for training and validation, Default None.

    • test_selection (Union[List[int], List[List[int]], None], default: None) – (Optional) a list of event id’s used for testing, -Default None.

      • +Defaults to None.

    • train_dataloader_kwargs (Optional[Dict[str, Any]], default: None) – Arguments for the training DataLoader, -Default None.

      • +Defaults{“batch_size”: 2, “num_workers”: 1}.

    • validation_dataloader_kwargs (Optional[Dict[str, Any]], default: None) – Arguments for the validation -DataLoader, Default None.

      • +DataLoader. Defaults to +train_dataloader_kwargs.

    • test_dataloader_kwargs (Optional[Dict[str, Any]], default: None) – Arguments for the test DataLoader, -Default None.

      • +Defaults to train_dataloader_kwargs.

    • train_val_split (Optional) – Split ratio for training and validation sets. Default is [0.9, 0.10].

    • split_seed (int, default: 42) – seed used for shuffling and splitting selections into @@ -630,7 +665,7 @@

    -property train_dataloader: DataLoader
    +property train_dataloader: DataLoader

    Prepare and return the training DataLoader.

    Returns:
    @@ -643,7 +678,7 @@
    -property val_dataloader: DataLoader
    +property val_dataloader: DataLoader

    Prepare and return the validation DataLoader.

    Returns:
    @@ -656,7 +691,7 @@
    -property test_dataloader: DataLoader
    +property test_dataloader: DataLoader

    Prepare and return the test DataLoader.

    Returns:
    @@ -709,12 +744,12 @@ - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.data.dataset.dataset.html b/api/graphnet.data.dataset.dataset.html index 3d311fc7b..264998e96 100644 --- a/api/graphnet.data.dataset.dataset.html +++ b/api/graphnet.data.dataset.dataset.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -340,8 +367,6 @@ -
  • @@ -562,14 +587,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -612,8 +637,6 @@
    @@ -696,7 +713,7 @@

    Dict[str, Label]

    Parameters:
    -

    cfg (dict) –

    +

    cfg (dict)

    @@ -752,8 +769,8 @@ events ~ event_no % 5 > 0”).

  • graph_definition (GraphDefinition) – Method that defines the graph representation.

  • labels (Optional[Dict[str, Any]], default: None) – Dictionary of labels to be added to the dataset.

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • +

  • args (Any)

    • +

  • kwargs (Any)

    • Return type:
    @@ -769,7 +786,7 @@

    Union[Dataset, EnsembleDataset, Dict[str, Dataset], Dict[str, EnsembleDataset]]

    Parameters:
    -

    source (DatasetConfig | str) –

    +

    source (DatasetConfig | str)

    @@ -782,7 +799,7 @@

    EnsembleDataset

    Parameters:
    -

    datasets (List[Dataset]) –

    +

    datasets (List[Dataset])

    @@ -814,7 +831,7 @@
    Return type:
    -

    List[Tuple[Any, ...]]

    +

    ndarray

    Returns:

    @@ -825,7 +842,7 @@

    Raises:
    -

    ColumnMissingException – If one or more element in columns is not +

    ColumnMissingException – If one or more element in columns is not present in table.

    @@ -840,8 +857,8 @@
    Parameters:
    @@ -908,7 +925,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.data.dataset.html b/api/graphnet.data.dataset.html index 9aa7ec0ad..ea9dde565 100644 --- a/api/graphnet.data.dataset.html +++ b/api/graphnet.data.dataset.html @@ -123,10 +123,9 @@ - + - @@ -285,14 +284,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -398,6 +425,13 @@ constants + +
  • + + + curated_datamodule + +
  • @@ -426,15 +460,15 @@ datamodule +
    • +
  • - pipeline + datasets -
    • -
  • @@ -446,14 +480,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -522,7 +556,6 @@
    Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.data.dataset.parquet.html b/api/graphnet.data.dataset.parquet.html index 19a432558..49717e54e 100644 --- a/api/graphnet.data.dataset.parquet.html +++ b/api/graphnet.data.dataset.parquet.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -406,6 +433,13 @@ constants + +
  • + + + curated_datamodule + +
  • @@ -434,15 +468,15 @@ datamodule +
    • +
  • - pipeline + datasets -
    • -
  • @@ -454,14 +488,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -571,7 +605,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.data.dataset.parquet.parquet_dataset.html b/api/graphnet.data.dataset.parquet.parquet_dataset.html index 3cff0e856..fc8339df5 100644 --- a/api/graphnet.data.dataset.parquet.parquet_dataset.html +++ b/api/graphnet.data.dataset.parquet.parquet_dataset.html @@ -123,10 +123,9 @@ - + - @@ -287,14 +286,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -432,6 +459,13 @@ constants + +
  • + + + curated_datamodule + +
  • @@ -460,15 +494,15 @@ datamodule +
    • +
  • - pipeline + datasets -
    • -
  • @@ -480,14 +514,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -549,17 +583,21 @@

    parquet_dataset

    -

    Dataset class(es) for reading from Parquet files.

    +

    Base Dataset class(es) used in GraphNeT.

    class graphnet.data.dataset.parquet.parquet_dataset.ParquetDataset(*args, **kwargs)[source]

    Bases: Dataset

    -

    Pytorch dataset for reading from Parquet files.

    +

    Dataset class for Parquet-files converted with ParquetWriter.

    Construct Dataset.

    +
    +

    NOTE: DataLoaders using this Dataset should have +“multiprocessing_context = ‘spawn’” set to avoid thread locking.

    +
    Parameters:
      -

    • path (Union[str, List[str]]) – Path to the file(s) from which this Dataset should read.

      • +

    • path (str) – Path to the file(s) from which this Dataset should read.

    • pulsemaps (Union[str, List[str]]) – Name(s) of the pulse map series that should be used to construct the nodes on the individual graph objects, and their features. Multiple pulse series maps can be used, e.g., when @@ -579,11 +617,8 @@

    • string_selection (Optional[List[int]], default: None) – Subset of strings for which data should be read and used to construct graph objects. Defaults to None, meaning all strings for which data exists are used.

      • -

    • selection (Union[str, List[int], List[List[int]], None], default: None) – The events that should be read. This can be given either -as list of indicies (in index_column); or a string-based -selection used to query the Dataset for events passing the -selection. Defaults to None, meaning that all events in the -input files are read.

      • +

    • selection (Union[str, List[int], List[List[int]], None], default: None) – The batch ids to include in the dataset. +Defaults to None, meaning that batches are read.

    • dtype (dtype, default: torch.float32) – Type of the feature tensor on the graph objects returned.

    • loss_weight_table (Optional[str], default: None) – Name of the table containing per-event loss weights.

      • @@ -601,9 +636,10 @@ “10000 random events ~ event_no % 5 > 0” or “20% random events ~ event_no % 5 > 0”).

    • graph_definition (GraphDefinition) – Method that defines the graph representation.

      • -

    • labels (Optional[Dict[str, Any]], default: None) – Dictionary of labels to be added to the dataset.

      • -

    • args (Any) –

      • -

    • kwargs (Any) –

      • +

    • cache_size (int, default: 1) – Number of batches to cache in memory. +Must be at least 1. Defaults to 1.

      • +

    • args (Any)

      • +

    • kwargs (Any)

    Return type:
    @@ -613,19 +649,35 @@
    query_table(table, columns, sequential_index, selection)[source]
    -

    Query table at a specific index, optionally with some selection.

    +

    Query a table at a specific index, optionally with some selection.

    -
    Return type:
    -

    List[Tuple[Any, ...]]

    -
    -
    Parameters:
    -
      -

    • table (str) –

      • -

    • columns (List[str] | str) –

      • -

    • sequential_index (int | None) –

      • -

    • selection (str | None) –

      • +
      Parameters:
      +
        +

      • table (str) – Table to be queried.

        • +

      • columns (Union[List[str], str]) – Columns to read out.

        • +

      • sequential_index (Optional[int], default: None) – Sequentially numbered index +(i.e. in [0,len(self))) of the event to query. This _may_ +differ from the indexation used in self._indices. If no value +is provided, the entire column is returned.

        • +

      • selection (Optional[str], default: None) – Selection to be imposed before reading out data. +Defaults to None.

      +
      Return type:
      +

      ndarray

      +
      +
      Returns:
      +

      +
      List of tuples containing the values in columns. If the table

      contains only scalar data for columns, a list of length 1 is +returned

      +
      +
      +

      +
      +
      Raises:
      +

      ColumnMissingException – If one or more element in columns is not + present in table.

      +
    @@ -678,7 +730,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.data.dataset.sqlite.html b/api/graphnet.data.dataset.sqlite.html index d147d8aaa..3d5ee0258 100644 --- a/api/graphnet.data.dataset.sqlite.html +++ b/api/graphnet.data.dataset.sqlite.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -406,6 +433,13 @@ constants + +
  • + + + curated_datamodule + +
  • @@ -434,15 +468,15 @@ datamodule +
    • +
  • - pipeline + datasets -
    • -
  • @@ -454,14 +488,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -571,7 +605,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.data.dataset.sqlite.sqlite_dataset.html b/api/graphnet.data.dataset.sqlite.sqlite_dataset.html index c5c664424..c0ff5ffb0 100644 --- a/api/graphnet.data.dataset.sqlite.sqlite_dataset.html +++ b/api/graphnet.data.dataset.sqlite.sqlite_dataset.html @@ -123,10 +123,9 @@ - + - @@ -287,14 +286,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -432,6 +459,13 @@ constants + +
  • + + + curated_datamodule + +
  • @@ -460,15 +494,15 @@ datamodule +
    • +
  • - pipeline + datasets -
    • -
  • @@ -480,14 +514,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -602,8 +636,8 @@ events ~ event_no % 5 > 0”).

  • graph_definition (GraphDefinition) – Method that defines the graph representation.

  • labels (Optional[Dict[str, Any]], default: None) – Dictionary of labels to be added to the dataset.

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • +

  • args (Any)

    • +

  • kwargs (Any)

    • Return type:
    @@ -620,10 +654,10 @@
    Parameters:
      -

    • table (str) –

      • -

    • columns (List[str] | str) –

      • -

    • sequential_index (int | None) –

      • -

    • selection (str | None) –

      • +

    • table (str)

      • +

    • columns (List[str] | str)

      • +

    • sequential_index (int | None)

      • +

    • selection (str | None)

    @@ -678,7 +712,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.data.pipeline.html b/api/graphnet.data.extractors.combine_extractors.html similarity index 70% rename from api/graphnet.data.pipeline.html rename to api/graphnet.data.extractors.combine_extractors.html index d7167dca9..02c7876a4 100644 --- a/api/graphnet.data.pipeline.html +++ b/api/graphnet.data.extractors.combine_extractors.html @@ -61,7 +61,7 @@ - pipeline — graphnet documentation + combine_extractors — graphnet documentation + + + + + + + + + + + + + + + + internal — graphnet documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
    + +
    + + +
    + + + + +
    +
    + +
    +
    +
    + +
    +
    +
    +
    +
    +
    + + +
    +
    +
    + +
    + +
    +
    +
    +
    + + + + + \ No newline at end of file diff --git a/api/graphnet.data.extractors.internal.parquet_extractor.html b/api/graphnet.data.extractors.internal.parquet_extractor.html new file mode 100644 index 000000000..c2baa33b5 --- /dev/null +++ b/api/graphnet.data.extractors.internal.parquet_extractor.html @@ -0,0 +1,673 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + parquet_extractor — graphnet documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
    + +
    + + +
    + + + + +
    +
    + +
    +
    +
    + +
    +
    +
    +
    +
    +
    + + +
    +
    +
    + +
    +
    + +
    +

    parquet_extractor

    +

    Parquet Extractor for conversion from internal parquet format.

    +
    +
    +class graphnet.data.extractors.internal.parquet_extractor.ParquetExtractor(extractor_name)[source]
    +

    Bases: Extractor

    +

    Class for extracting information from internal GraphNeT parquet files.

    +

    Contains functionality required to extract data from internal parquet +files, i.e files saved using the ParquetWriter. This allows for conversion +between internal data formats.

    +

    Construct ParquetExtractor.

    +
    +
    Parameters:
    +
      +

    • extractor_name (str) – Name of the ParquetExtractor instance.

      • +

    • data (Used to keep track of the provenance of different)

      • +
    +
    +
    +

    :param : +:param and to name tables to which this data is saved.:

    +
    +
    + + +
    +
    +
    +
    +
    + + + + + \ No newline at end of file diff --git a/api/graphnet.data.extractors.liquido.h5_extractor.html b/api/graphnet.data.extractors.liquido.h5_extractor.html new file mode 100644 index 000000000..e277cc317 --- /dev/null +++ b/api/graphnet.data.extractors.liquido.h5_extractor.html @@ -0,0 +1,713 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + h5_extractor — graphnet documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
    + +
    + + +
    + + + + +
    +
    + +
    +
    +
    + +
    +
    +
    +
    +
    +
    + + +
    +
    +
    + +
    +
    + +
    +

    h5_extractor

    +

    H5 Extractor for LiquidO data files.

    +
    +
    +class graphnet.data.extractors.liquido.h5_extractor.H5Extractor(extractor_name, column_names)[source]
    +

    Bases: Extractor

    +

    Class for extracting information from LiquidO h5 files.

    +

    Construct H5Extractor.

    +
    +
    Parameters:
    +
      +

    • extractor_name (str) – Name of the ParquetExtractor instance.

      • +

    • data (Used to keep track of the provenance of different)

      • +

    • column_names (List[str])

      • +
    +
    +
    +

    :param : +:param and to name tables to which this data is saved.: +:type column_names: List[str] +:param column_names: Name of the columns in extractor_name.

    +
    +
    +
    +class graphnet.data.extractors.liquido.h5_extractor.H5HitExtractor[source]
    +

    Bases: H5Extractor

    +

    Extractor for HitData in LiquidO H5 files.

    +

    Extractor for HitData in LiquidO H5 files.

    +
    +
    +
    +
    +
    +class graphnet.data.extractors.liquido.h5_extractor.H5TruthExtractor[source]
    +

    Bases: H5Extractor

    +

    Extractor for TruthData in LiquidO H5 files.

    +

    Extractor for TruthData in LiquidO H5 files.

    +
    +
    +
    +
    + + +
    +
    +
    +
    +
    + + + + + \ No newline at end of file diff --git a/api/graphnet.data.extractors.liquido.html b/api/graphnet.data.extractors.liquido.html new file mode 100644 index 000000000..a2b3e15f9 --- /dev/null +++ b/api/graphnet.data.extractors.liquido.html @@ -0,0 +1,642 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + liquido — graphnet documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
    + +
    + + +
    + + + + +
    +
    + +
    +
    +
    + +
    +
    +
    +
    +
    +
    + + +
    +
    +
    + +
    + +
    +
    +
    +
    + + + + + \ No newline at end of file diff --git a/api/graphnet.data.extractors.prometheus.html b/api/graphnet.data.extractors.prometheus.html new file mode 100644 index 000000000..8afc1a6f2 --- /dev/null +++ b/api/graphnet.data.extractors.prometheus.html @@ -0,0 +1,642 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + prometheus — graphnet documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
    + +
    + + +
    + + + + +
    +
    + +
    +
    +
    + +
    +
    +
    +
    +
    +
    + + +
    +
    +
    + +
    + +
    +
    +
    +
    + + + + + \ No newline at end of file diff --git a/api/graphnet.data.extractors.prometheus.prometheus_extractor.html b/api/graphnet.data.extractors.prometheus.prometheus_extractor.html new file mode 100644 index 000000000..6597c78f4 --- /dev/null +++ b/api/graphnet.data.extractors.prometheus.prometheus_extractor.html @@ -0,0 +1,724 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + prometheus_extractor — graphnet documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
    + +
    + + +
    + + + + +
    +
    + +
    +
    +
    + +
    +
    +
    +
    +
    +
    + + +
    +
    +
    + +
    +
    + +
    +

    prometheus_extractor

    +

    Parquet Extractor for conversion of simulation files from PROMETHEUS.

    +
    +
    +class graphnet.data.extractors.prometheus.prometheus_extractor.PrometheusExtractor(extractor_name, columns)[source]
    +

    Bases: Extractor

    +

    Class for extracting information from PROMETHEUS parquet files.

    +

    Contains functionality required to extract data from PROMETHEUS parquet +files.

    +

    Construct PrometheusExtractor.

    +
    +
    Parameters:
    +
      +

    • extractor_name (str) – Name of the PrometheusExtractor instance.

      • +

    • data (Used to keep track of the provenance of different)

      • +

    • columns (List[str])

      • +
    +
    +
    +

    :param : +:param and to name tables to which this data is saved.: +:type columns: List[str] +:param columns: List of column names to extract from the table.

    +
    +
    +
    +class graphnet.data.extractors.prometheus.prometheus_extractor.PrometheusTruthExtractor(table_name)[source]
    +

    Bases: PrometheusExtractor

    +

    Class for extracting event level truth from Prometheus parquet files.

    +

    This Extractor will “initial_state” i.e. neutrino truth.

    +

    Construct PrometheusTruthExtractor.

    +
    +
    Parameters:
    +

    table_name (str, default: 'mc_truth') – Name of the table in the parquet files that contain +event-level truth. Defaults to “mc_truth”.

    +
    +
    +
    +
    +
    +class graphnet.data.extractors.prometheus.prometheus_extractor.PrometheusFeatureExtractor(table_name)[source]
    +

    Bases: PrometheusExtractor

    +

    Class for extracting pulses/photons from Prometheus parquet files.

    +

    Construct PrometheusFeatureExtractor.

    +
    +
    Parameters:
    +

    table_name (str, default: 'photons') – Name of table in parquet files that contain the +photons/pulses. Defaults to “photons”.

    +
    +
    +
    +
    + + +
    +
    +
    +
    +
    + + + + + \ No newline at end of file diff --git a/api/graphnet.data.html b/api/graphnet.data.html index ea5ca2d92..115adf908 100644 --- a/api/graphnet.data.html +++ b/api/graphnet.data.html @@ -123,10 +123,9 @@ - + - @@ -284,14 +283,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -376,6 +403,13 @@ constants + +
  • + + + curated_datamodule + +
  • @@ -404,15 +438,15 @@ datamodule +
    • +
  • - pipeline + datasets -
    • -
  • @@ -424,14 +458,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -496,6 +530,10 @@
  • extractors
    • @@ -510,6 +548,9 @@
  • readers
  • sqlite
      @@ -539,6 +580,11 @@
    • TRUTH
    • +
  • curated_datamodule +
  • dataclasses
    • -
  • pipeline -
    • @@ -614,7 +656,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.data.parquet.deprecated_methods.html b/api/graphnet.data.parquet.deprecated_methods.html index 6d569ad59..d2404f15e 100644 --- a/api/graphnet.data.parquet.deprecated_methods.html +++ b/api/graphnet.data.parquet.deprecated_methods.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -399,6 +426,13 @@ constants + +
  • + + + curated_datamodule + +
  • @@ -427,15 +461,15 @@ datamodule +
    • +
  • - pipeline + datasets -
    • -
  • @@ -447,14 +481,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -595,7 +629,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.data.parquet.html b/api/graphnet.data.parquet.html index 8f91610c1..b81779746 100644 --- a/api/graphnet.data.parquet.html +++ b/api/graphnet.data.parquet.html @@ -123,10 +123,9 @@ - + - @@ -285,14 +284,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -384,6 +411,13 @@ constants + +
  • + + + curated_datamodule + +
  • @@ -412,15 +446,15 @@ datamodule +
    • +
  • - pipeline + datasets -
    • -
  • @@ -432,14 +466,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -549,7 +583,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.data.pre_configured.dataconverters.html b/api/graphnet.data.pre_configured.dataconverters.html index 11a6c31f9..00db438c7 100644 --- a/api/graphnet.data.pre_configured.dataconverters.html +++ b/api/graphnet.data.pre_configured.dataconverters.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -350,6 +377,8 @@
  • I3ToParquetConverter
  • I3ToSQLiteConverter +
    • +
  • ParquetToSQLiteConverter
    • @@ -369,6 +398,13 @@ I3ToSQLiteConverter + +
  • + + + ParquetToSQLiteConverter + +
    • @@ -408,6 +444,13 @@ constants + +
  • + + + curated_datamodule + +
  • @@ -436,15 +479,15 @@ datamodule +
    • +
  • - pipeline + datasets -
    • -
  • @@ -456,14 +499,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -509,6 +552,8 @@
  • I3ToParquetConverter
  • I3ToSQLiteConverter +
    • +
  • ParquetToSQLiteConverter
    • @@ -588,6 +633,29 @@ +
    +
    +class graphnet.data.pre_configured.dataconverters.ParquetToSQLiteConverter(extractors, outdir, index_column, num_workers)[source]
    +

    Bases: DataConverter

    +

    Preconfigured DataConverter for converting Parquet to SQLite files.

    +

    This class converts Parquet files written by ParquetWriter to SQLite.

    +

    Convert internal Parquet files to SQLite.

    +
    +
    Parameters:
    +
      +

    • extractors (List[ParquetExtractor]) – The `Extractor`(s) that will be applied to the input +files.

      • +

    • outdir (str) – The directory to save the files in.

      • +

    • icetray_verbose – Set the level of verbosity of icetray. +Defaults to 0.

      • +

    • index_column (str, default: 'event_no') – Name of the event id column added to the events. +Defaults to “event_no”.

      • +

    • num_workers (int, default: 1) – The number of CPUs used for parallel processing. +Defaults to 1 (no multiprocessing).

      • +
    +
    +
    +
    @@ -637,7 +705,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.data.pre_configured.html b/api/graphnet.data.pre_configured.html index af2a6c837..997b98695 100644 --- a/api/graphnet.data.pre_configured.html +++ b/api/graphnet.data.pre_configured.html @@ -123,10 +123,9 @@ - + - @@ -285,14 +284,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -384,6 +411,13 @@ constants + +
  • + + + curated_datamodule + +
  • @@ -412,15 +446,15 @@ datamodule +
    • +
  • - pipeline + datasets -
    • -
  • @@ -432,14 +466,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -497,6 +531,7 @@
  • dataconverters
    • @@ -550,7 +585,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.data.readers.graphnet_file_reader.html b/api/graphnet.data.readers.graphnet_file_reader.html index 3daaee6ca..4c22c8a31 100644 --- a/api/graphnet.data.readers.graphnet_file_reader.html +++ b/api/graphnet.data.readers.graphnet_file_reader.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -432,6 +459,27 @@ i3reader + +
  • + + + internal_parquet_reader + + +
    • +
  • + + + liquido_reader + + +
    • +
  • + + + prometheus_reader + +
    • @@ -462,6 +510,13 @@ constants + +
  • + + + curated_datamodule + +
  • @@ -490,15 +545,15 @@ datamodule +
    • +
  • - pipeline + datasets -
    • -
  • @@ -510,14 +565,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -606,11 +661,11 @@
    Parameters:
      -

    • name (str | None) –

      • -

    • class_name (str | None) –

      • -

    • level (int) –

      • -

    • log_folder (str | None) –

      • -

    • kwargs (Any) –

      • +

    • name (str | None)

      • +

    • class_name (str | None)

      • +

    • level (int)

      • +

    • log_folder (str | None)

      • +

    • kwargs (Any)

    @@ -652,7 +707,7 @@

    Set `Extractor`(s) as member variable.

    Parameters:
    -

    extractors (Union[List[Extractor], List[I3Extractor]]) – A list of `Extractor`(s) to set as member variable.

    +

    extractors (Union[List[Extractor], List[I3Extractor], List[ParquetExtractor], List[H5Extractor], List[PrometheusExtractor]]) – A list of `Extractor`(s) to set as member variable.

    Return type:

    None

    @@ -722,7 +777,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.data.readers.html b/api/graphnet.data.readers.html index d0d0dc99b..d3866f275 100644 --- a/api/graphnet.data.readers.html +++ b/api/graphnet.data.readers.html @@ -123,10 +123,9 @@ - + - @@ -285,14 +284,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -361,6 +388,27 @@ i3reader + +
  • + + + internal_parquet_reader + + +
    • +
  • + + + liquido_reader + + +
    • +
  • + + + prometheus_reader + +
    • @@ -391,6 +439,13 @@ constants + +
  • + + + curated_datamodule + +
  • @@ -419,15 +474,15 @@ datamodule +
    • +
  • - pipeline + datasets -
    • -
  • @@ -439,14 +494,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -509,6 +564,18 @@
  • I3Reader
    • +
  • internal_parquet_reader +
    • +
  • liquido_reader +
    • +
  • prometheus_reader +
    • @@ -560,7 +627,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.data.readers.i3reader.html b/api/graphnet.data.readers.i3reader.html index 4c3732eac..c90dac6fe 100644 --- a/api/graphnet.data.readers.i3reader.html +++ b/api/graphnet.data.readers.i3reader.html @@ -123,13 +123,12 @@ - + - - + @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -387,6 +414,27 @@ + +
  • + + + internal_parquet_reader + + +
    • +
  • + + + liquido_reader + + +
    • +
  • + + + prometheus_reader + +
    • @@ -417,6 +465,13 @@ constants + +
  • + + + curated_datamodule + +
  • @@ -445,15 +500,15 @@ datamodule +
    • +
  • - pipeline + datasets -
    • -
  • @@ -465,14 +520,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -604,12 +659,12 @@ - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.pisa.plotting.html b/api/graphnet.data.readers.internal_parquet_reader.html similarity index 54% rename from api/graphnet.pisa.plotting.html rename to api/graphnet.data.readers.internal_parquet_reader.html index 8d9b9e9e8..4f155fada 100644 --- a/api/graphnet.pisa.plotting.html +++ b/api/graphnet.data.readers.internal_parquet_reader.html @@ -61,7 +61,7 @@ - plotting — graphnet documentation + internal_parquet_reader — graphnet documentation + + + + + + + + + + + + + + + + liquido_reader — graphnet documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
    + +
    + + +
    + + + + +
    +
    + +
    +
    +
    + +
    +
    +
    +
    +
    +
    + + +
    +
    +
    + +
    +
    + +
    +

    liquido_reader

    +

    Modules for reading data files from LiquidO.

    +
    +
    +class graphnet.data.readers.liquido_reader.LiquidOReader(name, class_name, level, log_folder, **kwargs)[source]
    +

    Bases: GraphNeTFileReader

    +

    A class for reading h5 files from LiquidO.

    +

    Construct Logger.

    +
    +
    Parameters:
    +
      +

    • name (str | None)

      • +

    • class_name (str | None)

      • +

    • level (int)

      • +

    • log_folder (str | None)

      • +

    • kwargs (Any)

      • +
    +
    +
    +
    +
    +find_files(path)[source]
    +

    Search folder(s) for h5 files.

    +
    +
    Parameters:
    +

    path (Union[str, List[str]]) – directory to search for h5 files.

    +
    +
    Return type:
    +

    List[str]

    +
    +
    Returns:
    +

    List of h5 files in the folders.

    +
    +
    +
    +
    +
    + + +
    +
    +
    +
    +
    + + + + + \ No newline at end of file diff --git a/api/graphnet.data.readers.prometheus_reader.html b/api/graphnet.data.readers.prometheus_reader.html new file mode 100644 index 000000000..8f3f65f31 --- /dev/null +++ b/api/graphnet.data.readers.prometheus_reader.html @@ -0,0 +1,687 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + prometheus_reader — graphnet documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
    + +
    + + +
    + + + + +
    +
    + +
    +
    +
    + +
    +
    +
    +
    +
    +
    + + +
    +
    +
    + +
    +
    + +
    +

    prometheus_reader

    +

    Modules for reading data files from the Prometheus project.

    +
    +
    +class graphnet.data.readers.prometheus_reader.PrometheusReader(name, class_name, level, log_folder, **kwargs)[source]
    +

    Bases: GraphNeTFileReader

    +

    A class for reading parquet files from Prometheus simulation.

    +

    Construct Logger.

    +
    +
    Parameters:
    +
      +

    • name (str | None)

      • +

    • class_name (str | None)

      • +

    • level (int)

      • +

    • log_folder (str | None)

      • +

    • kwargs (Any)

      • +
    +
    +
    +
    +
    +find_files(path)[source]
    +

    Search folder(s) for parquet files.

    +
    +
    Parameters:
    +

    path (Union[str, List[str]]) – directory to search for parquet files.

    +
    +
    Return type:
    +

    List[str]

    +
    +
    Returns:
    +

    List of parquet files in the folders.

    +
    +
    +
    +
    +
    + + +
    +
    +
    +
    +
    + + + + + \ No newline at end of file diff --git a/api/graphnet.data.sqlite.deprecated_methods.html b/api/graphnet.data.sqlite.deprecated_methods.html index 4f95c689d..804cd9851 100644 --- a/api/graphnet.data.sqlite.deprecated_methods.html +++ b/api/graphnet.data.sqlite.deprecated_methods.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -399,6 +426,13 @@ constants + +
  • + + + curated_datamodule + +
  • @@ -427,15 +461,15 @@ datamodule +
    • +
  • - pipeline + datasets -
    • -
  • @@ -447,14 +481,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -595,7 +629,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.data.sqlite.html b/api/graphnet.data.sqlite.html index afd47386c..132f28ddd 100644 --- a/api/graphnet.data.sqlite.html +++ b/api/graphnet.data.sqlite.html @@ -123,14 +123,13 @@ - + - - + @@ -285,14 +284,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -384,6 +411,13 @@ constants + +
  • + + + curated_datamodule + +
  • @@ -412,15 +446,15 @@ datamodule +
    • +
  • - pipeline + datasets -
    • -
  • @@ -432,14 +466,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -512,7 +546,7 @@
    Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.data.utilities.random.html b/api/graphnet.data.utilities.random.html index 6a8420331..9cfed03b3 100644 --- a/api/graphnet.data.utilities.random.html +++ b/api/graphnet.data.utilities.random.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -420,6 +447,13 @@ constants + +
  • + + + curated_datamodule + +
  • @@ -448,15 +482,15 @@ datamodule +
    • +
  • - pipeline + datasets -
    • -
  • @@ -468,14 +502,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -544,7 +578,7 @@

    • files_list – List of I3 file paths.

    • gcd_list (List[str]) – List of corresponding gcd file paths.

      • -

    • i3_list (List[str]) –

      • +

    • i3_list (List[str])

    Returns:
    @@ -605,7 +639,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.data.utilities.sqlite_utilities.html b/api/graphnet.data.utilities.sqlite_utilities.html index 9e771ae9c..a2da298c7 100644 --- a/api/graphnet.data.utilities.sqlite_utilities.html +++ b/api/graphnet.data.utilities.sqlite_utilities.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -492,6 +519,13 @@ constants + +
  • + + + curated_datamodule + +
  • @@ -520,15 +554,15 @@ datamodule +
    • +
  • - pipeline + datasets -
    • -
  • @@ -540,14 +574,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -631,7 +665,7 @@

    bool

    Parameters:
    -

    database_path (str) –

    +

    database_path (str)

    @@ -686,8 +720,8 @@
    Parameters:
    @@ -737,9 +771,9 @@
    Parameters:
    @@ -780,12 +814,12 @@
    Parameters:
    @@ -839,7 +873,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.data.utilities.string_selection_resolver.html b/api/graphnet.data.utilities.string_selection_resolver.html index 6d1927ebf..7e1256f12 100644 --- a/api/graphnet.data.utilities.string_selection_resolver.html +++ b/api/graphnet.data.utilities.string_selection_resolver.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -431,6 +458,13 @@ constants + +
  • + + + curated_datamodule + +
  • @@ -459,15 +493,15 @@ datamodule +
    • +
  • - pipeline + datasets -
    • -
  • @@ -479,14 +513,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -594,10 +628,10 @@
    Parameters:
      -

    • dataset (Dataset) –

      • -

    • index_column (str) –

      • -

    • seed (int | None) –

      • -

    • use_cache (bool) –

      • +

    • dataset (Dataset)

      • +

    • index_column (str)

      • +

    • seed (int | None)

      • +

    • use_cache (bool)

    @@ -614,7 +648,7 @@

    List[int]

    Parameters:
    -

    selection (str) –

    +

    selection (str)

    @@ -668,7 +702,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.data.writers.graphnet_writer.html b/api/graphnet.data.writers.graphnet_writer.html index 86cea8354..45d2c0945 100644 --- a/api/graphnet.data.writers.graphnet_writer.html +++ b/api/graphnet.data.writers.graphnet_writer.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -442,6 +469,13 @@ constants + +
  • + + + curated_datamodule + +
  • @@ -470,15 +504,15 @@ datamodule +
    • +
  • - pipeline + datasets -
    • -
  • @@ -490,14 +524,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -580,11 +614,11 @@
    Parameters:
      -

    • name (str | None) –

      • -

    • class_name (str | None) –

      • -

    • level (int) –

      • -

    • log_folder (str | None) –

      • -

    • kwargs (Any) –

      • +

    • name (str | None)

      • +

    • class_name (str | None)

      • +

    • level (int)

      • +

    • log_folder (str | None)

      • +

    • kwargs (Any)

    @@ -664,7 +698,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.data.writers.html b/api/graphnet.data.writers.html index afea72365..59d5ec37f 100644 --- a/api/graphnet.data.writers.html +++ b/api/graphnet.data.writers.html @@ -123,10 +123,9 @@ - + - @@ -285,14 +284,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -398,6 +425,13 @@ constants + +
  • + + + curated_datamodule + +
  • @@ -426,15 +460,15 @@ datamodule +
    • +
  • - pipeline + datasets -
    • -
  • @@ -446,14 +480,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -571,7 +605,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.data.writers.parquet_writer.html b/api/graphnet.data.writers.parquet_writer.html index 4c65807fe..2deaaf432 100644 --- a/api/graphnet.data.writers.parquet_writer.html +++ b/api/graphnet.data.writers.parquet_writer.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -424,6 +451,13 @@ constants + +
  • + + + curated_datamodule + +
  • @@ -452,15 +486,15 @@ datamodule +
    • +
  • - pipeline + datasets -
    • -
  • @@ -472,14 +506,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -544,37 +578,42 @@

    DataConverter for the Parquet backend.

    -class graphnet.data.writers.parquet_writer.ParquetWriter(name, class_name, level, log_folder, **kwargs)[source]
    +class graphnet.data.writers.parquet_writer.ParquetWriter(truth_table, index_column)[source]

    Bases: GraphNeTWriter

    Class for writing interim data format to Parquet.

    -

    Construct Logger.

    +

    Construct ParquetWriter.

    Parameters:
      -

    • name (str | None) –

      • -

    • class_name (str | None) –

      • -

    • level (int) –

      • -

    • log_folder (str | None) –

      • -

    • kwargs (Any) –

      • +

    • truth_table (str, default: 'truth') – Name of the tables containing event-level truth data. +defaults to “truth”.

      • +

    • index_column (str, default: 'event_no') – The column used for indexation. +Defaults to “event_no”.

    -merge_files(files, output_dir)[source]
    -

    Merge parquet files.

    +merge_files(files, output_dir, events_per_batch, num_workers)[source] +

    Convert files into shuffled batches.

    +
    +

    Events will be shuffled, and the resulting batches will constitute +random subsamples of the full dataset.

    +
    Parameters:
      -

    • files (List[str]) – input files for merging.

      • -

    • output_dir (str) – directory to store merged file(s) in.

      • +

    • files (List[str]) – Files converted to parquet. Note this argument is ignored +by this method, as these files are automatically found +using the output_dir.

      • +

    • output_dir (str) – The directory to store the batched data.

      • +

    • events_per_batch (int, default: 200000) – Number of events in each batch. +Defaults to 200000.

      • +

    • num_workers (int, default: 1) – Number of workers to use for merging. Defaults to 1.

    -
    Raises:
    -

    NotImplementedError –

    -
    -
    Return type:
    -

    None

    +
    Return type:
    +

    None

    @@ -628,7 +667,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.data.writers.sqlite_writer.html b/api/graphnet.data.writers.sqlite_writer.html index be3ac1b63..b9bff6f4f 100644 --- a/api/graphnet.data.writers.sqlite_writer.html +++ b/api/graphnet.data.writers.sqlite_writer.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -424,6 +451,13 @@ constants + +
  • + + + curated_datamodule + +
  • @@ -452,15 +486,15 @@ datamodule +
    • +
  • - pipeline + datasets -
    • -
  • @@ -472,14 +506,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -546,7 +580,7 @@ a deep-learning friendly file format.

    -class graphnet.data.writers.sqlite_writer.SQLiteWriter(merged_database_name, max_table_size)[source]
    +class graphnet.data.writers.sqlite_writer.SQLiteWriter(merged_database_name, max_table_size, index_column)[source]

    Bases: GraphNeTWriter

    A method for saving GraphNeT’s interim dataformat to SQLite.

    Initialize SQLiteWriter.

    @@ -562,12 +596,13 @@ you have many events, as tables exceeding 400 million rows tend to be noticably slower to query. Defaults to None (All events are put into a single database).

    +

  • index_column (str, default: 'event_no') – Name of column that contains event id.

    • -merge_files(files, output_dir)[source]
    +merge_files(files, output_dir, primary_key_rescue)[source]

    SQLite-specific method for merging output files/databases.

    Parameters:
    @@ -582,6 +617,9 @@ you have many events, as tables exceeding 400 million rows tend to be noticably slower to query. Defaults to None (All events are put into a single database.)

    +

  • primary_key_rescue (str, default: 'event_no') – The name of the columns on which the primary +key is constructed. This will only be used if it is not +possible to infer the primary key name.

    • Return type:
    @@ -639,7 +677,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.datasets.html b/api/graphnet.datasets.html new file mode 100644 index 000000000..2692462c3 --- /dev/null +++ b/api/graphnet.datasets.html @@ -0,0 +1,512 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + datasets — graphnet documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
    + +
    + + +
    + + + + +
    +
    + +
    +
    +
    + +
    +
    +
    +
    +
    +
    + + +
    +
    +
    + +
    + +
    +
    +
    +
    + + + + + \ No newline at end of file diff --git a/api/graphnet.datasets.prometheus_datasets.html b/api/graphnet.datasets.prometheus_datasets.html new file mode 100644 index 000000000..9f28dc08a --- /dev/null +++ b/api/graphnet.datasets.prometheus_datasets.html @@ -0,0 +1,666 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + prometheus_datasets — graphnet documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
    + +
    + + +
    + + + + +
    +
    + +
    +
    +
    + +
    +
    +
    +
    +
    +
    + + +
    +
    +
    + +
    +
    + +
    +

    prometheus_datasets

    +

    Public datasets from Prometheus Simulation.

    +
    +
    +class graphnet.datasets.prometheus_datasets.PublicPrometheusDataset(graph_definition, download_dir, truth, features, backend, train_dataloader_kwargs, validation_dataloader_kwargs, test_dataloader_kwargs)[source]
    +

    Bases: ERDAHostedDataset

    +

    A generic class for public Prometheus Datasets hosted using ERDA.

    +

    Construct CuratedDataset.

    +
    +
    Parameters:
    +
      +

    • graph_definition (GraphDefinition) – Method that defines the data representation.

      • +

    • download_dir (str) – Directory to download dataset to.

      • +

    • truth (Optional) – List of event-level truth to include. Will +include all available information if not given.

      • +

    • features (Optional) – List of input features from pulsemap to use. +If not given, all available features will be +used.

      • +

    • backend (Optional) – data backend to use. Either “parquet” or +“sqlite”. Defaults to “parquet”.

      • +

    • train_dataloader_kwargs (Optional) – Arguments for the training +DataLoader. Default None.

      • +

    • validation_dataloader_kwargs (Optional) – Arguments for the +validation DataLoader, Default None.

      • +

    • test_dataloader_kwargs (Optional) – Arguments for the test +DataLoader. Default None.

      • +
    +
    +
    +
    +
    +
    +class graphnet.datasets.prometheus_datasets.TRIDENTSmall(graph_definition, download_dir, truth, features, backend, train_dataloader_kwargs, validation_dataloader_kwargs, test_dataloader_kwargs)[source]
    +

    Bases: PublicPrometheusDataset

    +

    Public Dataset for Prometheus simulation of a TRIDENT geometry.

    +

    Contains ~ 1 million track events between 10 GeV - 10 TeV.

    +

    Construct CuratedDataset.

    +
    +
    Parameters:
    +
      +

    • graph_definition (GraphDefinition) – Method that defines the data representation.

      • +

    • download_dir (str) – Directory to download dataset to.

      • +

    • truth (Optional) – List of event-level truth to include. Will +include all available information if not given.

      • +

    • features (Optional) – List of input features from pulsemap to use. +If not given, all available features will be +used.

      • +

    • backend (Optional) – data backend to use. Either “parquet” or +“sqlite”. Defaults to “parquet”.

      • +

    • train_dataloader_kwargs (Optional) – Arguments for the training +DataLoader. Default None.

      • +

    • validation_dataloader_kwargs (Optional) – Arguments for the +validation DataLoader, Default None.

      • +

    • test_dataloader_kwargs (Optional) – Arguments for the test +DataLoader. Default None.

      • +
    +
    +
    +
    +
    +
    +class graphnet.datasets.prometheus_datasets.PONESmall(graph_definition, download_dir, truth, features, backend, train_dataloader_kwargs, validation_dataloader_kwargs, test_dataloader_kwargs)[source]
    +

    Bases: PublicPrometheusDataset

    +

    Public Dataset for Prometheus simulation of a P-ONE geometry.

    +

    Contains ~ 1 million track events between 10 GeV - 10 TeV.

    +

    Construct CuratedDataset.

    +
    +
    Parameters:
    +
      +

    • graph_definition (GraphDefinition) – Method that defines the data representation.

      • +

    • download_dir (str) – Directory to download dataset to.

      • +

    • truth (Optional) – List of event-level truth to include. Will +include all available information if not given.

      • +

    • features (Optional) – List of input features from pulsemap to use. +If not given, all available features will be +used.

      • +

    • backend (Optional) – data backend to use. Either “parquet” or +“sqlite”. Defaults to “parquet”.

      • +

    • train_dataloader_kwargs (Optional) – Arguments for the training +DataLoader. Default None.

      • +

    • validation_dataloader_kwargs (Optional) – Arguments for the +validation DataLoader, Default None.

      • +

    • test_dataloader_kwargs (Optional) – Arguments for the test +DataLoader. Default None.

      • +
    +
    +
    +
    +
    +
    +class graphnet.datasets.prometheus_datasets.BaikalGVDSmall(graph_definition, download_dir, truth, features, backend, train_dataloader_kwargs, validation_dataloader_kwargs, test_dataloader_kwargs)[source]
    +

    Bases: PublicPrometheusDataset

    +

    Public Dataset for Prometheus simulation of a Baikal-GVD geometry.

    +

    Contains ~ 1 million track events between 10 GeV - 10 TeV.

    +

    Construct CuratedDataset.

    +
    +
    Parameters:
    +
      +

    • graph_definition (GraphDefinition) – Method that defines the data representation.

      • +

    • download_dir (str) – Directory to download dataset to.

      • +

    • truth (Optional) – List of event-level truth to include. Will +include all available information if not given.

      • +

    • features (Optional) – List of input features from pulsemap to use. +If not given, all available features will be +used.

      • +

    • backend (Optional) – data backend to use. Either “parquet” or +“sqlite”. Defaults to “parquet”.

      • +

    • train_dataloader_kwargs (Optional) – Arguments for the training +DataLoader. Default None.

      • +

    • validation_dataloader_kwargs (Optional) – Arguments for the +validation DataLoader, Default None.

      • +

    • test_dataloader_kwargs (Optional) – Arguments for the test +DataLoader. Default None.

      • +
    +
    +
    +
    +
    + + +
    +
    +
    +
    +
    + + + + + \ No newline at end of file diff --git a/api/graphnet.datasets.test_dataset.html b/api/graphnet.datasets.test_dataset.html new file mode 100644 index 000000000..78409e055 --- /dev/null +++ b/api/graphnet.datasets.test_dataset.html @@ -0,0 +1,547 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + test_dataset — graphnet documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
    + +
    + + +
    + + + + +
    +
    + +
    +
    +
    + +
    +
    +
    +
    +
    +
    + + +
    +
    +
    + +
    +
    + +
    +

    test_dataset

    +

    A CuratedDataset for unit tests.

    +
    +
    +class graphnet.datasets.test_dataset.TestDataset(graph_definition, download_dir, truth, features, backend, train_dataloader_kwargs, validation_dataloader_kwargs, test_dataloader_kwargs)[source]
    +

    Bases: ERDAHostedDataset

    +

    A CuratedDataset class for unit tests of ERDAHosted Datasets.

    +

    This dataset should not be used outside the context of unit tests.

    +

    Construct CuratedDataset.

    +
    +
    Parameters:
    +
      +

    • graph_definition (GraphDefinition) – Method that defines the data representation.

      • +

    • download_dir (str) – Directory to download dataset to.

      • +

    • truth (Optional) – List of event-level truth to include. Will +include all available information if not given.

      • +

    • features (Optional) – List of input features from pulsemap to use. +If not given, all available features will be +used.

      • +

    • backend (Optional) – data backend to use. Either “parquet” or +“sqlite”. Defaults to “parquet”.

      • +

    • train_dataloader_kwargs (Optional) – Arguments for the training +DataLoader. Default None.

      • +

    • validation_dataloader_kwargs (Optional) – Arguments for the +validation DataLoader, Default None.

      • +

    • test_dataloader_kwargs (Optional) – Arguments for the test +DataLoader. Default None.

      • +
    +
    +
    +
    +
    + + +
    +
    +
    +
    +
    + + + + + \ No newline at end of file diff --git a/api/graphnet.deployment.deployer.html b/api/graphnet.deployment.deployer.html index f72da3725..94fe641f6 100644 --- a/api/graphnet.deployment.deployer.html +++ b/api/graphnet.deployment.deployer.html @@ -123,10 +123,9 @@ - + - @@ -285,14 +284,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -307,6 +334,13 @@ data + +
  • + + + datasets + +
  • @@ -380,14 +414,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -537,7 +571,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.deployment.deployment_module.html b/api/graphnet.deployment.deployment_module.html index a8241876c..72264e3cc 100644 --- a/api/graphnet.deployment.deployment_module.html +++ b/api/graphnet.deployment.deployment_module.html @@ -123,13 +123,12 @@ - + - - + @@ -285,14 +284,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -307,6 +334,13 @@ data + +
  • + + + datasets + +
  • @@ -369,14 +403,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -481,12 +515,12 @@ - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.deployment.html b/api/graphnet.deployment.html index 1bc16b07e..1abe19dfa 100644 --- a/api/graphnet.deployment.html +++ b/api/graphnet.deployment.html @@ -123,14 +123,13 @@ - + - - + @@ -284,14 +283,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -306,6 +333,13 @@ data + +
  • + + + datasets + +
  • @@ -354,14 +388,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -455,7 +489,7 @@
    Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.deployment.i3modules.html b/api/graphnet.deployment.i3modules.html index 2efa006ef..d18b6168e 100644 --- a/api/graphnet.deployment.i3modules.html +++ b/api/graphnet.deployment.i3modules.html @@ -123,10 +123,9 @@ - + - @@ -285,14 +284,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -307,6 +334,13 @@ data + +
  • + + + datasets + +
  • @@ -362,14 +396,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -475,7 +509,7 @@

    i3modulesSphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.deployment.icecube.cleaning_module.html b/api/graphnet.deployment.icecube.cleaning_module.html index 47c3569b6..40f5acf49 100644 --- a/api/graphnet.deployment.icecube.cleaning_module.html +++ b/api/graphnet.deployment.icecube.cleaning_module.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -308,6 +335,13 @@ data + +
  • + + + datasets + +
  • @@ -391,14 +425,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -539,7 +573,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.deployment.icecube.html b/api/graphnet.deployment.icecube.html index 9bc11ad9e..9e0686597 100644 --- a/api/graphnet.deployment.icecube.html +++ b/api/graphnet.deployment.icecube.html @@ -123,10 +123,9 @@ - + - @@ -285,14 +284,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -307,6 +334,13 @@ data + +
  • + + + datasets + +
  • @@ -376,14 +410,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -497,7 +531,7 @@

    icecube Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.deployment.icecube.i3deployer.html b/api/graphnet.deployment.icecube.i3deployer.html index ef9795a2c..26ab51030 100644 --- a/api/graphnet.deployment.icecube.i3deployer.html +++ b/api/graphnet.deployment.icecube.i3deployer.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -308,6 +335,13 @@ data + +
  • + + + datasets + +
  • @@ -377,14 +411,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -484,7 +518,7 @@

    i3deployer Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.deployment.icecube.inference_module.html b/api/graphnet.deployment.icecube.inference_module.html index b9937cf35..4215022b9 100644 --- a/api/graphnet.deployment.icecube.inference_module.html +++ b/api/graphnet.deployment.icecube.inference_module.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -308,6 +335,13 @@ data + +
  • + + + datasets + +
  • @@ -391,14 +425,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -535,7 +569,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.exceptions.exceptions.html b/api/graphnet.exceptions.exceptions.html new file mode 100644 index 000000000..79d8e18be --- /dev/null +++ b/api/graphnet.exceptions.exceptions.html @@ -0,0 +1,517 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + exceptions — graphnet documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
    + +
    + + +
    + + + + +
    +
    + +
    +
    +
    + +
    +
    +
    +
    +
    +
    + + +
    +
    +
    + +
    +
    + +
    +

    exceptions

    +

    Module containing GraphNeT-specific Exceptions.

    +
    +
    +exception graphnet.exceptions.exceptions.ColumnMissingException[source]
    +

    Bases: Exception

    +

    Exception to indicate a missing column in a dataset.

    +
    +
    + + +
    +
    +
    +
    +
    + + + + + \ No newline at end of file diff --git a/api/graphnet.pisa.html b/api/graphnet.exceptions.html similarity index 83% rename from api/graphnet.pisa.html rename to api/graphnet.exceptions.html index a411dfc87..812c1837d 100644 --- a/api/graphnet.pisa.html +++ b/api/graphnet.exceptions.html @@ -61,7 +61,7 @@ - pisa — graphnet documentation + exceptions — graphnet documentation + + + + + + + + + + + + + + + + liquido — graphnet documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
    + +
    + + +
    + + + + +
    +
    + +
    +
    +
    + +
    +
    +
    +
    +
    +
    + + +
    +
    +
    + +
    +
    + +
    +

    liquido

    +

    LiquidO-specific Detector class(es).

    +
    +
    +class graphnet.models.detector.liquido.LiquidO_v1(*args, **kwargs)[source]
    +

    Bases: Detector

    +

    Detector class for LiquidO prototype.

    +

    Construct Detector.

    +
    +
    Parameters:
    +
      +

    • args (Any)

      • +

    • kwargs (Any)

      • +
    +
    +
    Return type:
    +

    object

    +
    +
    +
    +
    +geometry_table_path = '/home/runner/.local/lib/python3.10/data/geometry_tables/liquid-o/liquido_v1.parquet'
    +
    +
    +
    +xyz = ['sipm_x', 'sipm_y', 'sipm_z']
    +
    +
    +
    +string_id_column = 'fiber_id'
    +
    +
    +
    +sensor_id_column = 'sipm_id'
    +
    +
    +
    +feature_map()[source]
    +

    Map standardization functions to each dimension.

    +
    +
    Return type:
    +

    Dict[str, Callable]

    +
    +
    +
    +
    +
    + + +
    +
    +
    +
    +
    + + + + + \ No newline at end of file diff --git a/api/graphnet.models.detector.prometheus.html b/api/graphnet.models.detector.prometheus.html index e912b56e5..ace5f174d 100644 --- a/api/graphnet.models.detector.prometheus.html +++ b/api/graphnet.models.detector.prometheus.html @@ -123,14 +123,13 @@ - + - - + @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -308,6 +335,13 @@ data + +
  • + + + datasets + +
  • @@ -315,6 +349,13 @@ deployment +
    • +
  • + + + exceptions + +
  • @@ -346,6 +387,13 @@ icecube +
    • +
  • + + + liquido + +
  • @@ -361,6 +409,104 @@ - - - - - - -
    -
    -
    - -
    • +
  • + + + training + + +
    • +
  • + + + utilities + + +
    • +
  • + + + constants + + +
    • + + + + + + + + + +
    +
    +
    + +

    +
    +class graphnet.models.detector.prometheus.IceCube86Prometheus(*args, **kwargs)[source]
    +

    Bases: Detector

    +

    Detector class for Prometheus IceCube86.

    +

    Construct Detector.

    +
    +
    Parameters:
    +
      +

    • args (Any)

      • +

    • kwargs (Any)

      • +
    +
    +
    Return type:
    +

    object

    +
    +
    +
    +
    +geometry_table_path = '/home/runner/.local/lib/python3.10/data/geometry_tables/prometheus/icecube86.parquet'
    +
    +
    +
    +xyz = ['sensor_pos_x', 'sensor_pos_y', 'sensor_pos_z']
    +
    +
    +
    +string_id_column = 'sensor_string_id'
    +
    +
    +
    +sensor_id_column = 'sensor_id'
    +
    +
    +
    +feature_map()[source]
    +

    Map standardization functions to each dimension.

    +
    +
    Return type:
    +

    Dict[str, Callable]

    +
    +
    +
    +
    +
    +
    +class graphnet.models.detector.prometheus.IceCubeDeepCore8(*args, **kwargs)[source]
    +

    Bases: Detector

    +

    Detector class for Prometheus IceCubeDeepCore8.

    +

    Construct Detector.

    +
    +
    Parameters:
    +
      +

    • args (Any)

      • +

    • kwargs (Any)

      • +
    +
    +
    Return type:
    +

    object

    +
    +
    +
    +
    +geometry_table_path = '/home/runner/.local/lib/python3.10/data/geometry_tables/prometheus/icecube_deepcore.parquet'
    +
    +
    +
    +xyz = ['sensor_pos_x', 'sensor_pos_y', 'sensor_pos_z']
    +
    +
    +
    +string_id_column = 'sensor_string_id'
    +
    +
    +
    +sensor_id_column = 'sensor_id'
    +
    +
    +
    +feature_map()[source]
    +

    Map standardization functions to each dimension.

    +
    +
    Return type:
    +

    Dict[str, Callable]

    +
    +
    +
    +
    +
    +
    +class graphnet.models.detector.prometheus.IceCubeGen2(*args, **kwargs)[source]
    +

    Bases: Detector

    +

    Detector class for Prometheus IceCubeGen2.

    +

    Construct Detector.

    +
    +
    Parameters:
    +
      +

    • args (Any)

      • +

    • kwargs (Any)

      • +
    +
    +
    Return type:
    +

    object

    +
    +
    +
    +
    +geometry_table_path = '/home/runner/.local/lib/python3.10/data/geometry_tables/prometheus/icecube_gen2.parquet'
    +
    +
    +
    +xyz = ['sensor_pos_x', 'sensor_pos_y', 'sensor_pos_z']
    +
    +
    +
    +string_id_column = 'sensor_string_id'
    +
    +
    +
    +sensor_id_column = 'sensor_id'
    +
    +
    +
    +feature_map()[source]
    +

    Map standardization functions to each dimension.

    +
    +
    Return type:
    +

    Dict[str, Callable]

    +
    +
    +
    +
    +
    +
    +class graphnet.models.detector.prometheus.PONETriangle(*args, **kwargs)[source]
    +

    Bases: Detector

    +

    Detector class for Prometheus PONE Triangle.

    +

    Construct Detector.

    +
    +
    Parameters:
    +
      +

    • args (Any)

      • +

    • kwargs (Any)

      • +
    +
    +
    Return type:
    +

    object

    +
    +
    +
    +
    +geometry_table_path = '/home/runner/.local/lib/python3.10/data/geometry_tables/prometheus/pone_triangle.parquet'
    +
    +
    +
    +xyz = ['sensor_pos_x', 'sensor_pos_y', 'sensor_pos_z']
    +
    +
    +
    +string_id_column = 'sensor_string_id'
    +
    +
    +
    +sensor_id_column = 'sensor_id'
    +
    +
    +
    +feature_map()[source]
    +

    Map standardization functions to each dimension.

    +
    +
    Return type:
    +

    Dict[str, Callable]

    +
    +
    +
    +
    +
    class graphnet.models.detector.prometheus.Prometheus(*args, **kwargs)[source]
    -

    Bases: ORCA150

    -

    Reference to ORCA150.

    +

    Bases: ORCA150SuperDense

    +

    Reference to ORCA150SuperDense.

    Construct Detector.

    Parameters:
      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • +

    • args (Any)

      • +

    • kwargs (Any)

    Return type:
    @@ -650,7 +1952,7 @@
    Return type:
    @@ -598,7 +639,7 @@

    Tensor

    Parameters:
    -

    data (Data) –

    +

    data (Data)

    @@ -652,7 +693,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.models.gnn.convnet.html b/api/graphnet.models.gnn.convnet.html index 2ff5cc25d..dd7af7e29 100644 --- a/api/graphnet.models.gnn.convnet.html +++ b/api/graphnet.models.gnn.convnet.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -308,6 +335,13 @@ data + +
  • + + + datasets + +
  • @@ -315,6 +349,13 @@ deployment +
    • +
  • + + + exceptions + +
  • @@ -445,6 +486,13 @@ task +
    • +
  • + + + transformer + +
  • @@ -482,13 +530,6 @@
    • - -
  • - - - pisa - -
  • @@ -565,8 +606,8 @@ output layer.

  • nb_intermediate (int, default: 128) – Number of nodes in intermediate layer(s).

  • dropout_ratio (float, default: 0.3) – Fraction of nodes to drop.

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • +

  • args (Any)

    • +

  • kwargs (Any)

    • Return type:
    @@ -582,7 +623,7 @@

    Tensor

    Parameters:
    -

    data (Data) –

    +

    data (Data)

    @@ -636,7 +677,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.models.gnn.dynedge.html b/api/graphnet.models.gnn.dynedge.html index 2c625cd19..8bed660e2 100644 --- a/api/graphnet.models.gnn.dynedge.html +++ b/api/graphnet.models.gnn.dynedge.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -308,6 +335,13 @@ data + +
  • + + + datasets + +
  • @@ -315,6 +349,13 @@ deployment +
    • +
  • + + + exceptions + +
  • @@ -445,6 +486,13 @@ task +
    • +
  • + + + transformer + +
  • @@ -482,13 +530,6 @@
    • - -
  • - - - pisa - -
  • @@ -587,13 +628,13 @@ after global pooling. The alternative is to added (distribute) them to the individual nodes before any convolutional operations.

    • -

  • activation_layer (Optional[Callable], default: None) – The activation function to use in the model.

    • +

  • activation_layer (Optional[str], default: None) – The activation function to use in the model.

  • add_norm_layer (bool, default: False) – Whether to add a normalization layer after each linear layer.

  • skip_readout (bool, default: False) – Whether to skip the readout layer(s). If True, the output of the last post-processing layer is returned directly.

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • +

  • args (Any)

    • +

  • kwargs (Any)

    • Return type:
    @@ -609,7 +650,7 @@

    Tensor

    Parameters:
    -

    data (Data) –

    +

    data (Data)

    @@ -663,7 +704,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.models.gnn.dynedge_jinst.html b/api/graphnet.models.gnn.dynedge_jinst.html index e92659e50..4e1642a04 100644 --- a/api/graphnet.models.gnn.dynedge_jinst.html +++ b/api/graphnet.models.gnn.dynedge_jinst.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -308,6 +335,13 @@ data + +
  • + + + datasets + +
  • @@ -315,6 +349,13 @@ deployment +
    • +
  • + + + exceptions + +
  • @@ -445,6 +486,13 @@ task +
    • +
  • + + + transformer + +
  • @@ -482,13 +530,6 @@
    • - -
  • - - - pisa - -
  • @@ -562,8 +603,8 @@

  • nb_inputs (int) – Number of input features.

  • nb_outputs – Number of output features.

  • layer_size_scale (int, default: 4) – Integer that scales the size of hidden layers.

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • +

  • args (Any)

    • +

  • kwargs (Any)

    • Return type:
    @@ -579,7 +620,7 @@

    Tensor

    Parameters:
    -

    data (Data) –

    +

    data (Data)

    @@ -633,7 +674,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.models.gnn.dynedge_kaggle_tito.html b/api/graphnet.models.gnn.dynedge_kaggle_tito.html index 93f3d6a20..891f743da 100644 --- a/api/graphnet.models.gnn.dynedge_kaggle_tito.html +++ b/api/graphnet.models.gnn.dynedge_kaggle_tito.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -308,6 +335,13 @@ data + +
  • + + + datasets + +
  • @@ -315,6 +349,13 @@ deployment +
    • +
  • + + + exceptions + +
  • @@ -445,6 +486,13 @@ task +
    • +
  • + + + transformer + +
  • @@ -482,13 +530,6 @@
    • - -
  • - - - pisa - -
  • @@ -580,8 +621,8 @@

  • n_head (int, default: 8) – The number of heads to use in the DynTrans layer.

  • nb_neighbours (int, default: 8) – The number of neighbours to use in the DynTrans layer.

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • +

  • args (Any)

    • +

  • kwargs (Any)

    • Return type:
    @@ -597,7 +638,7 @@

    Tensor

    Parameters:
    -

    data (Data) –

    +

    data (Data)

    @@ -651,7 +692,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.models.gnn.gnn.html b/api/graphnet.models.gnn.gnn.html index a7cb5d36a..d9e11f75c 100644 --- a/api/graphnet.models.gnn.gnn.html +++ b/api/graphnet.models.gnn.gnn.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -308,6 +335,13 @@ data + +
  • + + + datasets + +
  • @@ -315,6 +349,13 @@ deployment +
    • +
  • + + + exceptions + +
  • @@ -463,6 +504,13 @@ task +
    • +
  • + + + transformer + +
  • @@ -500,13 +548,6 @@
    • - -
  • - - - pisa - -
  • @@ -580,8 +621,8 @@
    Parameters:
      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • +

    • args (Any)

      • +

    • kwargs (Any)

    Return type:
    @@ -607,7 +648,7 @@

    Tensor

    Parameters:
    -

    data (Data) –

    +

    data (Data)

    @@ -661,7 +702,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.models.gnn.html b/api/graphnet.models.gnn.html index d5dff7670..1e8916ed2 100644 --- a/api/graphnet.models.gnn.html +++ b/api/graphnet.models.gnn.html @@ -123,10 +123,9 @@ - + - @@ -285,14 +284,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -307,6 +334,13 @@ data + +
  • + + + datasets + +
  • @@ -314,6 +348,13 @@ deployment +
    • +
  • + + + exceptions + +
  • @@ -419,6 +460,13 @@ task +
    • +
  • + + + transformer + +
  • @@ -456,13 +504,6 @@
    • - -
  • - - - pisa - -
  • @@ -594,7 +635,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.models.gnn.icemix.html b/api/graphnet.models.gnn.icemix.html index 47931ca5a..3330d98f8 100644 --- a/api/graphnet.models.gnn.icemix.html +++ b/api/graphnet.models.gnn.icemix.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -308,6 +335,13 @@ data + +
  • + + + datasets + +
  • @@ -315,6 +349,13 @@ deployment +
    • +
  • + + + exceptions + +
  • @@ -454,6 +495,13 @@ task +
    • +
  • + + + transformer + +
  • @@ -491,13 +539,6 @@
    • - -
  • - - - pisa - -
  • @@ -576,7 +617,8 @@
    Parameters:

    • hidden_dim (int, default: 384) – The latent feature dimension.

      • -

    • seq_length (int, default: 128) – The base feature dimension.

      • +

    • mlp_ratio (int, default: 4) – Mlp expansion ratio of FourierEncoder and Transformer.

      • +

    • seq_length (int, default: 192) – The base feature dimension.

    • depth (int, default: 12) – The depth of the transformer.

    • head_size (int, default: 32) – The size of the attention heads.

    • depth_rel (int, default: 4) – The depth of the relative transformer.

      • @@ -588,8 +630,9 @@ provided, DynEdge will be initialized with the original Kaggle Competition settings. If include_dynedge is False, this argument have no impact.

      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • +

    • n_features (int, default: 6) – The number of features in the input data.

      • +

    • args (Any)

      • +

    • kwargs (Any)

    Return type:
    @@ -615,7 +658,7 @@

    Tensor

    Parameters:
    -

    data (Data) –

    +

    data (Data)

    @@ -669,7 +712,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.models.graphs.edges.edges.html b/api/graphnet.models.graphs.edges.edges.html index 13f2d9245..d99618b17 100644 --- a/api/graphnet.models.graphs.edges.edges.html +++ b/api/graphnet.models.graphs.edges.edges.html @@ -123,10 +123,9 @@ - + - @@ -287,14 +286,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -309,6 +336,13 @@ data + +
  • + + + datasets + +
  • @@ -316,6 +350,13 @@ deployment +
    • +
  • + + + exceptions + +
  • @@ -473,6 +514,13 @@ task +
    • +
  • + + + transformer + +
  • @@ -510,13 +558,6 @@
    • - -
  • - - - pisa - -
  • @@ -592,8 +633,8 @@
    Parameters:
      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • +

    • args (Any)

      • +

    • kwargs (Any)

    Return type:
    @@ -631,11 +672,11 @@

    • nb_nearest_neighbours (int) – number of neighbours.

    • columns (List[int], default: [0, 1, 2]) – Node features to use for distance calculation.

      • -

    • [0 (Defaults to) –

      • -

    • 1 –

      • -

    • 2]. –

      • -

    • args (Any) –

      • -

    • kwargs (Any) –

      • +

    • [0 (Defaults to)

      • +

    • 1

      • +

    • 2].

      • +

    • args (Any)

      • +

    • kwargs (Any)

    Return type:
    @@ -657,11 +698,11 @@

    • radius (float) – radius of sphere

    • columns (List[int], default: [0, 1, 2]) – columns of the node feature matrix used.

      • -

    • [0 (Defaults to) –

      • -

    • 1 –

      • -

    • 2]. –

      • -

    • args (Any) –

      • -

    • kwargs (Any) –

      • +

    • [0 (Defaults to)

      • +

    • 1

      • +

    • 2].

      • +

    • args (Any)

      • +

    • kwargs (Any)

    Return type:
    @@ -679,8 +720,8 @@
    Parameters:
      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • +

    • args (Any)

      • +

    • kwargs (Any)

    Return type:
    @@ -737,7 +778,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.models.graphs.edges.html b/api/graphnet.models.graphs.edges.html index d6afe8a37..8906969b4 100644 --- a/api/graphnet.models.graphs.edges.html +++ b/api/graphnet.models.graphs.edges.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -308,6 +335,13 @@ data +
    • +
  • + + + datasets + +
  • @@ -315,6 +349,13 @@ deployment +
    • +
  • + + + exceptions + +
  • @@ -420,6 +461,13 @@ task +
    • +
  • + + + transformer + +
  • @@ -457,13 +505,6 @@
    • - -
  • - - - pisa - -
  • @@ -582,7 +623,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.models.graphs.edges.minkowski.html b/api/graphnet.models.graphs.edges.minkowski.html index b1401e5d6..78d5165b9 100644 --- a/api/graphnet.models.graphs.edges.minkowski.html +++ b/api/graphnet.models.graphs.edges.minkowski.html @@ -123,10 +123,9 @@ - + - @@ -287,14 +286,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -309,6 +336,13 @@ data + +
  • + + + datasets + +
  • @@ -316,6 +350,13 @@ deployment +
    • +
  • + + + exceptions + +
  • @@ -444,6 +485,13 @@ task +
    • +
  • + + + transformer + +
  • @@ -481,13 +529,6 @@
    • - -
  • - - - pisa - -
  • @@ -582,8 +623,8 @@ nearest neighbours.

  • space_coords (Optional[List[int]], default: None) – Coordinates of x, y, z.

  • time_coord (Optional[int], default: 3) – Coordinate of time.

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • +

  • args (Any)

    • +

  • kwargs (Any)

    • Return type:
    @@ -640,7 +681,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.models.graphs.graph_definition.html b/api/graphnet.models.graphs.graph_definition.html index 9842afef9..892a56090 100644 --- a/api/graphnet.models.graphs.graph_definition.html +++ b/api/graphnet.models.graphs.graph_definition.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -308,6 +335,13 @@ data + +
  • + + + datasets + +
  • @@ -315,6 +349,13 @@ deployment +
    • +
  • + + + exceptions + +
  • @@ -431,6 +472,13 @@ task +
    • +
  • + + + transformer + +
  • @@ -468,13 +516,6 @@
    • - -
  • - - - pisa - -
  • @@ -578,8 +619,8 @@ sensor listed here will be removed from the graph. Defaults to None.

  • string_mask (Optional[List[int]], default: None) – A list of string id’s to be masked from the graph. Defaults to None.

  • sort_by (Optional[str], default: None) – Name of node feature to sort by. Defaults to None.

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • +

  • args (Any)

    • +

  • kwargs (Any)

    • Return type:
    @@ -664,7 +705,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.models.graphs.graphs.html b/api/graphnet.models.graphs.graphs.html index e904aef71..6f19f2668 100644 --- a/api/graphnet.models.graphs.graphs.html +++ b/api/graphnet.models.graphs.graphs.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -308,6 +335,13 @@ data + +
  • + + + datasets + +
  • @@ -315,6 +349,13 @@ deployment +
    • +
  • + + + exceptions + +
  • @@ -420,6 +461,13 @@ task +
    • +
  • + + + transformer + +
  • @@ -457,13 +505,6 @@
    • - -
  • - - - pisa - -
  • @@ -541,11 +582,11 @@ Defaults to None.

  • nb_nearest_neighbours (int, default: 8) – Number of edges for each node. Defaults to 8.

  • columns (List[int], default: [0, 1, 2]) – node feature columns used for distance calculation

    • -

  • [0 (. Defaults to) –

    • -

  • 1 –

    • -

  • 2]. –

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • +

  • [0 (. Defaults to)

    • +

  • 1

    • +

  • 2].

    • +

  • args (Any)

    • +

  • kwargs (Any)

    • Return type:
    @@ -602,7 +643,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.models.graphs.html b/api/graphnet.models.graphs.html index 2507abc16..b5649038b 100644 --- a/api/graphnet.models.graphs.html +++ b/api/graphnet.models.graphs.html @@ -123,10 +123,9 @@ - + - @@ -285,14 +284,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -307,6 +334,13 @@ data + +
  • + + + datasets + +
  • @@ -314,6 +348,13 @@ deployment +
    • +
  • + + + exceptions + +
  • @@ -405,6 +446,13 @@ task +
    • +
  • + + + transformer + +
  • @@ -442,13 +490,6 @@
    • - -
  • - - - pisa - -
  • @@ -585,7 +626,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.models.graphs.nodes.html b/api/graphnet.models.graphs.nodes.html index b8b2b714e..bebf84303 100644 --- a/api/graphnet.models.graphs.nodes.html +++ b/api/graphnet.models.graphs.nodes.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -308,6 +335,13 @@ data + +
  • + + + datasets + +
  • @@ -315,6 +349,13 @@ deployment +
    • +
  • + + + exceptions + +
  • @@ -413,6 +454,13 @@ task +
    • +
  • + + + transformer + +
  • @@ -450,13 +498,6 @@
    • - -
  • - - - pisa - -
  • @@ -571,7 +612,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.models.graphs.nodes.nodes.html b/api/graphnet.models.graphs.nodes.nodes.html index 42398f811..845670a3d 100644 --- a/api/graphnet.models.graphs.nodes.nodes.html +++ b/api/graphnet.models.graphs.nodes.nodes.html @@ -123,10 +123,9 @@ - + - @@ -287,14 +286,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -309,6 +336,13 @@ data + +
  • + + + datasets + +
  • @@ -316,6 +350,13 @@ deployment +
    • +
  • + + + exceptions + +
  • @@ -502,6 +543,13 @@ task +
    • +
  • + + + transformer + +
  • @@ -539,13 +587,6 @@
    • - -
  • - - - pisa - -
  • @@ -629,8 +670,8 @@
    Parameters:
      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • +

    • args (Any)

      • +

    • kwargs (Any)

    Return type:
    @@ -645,7 +686,7 @@
    Parameters:

    • x (tensor) – standardized node features with shape ´[num_pulses, d]´,

      • -

    • features. (where ´d´ is the number of node) –

      • +

    • features. (where ´d´ is the number of node)

    • node_feature_names – list of names for each column in ´x´.

    @@ -685,7 +726,7 @@
    Parameters:

    • input_feature_names (List[str]) – List of column names of the input to the

      • -

    • definition. (node) –

      • +

    • definition. (node)

    Return type:
    @@ -703,8 +744,8 @@
    Parameters:
      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • +

    • args (Any)

      • +

    • kwargs (Any)

    Return type:
    @@ -729,8 +770,8 @@

  • percentiles (List[int]) – List of percentiles. E.g. [10, 50, 90].

  • add_counts (bool, default: True) – If True, number of duplicates is added to output array.

  • input_feature_names (Optional[List[str]], default: None) – (Optional) column names for input features.

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • +

  • args (Any)

    • +

  • kwargs (Any)

    • Return type:
    @@ -752,8 +793,8 @@

  • time_column (str, default: 'dom_time') – Name of time column.

  • charge_column (str, default: 'charge') – Name of charge column.

  • max_activations (Optional[int], default: None) – Maximum number of activations to include in the time series.

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • +

  • args (Any)

    • +

  • kwargs (Any)

    • Return type:
    @@ -774,12 +815,16 @@
    Parameters:

    • input_feature_names (Optional[List[str]], default: None) – Column names for input features. Minimum

      • -

    • names. (required features are z coordinate and hlc column) –

      • +

    • names. (required features are z coordinate and hlc column)

    • max_pulses (int, default: 768) – Maximum number of pulses to keep in the event.

    • z_name (str, default: 'dom_z') – Name of the z-coordinate column.

      • -

    • hlc_name (str, default: 'hlc') – Name of the Hard Local Coincidence Check column.

      • -

    • args (Any) –

      • -

    • kwargs (Any) –

      • +

    • hlc_name (Optional[str], default: 'hlc') – Name of the Hard Local Coincidence Check column.

      • +

    • add_ice_properties (bool, default: True) – If True, scattering and absoption length of

      • +

    • coordinate. (ice in IceCube are added to the feature set based on z)

      • +

    • ice_args (Dict[str, Optional[float]], default: {'z_offset': None, 'z_scaling': None}) – Offset and scaling of the z coordinate in the Detector,

      • +

    • data. (to be able to make similar conversion in the ice)

      • +

    • args (Any)

      • +

    • kwargs (Any)

    Return type:
    @@ -836,7 +881,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.models.graphs.utils.html b/api/graphnet.models.graphs.utils.html index e80c9c7d5..4fc59ed86 100644 --- a/api/graphnet.models.graphs.utils.html +++ b/api/graphnet.models.graphs.utils.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -308,6 +335,13 @@ data +
    • +
  • + + + datasets + +
  • @@ -315,6 +349,13 @@ deployment +
    • +
  • + + + exceptions + +
  • @@ -456,6 +497,13 @@ task +
    • +
  • + + + transformer + +
  • @@ -493,13 +541,6 @@
    • - -
  • - - - pisa - -
  • @@ -629,8 +670,8 @@
    Parameters:
      -

    • feature_names (List[str]) –

      • -

    • cluster_on (List[str]) –

      • +

    • feature_names (List[str])

      • +

    • cluster_on (List[str])

    @@ -661,7 +702,7 @@

  • cluster_indices (List[int]) – List of column indices on which the clusters are constructed.

  • percentiles (List[int]) – percentiles used to summarize x. E.g. [10,50,90].

    • -

  • add_counts (bool) –

    • +

  • add_counts (bool)

    • Return type:
    @@ -674,7 +715,7 @@
    -graphnet.models.graphs.utils.ice_transparency()[source]
    +graphnet.models.graphs.utils.ice_transparency(z_offset, z_scaling)[source]

    Return interpolation functions for optical properties of IceCube.

    NOTE: The resulting interpolation functions assumes that the @@ -682,8 +723,14 @@ Any deviation from this scaling method results in inaccurate results.

    -
    Returns:
    -

    +
    Parameters:
    +
      +

    • z_offset (Optional[float], default: None) – Offset to be added to the depth of the DOM.

      • +

    • z_scaling (Optional[float], default: None) – Scaling factor to be applied to the depth of the DOM.

      • +
    +
    +
    Returns:
    +

    Function that takes a normalized depth and returns the

    corresponding normalized scattering length.

    f_absorption: Function that takes a normalized depth and returns the

    corresponding normalized absorption length.

    @@ -691,8 +738,8 @@

    -
    Return type:
    -

    f_scattering

    +
    Return type:
    +

    f_scattering

    @@ -745,7 +792,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.models.html b/api/graphnet.models.html index 15ae7feb7..fbf317188 100644 --- a/api/graphnet.models.html +++ b/api/graphnet.models.html @@ -123,14 +123,14 @@ - + + - - + @@ -284,14 +284,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -306,6 +334,13 @@ data + +
  • + + + datasets + +
  • @@ -313,6 +348,13 @@ deployment +
    • +
  • + + + exceptions + +
  • @@ -369,6 +411,13 @@ task +
    • +
  • + + + transformer + +
  • @@ -406,13 +455,6 @@
    • - -
  • - - - pisa - -
  • @@ -479,6 +521,7 @@
  • detector
    • @@ -510,6 +553,10 @@
  • task
    • +
  • transformer +

    • Submodules

    @@ -557,7 +604,7 @@
    @@ -630,7 +671,7 @@

    Model

    Parameters:
    -

    path (str) –

    +

    path (str)

    @@ -643,7 +684,7 @@

    None

    Parameters:
    -

    path (str) –

    +

    path (str)

    @@ -657,8 +698,8 @@
    Parameters:
    @@ -675,7 +716,7 @@

  • load_modules (Optional[List[str]], default: None) – List of modules used in the definition of the model which, as a consequence, need to be loaded into the global namespace. Defaults to loading torch.

    • -

  • source (ModelConfig | str) –

    • +

  • source (ModelConfig | str)

    • Raises:
    @@ -696,7 +737,7 @@

    None

    Parameters:
    -

    verbose_print (bool) –

    +

    verbose_print (bool)

    @@ -724,8 +765,8 @@
    Parameters:
    @@ -780,7 +821,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.models.rnn.html b/api/graphnet.models.rnn.html index 260861d9f..6fa9b2771 100644 --- a/api/graphnet.models.rnn.html +++ b/api/graphnet.models.rnn.html @@ -123,10 +123,9 @@ - + - @@ -285,14 +284,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -307,6 +334,13 @@ data + +
  • + + + datasets + +
  • @@ -314,6 +348,13 @@ deployment +
    • +
  • + + + exceptions + +
  • @@ -377,6 +418,13 @@ task +
    • +
  • + + + transformer + +
  • @@ -414,13 +462,6 @@
    • - -
  • - - - pisa - -
  • @@ -528,7 +569,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.models.rnn.node_rnn.html b/api/graphnet.models.rnn.node_rnn.html index 28807ca58..445c54760 100644 --- a/api/graphnet.models.rnn.node_rnn.html +++ b/api/graphnet.models.rnn.node_rnn.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -308,6 +335,13 @@ data + +
  • + + + datasets + +
  • @@ -315,6 +349,13 @@ deployment +
    • +
  • + + + exceptions + +
  • @@ -412,6 +453,13 @@ task +
    • +
  • + + + transformer + +
  • @@ -449,13 +497,6 @@
    • - -
  • - - - pisa - -
  • @@ -543,8 +584,8 @@

  • features_subset (Optional[List[int]], default: None) – The subset of latent features on each node that are used as metric dimensions when performing the k-nearest neighbours clustering. Defaults to [0,1,2,3]

  • dropout (float, default: 0.5) – Dropout fraction to use in the RNN. Defaults to 0.5.

  • embedding_dim (int, default: 0) – Embedding dimension of the RNN. Defaults to no embedding.

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • +

  • args (Any)

    • +

  • kwargs (Any)

    • Return type:
    @@ -573,7 +614,7 @@

    Tensor

    Parameters:
    -

    data (Data) –

    +

    data (Data)

    @@ -627,7 +668,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.models.standard_averaged_model.html b/api/graphnet.models.standard_averaged_model.html index 271f4d19e..e57f946c4 100644 --- a/api/graphnet.models.standard_averaged_model.html +++ b/api/graphnet.models.standard_averaged_model.html @@ -123,10 +123,9 @@ - + - @@ -285,14 +284,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -307,6 +334,13 @@ data + +
  • + + + datasets + +
  • @@ -314,6 +348,13 @@ deployment +
    • +
  • + + + exceptions + +
  • @@ -361,6 +402,13 @@ task +
    • +
  • + + + transformer + +
  • @@ -468,13 +516,6 @@
    • - -
  • - - - pisa - -
  • @@ -552,8 +593,8 @@
    Parameters:
      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • +

    • args (Any)

      • +

    • kwargs (Any)

    Return type:
    @@ -570,8 +611,8 @@
    Parameters:
      -

    • train_batch (Data | List[Data]) –

      • -

    • batch_idx (int) –

      • +

    • train_batch (Data | List[Data])

      • +

    • batch_idx (int)

    @@ -586,8 +627,8 @@
    Parameters:
      -

    • val_batch (Data | List[Data]) –

      • -

    • batch_idx (int) –

      • +

    • val_batch (Data | List[Data])

      • +

    • batch_idx (int)

    @@ -602,10 +643,10 @@
    Parameters:
      -

    • epoch (int) –

      • -

    • batch_idx (int) –

      • -

    • optimizer (Type[Optimizer]) –

      • -

    • optimizer_closure (Callable[[], Any] | None) –

      • +

    • epoch (int)

      • +

    • batch_idx (int)

      • +

    • optimizer (Type[Optimizer])

      • +

    • optimizer_closure (Callable[[], Any] | None)

    @@ -620,8 +661,8 @@
    Parameters:
      -

    • path (str | Dict) –

      • -

    • kargs (Any | None) –

      • +

    • path (str | Dict)

      • +

    • kargs (Any | None)

    @@ -686,7 +727,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.models.standard_model.html b/api/graphnet.models.standard_model.html index b6edf21db..9353890c2 100644 --- a/api/graphnet.models.standard_model.html +++ b/api/graphnet.models.standard_model.html @@ -123,10 +123,9 @@ - + - @@ -285,14 +284,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -307,6 +334,13 @@ data + +
  • + + + datasets + +
  • @@ -314,6 +348,13 @@ deployment +
    • +
  • + + + exceptions + +
  • @@ -361,6 +402,13 @@ task +
    • +
  • + + + transformer + +
  • @@ -540,13 +588,6 @@
    • - -
  • - - - pisa - -
  • @@ -642,8 +683,8 @@
    Parameters:
      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • +

    • args (Any)

      • +

    • kwargs (Any)

    Return type:
    @@ -660,18 +701,18 @@
    Parameters:
      -

    • train_dataloader (DataLoader) –

      • -

    • val_dataloader (DataLoader | None) –

      • -

    • max_epochs (int) –

      • -

    • early_stopping_patience (int) –

      • -

    • gpus (List[int] | int | None) –

      • -

    • callbacks (List[Callback] | None) –

      • -

    • ckpt_path (str | None) –

      • -

    • logger (Logger | None) –

      • -

    • log_every_n_steps (int) –

      • -

    • gradient_clip_val (float | None) –

      • -

    • distribution_strategy (str | None) –

      • -

    • trainer_kwargs (Any) –

      • +

    • train_dataloader (DataLoader)

      • +

    • val_dataloader (DataLoader | None)

      • +

    • max_epochs (int)

      • +

    • early_stopping_patience (int)

      • +

    • gpus (List[int] | int | None)

      • +

    • callbacks (List[Callback] | None)

      • +

    • ckpt_path (str | None)

      • +

    • logger (Logger | None)

      • +

    • log_every_n_steps (int)

      • +

    • gradient_clip_val (float | None)

      • +

    • distribution_strategy (str | None)

      • +

    • trainer_kwargs (Any)

    @@ -705,7 +746,7 @@

    List[Union[Tensor, Data]]

    Parameters:
    -

    data (Data | List[Data]) –

    +

    data (Data | List[Data])

    @@ -721,8 +762,8 @@
    Parameters:
      -

    • batch (List[Data]) –

      • -

    • batch_idx (int) –

      • +

    • batch (List[Data])

      • +

    • batch_idx (int)

    @@ -737,8 +778,8 @@
    Parameters:
      -

    • train_batch (Data | List[Data]) –

      • -

    • batch_idx (int) –

      • +

    • train_batch (Data | List[Data])

      • +

    • batch_idx (int)

    @@ -753,8 +794,8 @@
    Parameters:
      -

    • val_batch (Data | List[Data]) –

      • -

    • batch_idx (int) –

      • +

    • val_batch (Data | List[Data])

      • +

    • batch_idx (int)

    @@ -769,9 +810,9 @@
    Parameters:
      -

    • preds (Tensor) –

      • -

    • data (List[Data]) –

      • -

    • verbose (bool) –

      • +

    • preds (Tensor)

      • +

    • data (List[Data])

      • +

    • verbose (bool)

    @@ -795,7 +836,7 @@

    Model

    Parameters:
    -

    mode (bool) –

    +

    mode (bool)

    @@ -809,9 +850,9 @@
    Parameters:
      -

    • dataloader (DataLoader) –

      • -

    • gpus (List[int] | int | None) –

      • -

    • distribution_strategy (str | None) –

      • +

    • dataloader (DataLoader)

      • +

    • gpus (List[int] | int | None)

      • +

    • distribution_strategy (str | None)

    @@ -828,11 +869,11 @@
    Parameters:
      -

    • dataloader (DataLoader) –

      • -

    • prediction_columns (List[str] | None) –

      • -

    • additional_attributes (List[str] | None) –

      • -

    • gpus (List[int] | int | None) –

      • -

    • distribution_strategy (str | None) –

      • +

    • dataloader (DataLoader)

      • +

    • prediction_columns (List[str] | None)

      • +

    • additional_attributes (List[str] | None)

      • +

    • gpus (List[int] | int | None)

      • +

    • distribution_strategy (str | None)

    @@ -887,7 +928,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.models.task.classification.html b/api/graphnet.models.task.classification.html index d37dabeb0..a9f149d0f 100644 --- a/api/graphnet.models.task.classification.html +++ b/api/graphnet.models.task.classification.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -308,6 +335,13 @@ data + +
  • + + + datasets + +
  • @@ -315,6 +349,13 @@ deployment +
    • +
  • + + + exceptions + +
  • @@ -482,6 +523,13 @@
    • + +
  • + + + transformer + +
  • @@ -519,13 +567,6 @@
    • - -
  • - - - pisa - -
  • @@ -616,8 +657,8 @@
    Parameters:
      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • +

    • args (Any)

      • +

    • kwargs (Any)

    Return type:
    @@ -637,8 +678,8 @@

  • hidden_size (int) – The number of columns in the output of the last latent layer of Model using this Task. Available through Model.nb_outputs

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • +

  • args (Any)

    • +

  • kwargs (Any)

    • Return type:
    @@ -670,8 +711,8 @@

  • hidden_size (int) – The number of columns in the output of the last latent layer of Model using this Task. Available through Model.nb_outputs

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • +

  • args (Any)

    • +

  • kwargs (Any)

    • Return type:
    @@ -740,7 +781,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.models.task.html b/api/graphnet.models.task.html index d6336a83f..458218d44 100644 --- a/api/graphnet.models.task.html +++ b/api/graphnet.models.task.html @@ -123,10 +123,9 @@ - + - @@ -285,14 +284,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -307,6 +334,13 @@ data +
    • +
  • + + + datasets + +
  • @@ -314,6 +348,13 @@ deployment +
    • +
  • + + + exceptions + +
  • @@ -391,6 +432,13 @@
    • + +
  • + + + transformer + +
  • @@ -428,13 +476,6 @@
    • - -
  • - - - pisa - -
  • @@ -568,7 +609,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.models.task.reconstruction.html b/api/graphnet.models.task.reconstruction.html index 77ad75bcc..b335f1754 100644 --- a/api/graphnet.models.task.reconstruction.html +++ b/api/graphnet.models.task.reconstruction.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -308,6 +335,13 @@ data + +
  • + + + datasets + +
  • @@ -315,6 +349,13 @@ deployment +
    • +
  • + + + exceptions + +
  • @@ -891,6 +932,13 @@
    • + +
  • + + + transformer + +
  • @@ -928,13 +976,6 @@
    • - -
  • - - - pisa - -
  • @@ -1131,8 +1172,8 @@

  • hidden_size (int) – The number of columns in the output of the last latent layer of Model using this Task. Available through Model.nb_outputs

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • +

  • args (Any)

    • +

  • kwargs (Any)

    • Return type:
    @@ -1164,8 +1205,8 @@

  • hidden_size (int) – The number of columns in the output of the last latent layer of Model using this Task. Available through Model.nb_outputs

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • +

  • args (Any)

    • +

  • kwargs (Any)

    • Return type:
    @@ -1197,8 +1238,8 @@

  • hidden_size (int) – The number of columns in the output of the last latent layer of Model using this Task. Available through Model.nb_outputs

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • +

  • args (Any)

    • +

  • kwargs (Any)

    • Return type:
    @@ -1230,8 +1271,8 @@

  • hidden_size (int) – The number of columns in the output of the last latent layer of Model using this Task. Available through Model.nb_outputs

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • +

  • args (Any)

    • +

  • kwargs (Any)

    • Return type:
    @@ -1263,8 +1304,8 @@

  • hidden_size (int) – The number of columns in the output of the last latent layer of Model using this Task. Available through Model.nb_outputs

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • +

  • args (Any)

    • +

  • kwargs (Any)

    • Return type:
    @@ -1296,8 +1337,8 @@

  • hidden_size (int) – The number of columns in the output of the last latent layer of Model using this Task. Available through Model.nb_outputs

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • +

  • args (Any)

    • +

  • kwargs (Any)

    • Return type:
    @@ -1329,8 +1370,8 @@

  • hidden_size (int) – The number of columns in the output of the last latent layer of Model using this Task. Available through Model.nb_outputs

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • +

  • args (Any)

    • +

  • kwargs (Any)

    • Return type:
    @@ -1362,8 +1403,8 @@

  • hidden_size (int) – The number of columns in the output of the last latent layer of Model using this Task. Available through Model.nb_outputs

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • +

  • args (Any)

    • +

  • kwargs (Any)

    • Return type:
    @@ -1395,8 +1436,8 @@

  • hidden_size (int) – The number of columns in the output of the last latent layer of Model using this Task. Available through Model.nb_outputs

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • +

  • args (Any)

    • +

  • kwargs (Any)

    • Return type:
    @@ -1428,8 +1469,8 @@

  • hidden_size (int) – The number of columns in the output of the last latent layer of Model using this Task. Available through Model.nb_outputs

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • +

  • args (Any)

    • +

  • kwargs (Any)

    • Return type:
    @@ -1461,8 +1502,8 @@

  • hidden_size (int) – The number of columns in the output of the last latent layer of Model using this Task. Available through Model.nb_outputs

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • +

  • args (Any)

    • +

  • kwargs (Any)

    • Return type:
    @@ -1494,8 +1535,8 @@

  • hidden_size (int) – The number of columns in the output of the last latent layer of Model using this Task. Available through Model.nb_outputs

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • +

  • args (Any)

    • +

  • kwargs (Any)

    • Return type:
    @@ -1528,8 +1569,8 @@

  • hidden_size (int) – The number of columns in the output of the last latent layer of Model using this Task. Available through Model.nb_outputs

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • +

  • args (Any)

    • +

  • kwargs (Any)

    • Return type:
    @@ -1598,7 +1639,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.models.task.task.html b/api/graphnet.models.task.task.html index b842f56bf..996dd3892 100644 --- a/api/graphnet.models.task.task.html +++ b/api/graphnet.models.task.task.html @@ -123,13 +123,12 @@ - + - - + @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -308,6 +335,13 @@ data + +
  • + + + datasets + +
  • @@ -315,6 +349,13 @@ deployment +
    • +
  • + + + exceptions + +
  • @@ -596,6 +637,13 @@
    • + +
  • + + + transformer + +
  • @@ -633,13 +681,6 @@
    • - -
  • - - - pisa - -
  • @@ -785,8 +826,8 @@ is tested on the range [-1e6, 1e6].

  • loss_weight (Optional[str], default: None) – Name of the attribute in data containing per-event loss weights.

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • +

  • args (Any)

    • +

  • kwargs (Any)

    • Return type:
    @@ -844,8 +885,8 @@

  • hidden_size (int) – The number of columns in the output of the last latent layer of Model using this Task. Available through Model.nb_outputs

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • +

  • args (Any)

    • +

  • kwargs (Any)

    • Return type:
    @@ -863,8 +904,8 @@
    Parameters:
    @@ -885,7 +926,7 @@

    Union[Tensor, Data]

    Parameters:
    -

    x (Tensor | Data) –

    +

    x (Tensor | Data)

    @@ -904,8 +945,8 @@

  • hidden_size (int) – The number of columns in the output of the last latent layer of Model using this Task. Available through Model.nb_outputs

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • +

  • args (Any)

    • +

  • kwargs (Any)

    • Return type:
    @@ -927,8 +968,8 @@
    Parameters:
    @@ -947,8 +988,8 @@
    Parameters:
      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • +

    • args (Any)

      • +

    • kwargs (Any)

    Return type:
    @@ -984,8 +1025,8 @@

  • hidden_size – The number of columns in the output of the last latent layer of Model using this Task. Available through Model.nb_outputs

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • +

  • args (Any)

    • +

  • kwargs (Any)

    • Return type:
    @@ -1012,8 +1053,8 @@
    Parameters:
      -

    • x (Tensor | Data) –

      • -

    • jacobian (Tensor | None) –

      • +

    • x (Tensor | Data)

      • +

    • jacobian (Tensor | None)

    @@ -1065,12 +1106,12 @@ - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.models.transformer.html b/api/graphnet.models.transformer.html new file mode 100644 index 000000000..e492e61d1 --- /dev/null +++ b/api/graphnet.models.transformer.html @@ -0,0 +1,583 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + transformer — graphnet documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
    + +
    + + +
    + + + + +
    +
    + +
    +
    +
    + +
    +
    +
    +
    +
    +
    + + +
    +
    +
    + +
    +
    + +
    +

    transformer

    +

    Transformer-specific modules.

    +

    Submodules

    +
    + +
    +
    + + +
    +
    +
    +
    +
    + + + + + \ No newline at end of file diff --git a/api/graphnet.models.transformer.iseecube.html b/api/graphnet.models.transformer.iseecube.html new file mode 100644 index 000000000..7b5e1e52b --- /dev/null +++ b/api/graphnet.models.transformer.iseecube.html @@ -0,0 +1,654 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + iseecube — graphnet documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
    + +
    + + +
    + + + + +
    +
    + +
    +
    +
    + +
    +
    +
    +
    +
    +
    + + +
    +
    +
    + +
    +
    + +
    +

    iseecube

    +

    Implementation of ISeeCube Transformer architecture used in.

    +

    https://github.com/ChenLi2049/ISeeCube/

    +
    +
    +class graphnet.models.transformer.iseecube.ISeeCube(*args, **kwargs)[source]
    +

    Bases: GNN

    +

    ISeeCube model.

    +

    Construct ISeeCube.

    +
    +
    Parameters:
    +
      +

    • hidden_dim (int, default: 384) – The latent feature dimension.

      • +

    • seq_length (int, default: 196) – The number of pulses in a neutrino event.

      • +

    • num_layers (int, default: 16) – The depth of the transformer.

      • +

    • num_heads (int, default: 12) – The number of the attention heads.

      • +

    • mlp_dim (int, default: 1536) – The mlp dimension of FourierEncoder and Transformer.

      • +

    • rel_pos_buckets (int, default: 32) – Relative position buckets for relative position +bias.

      • +

    • max_rel_pos (int, default: 256) – Maximum relative position for relative position bias.

      • +

    • num_register_tokens (int, default: 3) – The number of register tokens.

      • +

    • scaled_emb (bool, default: False) – Whether to scale the sinusoidal positional embeddings.

      • +

    • n_features (int, default: 6) – The number of features in the input data.

      • +

    • args (Any)

      • +

    • kwargs (Any)

      • +
    +
    +
    Return type:
    +

    object

    +
    +
    +
    +
    +forward(data)[source]
    +

    Apply learnable forward pass.

    +
    +
    Return type:
    +

    Tensor

    +
    +
    Parameters:
    +

    data (Data)

    +
    +
    +
    +
    +
    + + +
    +
    +
    +
    +
    + + + + + \ No newline at end of file diff --git a/api/graphnet.models.utils.html b/api/graphnet.models.utils.html index 8f52d93c0..41f1210f7 100644 --- a/api/graphnet.models.utils.html +++ b/api/graphnet.models.utils.html @@ -123,13 +123,12 @@ - + - - + @@ -285,14 +284,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -307,6 +334,13 @@ data + +
  • + + + datasets + +
  • @@ -314,6 +348,13 @@ deployment +
    • +
  • + + + exceptions + +
  • @@ -361,6 +402,13 @@ task +
    • +
  • + + + transformer + +
  • @@ -448,13 +496,6 @@
    • - -
  • - - - pisa - -
  • @@ -533,9 +574,9 @@
    Parameters:
      -

    • x (Tensor) –

      • -

    • edge_index (LongTensor) –

      • -

    • batch (Batch) –

      • +

    • x (Tensor)

      • +

    • edge_index (LongTensor)

      • +

    • batch (Batch)

    @@ -589,7 +630,7 @@
    Parameters:

    • x (Tensor) – array-like tensor with shape [n,d] where n is the total number

      • -

    • features. (of pulses in the batch and d is the number of node) –

      • +

    • features. (of pulses in the batch and d is the number of node)

    • batch_idx (LongTensor) – a LongTensor identifying which row in x belongs to which training example. E.g. torch_geometric.data.Batch.batch.

      • @@ -638,12 +679,12 @@ - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.pisa.fitting.html b/api/graphnet.pisa.fitting.html deleted file mode 100644 index c40fe61bf..000000000 --- a/api/graphnet.pisa.fitting.html +++ /dev/null @@ -1,673 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - fitting — graphnet documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Skip to content -
      - -
      - - -
      - - - - -
      -
      - -
      -
      -
      - -
      -
      -
      -
      -
      -
      - - -
      -
      -
      - -
      -
      - -
      -

      fitting

      -

      Functions and classes for fitting contours using PISA.

      -
      -
      -graphnet.pisa.fitting.config_updater(config_path, new_config_path, dummy_section)[source]
      -

      Update config files and saves them to file.

      -
      -
      Parameters:
      -
        -

      • config_path (str) – Path to original config file.

        • -

      • new_config_path (Optional[str], default: None) – Path to save updated config file.

        • -

      • dummy_section (str, default: 'temp') – Dummy section name to use for config files without -section headers.

        • -
      -
      -
      Yields:
      -

      ConfigUpdater instance for programatically updating config file.

      -
      -
      Return type:
      -

      ConfigUpdater

      -
      -
      -
      -
      -
      -class graphnet.pisa.fitting.WeightFitter(database_path, truth_table, index_column, statistical_fit)[source]
      -

      Bases: object

      -

      Class for fitting weights using PISA.

      -

      Construct WeightFitter.

      -
      -
      Parameters:
      -
        -

      • database_path (str) –

        • -

      • truth_table (str) –

        • -

      • index_column (str) –

        • -

      • statistical_fit (bool) –

        • -
      -
      -
      -
      -
      -fit_weights(config_outdir, weight_name, pisa_config_dict, add_to_database)[source]
      -

      Fit flux weights to each neutrino event in self._database_path.

      -

      If statistical_fit=True, only statistical effects are accounted for. -If True, certain systematic effects are included, but not -hypersurfaces.

      -
      -
      Parameters:
      -
        -

      • config_outdir (str) – The output directory in which to store the -configuration.

        • -

      • weight_name (str, default: '') – The name of the weight. If add_to_database=True, -this will be the name of the table.

        • -

      • pisa_config_dict (Optional[Dict], default: None) – The dictionary of PISA configurations. Can be -used to change assumptions regarding the fit.

        • -

      • add_to_database (bool, default: False) – If True, a table will be added to the database -called weight_name with two columns: -[index_column, weight_name]

        • -
      -
      -
      Return type:
      -

      DataFrame

      -
      -
      Returns:
      -

      A dataframe with columns [index_column, weight_name].

      -
      -
      -
      -
      -
      -
      -class graphnet.pisa.fitting.ContourFitter(outdir, pipeline_path, post_fix, model_name, include_retro, statistical_fit)[source]
      -

      Bases: object

      -

      Class for fitting contours using PISA.

      -

      Construct ContourFitter.

      -
      -
      Parameters:
      -
        -

      • outdir (str) –

        • -

      • pipeline_path (str) –

        • -

      • post_fix (str) –

        • -

      • model_name (str) –

        • -

      • include_retro (bool) –

        • -

      • statistical_fit (bool) –

        • -
      -
      -
      -
      -
      -fit_1d_contour(run_name, config_dict, grid_size, n_workers, theta23_minmax=(36.0, 54.0), dm31_minmax=(2.3, 2.7))[source]
      -

      Fit 1D contours.

      -
      -
      Return type:
      -

      None

      -
      -
      Parameters:
      -
        -

      • run_name (str) –

        • -

      • config_dict (Dict) –

        • -

      • grid_size (int) –

        • -

      • n_workers (int) –

        • -

      • theta23_minmax (Tuple[float, float]) –

        • -

      • dm31_minmax (Tuple[float, float]) –

        • -
      -
      -
      -
      -
      -
      -fit_2d_contour(run_name, config_dict, grid_size, n_workers, theta23_minmax=(36.0, 54.0), dm31_minmax=(2.3, 2.7))[source]
      -

      Fit 2D contours.

      -
      -
      Return type:
      -

      None

      -
      -
      Parameters:
      -
        -

      • run_name (str) –

        • -

      • config_dict (Dict) –

        • -

      • grid_size (int) –

        • -

      • n_workers (int) –

        • -

      • theta23_minmax (Tuple[float, float]) –

        • -

      • dm31_minmax (Tuple[float, float]) –

        • -
      -
      -
      -
      -
      -
      - - -
      -
      -
      -
      -
      - - - - - \ No newline at end of file diff --git a/api/graphnet.training.callbacks.html b/api/graphnet.training.callbacks.html index 30f76fb50..0d5fbee57 100644 --- a/api/graphnet.training.callbacks.html +++ b/api/graphnet.training.callbacks.html @@ -123,10 +123,9 @@ - + - @@ -285,14 +284,42 @@
    • - Install + Installation
    • - Contribute + Models In GraphNeT + + +
      • +
    • + + + Datasets In GraphNeT + + +
      • +
    • + + + Data Conversion in GraphNeT + + +
      • +
    • + + + Integrating New Experiments into GraphNeT + + +
      • +
    • + + + Contributing To GraphNeT
      • @@ -307,6 +334,13 @@ data + +
    • + + + datasets + +
    • @@ -318,14 +352,14 @@
    • - models + exceptions
    • - pisa + models
      • @@ -652,8 +686,8 @@
      Parameters:
        -

      • refresh_rate (int) –

        • -

      • process_position (int) –

        • +

      • refresh_rate (int)

        • +

      • process_position (int)

      @@ -707,8 +741,8 @@
    Parameters:
      -

    • trainer (Trainer) –

      • -

    • model (LightningModule) –

      • +

    • trainer (Trainer)

      • +

    • model (LightningModule)

    @@ -726,8 +760,8 @@
    Parameters:
      -

    • trainer (Trainer) –

      • -

    • model (LightningModule) –

      • +

    • trainer (Trainer)

      • +

    • model (LightningModule)

    @@ -743,8 +777,8 @@
    Parameters:
      -

    • trainer (Trainer) –

      • -

    • model (LightningModule) –

      • +

    • trainer (Trainer)

      • +

    • model (LightningModule)

    @@ -883,7 +917,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.training.html b/api/graphnet.training.html index 43a1760a0..caa444970 100644 --- a/api/graphnet.training.html +++ b/api/graphnet.training.html @@ -123,14 +123,13 @@ - + - - + @@ -284,14 +283,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -306,6 +333,13 @@ data + +
  • + + + datasets + +
  • @@ -317,14 +351,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -433,6 +467,7 @@
  • labels
  • loss_functions
    • @@ -388,6 +424,13 @@ Direction + +
  • + + + Track + +
    • @@ -453,6 +496,8 @@
  • Direction +
    • +
  • Track
    • @@ -507,6 +552,28 @@ +
    +
    +class graphnet.training.labels.Track(key, pid_key, interaction_key)[source]
    +

    Bases: Label

    +

    Class for producing NuMuCC label.

    +

    Label is set to 1 if the event is a NuMu CC event, else 0.

    +

    Construct Track label.

    +
    +
    Parameters:
    +
      +

    • key (str, default: 'track') – The name of the field in Data where the label will be +stored. That is, graph[key] = label.

      • +

    • pid_key (str, default: 'pid') – The name of the pre-existing key in graph that will +be used to access the pdg encoding, used when calculating +the direction.

      • +

    • interaction_key (str, default: 'interaction_type') – The name of the pre-existing key in graph that +will be used to access the interaction type (1 denoting CC), +used when calculating the direction.

      • +
    +
    +
    +
    @@ -556,7 +623,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.training.loss_functions.html b/api/graphnet.training.loss_functions.html index bcf94e1bb..f348c299e 100644 --- a/api/graphnet.training.loss_functions.html +++ b/api/graphnet.training.loss_functions.html @@ -123,10 +123,9 @@ - + - @@ -285,14 +284,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -307,6 +334,13 @@ data + +
  • + + + datasets + +
  • @@ -318,14 +352,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -641,8 +675,8 @@
    Parameters:
      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • +

    • args (Any)

      • +

    • kwargs (Any)

    Return type:
    @@ -660,7 +694,7 @@

  • target (Tensor) – Tensor containing targets. Shape [N,T]

  • return_elements (bool, default: False) – Whether elementwise loss terms should be returned. The alternative is to return the averaged loss across examples.

    • -

  • weights (Tensor | None) –

    • +

  • weights (Tensor | None)

    • Return type:
    @@ -682,8 +716,8 @@
    Parameters:
      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • +

    • args (Any)

      • +

    • kwargs (Any)

    Return type:
    @@ -700,8 +734,8 @@
    Parameters:
      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • +

    • args (Any)

      • +

    • kwargs (Any)

    Return type:
    @@ -719,8 +753,8 @@
    Parameters:
      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • +

    • args (Any)

      • +

    • kwargs (Any)

    Return type:
    @@ -740,8 +774,8 @@
    Parameters:
      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • +

    • args (Any)

      • +

    • kwargs (Any)

    Return type:
    @@ -760,8 +794,8 @@
    Parameters:
      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • +

    • args (Any)

      • +

    • kwargs (Any)

    Return type:
    @@ -806,9 +840,9 @@
    Parameters:
      -

    • ctx (Any) –

      • -

    • m (int) –

      • -

    • kappa (Tensor) –

      • +

    • ctx (Any)

      • +

    • m (int)

      • +

    • kappa (Tensor)

    @@ -823,8 +857,8 @@
    Parameters:
      -

    • ctx (Any) –

      • -

    • grad_output (Tensor) –

      • +

    • ctx (Any)

      • +

    • grad_output (Tensor)

    @@ -841,8 +875,8 @@
    Parameters:
      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • +

    • args (Any)

      • +

    • kwargs (Any)

    Return type:
    @@ -859,8 +893,8 @@
    Parameters:
      -

    • m (int) –

      • -

    • kappa (Tensor) –

      • +

    • m (int)

      • +

    • kappa (Tensor)

    @@ -876,8 +910,8 @@
    Parameters:
      -

    • m (int) –

      • -

    • kappa (Tensor) –

      • +

    • m (int)

      • +

    • kappa (Tensor)

    @@ -896,9 +930,9 @@
    Parameters:
      -

    • m (int) –

      • -

    • kappa (Tensor) –

      • -

    • kappa_switch (float) –

      • +

    • m (int)

      • +

    • kappa (Tensor)

      • +

    • kappa_switch (float)

    @@ -913,8 +947,8 @@
    Parameters:
      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • +

    • args (Any)

      • +

    • kwargs (Any)

    Return type:
    @@ -931,8 +965,8 @@
    Parameters:
      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • +

    • args (Any)

      • +

    • kwargs (Any)

    Return type:
    @@ -949,8 +983,8 @@
    Parameters:
      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • +

    • args (Any)

      • +

    • kwargs (Any)

    Return type:
    @@ -1007,7 +1041,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.training.utils.html b/api/graphnet.training.utils.html index e974931d6..616e7ff8c 100644 --- a/api/graphnet.training.utils.html +++ b/api/graphnet.training.utils.html @@ -123,10 +123,9 @@ - + - @@ -285,14 +284,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -307,6 +334,13 @@ data + +
  • + + + datasets + +
  • @@ -318,14 +352,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -518,7 +552,7 @@

    Batch

    Parameters:
    -

    graphs (List[Data]) –

    +

    graphs (List[Data])

    @@ -533,7 +567,7 @@ last elements, which will always be 0 and 1 respectively.

    Parameters:
    -

    batch_splits (List[float]) –

    +

    batch_splits (List[float])

    @@ -547,24 +581,24 @@
    Parameters:
      -

    • db (str) –

      • -

    • pulsemaps (str | List[str]) –

      • -

    • graph_definition (GraphDefinition) –

      • -

    • features (List[str]) –

      • -

    • truth (List[str]) –

      • -

    • batch_size (int) –

      • -

    • shuffle (bool) –

      • -

    • selection (List[int] | None) –

      • -

    • num_workers (int) –

      • -

    • persistent_workers (bool) –

      • -

    • node_truth (List[str] | None) –

      • -

    • truth_table (str) –

      • -

    • node_truth_table (str | None) –

      • -

    • string_selection (List[int] | None) –

      • -

    • loss_weight_table (str | None) –

      • -

    • loss_weight_column (str | None) –

      • -

    • index_column (str) –

      • -

    • labels (Dict[str, Callable] | None) –

      • +

    • db (str)

      • +

    • pulsemaps (str | List[str])

      • +

    • graph_definition (GraphDefinition)

      • +

    • features (List[str])

      • +

    • truth (List[str])

      • +

    • batch_size (int)

      • +

    • shuffle (bool)

      • +

    • selection (List[int] | None)

      • +

    • num_workers (int)

      • +

    • persistent_workers (bool)

      • +

    • node_truth (List[str] | None)

      • +

    • truth_table (str)

      • +

    • node_truth_table (str | None)

      • +

    • string_selection (List[int] | None)

      • +

    • loss_weight_table (str | None)

      • +

    • loss_weight_column (str | None)

      • +

    • index_column (str)

      • +

    • labels (Dict[str, Callable] | None)

    @@ -579,26 +613,26 @@
    Parameters:
      -

    • db (str) –

      • -

    • graph_definition (GraphDefinition) –

      • -

    • selection (List[int] | None) –

      • -

    • pulsemaps (str | List[str]) –

      • -

    • features (List[str]) –

      • -

    • truth (List[str]) –

      • -

    • batch_size (int) –

      • -

    • database_indices (List[int] | None) –

      • -

    • seed (int) –

      • -

    • test_size (float) –

      • -

    • num_workers (int) –

      • -

    • persistent_workers (bool) –

      • -

    • node_truth (str | None) –

      • -

    • truth_table (str) –

      • -

    • node_truth_table (str | None) –

      • -

    • string_selection (List[int] | None) –

      • -

    • loss_weight_column (str | None) –

      • -

    • loss_weight_table (str | None) –

      • -

    • index_column (str) –

      • -

    • labels (Dict[str, Callable] | None) –

      • +

    • db (str)

      • +

    • graph_definition (GraphDefinition)

      • +

    • selection (List[int] | None)

      • +

    • pulsemaps (str | List[str])

      • +

    • features (List[str])

      • +

    • truth (List[str])

      • +

    • batch_size (int)

      • +

    • database_indices (List[int] | None)

      • +

    • seed (int)

      • +

    • test_size (float)

      • +

    • num_workers (int)

      • +

    • persistent_workers (bool)

      • +

    • node_truth (str | None)

      • +

    • truth_table (str)

      • +

    • node_truth_table (str | None)

      • +

    • string_selection (List[int] | None)

      • +

    • loss_weight_column (str | None)

      • +

    • loss_weight_table (str | None)

      • +

    • index_column (str)

      • +

    • labels (Dict[str, Callable] | None)

    @@ -613,12 +647,12 @@
    Parameters:
    @@ -633,11 +667,11 @@
    Parameters:
    @@ -707,7 +741,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.training.weight_fitting.html b/api/graphnet.training.weight_fitting.html index 703da8cd7..f3b969fc9 100644 --- a/api/graphnet.training.weight_fitting.html +++ b/api/graphnet.training.weight_fitting.html @@ -123,10 +123,9 @@ - + - @@ -285,14 +284,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -307,6 +334,13 @@ data + +
  • + + + datasets + +
  • @@ -318,14 +352,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -490,9 +524,9 @@
    Parameters:
      -

    • database_path (str) –

      • -

    • truth_table (str) –

      • -

    • index_column (str) –

      • +

    • database_path (str)

      • +

    • truth_table (str)

      • +

    • index_column (str)

    @@ -538,9 +572,9 @@
    Parameters:
      -

    • database_path (str) –

      • -

    • truth_table (str) –

      • -

    • index_column (str) –

      • +

    • database_path (str)

      • +

    • truth_table (str)

      • +

    • index_column (str)

    @@ -556,9 +590,9 @@
    Parameters:
      -

    • database_path (str) –

      • -

    • truth_table (str) –

      • -

    • index_column (str) –

      • +

    • database_path (str)

      • +

    • truth_table (str)

      • +

    • index_column (str)

    @@ -612,7 +646,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.utilities.argparse.html b/api/graphnet.utilities.argparse.html index 306ca3b0d..57526f2b8 100644 --- a/api/graphnet.utilities.argparse.html +++ b/api/graphnet.utilities.argparse.html @@ -123,10 +123,9 @@ - + - @@ -285,14 +284,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -307,6 +334,13 @@ data + +
  • + + + datasets + +
  • @@ -318,14 +352,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -534,7 +568,7 @@

    Construct Options.

    Parameters:
    -

    options (str | Tuple[str, Any]) –

    +

    options (str | Tuple[str, Any])

    @@ -546,7 +580,7 @@

    bool

    Parameters:
    -

    option (str) –

    +

    option (str)

    @@ -559,7 +593,7 @@

    Optional[Any]

    Parameters:
    -

    option (str) –

    +

    option (str)

    @@ -573,8 +607,8 @@
    Parameters:
      -

    • usage (str | None) –

      • -

    • description (str | None) –

      • +

    • usage (str | None)

      • +

    • description (str | None)

    @@ -592,7 +626,7 @@

    ArgumentParser

    Parameters:
    -

    args (str | Tuple[str, Any]) –

    +

    args (str | Tuple[str, Any])

    @@ -646,7 +680,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.utilities.config.base_config.html b/api/graphnet.utilities.config.base_config.html index a43d9ac48..4212984a0 100644 --- a/api/graphnet.utilities.config.base_config.html +++ b/api/graphnet.utilities.config.base_config.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -308,6 +335,13 @@ data + +
  • + + + datasets + +
  • @@ -319,14 +353,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -607,7 +641,7 @@

    BaseConfig

    Parameters:
    -

    path (str) –

    +

    path (str)

    @@ -620,7 +654,7 @@

    Optional[str]

    Parameters:
    -

    path (str | None) –

    +

    path (str | None)

    @@ -663,9 +697,9 @@
    Parameters:
    @@ -719,7 +753,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.utilities.config.configurable.html b/api/graphnet.utilities.config.configurable.html index c8d3bec55..1b48bdbd5 100644 --- a/api/graphnet.utilities.config.configurable.html +++ b/api/graphnet.utilities.config.configurable.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -308,6 +335,13 @@ data + +
  • + + + datasets + +
  • @@ -319,14 +353,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -565,7 +599,7 @@

    None

    Parameters:
    -

    path (str) –

    +

    path (str)

    @@ -578,7 +612,7 @@

    Any

    Parameters:
    -

    source (BaseConfig | str) –

    +

    source (BaseConfig | str)

    @@ -632,7 +666,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.utilities.config.dataset_config.html b/api/graphnet.utilities.config.dataset_config.html index d7f81f110..f643e6c4d 100644 --- a/api/graphnet.utilities.config.dataset_config.html +++ b/api/graphnet.utilities.config.dataset_config.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -308,6 +335,13 @@ data + +
  • + + + datasets + +
  • @@ -319,14 +353,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -843,22 +877,22 @@
    Parameters:
      -

    • path (str | List[str]) –

      • -

    • pulsemaps (str | List[str]) –

      • -

    • features (List[str]) –

      • -

    • truth (List[str]) –

      • -

    • node_truth (List[str] | None) –

      • -

    • index_column (str) –

      • -

    • truth_table (str) –

      • -

    • node_truth_table (str | None) –

      • -

    • string_selection (List[int] | None) –

      • -

    • selection (str | List[str] | List[int | List[int]] | Dict[str, str | List[str]] | None) –

      • -

    • loss_weight_table (str | None) –

      • -

    • loss_weight_column (str | None) –

      • -

    • loss_weight_default_value (float | None) –

      • -

    • seed (int | None) –

      • -

    • graph_definition (Any) –

      • -

    • labels (Dict[str, Any] | None) –

      • +

    • path (str | List[str])

      • +

    • pulsemaps (str | List[str])

      • +

    • features (List[str])

      • +

    • truth (List[str])

      • +

    • node_truth (List[str] | None)

      • +

    • index_column (str)

      • +

    • truth_table (str)

      • +

    • node_truth_table (str | None)

      • +

    • string_selection (List[int] | None)

      • +

    • selection (str | List[str] | List[int | List[int]] | Dict[str, str | List[str]] | None)

      • +

    • loss_weight_table (str | None)

      • +

    • loss_weight_column (str | None)

      • +

    • loss_weight_default_value (float | None)

      • +

    • seed (int | None)

      • +

    • graph_definition (Any)

      • +

    • labels (Dict[str, Any] | None)

    @@ -951,7 +985,7 @@
    -model_fields: ClassVar[dict[str, FieldInfo]] = {'features': FieldInfo(annotation=List[str], required=True), 'graph_definition': FieldInfo(annotation=Any, required=False), 'index_column': FieldInfo(annotation=str, required=False, default='event_no'), 'labels': FieldInfo(annotation=Union[Dict[str, Any], NoneType], required=False), 'loss_weight_column': FieldInfo(annotation=Union[str, NoneType], required=False), 'loss_weight_default_value': FieldInfo(annotation=Union[float, NoneType], required=False), 'loss_weight_table': FieldInfo(annotation=Union[str, NoneType], required=False), 'node_truth': FieldInfo(annotation=Union[List[str], NoneType], required=False), 'node_truth_table': FieldInfo(annotation=Union[str, NoneType], required=False), 'path': FieldInfo(annotation=Union[str, List[str]], required=True), 'pulsemaps': FieldInfo(annotation=Union[str, List[str]], required=True), 'seed': FieldInfo(annotation=Union[int, NoneType], required=False), 'selection': FieldInfo(annotation=Union[str, List[str], List[Union[int, List[int]]], Dict[str, Union[str, List[str]]], NoneType], required=False), 'string_selection': FieldInfo(annotation=Union[List[int], NoneType], required=False), 'truth': FieldInfo(annotation=List[str], required=True), 'truth_table': FieldInfo(annotation=str, required=False, default='truth')}
    +model_fields: ClassVar[dict[str, FieldInfo]] = {'features': FieldInfo(annotation=List[str], required=True), 'graph_definition': FieldInfo(annotation=Any, required=False, default=None), 'index_column': FieldInfo(annotation=str, required=False, default='event_no'), 'labels': FieldInfo(annotation=Union[Dict[str, Any], NoneType], required=False, default=None), 'loss_weight_column': FieldInfo(annotation=Union[str, NoneType], required=False, default=None), 'loss_weight_default_value': FieldInfo(annotation=Union[float, NoneType], required=False, default=None), 'loss_weight_table': FieldInfo(annotation=Union[str, NoneType], required=False, default=None), 'node_truth': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None), 'node_truth_table': FieldInfo(annotation=Union[str, NoneType], required=False, default=None), 'path': FieldInfo(annotation=Union[str, List[str]], required=True), 'pulsemaps': FieldInfo(annotation=Union[str, List[str]], required=True), 'seed': FieldInfo(annotation=Union[int, NoneType], required=False, default=None), 'selection': FieldInfo(annotation=Union[str, List[str], List[Union[int, List[int]]], Dict[str, Union[str, List[str]]], NoneType], required=False, default=None), 'string_selection': FieldInfo(annotation=Union[List[int], NoneType], required=False, default=None), 'truth': FieldInfo(annotation=List[str], required=True), 'truth_table': FieldInfo(annotation=str, required=False, default='truth')}

    Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

    This replaces Model.__fields__ from Pydantic V1.

    @@ -966,7 +1000,7 @@

    Callable

    Parameters:
    -

    init_fn (Callable) –

    +

    init_fn (Callable)

    @@ -1031,7 +1065,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.utilities.config.html b/api/graphnet.utilities.config.html index 88ea67d59..12c82520e 100644 --- a/api/graphnet.utilities.config.html +++ b/api/graphnet.utilities.config.html @@ -123,10 +123,9 @@ - + - @@ -285,14 +284,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -307,6 +334,13 @@ data + +
  • + + + datasets + +
  • @@ -318,14 +352,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -574,7 +608,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.utilities.config.model_config.html b/api/graphnet.utilities.config.model_config.html index 39894fd70..1b5d5a3ed 100644 --- a/api/graphnet.utilities.config.model_config.html +++ b/api/graphnet.utilities.config.model_config.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -308,6 +335,13 @@ data + +
  • + + + datasets + +
  • @@ -319,14 +353,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -636,8 +670,8 @@
    Parameters:
      -

    • class_name (str) –

      • -

    • arguments (Dict[str, Any]) –

      • +

    • class_name (str)

      • +

    • arguments (Dict[str, Any])

    @@ -689,7 +723,7 @@

    Callable

    Parameters:
    -

    init_fn (Callable) –

    +

    init_fn (Callable)

    @@ -754,7 +788,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.utilities.config.parsing.html b/api/graphnet.utilities.config.parsing.html index b2100d068..81328ad85 100644 --- a/api/graphnet.utilities.config.parsing.html +++ b/api/graphnet.utilities.config.parsing.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -308,6 +335,13 @@ data + +
  • + + + datasets + +
  • @@ -319,14 +353,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -571,9 +605,9 @@
    Parameters:
    @@ -587,7 +621,7 @@

    List[ModuleType]

    Parameters:
    -

    packages (module) –

    +

    packages (ModuleType)

    @@ -600,7 +634,7 @@

    Dict[str, type]

    Parameters:
    -

    packages (module) –

    +

    packages (ModuleType)

    @@ -613,7 +647,7 @@

    bool

    Parameters:
    -

    obj (module) –

    +

    obj (ModuleType)

    @@ -626,7 +660,7 @@

    bool

    Parameters:
    -

    obj (type) –

    +

    obj (type)

    @@ -639,7 +673,7 @@

    Dict[str, type]

    Parameters:
    -

    module (module) –

    +

    module (ModuleType)

    @@ -692,7 +726,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.utilities.config.training_config.html b/api/graphnet.utilities.config.training_config.html index fb1647bf3..e17e2faf3 100644 --- a/api/graphnet.utilities.config.training_config.html +++ b/api/graphnet.utilities.config.training_config.html @@ -123,10 +123,9 @@ - + - @@ -286,14 +285,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -308,6 +335,13 @@ data + +
  • + + + datasets + +
  • @@ -319,14 +353,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -599,10 +633,10 @@
    Parameters:
      -

    • target (str | List[str]) –

      • -

    • early_stopping_patience (int) –

      • -

    • fit (Dict[str, Any]) –

      • -

    • dataloader (Dict[str, Any]) –

      • +

    • target (str | List[str])

      • +

    • early_stopping_patience (int)

      • +

    • fit (Dict[str, Any])

      • +

    • dataloader (Dict[str, Any])

    @@ -689,7 +723,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.utilities.decorators.html b/api/graphnet.utilities.decorators.html index 854e94e51..65f3bd085 100644 --- a/api/graphnet.utilities.decorators.html +++ b/api/graphnet.utilities.decorators.html @@ -123,10 +123,9 @@ - + - @@ -285,14 +284,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -307,6 +334,13 @@ data + +
  • + + + datasets + +
  • @@ -318,14 +352,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -491,7 +525,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.utilities.deprecation_tools.html b/api/graphnet.utilities.deprecation_tools.html index 4d0500613..c15157044 100644 --- a/api/graphnet.utilities.deprecation_tools.html +++ b/api/graphnet.utilities.deprecation_tools.html @@ -123,10 +123,9 @@ - + - @@ -285,14 +284,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -307,6 +334,13 @@ data + +
  • + + + datasets + +
  • @@ -318,14 +352,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -530,7 +564,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.utilities.filesys.html b/api/graphnet.utilities.filesys.html index d2965bd8b..2dd5ba95a 100644 --- a/api/graphnet.utilities.filesys.html +++ b/api/graphnet.utilities.filesys.html @@ -123,10 +123,9 @@ - + - @@ -285,14 +284,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -307,6 +334,13 @@ data + +
  • + + + datasets + +
  • @@ -318,14 +352,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -505,7 +539,7 @@

    bool

    Parameters:
    -

    filename (str) –

    +

    filename (str)

    @@ -518,7 +552,7 @@

    bool

    Parameters:
    -

    filename (str) –

    +

    filename (str)

    @@ -532,8 +566,8 @@
    Parameters:
    @@ -612,7 +646,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.utilities.html b/api/graphnet.utilities.html index a587baa9c..328307d19 100644 --- a/api/graphnet.utilities.html +++ b/api/graphnet.utilities.html @@ -123,10 +123,9 @@ - + - @@ -284,14 +283,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -306,6 +333,13 @@ data + +
  • + + + datasets + +
  • @@ -317,14 +351,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -478,7 +512,6 @@
  • imports
    • @@ -542,7 +575,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.utilities.imports.html b/api/graphnet.utilities.imports.html index c91150b43..914c0993c 100644 --- a/api/graphnet.utilities.imports.html +++ b/api/graphnet.utilities.imports.html @@ -123,10 +123,9 @@ - + - @@ -285,14 +284,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -307,6 +334,13 @@ data + +
  • + + + datasets + +
  • @@ -318,14 +352,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -394,8 +428,6 @@
  • has_torch_package()
    • -
  • has_pisa_package() -
  • requires_icecube()
    • @@ -416,13 +448,6 @@ has_torch_package() - -
  • - - - has_pisa_package() - -
  • @@ -478,8 +503,6 @@
  • has_torch_package()
    • -
  • has_pisa_package() -
  • requires_icecube()
    • @@ -517,16 +540,6 @@
    -
    -graphnet.utilities.imports.has_pisa_package()[source]
    -

    Check whether the pisa package is available.

    -
    -
    Return type:
    -

    bool

    -
    -
    -
    -
    graphnet.utilities.imports.requires_icecube(test_function)[source]

    Decorate test_function for use only if icecube module is present.

    @@ -535,7 +548,7 @@

    Callable

    Parameters:
    -

    test_function (Callable) –

    +

    test_function (Callable)

    @@ -588,7 +601,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.utilities.logging.html b/api/graphnet.utilities.logging.html index af5990025..7357510b4 100644 --- a/api/graphnet.utilities.logging.html +++ b/api/graphnet.utilities.logging.html @@ -123,10 +123,9 @@ - + - @@ -285,14 +284,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -307,6 +334,13 @@ data + +
  • + + + datasets + +
  • @@ -318,14 +352,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -635,7 +669,7 @@

    bool

    Parameters:
    -

    record (LogRecord) –

    +

    record (LogRecord)

    @@ -654,11 +688,11 @@
    Parameters:
      -

    • name (str | None) –

      • -

    • class_name (str | None) –

      • -

    • level (int) –

      • -

    • log_folder (str | None) –

      • -

    • kwargs (Any) –

      • +

    • name (str | None)

      • +

    • class_name (str | None)

      • +

    • level (int)

      • +

    • log_folder (str | None)

      • +

    • kwargs (Any)

    @@ -671,7 +705,7 @@

    None

    Parameters:
    -

    level (int) –

    +

    level (int)

    @@ -685,9 +719,9 @@
    Parameters:
    @@ -702,9 +736,9 @@
    Parameters:
    @@ -719,9 +753,9 @@
    Parameters:
    @@ -736,9 +770,9 @@
    Parameters:
    @@ -753,9 +787,9 @@
    Parameters:
    @@ -769,7 +803,7 @@

    None

    Parameters:
    -

    msg (str) –

    +

    msg (str)

    @@ -838,7 +872,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/graphnet.utilities.maths.html b/api/graphnet.utilities.maths.html index cfe0b90e2..45e2a8f40 100644 --- a/api/graphnet.utilities.maths.html +++ b/api/graphnet.utilities.maths.html @@ -123,10 +123,9 @@ - + - @@ -285,14 +284,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -307,6 +334,13 @@ data + +
  • + + + datasets + +
  • @@ -318,14 +352,14 @@
  • - models + exceptions
  • - pisa + models
    • @@ -472,7 +506,7 @@

    Tensor

    Parameters:
    -

    tensor (Tensor) –

    +

    tensor (Tensor)

    @@ -525,7 +559,7 @@ Created using - Sphinx 7.2.6. + Sphinx 7.3.7. and Material for Sphinx diff --git a/api/modules.html b/api/modules.html index 11cc56b2f..eb8ad7c85 100644 --- a/api/modules.html +++ b/api/modules.html @@ -123,10 +123,10 @@ - + + - @@ -281,14 +281,42 @@
  • - Install + Installation
  • - Contribute + Models In GraphNeT + + +
    • +
  • + + + Datasets In GraphNeT + + +
    • +
  • + + + Data Conversion in GraphNeT + + +
    • +
  • + + + Integrating New Experiments into GraphNeT + + +
    • +
  • + + + Contributing To GraphNeT
    • @@ -327,9 +355,10 @@

    srcAPI