From 92855c8969503dc63bbb608c93add340ec4b6ebc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andreas=20S=C3=B8gaard?= Date: Mon, 5 Feb 2024 05:27:27 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20Aske-Ros?= =?UTF-8?q?ted/graphnet@b686dd72d5840b8e6621ac04e7abc3ac1e7ccadd=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- _modules/graphnet/data/dataloader.html | 457 ------- _modules/graphnet/data/dataset/dataset.html | 1089 ----------------- .../data/dataset/parquet/parquet_dataset.html | 500 -------- .../data/dataset/sqlite/sqlite_dataset.html | 515 -------- _modules/graphnet/data/pipeline.html | 593 --------- .../deployment/i3modules/graphnet_module.html | 817 ------------- _modules/graphnet/models/coarsening.html | 708 ----------- .../graphnet/models/components/layers.html | 579 --------- _modules/graphnet/models/components/pool.html | 656 ---------- _modules/graphnet/models/gnn/convnet.html | 484 -------- _modules/graphnet/models/gnn/dynedge.html | 691 ----------- .../graphnet/models/gnn/dynedge_jinst.html | 519 -------- .../models/gnn/dynedge_kaggle_tito.html | 633 ---------- _modules/graphnet/models/gnn/gnn.html | 401 ------ .../graphnet/models/graphs/edges/edges.html | 559 --------- .../models/graphs/edges/minkowski.html | 464 ------- .../models/graphs/graph_definition.html | 815 ------------ _modules/graphnet/models/graphs/graphs.html | 419 ------- .../graphnet/models/graphs/nodes/nodes.html | 591 --------- _modules/graphnet/models/graphs/utils.html | 532 -------- _modules/graphnet/models/standard_model.html | 912 -------------- .../graphnet/models/task/classification.html | 411 ------- .../graphnet/models/task/reconstruction.html | 632 ---------- _modules/graphnet/models/task/task.html | 844 ------------- _modules/graphnet/models/utils.html | 430 ------- _modules/graphnet/training/utils.html | 697 ----------- _modules/index.html | 26 - 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Source code for graphnet.data.dataloader

-"""Base `Dataloader` class(es) used in `graphnet`."""
-
-from typing import Any, Callable, Dict, List, Union
-
-import torch.utils.data
-from torch_geometric.data import Batch, Data
-
-from graphnet.data.dataset import Dataset
-from graphnet.utilities.config import DatasetConfig
-
-
-

-[docs]
-def collate_fn(graphs: List[Data]) -> Batch:
-    """Remove graphs with less than two DOM hits.
-
-    Should not occur in "production.
-    """
-    graphs = [g for g in graphs if g.n_pulses > 1]
-    return Batch.from_data_list(graphs)

-
-
-
-

-[docs]
-def do_shuffle(selection_name: str) -> bool:
-    """Check whether to shuffle selection with name `selection_name`."""
-    return "train" in selection_name.lower()

-
-
-
-

-[docs]
-class DataLoader(torch.utils.data.DataLoader):
-    """Class for loading data from a `Dataset`."""
-
-    def __init__(
-        self,
-        dataset: Dataset,
-        batch_size: int = 1,
-        shuffle: bool = False,
-        num_workers: int = 10,
-        persistent_workers: bool = True,
-        collate_fn: Callable = collate_fn,
-        prefetch_factor: int = 2,
-        **kwargs: Any,
-    ) -> None:
-        """Construct `DataLoader`."""
-        # Base class constructor
-        super().__init__(
-            dataset,
-            batch_size=batch_size,
-            shuffle=shuffle,
-            num_workers=num_workers,
-            collate_fn=collate_fn,
-            persistent_workers=persistent_workers,
-            prefetch_factor=prefetch_factor,
-            **kwargs,
-        )
-
-

-[docs]
-    @classmethod
-    def from_dataset_config(
-        cls,
-        config: DatasetConfig,
-        **kwargs: Any,
-    ) -> Union["DataLoader", Dict[str, "DataLoader"]]:
-        """Construct `DataLoader`s based on selections in `DatasetConfig`."""
-        if isinstance(config.selection, dict):
-            assert "shuffle" not in kwargs, (
-                "When passing a `DatasetConfig` with multiple selections, "
-                "`shuffle` is automatically inferred from the selection name, "
-                "and thus should not specified as an argument."
-            )
-            datasets = Dataset.from_config(config)
-            assert isinstance(datasets, dict)
-            data_loaders: Dict[str, DataLoader] = {}
-            for name, dataset in datasets.items():
-                data_loaders[name] = cls(
-                    dataset,
-                    shuffle=do_shuffle(name),
-                    **kwargs,
-                )
-
-            return data_loaders
-
-        else:
-            assert "shuffle" in kwargs, (
-                "When passing a `DatasetConfig` with a single selections, you "
-                "need to specify `shuffle` as an argument."
-            )
-            dataset = Dataset.from_config(config)
-            assert isinstance(dataset, Dataset)
-            return cls(dataset, **kwargs)

-

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Source code for graphnet.data.dataset.dataset

-"""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 torch
-from torch_geometric.data import Data
-
-from graphnet.constants import GRAPHNET_ROOT_DIR
-from graphnet.data.utilities.string_selection_resolver import (
-    StringSelectionResolver,
-)
-from graphnet.training.labels import Label
-from graphnet.utilities.config import (
-    Configurable,
-    DatasetConfig,
-    DatasetConfigSaverABCMeta,
-)
-from graphnet.utilities.config.parsing import traverse_and_apply
-from graphnet.utilities.logging import Logger
-from graphnet.models.graphs import GraphDefinition
-
-from graphnet.utilities.config.parsing import (
-    get_all_grapnet_classes,
-)
-
-
-

-[docs]
-class ColumnMissingException(Exception):
-    """Exception to indicate a missing column in a dataset."""

-
-
-
-

-[docs]
-def load_module(class_name: str) -> Type:
-    """Load graphnet module from string name.
-
-    Args:
-        class_name: name of class
-
-    Returns:
-        graphnet module.
-    """
-    # Get a lookup for all classes in `graphnet`
-    import graphnet.data
-    import graphnet.models
-    import graphnet.training
-
-    namespace_classes = get_all_grapnet_classes(
-        graphnet.data, graphnet.models, graphnet.training
-    )
-    return namespace_classes[class_name]

-
-
-
-

-[docs]
-def parse_graph_definition(cfg: dict) -> GraphDefinition:
-    """Construct GraphDefinition from DatasetConfig."""
-    assert cfg["graph_definition"] is not None
-
-    args = cfg["graph_definition"]["arguments"]
-    classes = {}
-    for arg in args.keys():
-        if isinstance(args[arg], dict):
-            if "class_name" in args[arg].keys():
-                classes[arg] = load_module(args[arg]["class_name"])(
-                    **args[arg]["arguments"]
-                )
-        if arg == "dtype":
-            args[arg] = eval(args[arg])  # converts string to class
-
-    new_cfg = deepcopy(args)
-    new_cfg.update(classes)
-    graph_definition = load_module(cfg["graph_definition"]["class_name"])(
-        **new_cfg
-    )
-    return graph_definition

-
-
-
-

-[docs]
-class Dataset(
-    Logger,
-    Configurable,
-    torch.utils.data.Dataset,
-    ABC,
-    metaclass=DatasetConfigSaverABCMeta,
-):
-    """Base Dataset class for reading from any intermediate file format."""
-
-    # Class method(s)
-

-[docs]
-    @classmethod
-    def from_config(  # type: ignore[override]
-        cls,
-        source: Union[DatasetConfig, str],
-    ) -> Union[
-        "Dataset",
-        "EnsembleDataset",
-        Dict[str, "Dataset"],
-        Dict[str, "EnsembleDataset"],
-    ]:
-        """Construct `Dataset` instance from `source` configuration."""
-        if isinstance(source, str):
-            source = DatasetConfig.load(source)
-
-        assert isinstance(source, DatasetConfig), (
-            f"Argument `source` of type ({type(source)}) is not a "
-            "`DatasetConfig`"
-        )
-
-        assert (
-            "graph_definition" in source.dict().keys()
-        ), "`DatasetConfig` incompatible with current GraphNeT version."
-
-        # Parse set of `selection``.
-        if isinstance(source.selection, dict):
-            return cls._construct_datasets_from_dict(source)
-        elif (
-            isinstance(source.selection, list)
-            and len(source.selection)
-            and isinstance(source.selection[0], str)
-        ):
-            return cls._construct_dataset_from_list_of_strings(source)
-
-        cfg = source.dict()
-        if cfg["graph_definition"] is not None:
-            cfg["graph_definition"] = parse_graph_definition(cfg)
-        return source._dataset_class(**cfg)

-
-
-

-[docs]
-    @classmethod
-    def concatenate(
-        cls,
-        datasets: List["Dataset"],
-    ) -> "EnsembleDataset":
-        """Concatenate multiple `Dataset`s into one instance."""
-        return EnsembleDataset(datasets)

-
-
-    @classmethod
-    def _construct_datasets_from_dict(
-        cls, config: DatasetConfig
-    ) -> Dict[str, "Dataset"]:
-        """Construct `Dataset` for each entry in dict `self.selection`."""
-        assert isinstance(config.selection, dict)
-        datasets: Dict[str, "Dataset"] = {}
-        selections: Dict[str, Union[str, List]] = deepcopy(config.selection)
-        for key, selection in selections.items():
-            config.selection = selection
-            dataset = Dataset.from_config(config)
-            assert isinstance(dataset, (Dataset, EnsembleDataset))
-            datasets[key] = dataset
-
-        # Reset `selections`.
-        config.selection = selections
-
-        return datasets
-
-    @classmethod
-    def _construct_dataset_from_list_of_strings(
-        cls, config: DatasetConfig
-    ) -> "Dataset":
-        """Construct `Dataset` for each entry in list `self.selection`."""
-        assert isinstance(config.selection, list)
-        datasets: List["Dataset"] = []
-        selections: List[str] = deepcopy(cast(List[str], config.selection))
-        for selection in selections:
-            config.selection = selection
-            dataset = Dataset.from_config(config)
-            assert isinstance(dataset, Dataset)
-            datasets.append(dataset)
-
-        # Reset `selections`.
-        config.selection = selections
-
-        return cls.concatenate(datasets)
-
-    @classmethod
-    def _resolve_graphnet_paths(
-        cls, path: Union[str, List[str]]
-    ) -> Union[str, List[str]]:
-        if isinstance(path, list):
-            return [cast(str, cls._resolve_graphnet_paths(p)) for p in path]
-
-        assert isinstance(path, str)
-        return (
-            path.replace("$graphnet", GRAPHNET_ROOT_DIR)
-            .replace("$GRAPHNET", GRAPHNET_ROOT_DIR)
-            .replace("${graphnet}", GRAPHNET_ROOT_DIR)
-            .replace("${GRAPHNET}", GRAPHNET_ROOT_DIR)
-        )
-
-    def __init__(
-        self,
-        path: Union[str, List[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,
-    ):
-        """Construct Dataset.
-
-        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 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.
-            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.
-        """
-        # Base class constructor
-        super().__init__(name=__name__, class_name=self.__class__.__name__)
-
-        # Check(s)
-        if isinstance(pulsemaps, str):
-            pulsemaps = [pulsemaps]
-
-        assert isinstance(features, (list, tuple))
-        assert isinstance(truth, (list, tuple))
-
-        # Resolve reference to `$GRAPHNET` in path(s)
-        path = self._resolve_graphnet_paths(path)
-
-        # Member variable(s)
-        self._path = path
-        self._selection = None
-        self._pulsemaps = pulsemaps
-        self._features = [index_column] + 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)
-
-        if node_truth is not None:
-            assert isinstance(node_truth_table, str)
-            if isinstance(node_truth, str):
-                node_truth = [node_truth]
-
-        self._node_truth = node_truth
-        self._node_truth_table = node_truth_table
-
-        if string_selection is not None:
-            self.warning(
-                (
-                    "String selection detected.\n "
-                    f"Accepted strings: {string_selection}\n "
-                    "All other strings are ignored!"
-                )
-            )
-            if isinstance(string_selection, int):
-                string_selection = [string_selection]
-
-        self._string_selection = string_selection
-
-        self._selection = None
-        if self._string_selection:
-            self._selection = f"string in {str(tuple(self._string_selection))}"
-
-        self._loss_weight_column = loss_weight_column
-        self._loss_weight_table = loss_weight_table
-        if (self._loss_weight_table is None) and (
-            self._loss_weight_column is not None
-        ):
-            self.warning("Error: no loss weight table specified")
-            assert isinstance(self._loss_weight_table, str)
-        if (self._loss_weight_table is not None) and (
-            self._loss_weight_column is None
-        ):
-            self.warning("Error: no loss weight column specified")
-            assert isinstance(self._loss_weight_column, str)
-
-        self._dtype = dtype
-
-        self._label_fns: Dict[str, Callable[[Data], Any]] = {}
-
-        self._string_selection_resolver = StringSelectionResolver(
-            self,
-            index_column=index_column,
-            seed=seed,
-        )
-
-        # Implementation-specific initialisation.
-        self._init()
-
-        # Set unique indices
-        self._indices: Union[List[int], List[List[int]]]
-        if selection is None:
-            self._indices = self._get_all_indices()
-        elif isinstance(selection, str):
-            self._indices = self._resolve_string_selection_to_indices(
-                selection
-            )
-        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()
-
-    # Properties
-    @property
-    def path(self) -> Union[str, List[str]]:
-        """Path to the file(s) from which this `Dataset` reads."""
-        return self._path
-
-    @property
-    def truth_table(self) -> str:
-        """Name of the table containing event-level truth information."""
-        return self._truth_table
-
-    # Abstract method(s)
-    @abstractmethod
-    def _init(self) -> None:
-        """Set internal representation needed to read data from input file."""
-
-    def _post_init(self) -> None:
-        """Implementation-specific code executed after the main constructor."""
-
-    @abstractmethod
-    def _get_all_indices(self) -> List[int]:
-        """Return a list of all unique values in `self._index_column`."""
-
-    @abstractmethod
-    def _get_event_index(
-        self, sequential_index: Optional[int]
-    ) -> Optional[int]:
-        """Return the event index corresponding to a `sequential_index`."""
-
-

-[docs]
-    @abstractmethod
-    def query_table(
-        self,
-        table: str,
-        columns: Union[List[str], str],
-        sequential_index: Optional[int] = None,
-        selection: Optional[str] = None,
-    ) -> List[Tuple[Any, ...]]:
-        """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`.
-        """

-
-
-    # Public method(s)
-

-[docs]
-    def add_label(
-        self, fn: Callable[[Data], Any], key: Optional[str] = None
-    ) -> None:
-        """Add custom graph label define using function `fn`."""
-        if isinstance(fn, Label):
-            key = fn.key
-        assert isinstance(
-            key, str
-        ), "Please specify a key for the custom label to be added."
-        assert (
-            key not in self._label_fns
-        ), f"A custom label {key} has already been defined."
-        self._label_fns[key] = fn

-
-
-    def __len__(self) -> int:
-        """Return number of graphs in `Dataset`."""
-        return len(self._indices)
-
-    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}]"
-            )
-        features, truth, node_truth, loss_weight = self._query(
-            sequential_index
-        )
-        graph = self._create_graph(features, truth, node_truth, loss_weight)
-        return graph
-
-    # Internal method(s)
-    def _resolve_string_selection_to_indices(
-        self, selection: str
-    ) -> List[int]:
-        """Resolve selection as string to list of indices.
-
-        Selections are expected to have pandas.DataFrame.query-compatible
-        syntax, e.g., ``` "event_no % 5 > 0" ``` Selections may also specify a
-        fixed number of events to randomly sample, e.g., ``` "10000 random
-        events ~ event_no % 5 > 0" "20% random events ~ event_no % 5 > 0" ```
-        """
-        return self._string_selection_resolver.resolve(selection)
-
-    def _remove_missing_columns(self) -> None:
-        """Remove columns that are not present in the input file.
-
-        Columns are removed from `self._features` and `self._truth`.
-        """
-        # Check if table is completely empty
-        if len(self) == 0:
-            self.warning("Dataset is empty.")
-            return
-
-        # Find missing features
-        missing_features_set = set(self._features)
-        for pulsemap in self._pulsemaps:
-            missing = self._check_missing_columns(self._features, pulsemap)
-            missing_features_set = missing_features_set.intersection(missing)
-
-        missing_features = list(missing_features_set)
-
-        # Find missing truth variables
-        missing_truth_variables = self._check_missing_columns(
-            self._truth, self._truth_table
-        )
-
-        # Remove missing features
-        if missing_features:
-            self.warning(
-                "Removing the following (missing) features: "
-                + ", ".join(missing_features)
-            )
-            for missing_feature in missing_features:
-                self._features.remove(missing_feature)
-
-        # Remove missing truth variables
-        if missing_truth_variables:
-            self.warning(
-                (
-                    "Removing the following (missing) truth variables: "
-                    + ", ".join(missing_truth_variables)
-                )
-            )
-            for missing_truth_variable in missing_truth_variables:
-                self._truth.remove(missing_truth_variable)
-
-    def _check_missing_columns(
-        self,
-        columns: List[str],
-        table: str,
-    ) -> List[str]:
-        """Return a list missing columns in `table`."""
-        for column in columns:
-            try:
-                self.query_table(table, [column], 0)
-            except ColumnMissingException:
-                if table not in self._missing_variables:
-                    self._missing_variables[table] = []
-                self._missing_variables[table].append(column)
-            except IndexError:
-                self.warning(f"Dataset contains no entries for {column}")
-
-        return self._missing_variables.get(table, [])
-
-    def _query(
-        self, sequential_index: int
-    ) -> Tuple[
-        List[Tuple[float, ...]],
-        Tuple[Any, ...],
-        Optional[List[Tuple[Any, ...]]],
-        Optional[float],
-    ]:
-        """Query file for event features and truth information.
-
-        The returned lists have lengths corresponding to the number of pulses
-        in the event. Their constituent tuples have lengths corresponding to
-        the number of features/attributes in each output
-
-        Args:
-            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`.
-
-        Returns:
-            Tuple containing pulse-level event features; event-level truth
-                information; pulse-level truth information; and event-level
-                loss weights, respectively.
-        """
-        features = []
-        for pulsemap in self._pulsemaps:
-            features_pulsemap = self.query_table(
-                pulsemap, self._features, sequential_index, self._selection
-            )
-            features.extend(features_pulsemap)
-
-        truth: Tuple[Any, ...] = 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(
-                self._node_truth_table,
-                self._node_truth,
-                sequential_index,
-                self._selection,
-            )
-        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(
-                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
-
-        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,
-        loss_weight: Optional[float] = None,
-    ) -> Data:
-        """Create Pytorch Data (i.e. graph) object.
-
-        Args:
-            features: List of tuples, containing event features.
-            truth: List of tuples, containing truth information.
-            node_truth: List of tuples, containing node-level truth.
-            loss_weight: A weight associated with the event for weighing the
-                loss.
-
-        Returns:
-            Graph object.
-        """
-        # Convert nested list to simple dict
-        truth_dict = {
-            key: truth[index] for index, key in enumerate(self._truth)
-        }
-
-        # Define custom labels
-        labels_dict = self._get_labels(truth_dict)
-
-        # 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]
-                for index, key in enumerate(self._node_truth)
-            }
-
-        # Create list of truth dicts with labels
-        truth_dicts = [labels_dict, truth_dict]
-        if node_truth is not None:
-            truth_dicts.append(node_truth_dict)
-
-        # Catch cases with no reconstructed pulses
-        if len(features):
-            node_features = np.asarray(features)[
-                :, 1:
-            ]  # first entry is index column
-        else:
-            node_features = np.array([]).reshape((0, len(self._features) - 1))
-
-        # 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
-            truth_dicts=truth_dicts,
-            custom_label_functions=self._label_fns,
-            loss_weight_column=self._loss_weight_column,
-            loss_weight=loss_weight,
-            loss_weight_default_value=self._loss_weight_default_value,
-            data_path=self._path,
-        )
-        return graph
-
-    def _get_labels(self, truth_dict: Dict[str, Any]) -> Dict[str, Any]:
-        """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]`?
-                "v_e": int(abs_pid == 12),
-                "v_u": int(abs_pid == 14),
-                "v_t": int(abs_pid == 16),
-                "track": int(
-                    (abs_pid == 14) & (truth_dict["interaction_type"] == 1)
-                ),
-                "dbang": self._get_dbang_label(truth_dict),
-                "corsika": int(abs_pid > 20),
-            }
-        else:
-            labels_dict = {
-                self._index_column: truth_dict[self._index_column],
-                "muon": -1,
-                "muon_stopped": -1,
-                "noise": -1,
-                "neutrino": -1,
-                "v_e": -1,
-                "v_u": -1,
-                "v_t": -1,
-                "track": -1,
-                "dbang": -1,
-                "corsika": -1,
-            }
-        return labels_dict
-
-    def _get_dbang_label(self, truth_dict: Dict[str, Any]) -> int:
-        """Get label for double-bang classification."""
-        try:
-            label = int(truth_dict["dbang_decay_length"] > -1)
-            return label
-        except KeyError:
-            return -1

-
-
-
-

-[docs]
-class EnsembleDataset(torch.utils.data.ConcatDataset):
-    """Construct a single dataset from a collection of datasets."""
-
-    def __init__(self, datasets: Iterable[Dataset]) -> None:
-        """Construct a single dataset from a collection of datasets.
-
-        Args:
-            datasets: A collection of Datasets
-        """
-        super().__init__(datasets=datasets)

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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
-
-import numpy as np
-import awkward as ak
-
-from graphnet.data.dataset.dataset import Dataset, ColumnMissingException
-
-
-

-[docs]
-class ParquetDataset(Dataset):
-    """Pytorch dataset for reading from Parquet files."""
-
-    # 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 _get_all_indices(self) -> List[int]:
-        return np.arange(
-            len(
-                ak.to_numpy(
-                    self._parquet_hook[self._truth_table][self._index_column]
-                ).tolist()
-            )
-        ).tolist()
-
-    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)})."
-        )
-        nb_elements = array_lengths[0]
-
-        # Broadcast scalars
-        for key in dictionary:
-            value = dictionary[key]
-            if np.isscalar(value):
-                dictionary[key] = np.repeat(
-                    value, repeats=nb_elements
-                ).tolist()
-
-        return list(map(tuple, list(zip(*dictionary.values()))))
-
-

-[docs]
-    def query_table(
-        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
-
-        output = ak_array.to_list()
-
-        result: List[Tuple[Any, ...]] = []
-
-        # Querying single index
-        if isinstance(output, dict):
-            assert list(output.keys()) == columns
-            result = self._format_dictionary_result(output)
-
-        # Querying entire columm
-        elif isinstance(output, list):
-            for dictionary in output:
-                assert list(dictionary.keys()) == columns
-                result.extend(self._format_dictionary_result(dictionary))
-
-        return result

-

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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
-import pandas as pd
-import sqlite3
-
-from graphnet.data.dataset.dataset import Dataset, ColumnMissingException
-
-
-

-[docs]
-class SQLiteDataset(Dataset):
-    """Pytorch dataset for reading data from SQLite databases."""
-
-    # Implementing abstract method(s)
-    def _init(self) -> None:
-        # Check(s)
-        self._database_list: Optional[List[str]]
-        if isinstance(self._path, list):
-            self._database_list = self._path
-            self._all_connections_established = False
-            self._all_connections: List[sqlite3.Connection] = []
-        else:
-            self._database_list = None
-            assert isinstance(self._path, str)
-            assert self._path.endswith(
-                ".db"
-            ), f"Format of input file `{self._path}` is not supported."
-
-        if self._database_list is not None:
-            self._current_database: Optional[int] = None
-
-        # Set custom member variable(s)
-        self._features_string = ", ".join(self._features)
-        self._truth_string = ", ".join(self._truth)
-        if self._node_truth:
-            self._node_truth_string = ", ".join(self._node_truth)
-
-        self._conn: Optional[sqlite3.Connection] = None
-
-    def _post_init(self) -> None:
-        self._close_connection()
-
-

-[docs]
-    def query_table(
-        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)
-        if isinstance(columns, list):
-            columns = ", ".join(columns)
-
-        if not selection:  # I.e., `None` or `""`
-            selection = "1=1"  # Identically true, to select all
-
-        index = self._get_event_index(sequential_index)
-
-        # Query table
-        assert index is not None
-        self._establish_connection(index)
-        try:
-            assert self._conn
-            if sequential_index is None:
-                combined_selections = selection
-            else:
-                combined_selections = (
-                    f"{self._index_column} = {index} and {selection}"
-                )
-
-            result = self._conn.execute(
-                f"SELECT {columns} FROM {table} WHERE "
-                f"{combined_selections}"
-            ).fetchall()
-        except sqlite3.OperationalError as e:
-            if "no such column" in str(e):
-                raise ColumnMissingException(str(e))
-            else:
-                raise e
-        return result

-
-
-    def _get_all_indices(self) -> List[int]:
-        self._establish_connection(0)
-        indices = pd.read_sql_query(
-            f"SELECT {self._index_column} FROM {self._truth_table}", self._conn
-        )
-        self._close_connection()
-        return indices.values.ravel().tolist()
-
-    def _get_event_index(
-        self, sequential_index: Optional[int]
-    ) -> Optional[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_
-            else:
-                assert isinstance(index_, list)
-                index = index_[0]
-        return index
-
-    # Custom, internal method(s)
-    # @TODO: Is it necessary to return anything here?
-    def _establish_connection(self, i: int) -> "SQLiteDataset":
-        """Make sure that a sqlite3 connection is open."""
-        if self._database_list is None:
-            assert isinstance(self._path, str)
-            if self._conn is None:
-                self._conn = sqlite3.connect(self._path)
-        else:
-            indices = self._indices[i]
-            assert isinstance(indices, list)
-            if self._conn is None:
-                if self._all_connections_established is False:
-                    self._all_connections = []
-                    for database in self._database_list:
-                        con = sqlite3.connect(database)
-                        self._all_connections.append(con)
-                    self._all_connections_established = True
-                self._conn = self._all_connections[indices[1]]
-            if indices[1] != self._current_database:
-                self._conn = self._all_connections[indices[1]]
-                self._current_database = indices[1]
-        return self
-
-    # @TODO: Is it necessary to return anything here?
-    def _close_connection(self) -> "SQLiteDataset":
-        """Make sure that no sqlite3 connection is open.
-
-        This is necessary to calls this before passing to
-        `torch.DataLoader` such that the dataset replica on each worker
-        is required to create its own connection (thereby avoiding
-        `sqlite3.DatabaseError: database disk image is malformed` errors
-        due to inability to use sqlite3 connection accross processes.
-        """
-        if self._conn is not None:
-            self._conn.close()
-            del self._conn
-            self._conn = None
-        if self._database_list is not None:
-            if self._all_connections_established:
-                for con in self._all_connections:
-                    con.close()
-                del self._all_connections
-                self._all_connections_established = False
-                self._conn = None
-        return self

-
-
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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.sqlite.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
-            )

-
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Source code for graphnet.deployment.i3modules.graphnet_module

-"""Class(es) for deploying GraphNeT models in icetray as I3Modules."""
-from abc import abstractmethod
-from typing import TYPE_CHECKING, Any, List, Union, Dict, Tuple, Optional
-
-import dill
-import numpy as np
-import torch
-from torch_geometric.data import Data, Batch
-
-from graphnet.data.extractors import (
-    I3FeatureExtractor,
-    I3FeatureExtractorIceCubeUpgrade,
-)
-from graphnet.models import Model, StandardModel
-from graphnet.models.graphs import GraphDefinition
-from graphnet.utilities.imports import has_icecube_package
-from graphnet.utilities.config import ModelConfig
-
-if has_icecube_package() or TYPE_CHECKING:
-    from icecube.icetray import (
-        I3Module,
-        I3Frame,
-    )  # pyright: reportMissingImports=false
-    from icecube.dataclasses import (
-        I3Double,
-        I3MapKeyVectorDouble,
-    )  # pyright: reportMissingImports=false
-    from icecube import dataclasses, dataio, icetray
-
-
-

-[docs]
-class GraphNeTI3Module:
-    """Base I3 Module for GraphNeT.
-
-    Contains methods for extracting pulsemaps, producing graphs and writing to
-    frames.
-    """
-
-    def __init__(
-        self,
-        graph_definition: GraphDefinition,
-        pulsemap: str,
-        features: List[str],
-        pulsemap_extractor: Union[
-            List[I3FeatureExtractor], I3FeatureExtractor
-        ],
-        gcd_file: str,
-    ):
-        """I3Module Constructor.
-
-        Arguments:
-            graph_definition: An instance of GraphDefinition.  E.g. KNNGraph.
-            pulsemap: the pulse map on which the module functions
-            features: the features that is used from the pulse map.
-                      E.g. [dom_x, dom_y, dom_z, charge]
-            pulsemap_extractor: The I3FeatureExtractor used to extract the
-                                pulsemap from the I3Frames
-            gcd_file: Path to the associated gcd-file.
-        """
-        assert isinstance(graph_definition, GraphDefinition)
-        self._graph_definition = graph_definition
-        self._pulsemap = pulsemap
-        self._features = features
-        assert isinstance(gcd_file, str), "gcd_file must be string"
-        self._gcd_file = gcd_file
-        if isinstance(pulsemap_extractor, list):
-            self._i3_extractors = pulsemap_extractor
-        else:
-            self._i3_extractors = [pulsemap_extractor]
-
-        for i3_extractor in self._i3_extractors:
-            i3_extractor.set_files(i3_file="", gcd_file=self._gcd_file)
-
-    @abstractmethod
-    def __call__(self, frame: I3Frame) -> bool:
-        """Define here how the module acts on the frame.
-
-        Must return True if successful.
-
-        Return True # SUPER IMPORTANT
-        """
-
-    def _make_graph(
-        self, frame: I3Frame
-    ) -> Data:  # py-l-i-n-t-:- -d-i-s-able=invalid-name
-        """Process Physics I3Frame into graph."""
-        # Extract features
-        input_features = self._extract_feature_array_from_frame(frame)
-        # Prepare graph data
-        if len(input_features) > 0:
-            data = self._graph_definition(
-                input_features=input_features,
-                input_feature_names=self._features,
-            )
-            return Batch.from_data_list([data])
-        else:
-            return None
-
-    def _extract_feature_array_from_frame(self, frame: I3Frame) -> np.array:
-        """Apply the I3FeatureExtractors to the I3Frame.
-
-        Arguments:
-            frame: Physics I3Frame (PFrame)
-
-        Returns:
-            array with pulsemap
-        """
-        features = None
-        for i3extractor in self._i3_extractors:
-            feature_dict = i3extractor(frame)
-            features_pulsemap = np.array(
-                [feature_dict[key] for key in self._features]
-            ).T
-            if features is None:
-                features = features_pulsemap
-            else:
-                features = np.concatenate(
-                    (features, features_pulsemap), axis=0
-                )
-        return features
-
-    def _add_to_frame(self, frame: I3Frame, data: Dict[str, Any]) -> I3Frame:
-        """Add every field in data to I3Frame.
-
-        Arguments:
-            frame: I3Frame (physics)
-            data: Dictionary containing content that will be written to frame.
-
-        Returns:
-            frame: Same I3Frame as input, but with the new entries
-        """
-        assert isinstance(
-            data, dict
-        ), f"data must be of type dict. Got {type(data)}"
-        for key in data.keys():
-            if key not in frame:
-                frame.Put(key, data[key])
-        return frame

-
-
-
-

-[docs]
-class I3InferenceModule(GraphNeTI3Module):
-    """General class for inference on i3 frames."""
-
-    def __init__(
-        self,
-        pulsemap: str,
-        features: List[str],
-        pulsemap_extractor: Union[
-            List[I3FeatureExtractor], I3FeatureExtractor
-        ],
-        model_config: Union[ModelConfig, str],
-        state_dict: str,
-        model_name: str,
-        gcd_file: str,
-        prediction_columns: Optional[Union[List[str], str]] = None,
-    ):
-        """General class for inference on I3Frames (physics).
-
-        Arguments:
-            pulsemap: the pulsmap that the model is expecting as input.
-            features: the features of the pulsemap that the model is expecting.
-            pulsemap_extractor: The extractor used to extract the pulsemap.
-            model_config: The ModelConfig (or path to it) that summarizes the
-                            model used for inference.
-            state_dict: Path to state_dict containing the learned weights.
-            model_name: The name used for the model. Will help define the
-                        named entry in the I3Frame. E.g. "dynedge".
-            gcd_file: path to associated gcd file.
-            prediction_columns: column names for the predictions of the model.
-                               Will help define the named entry in the I3Frame.
-                                E.g. ['energy_reco']. Optional.
-        """
-        # Construct model & load weights
-        self.model = Model.from_config(model_config, trust=True)
-        self.model.load_state_dict(state_dict)
-
-        super().__init__(
-            pulsemap=pulsemap,
-            features=features,
-            pulsemap_extractor=pulsemap_extractor,
-            gcd_file=gcd_file,
-            graph_definition=self.model._graph_definition,
-        )
-        self.model.inference()
-
-        self.model.to("cpu")
-        if prediction_columns is not None:
-            if isinstance(prediction_columns, str):
-                self.prediction_columns = [prediction_columns]
-            else:
-                self.prediction_columns = prediction_columns
-        else:
-            self.prediction_columns = self.model.prediction_labels
-
-        self.model_name = model_name
-
-    def __call__(self, frame: I3Frame) -> bool:
-        """Write predictions from model to frame."""
-        # inference
-        graph = self._make_graph(frame)
-        if graph is not None:
-            predictions = self._inference(graph)
-        else:
-            predictions = np.repeat(
-                [np.nan], len(self.prediction_columns)
-            ).reshape(-1, len(self.prediction_columns))
-        # Check dimensions of predictions and prediction columns
-        if len(predictions.shape) > 1:
-            dim = predictions.shape[1]
-        else:
-            dim = len(predictions)
-        assert dim == len(
-            self.prediction_columns
-        ), f"""predictions have shape {dim} but \n
-            prediction columns have [{self.prediction_columns}]"""
-
-        # Build Dictionary of predictions
-        data = {}
-        assert predictions.shape[0] == 1
-        for i in range(dim if isinstance(dim, int) else len(dim)):
-            try:
-                assert len(predictions[:, i]) == 1
-                data[
-                    self.model_name + "_" + self.prediction_columns[i]
-                ] = I3Double(float(predictions[:, i][0]))
-            except IndexError:
-                data[
-                    self.model_name + "_" + self.prediction_columns[i]
-                ] = I3Double(predictions[0])
-
-        # Submission methods
-        frame = self._add_to_frame(frame=frame, data=data)
-        return True
-
-    def _inference(self, data: Data) -> np.ndarray:
-        # Perform inference
-        task_predictions = self.model(data)
-        assert (
-            len(task_predictions) == 1
-        ), f"""This method assumes a single task. \n
-               Got {len(task_predictions)} tasks."""
-        return self.model(data)[0].detach().numpy()

-
-
-
-

-[docs]
-class I3PulseCleanerModule(I3InferenceModule):
-    """A specialized module for pulse cleaning.
-
-    It is assumed that the model provided has been trained for this.
-    """
-
-    def __init__(
-        self,
-        pulsemap: str,
-        features: List[str],
-        pulsemap_extractor: Union[
-            List[I3FeatureExtractor], I3FeatureExtractor
-        ],
-        model_config: str,
-        state_dict: str,
-        model_name: str,
-        *,
-        gcd_file: str,
-        threshold: float = 0.7,
-        discard_empty_events: bool = False,
-        prediction_columns: Optional[Union[List[str], str]] = None,
-    ):
-        """General class for inference on I3Frames (physics).
-
-        Arguments:
-            pulsemap: the pulsmap that the model is expecting as input
-                     (the one that is being cleaned).
-            features: the features of the pulsemap that the model is expecting.
-            pulsemap_extractor: The extractor used to extract the pulsemap.
-            model_config: The ModelConfig (or path to it) that summarizes the
-                            model used for inference.
-            state_dict: Path to state_dict containing the learned weights.
-            model_name: The name used for the model. Will help define the named
-                        entry in the I3Frame. E.g. "dynedge".
-            gcd_file: path to associated gcd file.
-            threshold: the threshold for being considered a positive case.
-                        E.g., predictions >= threshold will be considered
-                        to be signal, all else noise.
-            discard_empty_events: When true, this flag will eliminate events
-                            whose cleaned pulse series are empty. Can be used
-                            to speed up processing especially for noise
-                            simulation, since it will not do any writing or
-                            further calculations.
-            prediction_columns: column names for the predictions of the model.
-                            Will help define the named entry in the I3Frame.
-                            E.g. ['energy_reco']. Optional.
-        """
-        super().__init__(
-            pulsemap=pulsemap,
-            features=features,
-            pulsemap_extractor=pulsemap_extractor,
-            model_config=model_config,
-            state_dict=state_dict,
-            model_name=model_name,
-            prediction_columns=prediction_columns,
-            gcd_file=gcd_file,
-        )
-        self._threshold = threshold
-        self._predictions_key = f"{pulsemap}_{model_name}_Predictions"
-        self._total_pulsemap_name = f"{pulsemap}_{model_name}_Pulses"
-        self._discard_empty_events = discard_empty_events
-
-    def __call__(self, frame: I3Frame) -> bool:
-        """Add a cleaned pulsemap to frame."""
-        # inference
-        gcd_file = self._gcd_file
-        graph = self._make_graph(frame)
-        if graph is None:  # If there is no pulses to clean
-            return False
-        predictions = self._inference(graph)
-        if self._discard_empty_events:
-            if sum(predictions > self._threshold) == 0:
-                return False
-
-        if len(predictions.shape) == 1:
-            predictions = predictions.reshape(-1, 1)
-
-        assert predictions.shape[1] == 1
-
-        # Build Dictionary of predictions
-        data = {}
-
-        predictions_map = self._construct_prediction_map(
-            frame=frame, predictions=predictions
-        )
-
-        # Adds the raw predictions to dictionary
-        if self._predictions_key not in frame.keys():
-            data[self._predictions_key] = predictions_map
-
-        # Create a pulse map mask, indicating the pulses that are over
-        # threshold (e.g. identified as signal) and therefore should be kept
-        # Using a lambda function to evaluate which pulses to keep by
-        # checking the prediction for each pulse
-        # (Adds the actual pulsemap to dictionary)
-        if self._total_pulsemap_name not in frame.keys():
-            data[
-                self._total_pulsemap_name
-            ] = dataclasses.I3RecoPulseSeriesMapMask(
-                frame,
-                self._pulsemap,
-                lambda om_key, index, pulse: predictions_map[om_key][index]
-                >= self._threshold,
-            )
-
-        # Submit predictions and general pulsemap
-        frame = self._add_to_frame(frame=frame, data=data)
-        data = {}
-        # Adds an additional pulsemap for each DOM type
-        if isinstance(
-            self._i3_extractors[0], I3FeatureExtractorIceCubeUpgrade
-        ):
-            mDOMMap, DEggMap, IceCubeMap = self._split_pulsemap_in_dom_types(
-                frame=frame, gcd_file=gcd_file
-            )
-
-            if f"{self._total_pulsemap_name}_mDOMs_Only" not in frame.keys():
-                data[
-                    f"{self._total_pulsemap_name}_mDOMs_Only"
-                ] = dataclasses.I3RecoPulseSeriesMap(mDOMMap)
-
-            if f"{self._total_pulsemap_name}_dEggs_Only" not in frame.keys():
-                data[
-                    f"{self._total_pulsemap_name}_dEggs_Only"
-                ] = dataclasses.I3RecoPulseSeriesMap(DEggMap)
-
-            if f"{self._total_pulsemap_name}_pDOMs_Only" not in frame.keys():
-                data[
-                    f"{self._total_pulsemap_name}_pDOMs_Only"
-                ] = dataclasses.I3RecoPulseSeriesMap(IceCubeMap)
-
-        # Submits the additional pulsemaps to the frame
-        frame = self._add_to_frame(frame=frame, data=data)
-
-        return True
-
-    def _split_pulsemap_in_dom_types(
-        self, frame: I3Frame, gcd_file: Any
-    ) -> Tuple[Dict[Any, Any], Dict[Any, Any], Dict[Any, Any]]:
-        """Will split the cleaned pulsemap into multiple pulsemaps.
-
-        Arguments:
-            frame: I3Frame (physics)
-            gcd_file: path to associated gcd file
-
-        Returns:
-            mDOMMap, DeGGMap, IceCubeMap
-        """
-        g = dataio.I3File(gcd_file)
-        gFrame = g.pop_frame()
-        while "I3Geometry" not in gFrame.keys():
-            gFrame = g.pop_frame()
-        omGeoMap = gFrame["I3Geometry"].omgeo
-
-        mDOMMap, DEggMap, IceCubeMap = {}, {}, {}
-        pulses = dataclasses.I3RecoPulseSeriesMap.from_frame(
-            frame, self._total_pulsemap_name
-        )
-        for P in pulses:
-            om = omGeoMap[P[0]]
-            if om.omtype == 130:  # "mDOM"
-                mDOMMap[P[0]] = P[1]
-            elif om.omtype == 120:  # "DEgg"
-                DEggMap[P[0]] = P[1]
-            elif om.omtype == 20:  # "IceCube / pDOM"
-                IceCubeMap[P[0]] = P[1]
-        return mDOMMap, DEggMap, IceCubeMap
-
-    def _construct_prediction_map(
-        self, frame: I3Frame, predictions: np.ndarray
-    ) -> I3MapKeyVectorDouble:
-        """Make a pulsemap from predictions (for all OM types).
-
-        Arguments:
-            frame: I3Frame (physics)
-            predictions: predictions from Model.
-
-        Returns:
-            predictions_map: a pulsemap from predictions
-        """
-        pulsemap = dataclasses.I3RecoPulseSeriesMap.from_frame(
-            frame, self._pulsemap
-        )
-
-        idx = 0
-        predictions = predictions.squeeze(1)
-        predictions_map = dataclasses.I3MapKeyVectorDouble()
-        for om_key, pulses in pulsemap.items():
-            num_pulses = len(pulses)
-            predictions_map[om_key] = predictions[
-                idx : idx + num_pulses
-            ].tolist()
-            idx += num_pulses
-
-        # Checks
-        assert idx == len(
-            predictions
-        ), """Not all predictions were mapped to pulses,\n
-            validation of predictions have failed."""
-
-        assert (
-            pulsemap.keys() == predictions_map.keys()
-        ), """Input pulse map and predictions map do \n
-              not contain exactly the same OMs"""
-        return predictions_map

-
-
- -
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- - - - - \ No newline at end of file diff --git a/_modules/graphnet/models/coarsening.html b/_modules/graphnet/models/coarsening.html deleted file mode 100644 index 301d35d73..000000000 --- a/_modules/graphnet/models/coarsening.html +++ /dev/null @@ -1,708 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - graphnet.models.coarsening — graphnet documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Skip to content -
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Source code for graphnet.models.coarsening

-"""Class(es) for coarsening operations (i.e., clustering, or local pooling)."""
-
-from abc import abstractmethod
-from typing import List, Optional, Union
-from copy import deepcopy
-import torch
-from torch import LongTensor, Tensor
-from torch_geometric.data import Data, Batch
-from sklearn.cluster import DBSCAN
-
-# from torch_geometric.utils import unbatch_edge_index
-from graphnet.models.components.pool import (
-    group_by,
-    avg_pool,
-    max_pool,
-    min_pool,
-    sum_pool,
-    avg_pool_x,
-    max_pool_x,
-    min_pool_x,
-    sum_pool_x,
-    std_pool_x,
-)
-from graphnet.models import Model
-
-# Utility method(s)
-from torch_geometric.utils import degree
-
-# NOTE: From [https://github.com/pyg-team/pytorch_geometric/pull/4903]
-# TODO:  Remove once bumping to torch_geometric>=2.1.0
-#       See [https://github.com/pyg-team/pytorch_geometric/blob/master/CHANGELOG.md]
-
-
-

-[docs]
-def unbatch_edge_index(edge_index: Tensor, batch: Tensor) -> List[Tensor]:
-    # noqa: D401
-    r"""Splits the :obj:`edge_index` according to a :obj:`batch` vector.
-
-    Args:
-        edge_index (Tensor): The edge_index tensor. Must be ordered.
-        batch (LongTensor): The batch vector
-            :math:`\mathbf{b} \in {\{ 0, \ldots, B-1\}}^N`, which assigns each
-            node to a specific example. Must be ordered.
-    :rtype: :class:`List[Tensor]`
-    """
-    deg = degree(batch, dtype=torch.int64)
-    ptr = torch.cat([deg.new_zeros(1), deg.cumsum(dim=0)[:-1]], dim=0)
-
-    edge_batch = batch[edge_index[0]]
-    edge_index = edge_index - ptr[edge_batch]
-    sizes = degree(edge_batch, dtype=torch.int64).cpu().tolist()
-    return edge_index.split(sizes, dim=1)

-
-
-
-

-[docs]
-class Coarsening(Model):
-    """Base class for coarsening operations."""
-
-    # Class variables
-    reduce_options = {
-        "avg": (avg_pool, avg_pool_x),
-        "min": (min_pool, min_pool_x),
-        "max": (max_pool, max_pool_x),
-        "sum": (sum_pool, sum_pool_x),
-    }
-
-    def __init__(
-        self,
-        reduce: str = "avg",
-        transfer_attributes: bool = True,
-    ):
-        """Construct `Coarsening`."""
-        assert reduce in self.reduce_options
-
-        (
-            self._reduce_method,
-            self._attribute_reduce_method,
-        ) = self.reduce_options[reduce]
-        self._do_transfer_attributes = transfer_attributes
-
-        # Base class constructor
-        super().__init__()
-
-    @abstractmethod
-    def _perform_clustering(self, data: Union[Data, Batch]) -> LongTensor:
-        """Cluster nodes in `data` by assigning a cluster index to each."""
-
-    def _additional_features(self, cluster: LongTensor, data: Batch) -> Tensor:
-        """Perform additional poolings of feature tensor `x` on `data`.
-
-        By default the nominal `pooling_method` is used for features as well.
-        This method can be overwritten for bespoke coarsening operations.
-        """
-
-    def _transfer_attributes(
-        self, cluster: LongTensor, original_data: Batch, pooled_data: Batch
-    ) -> Batch:
-        """Transfer attributes on `original_data` to `pooled_data`."""
-        # Check(s)
-        if not self._do_transfer_attributes:
-            return pooled_data
-
-        attributes = list(original_data._store.keys())
-        batch: Optional[LongTensor] = original_data.batch
-        for ix, attr in enumerate(attributes):
-            if attr not in pooled_data._store:
-                values: Tensor = getattr(original_data, attr)
-
-                attr_is_node_level_tensor = False
-                if isinstance(values, Tensor):
-                    if batch is None:
-                        attr_is_node_level_tensor = (
-                            values.dim() > 1 or values.size(dim=0) > 1
-                        )
-                    else:
-                        attr_is_node_level_tensor = (
-                            values.size() == original_data.batch.size()
-                        )
-
-                if attr_is_node_level_tensor:
-                    values = self._attribute_reduce_method(
-                        cluster,
-                        values,
-                        batch=torch.zeros_like(values, dtype=torch.int32),
-                    )[0]
-
-                setattr(pooled_data, attr, values)
-
-        return pooled_data
-
-

-[docs]
-    def forward(self, data: Union[Data, Batch]) -> Union[Data, Batch]:
-        """Perform coarsening operation."""
-        # Get tensor of cluster indices for each node.
-        cluster: LongTensor = self._perform_clustering(data)
-
-        # Check whether a graph has already been built. Otherwise, set a dummy
-        # connectivity, as this is required by pooling functions.
-        edge_index = data.edge_index
-        if edge_index is None:
-            data.edge_index = torch.tensor([[]], dtype=torch.int64)
-
-        # Pool `data` object, including `x`, `batch`. and `edge_index`.
-        pooled_data: Batch = self._reduce_method(cluster, data)
-
-        # Optionally overwrite feature tensor
-        x = self._additional_features(cluster, data)
-        if x is not None:
-            pooled_data.x = torch.cat(
-                (
-                    pooled_data.x,
-                    x,
-                ),
-                dim=1,
-            )
-
-        # Reset `edge_index` if necessary.
-        if edge_index is None:
-            data.edge_index = edge_index
-            pooled_data.edge_index = edge_index
-
-        # Transfer attributes on `data`, pooling as required.
-        pooled_data = self._transfer_attributes(cluster, data, pooled_data)
-
-        # Reconstruct Batch Attributes
-        if isinstance(data, Batch):  # if a Batch object
-            pooled_data = self._reconstruct_batch(data, pooled_data)
-        return pooled_data

-
-
-    def _reconstruct_batch(self, original: Data, pooled: Data) -> Data:
-        pooled = self._add_slice_dict(original, pooled)
-        pooled = self._add_inc_dict(original, pooled)
-        return pooled
-
-    def _add_slice_dict(self, original: Data, pooled: Data) -> Data:
-        # Copy original slice_dict and count nodes in each graph in pooled batch
-        slice_dict = deepcopy(original._slice_dict)
-        _, counts = torch.unique_consecutive(pooled.batch, return_counts=True)
-        # Reconstruct the entry in slice_dict for pulsemaps - only these are affected by pooling
-        pulsemap_slice = [0]
-        for i in range(len(counts)):
-            pulsemap_slice.append(pulsemap_slice[i] + counts[i].item())
-
-        # Identifies pulsemap entries in slice_dict and set them to pulsemap_slice
-        for field in slice_dict.keys():
-            if (original._num_graphs) == slice_dict[field][-1]:
-                pass  # not pulsemap, so skip
-            else:
-                slice_dict[field] = pulsemap_slice
-        pooled._slice_dict = slice_dict
-        return pooled
-
-    def _add_inc_dict(self, original: Data, pooled: Data) -> Data:
-        # not changed by coarsening
-        pooled._inc_dict = deepcopy(original._inc_dict)
-        return pooled

-
-
-
-

-[docs]
-class AttributeCoarsening(Coarsening):
-    """Coarsen pulses based on specified attributes."""
-
-    def __init__(
-        self,
-        attributes: List[str],
-        reduce: str = "avg",
-        transfer_attributes: bool = True,
-    ):
-        """Construct `SimpleCoarsening`."""
-        self._attributes = attributes
-
-        # Base class constructor
-        super().__init__(reduce, transfer_attributes)
-
-    def _perform_clustering(self, data: Union[Data, Batch]) -> LongTensor:
-        """Cluster nodes in `data` by assigning a cluster index to each."""
-        dom_index = group_by(data, self._attributes)
-        return dom_index

-
-
-
-

-[docs]
-class DOMCoarsening(Coarsening):
-    """Coarsen pulses to DOM-level."""
-
-    def __init__(
-        self,
-        reduce: str = "avg",
-        transfer_attributes: bool = True,
-        keys: Optional[List[str]] = None,
-    ):
-        """Cluster pulses on the same DOM."""
-        super().__init__(reduce, transfer_attributes)
-        if keys is None:
-            self._keys = [
-                "dom_x",
-                "dom_y",
-                "dom_z",
-                "rde",
-                "pmt_area",
-            ]
-        else:
-            self._keys = keys
-
-    def _perform_clustering(self, data: Union[Data, Batch]) -> LongTensor:
-        """Cluster nodes in `data` by assigning a cluster index to each."""
-        dom_index = group_by(data, self._keys)
-        return dom_index

-
-
-
-

-[docs]
-class CustomDOMCoarsening(DOMCoarsening):
-    """Coarsen pulses to DOM-level with additional attributes."""
-
-    def _additional_features(self, cluster: LongTensor, data: Data) -> Tensor:
-        """Perform Additional poolings of feature tensor `x` on `data`."""
-        batch = data.batch
-
-        features = data.features
-        if batch is not None:
-            features = [feats[0] for feats in features]
-
-        ix_time = features.index("dom_time")
-        ix_charge = features.index("charge")
-
-        time = data.x[:, ix_time]
-        charge = data.x[:, ix_charge]
-
-        x = torch.stack(
-            (
-                min_pool_x(cluster, time, batch)[0],
-                max_pool_x(cluster, time, batch)[0],
-                std_pool_x(cluster, time, batch)[0],
-                min_pool_x(cluster, charge, batch)[0],
-                max_pool_x(cluster, charge, batch)[0],
-                std_pool_x(cluster, charge, batch)[0],
-                sum_pool_x(cluster, torch.ones_like(charge), batch)[
-                    0
-                ],  # Num. nodes (pulses) per cluster (DOM)
-            ),
-            dim=1,
-        )
-
-        return x

-
-
-
-

-[docs]
-class DOMAndTimeWindowCoarsening(Coarsening):
-    """Coarsen pulses to DOM-level, with additional time-window clustering."""
-
-    def __init__(
-        self,
-        time_window: float,
-        reduce: str = "avg",
-        transfer_attributes: bool = True,
-        keys: List[str] = [
-            "dom_x",
-            "dom_y",
-            "dom_z",
-            "rde",
-            "pmt_area",
-        ],
-        time_key: str = "dom_time",
-    ):
-        """Cluster pulses on the same DOM within `time_window`."""
-        super().__init__(reduce, transfer_attributes)
-        self._time_window = time_window
-        self._cluster_method = DBSCAN(self._time_window, min_samples=1)
-        self._keys = keys
-        self._time_key = time_key
-
-    def _perform_clustering(self, data: Union[Data, Batch]) -> LongTensor:
-        """Cluster nodes in `data` by assigning a cluster index to each."""
-        dom_index = group_by(data, self._keys)
-        if data.batch is not None:
-            features = data.features[0]
-        else:
-            features = data.features
-
-        ix_time = features.index(self._time_key)
-        hit_times = data.x[:, ix_time]
-
-        # Scale up dom_index to make sure clusters are well separated
-        times_and_domids = torch.stack(
-            [
-                hit_times,
-                dom_index * self._time_window * 10,
-            ]
-        ).T
-        clusters = torch.tensor(
-            self._cluster_method.fit_predict(times_and_domids.cpu()),
-            device=hit_times.device,
-        )
-
-        return clusters

-
-
- -
-
-
-
-
- - - - - \ No newline at end of file diff --git a/_modules/graphnet/models/components/layers.html b/_modules/graphnet/models/components/layers.html deleted file mode 100644 index 80fbc5ec0..000000000 --- a/_modules/graphnet/models/components/layers.html +++ /dev/null @@ -1,579 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - graphnet.models.components.layers — graphnet documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Skip to content -
- -
- - -
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-
- -
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- -
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- - -
-
-
- -
-
- -

Source code for graphnet.models.components.layers

-"""Class(es) implementing layers to be used in `graphnet` models."""
-
-from typing import Any, Callable, Optional, Sequence, Union, List, Tuple
-
-import torch
-from torch.functional import Tensor
-from torch_geometric.nn import EdgeConv
-from torch_geometric.nn.pool import knn_graph
-from torch_geometric.typing import Adj, PairTensor
-from torch_geometric.nn.conv import MessagePassing
-from torch_geometric.nn.inits import reset
-from torch.nn.modules import TransformerEncoder, TransformerEncoderLayer
-from torch.nn.modules.normalization import LayerNorm
-from torch_geometric.utils import to_dense_batch
-from pytorch_lightning import LightningModule
-
-
-

-[docs]
-class DynEdgeConv(EdgeConv, LightningModule):
-    """Dynamical edge convolution layer."""
-
-    def __init__(
-        self,
-        nn: Callable,
-        aggr: str = "max",
-        nb_neighbors: int = 8,
-        features_subset: Optional[Union[Sequence[int], slice]] = None,
-        **kwargs: Any,
-    ):
-        """Construct `DynEdgeConv`.
-
-        Args:
-            nn: The MLP/torch.Module to be used within the `EdgeConv`.
-            aggr: Aggregation method to be used with `EdgeConv`.
-            nb_neighbors: Number of neighbours to be clustered after the
-                `EdgeConv` operation.
-            features_subset: Subset of features in `Data.x` that should be used
-                when dynamically performing the new graph clustering after the
-                `EdgeConv` operation. Defaults to all features.
-            **kwargs: Additional features to be passed to `EdgeConv`.
-        """
-        # Check(s)
-        if features_subset is None:
-            features_subset = slice(None)  # Use all features
-        assert isinstance(features_subset, (list, slice))
-
-        # Base class constructor
-        super().__init__(nn=nn, aggr=aggr, **kwargs)
-
-        # Additional member variables
-        self.nb_neighbors = nb_neighbors
-        self.features_subset = features_subset
-
-

-[docs]
-    def forward(
-        self, x: Tensor, edge_index: Adj, batch: Optional[Tensor] = None
-    ) -> Tensor:
-        """Forward pass."""
-        # Standard EdgeConv forward pass
-        x = super().forward(x, edge_index)
-
-        # Recompute adjacency
-        edge_index = knn_graph(
-            x=x[:, self.features_subset],
-            k=self.nb_neighbors,
-            batch=batch,
-        ).to(self.device)
-
-        return x, edge_index

-

-
-
-
-

-[docs]
-class EdgeConvTito(MessagePassing, LightningModule):
-    """Implementation of EdgeConvTito layer used in TITO solution for.
-
-    'IceCube - Neutrinos in Deep' kaggle competition.
-    """
-
-    def __init__(
-        self,
-        nn: Callable,
-        aggr: str = "max",
-        **kwargs: Any,
-    ):
-        """Construct `EdgeConvTito`.
-
-        Args:
-            nn: The MLP/torch.Module to be used within the `EdgeConvTito`.
-            aggr: Aggregation method to be used with `EdgeConvTito`.
-            **kwargs: Additional features to be passed to `EdgeConvTito`.
-        """
-        super().__init__(aggr=aggr, **kwargs)
-        self.nn = nn
-        self.reset_parameters()
-
-

-[docs]
-    def reset_parameters(self) -> None:
-        """Reset all learnable parameters of the module."""
-        reset(self.nn)

-
-
-

-[docs]
-    def forward(self, x: Union[Tensor, PairTensor], edge_index: Adj) -> Tensor:
-        """Forward pass."""
-        if isinstance(x, Tensor):
-            x = (x, x)
-        # propagate_type: (x: PairTensor)
-        return self.propagate(edge_index, x=x, size=None)

-
-
-

-[docs]
-    def message(self, x_i: Tensor, x_j: Tensor) -> Tensor:
-        """Edgeconvtito message passing."""
-        return self.nn(
-            torch.cat([x_i, x_j - x_i, x_j], dim=-1)
-        )  # EdgeConvTito

-
-
-    def __repr__(self) -> str:
-        """Print out module name."""
-        return f"{self.__class__.__name__}(nn={self.nn})"

-
-
-
-

-[docs]
-class DynTrans(EdgeConvTito, LightningModule):
-    """Implementation of dynTrans1 layer used in TITO solution for.
-
-    'IceCube - Neutrinos in Deep' kaggle competition.
-    """
-
-    def __init__(
-        self,
-        layer_sizes: Optional[List[int]] = None,
-        aggr: str = "max",
-        features_subset: Optional[Union[Sequence[int], slice]] = None,
-        n_head: int = 8,
-        **kwargs: Any,
-    ):
-        """Construct `DynTrans`.
-
-        Args:
-            nn: The MLP/torch.Module to be used within the `DynTrans`.
-            layer_sizes: List of layer sizes to be used in `DynTrans`.
-            aggr: Aggregation method to be used with `DynTrans`.
-            features_subset: Subset of features in `Data.x` that should be used
-                when dynamically performing the new graph clustering after the
-                `EdgeConv` operation. Defaults to all features.
-            n_head: Number of heads to be used in the multiheadattention models.
-            **kwargs: Additional features to be passed to `DynTrans`.
-        """
-        # Check(s)
-        if features_subset is None:
-            features_subset = slice(None)  # Use all features
-        assert isinstance(features_subset, (list, slice))
-
-        if layer_sizes is None:
-            layer_sizes = [256, 256, 256]
-        layers = []
-        for ix, (nb_in, nb_out) in enumerate(
-            zip(layer_sizes[:-1], layer_sizes[1:])
-        ):
-            if ix == 0:
-                nb_in *= 3  # edgeConv1
-            layers.append(torch.nn.Linear(nb_in, nb_out))
-            layers.append(torch.nn.LeakyReLU())
-        d_model = nb_out
-
-        # Base class constructor
-        super().__init__(nn=torch.nn.Sequential(*layers), aggr=aggr, **kwargs)
-
-        # Additional member variables
-        self.features_subset = features_subset
-
-        self.norm1 = LayerNorm(d_model, eps=1e-5)  # lNorm
-
-        # Transformer layer(s)
-        encoder_layer = TransformerEncoderLayer(
-            d_model=d_model,
-            nhead=n_head,
-            batch_first=True,
-            norm_first=False,
-        )
-        self._transformer_encoder = TransformerEncoder(
-            encoder_layer, num_layers=1
-        )
-
-

-[docs]
-    def forward(
-        self, x: Tensor, edge_index: Adj, batch: Optional[Tensor] = None
-    ) -> Tensor:
-        """Forward pass."""
-        x_out = super().forward(x, edge_index)
-
-        if x_out.shape[-1] == x.shape[-1]:
-            x = x + x_out
-        else:
-            x = x_out
-
-        x = self.norm1(x)  # lNorm
-
-        # Transformer layer
-        x, mask = to_dense_batch(x, batch)
-        x = self._transformer_encoder(x, src_key_padding_mask=~mask)
-        x = x[mask]
-
-        return x

-

-
-
- -
-
-
-
-
- - - - - \ No newline at end of file diff --git a/_modules/graphnet/models/components/pool.html b/_modules/graphnet/models/components/pool.html deleted file mode 100644 index 11ce78f3d..000000000 --- a/_modules/graphnet/models/components/pool.html +++ /dev/null @@ -1,656 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - graphnet.models.components.pool — graphnet documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Skip to content -
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Source code for graphnet.models.components.pool

-"""Functions for performing pooling/clustering/coarsening."""
-
-from typing import Any, Callable, List, Optional, Union
-
-import torch
-from torch import LongTensor, Tensor
-from torch_geometric.data import Data, Batch
-from torch_geometric.nn.pool.consecutive import consecutive_cluster
-from torch_geometric.nn.pool.pool import pool_edge, pool_batch, pool_pos
-from torch_scatter import scatter, scatter_std
-
-from torch_geometric.nn.pool import (
-    avg_pool,
-    max_pool,
-    avg_pool_x,
-    max_pool_x,
-)
-
-
-

-[docs]
-def min_pool(
-    cluster: LongTensor, data: Data, transform: Optional[Any] = None
-) -> Data:
-    """Perform min-pooling of `Data`.
-
-    Like `max_pool, just negating `data.x`.
-    """
-    data.x = -data.x
-    data_pooled = max_pool(
-        cluster,
-        data,
-        transform,
-    )
-    data.x = -data.x
-    data_pooled.x = -data_pooled.x
-    return data_pooled

-
-
-
-

-[docs]
-def min_pool_x(
-    cluster: LongTensor,
-    x: Tensor,
-    batch: LongTensor,
-    size: Optional[int] = None,
-) -> Tensor:
-    """Perform min-pooling of `Tensor`.
-
-    Like `max_pool_x, just negating `x`.
-    """
-    ret = max_pool_x(cluster, -x, batch, size)
-    if size is None:
-        return (-ret[0], ret[1])
-    else:
-        return -ret

-
-
-
-

-[docs]
-def sum_pool_and_distribute(
-    tensor: Tensor,
-    cluster_index: LongTensor,
-    batch: Optional[LongTensor] = None,
-) -> Tensor:
-    """Sum-pool values and distribute result to the individual nodes."""
-    if batch is None:
-        batch = torch.zeros(tensor.size(dim=0)).long()
-    tensor_pooled, _ = sum_pool_x(cluster_index, tensor, batch)
-    inv, _ = consecutive_cluster(cluster_index)
-    tensor_unpooled = tensor_pooled[inv]
-    return tensor_unpooled

-
-
-
-def _group_identical(
-    tensor: Tensor, batch: Optional[LongTensor] = None
-) -> LongTensor:
-    """Group rows in `tensor` that are identical.
-
-    Args:
-        tensor: Tensor of shape [N, F].
-        batch: Batch indices, to only group identical rows within batches.
-
-    Returns:
-        List of group indices, from 0 to num. groups - 1, assigning all
-            identical rows to the same group.
-    """
-    if batch is not None:
-        tensor = torch.cat((batch.unsqueeze(dim=1), tensor), dim=1)
-    return torch.unique(tensor, return_inverse=True, sorted=False, dim=0)[1]
-
-
-

-[docs]
-def group_by(data: Union[Data, Batch], keys: List[str]) -> LongTensor:
-    """Group nodes in `data` that have identical values of `keys`.
-
-    This grouping is done with in each event in case of batching. This allows
-    for, e.g., assigning the same index to all pulses on the same PMT or DOM in
-    the same event. This can be used for coarsening graphs, e.g., from pulse-
-    level to DOM-level by aggregating feature across each group returned by this
-    method.
-
-    Example:
-      Given:
-        data.f1 = [1,1,2,2,2]
-        data.f2 = [6,7,7,7,8]
-      Calls:
-        groupby(data, ['f1'])       -> [0, 0, 1, 1, 1]
-        groupby(data, ['f2'])       -> [0, 1, 1, 1, 2]
-        groupby(data, ['f1', 'f2']) -> [0, 1, 2, 2, 3]
-    """
-    features = [getattr(data, key) for key in keys]
-    tensor = torch.stack(features).T  # .int()  @TODO: Required? Use rounding?
-    batch = getattr(data, "batch", None)
-    index = _group_identical(tensor, batch)
-    return index

-
-
-
-

-[docs]
-def group_pulses_to_dom(data: Data) -> Data:
-    """Group pulses on the same DOM, using DOM and string number."""
-    data.dom_index = group_by(data, ["dom_number", "string"])
-    return data

-
-
-
-

-[docs]
-def group_pulses_to_pmt(data: Data) -> Data:
-    """Group pulses on the same PMT, using PMT, DOM, and string number."""
-    data.pmt_index = group_by(data, ["pmt_number", "dom_number", "string"])
-    return data

-
-
-
-# Below mirroring `torch_geometric.nn.pool.{avg,max}_pool.py`.
-def _sum_pool_x(
-    cluster: LongTensor, x: Tensor, size: Optional[int] = None
-) -> Tensor:
-    return scatter(x, cluster, dim=0, dim_size=size, reduce="sum")
-
-
-def _std_pool_x(
-    cluster: LongTensor, x: Tensor, size: Optional[int] = None
-) -> Tensor:
-    return scatter_std(x, cluster, dim=0, dim_size=size, unbiased=False)
-
-
-

-[docs]
-def sum_pool_x(
-    cluster: LongTensor,
-    x: Tensor,
-    batch: LongTensor,
-    size: Optional[int] = None,
-) -> Tensor:
-    r"""Sum-pool node features according to the clustering defined in `cluster`.
-
-    Args:
-        cluster: Cluster vector :math:`\mathbf{c} \in \{ 0,
-            \ldots, N - 1 \}^N`, which assigns each node to a specific cluster.
-        x: Node feature matrix
-            :math:`\mathbf{X} \in \mathbb{R}^{(N_1 + \ldots + N_B) \times F}`.
-        batch: Batch vector :math:`\mathbf{b} \in {\{ 0, \ldots,
-            B-1\}}^N`, which assigns each node to a specific example.
-        size: The maximum number of clusters in a single
-            example. This property is useful to obtain a batch-wise dense
-            representation, *e.g.* for applying FC layers, but should only be
-            used if the size of the maximum number of clusters per example is
-            known in advance.
-    """
-    if size is not None:
-        batch_size = int(batch.max().item()) + 1
-        return _sum_pool_x(cluster, x, batch_size * size), None
-
-    cluster, perm = consecutive_cluster(cluster)
-    x = _sum_pool_x(cluster, x)
-    batch = pool_batch(perm, batch)
-
-    return x, batch

-
-
-
-

-[docs]
-def std_pool_x(
-    cluster: LongTensor,
-    x: Tensor,
-    batch: LongTensor,
-    size: Optional[int] = None,
-) -> Tensor:
-    r"""Std-pool node features according to the clustering defined in `cluster`.
-
-    Args:
-        cluster: Cluster vector :math:`\mathbf{c} \in \{ 0,
-            \ldots, N - 1 \}^N`, which assigns each node to a specific cluster.
-        x: Node feature matrix
-            :math:`\mathbf{X} \in \mathbb{R}^{(N_1 + \ldots + N_B) \times F}`.
-        batch: Batch vector :math:`\mathbf{b} \in {\{ 0, \ldots,
-            B-1\}}^N`, which assigns each node to a specific example.
-        size: The maximum number of clusters in a single
-            example. This property is useful to obtain a batch-wise dense
-            representation, *e.g.* for applying FC layers, but should only be
-            used if the size of the maximum number of clusters per example is
-            known in advance.
-    """
-    if size is not None:
-        batch_size = int(batch.max().item()) + 1
-        return _std_pool_x(cluster, x, batch_size * size), None
-
-    cluster, perm = consecutive_cluster(cluster)
-    x = _std_pool_x(cluster, x)
-    batch = pool_batch(perm, batch)
-
-    return x, batch

-
-
-
-

-[docs]
-def sum_pool(
-    cluster: LongTensor, data: Data, transform: Optional[Callable] = None
-) -> Data:
-    r"""Pool and coarsen graph according to the clustering defined in `cluster`.
-
-    All nodes within the same cluster will be represented as one node.
-    Final node features are defined by the *sum* of features of all nodes
-    within the same cluster, node positions are averaged and edge indices are
-    defined to be the union of the edge indices of all nodes within the same
-    cluster.
-
-    Args:
-        cluster: Cluster vector :math:`\mathbf{c} \in \{ 0,
-            \ldots, N - 1 \}^N`, which assigns each node to a specific cluster.
-        data: Graph data object.
-        transform: A function/transform that takes in the
-            coarsened and pooled :obj:`torch_geometric.data.Data` object and
-            returns a transformed version.
-    """
-    cluster, perm = consecutive_cluster(cluster)
-
-    x = None if data.x is None else _sum_pool_x(cluster, data.x)
-    index, attr = pool_edge(cluster, data.edge_index, data.edge_attr)
-    batch = None if data.batch is None else pool_batch(perm, data.batch)
-    pos = None if data.pos is None else pool_pos(cluster, data.pos)
-
-    data = Batch(batch=batch, x=x, edge_index=index, edge_attr=attr, pos=pos)
-
-    if transform is not None:
-        data = transform(data)
-
-    return data

-
-
-
-

-[docs]
-def std_pool(
-    cluster: LongTensor, data: Data, transform: Optional[Callable] = None
-) -> Data:
-    r"""Pool and coarsen graph according to the clustering defined in `cluster`.
-
-    All nodes within the same cluster will be represented as one node.
-    Final node features are defined by the *std* of features of all nodes
-    within the same cluster, node positions are averaged and edge indices are
-    defined to be the union of the edge indices of all nodes within the same
-    cluster.
-
-    Args:
-        cluster: Cluster vector :math:`\mathbf{c} \in \{ 0,
-            \ldots, N - 1 \}^N`, which assigns each node to a specific cluster.
-        data: Graph data object.
-        transform: A function/transform that takes in the
-            coarsened and pooled :obj:`torch_geometric.data.Data` object and
-            returns a transformed version.
-    """
-    cluster, perm = consecutive_cluster(cluster)
-
-    x = None if data.x is None else _std_pool_x(cluster, data.x)
-    index, attr = pool_edge(cluster, data.edge_index, data.edge_attr)
-    batch = None if data.batch is None else pool_batch(perm, data.batch)
-    pos = None if data.pos is None else pool_pos(cluster, data.pos)
-
-    data = Batch(batch=batch, x=x, edge_index=index, edge_attr=attr, pos=pos)
-
-    if transform is not None:
-        data = transform(data)
-
-    return data

-
-
- -
-
-
-
-
- - - - - \ No newline at end of file diff --git a/_modules/graphnet/models/gnn/convnet.html b/_modules/graphnet/models/gnn/convnet.html deleted file mode 100644 index 9c1b3f2f7..000000000 --- a/_modules/graphnet/models/gnn/convnet.html +++ /dev/null @@ -1,484 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - graphnet.models.gnn.convnet — graphnet documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Skip to content -
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Source code for graphnet.models.gnn.convnet

-"""Implementation of the ConvNet GNN model architecture.
-
-Author: Martin Ha Minh
-"""
-
-import torch
-from torch import Tensor
-from torch.nn import BatchNorm1d, Linear, Dropout
-import torch.nn.functional as F
-from torch_geometric.nn import TAGConv, global_add_pool, global_max_pool
-from torch_geometric.data import Data
-
-from graphnet.models.gnn.gnn import GNN
-
-
-

-[docs]
-class ConvNet(GNN):
-    """ConvNet (convolutional network) model."""
-
-    def __init__(
-        self,
-        nb_inputs: int,
-        nb_outputs: int,
-        nb_intermediate: int = 128,
-        dropout_ratio: float = 0.3,
-    ):
-        """Construct `ConvNet`.
-
-        Args:
-            nb_inputs: Number of input features, i.e. dimension of input
-                layer.
-            nb_outputs: Number of prediction labels, i.e. dimension of
-                output layer.
-            nb_intermediate: Number of nodes in intermediate layer(s).
-            dropout_ratio: Fraction of nodes to drop.
-        """
-        # Base class constructor
-        super().__init__(nb_inputs, nb_outputs)
-
-        # Member variables
-        self.nb_intermediate = nb_intermediate
-        self.nb_intermediate2 = 6 * self.nb_intermediate
-
-        # Architecture configuration
-        self.conv1 = TAGConv(self.nb_inputs, self.nb_intermediate, 2)
-        self.conv2 = TAGConv(self.nb_intermediate, self.nb_intermediate, 2)
-        self.conv3 = TAGConv(self.nb_intermediate, self.nb_intermediate, 2)
-
-        self.batchnorm1 = BatchNorm1d(self.nb_intermediate2)
-
-        self.linear1 = Linear(self.nb_intermediate2, self.nb_intermediate2)
-        self.linear2 = Linear(self.nb_intermediate2, self.nb_intermediate2)
-        self.linear3 = Linear(self.nb_intermediate2, self.nb_intermediate2)
-        self.linear4 = Linear(self.nb_intermediate2, self.nb_intermediate2)
-        self.linear5 = Linear(self.nb_intermediate2, self.nb_intermediate2)
-
-        self.drop1 = Dropout(dropout_ratio)
-        self.drop2 = Dropout(dropout_ratio)
-        self.drop3 = Dropout(dropout_ratio)
-        self.drop4 = Dropout(dropout_ratio)
-        self.drop5 = Dropout(dropout_ratio)
-
-        self.out = Linear(self.nb_intermediate2, self.nb_outputs)
-
-

-[docs]
-    def forward(self, data: Data) -> Tensor:
-        """Apply learnable forward pass."""
-        # Convenience variables
-        x, edge_index, batch = data.x, data.edge_index, data.batch
-
-        # Graph convolutional operations
-        x = F.leaky_relu(self.conv1(x, edge_index))
-        x1 = torch.cat(
-            [
-                global_add_pool(x, batch),
-                global_max_pool(x, batch),
-            ],
-            dim=1,
-        )
-
-        x = F.leaky_relu(self.conv2(x, edge_index))
-        x2 = torch.cat(
-            [
-                global_add_pool(x, batch),
-                global_max_pool(x, batch),
-            ],
-            dim=1,
-        )
-
-        x = F.leaky_relu(self.conv3(x, edge_index))
-        x3 = torch.cat(
-            [
-                global_add_pool(x, batch),
-                global_max_pool(x, batch),
-            ],
-            dim=1,
-        )
-
-        # Skip-cat
-        x = torch.cat([x1, x2, x3], dim=1)
-
-        # Batch-normalising intermediate features
-        x = self.batchnorm1(x)
-
-        # Post-processing
-        x = F.leaky_relu(self.linear1(x))
-        x = self.drop1(x)
-        x = F.leaky_relu(self.linear2(x))
-        x = self.drop2(x)
-        x = F.leaky_relu(self.linear3(x))
-        x = self.drop3(x)
-        x = F.leaky_relu(self.linear4(x))
-        x = self.drop4(x)
-        x = F.leaky_relu(self.linear5(x))
-        x = self.drop5(x)
-
-        # Read-out
-        x = self.out(x)
-
-        return x

-

-
-
- -
-
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- - - - - \ No newline at end of file diff --git a/_modules/graphnet/models/gnn/dynedge.html b/_modules/graphnet/models/gnn/dynedge.html deleted file mode 100644 index 90dbb8077..000000000 --- a/_modules/graphnet/models/gnn/dynedge.html +++ /dev/null @@ -1,691 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - graphnet.models.gnn.dynedge — graphnet documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Skip to content -
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Source code for graphnet.models.gnn.dynedge

-"""Implementation of the DynEdge GNN model architecture."""
-from typing import List, Optional, Sequence, Tuple, Union
-
-import torch
-from torch import Tensor, LongTensor
-from torch_geometric.data import Data
-from torch_scatter import scatter_max, scatter_mean, scatter_min, scatter_sum
-
-from graphnet.models.components.layers import DynEdgeConv
-from graphnet.models.gnn.gnn import GNN
-from graphnet.models.utils import calculate_xyzt_homophily
-
-GLOBAL_POOLINGS = {
-    "min": scatter_min,
-    "max": scatter_max,
-    "sum": scatter_sum,
-    "mean": scatter_mean,
-}
-
-
-

-[docs]
-class DynEdge(GNN):
-    """DynEdge (dynamical edge convolutional) model."""
-
-    def __init__(
-        self,
-        nb_inputs: int,
-        *,
-        nb_neighbours: int = 8,
-        features_subset: Optional[Union[List[int], slice]] = None,
-        dynedge_layer_sizes: Optional[List[Tuple[int, ...]]] = None,
-        post_processing_layer_sizes: Optional[List[int]] = None,
-        readout_layer_sizes: Optional[List[int]] = None,
-        global_pooling_schemes: Optional[Union[str, List[str]]] = None,
-        add_global_variables_after_pooling: bool = False,
-    ):
-        """Construct `DynEdge`.
-
-        Args:
-            nb_inputs: Number of input features on each node.
-            nb_neighbours: Number of neighbours to used in the k-nearest
-                neighbour clustering which is performed after each (dynamical)
-                edge convolution.
-            features_subset: 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].
-            dynedge_layer_sizes: The layer sizes, or latent feature dimenions,
-                used in the `DynEdgeConv` layer. Each entry in
-                `dynedge_layer_sizes` corresponds to a single `DynEdgeConv`
-                layer; the integers in the corresponding tuple corresponds to
-                the layer sizes in the multi-layer perceptron (MLP) that is
-                applied within each `DynEdgeConv` layer. That is, a list of
-                size-two tuples means that all `DynEdgeConv` layers contain a
-                two-layer MLP.
-                Defaults to [(128, 256), (336, 256), (336, 256), (336, 256)].
-            post_processing_layer_sizes: Hidden layer sizes in the MLP
-                following the skip-concatenation of the outputs of each
-                `DynEdgeConv` layer. Defaults to [336, 256].
-            readout_layer_sizes: Hidden layer sizes in the MLP following the
-                post-processing _and_ optional global pooling. As this is the
-                last layer(s) in the model, the last layer in the read-out
-                yields the output of the `DynEdge` model. Defaults to [128,].
-            global_pooling_schemes: The list global pooling schemes to use.
-                Options are: "min", "max", "mean", and "sum".
-            add_global_variables_after_pooling: Whether to add global variables
-                after global pooling. The alternative is to  added (distribute)
-                them to the individual nodes before any convolutional
-                operations.
-        """
-        # Latent feature subset for computing nearest neighbours in DynEdge.
-        if features_subset is None:
-            features_subset = slice(0, 3)
-
-        # DynEdge layer sizes
-        if dynedge_layer_sizes is None:
-            dynedge_layer_sizes = [
-                (
-                    128,
-                    256,
-                ),
-                (
-                    336,
-                    256,
-                ),
-                (
-                    336,
-                    256,
-                ),
-                (
-                    336,
-                    256,
-                ),
-            ]
-
-        assert isinstance(dynedge_layer_sizes, list)
-        assert len(dynedge_layer_sizes)
-        assert all(isinstance(sizes, tuple) for sizes in dynedge_layer_sizes)
-        assert all(len(sizes) > 0 for sizes in dynedge_layer_sizes)
-        assert all(
-            all(size > 0 for size in sizes) for sizes in dynedge_layer_sizes
-        )
-
-        self._dynedge_layer_sizes = dynedge_layer_sizes
-
-        # Post-processing layer sizes
-        if post_processing_layer_sizes is None:
-            post_processing_layer_sizes = [
-                336,
-                256,
-            ]
-
-        assert isinstance(post_processing_layer_sizes, list)
-        assert len(post_processing_layer_sizes)
-        assert all(size > 0 for size in post_processing_layer_sizes)
-
-        self._post_processing_layer_sizes = post_processing_layer_sizes
-
-        # Read-out layer sizes
-        if readout_layer_sizes is None:
-            readout_layer_sizes = [
-                128,
-            ]
-
-        assert isinstance(readout_layer_sizes, list)
-        assert len(readout_layer_sizes)
-        assert all(size > 0 for size in readout_layer_sizes)
-
-        self._readout_layer_sizes = readout_layer_sizes
-
-        # Global pooling scheme(s)
-        if isinstance(global_pooling_schemes, str):
-            global_pooling_schemes = [global_pooling_schemes]
-
-        if isinstance(global_pooling_schemes, list):
-            for pooling_scheme in global_pooling_schemes:
-                assert (
-                    pooling_scheme in GLOBAL_POOLINGS
-                ), f"Global pooling scheme {pooling_scheme} not supported."
-        else:
-            assert global_pooling_schemes is None
-
-        self._global_pooling_schemes = global_pooling_schemes
-
-        if add_global_variables_after_pooling:
-            assert self._global_pooling_schemes, (
-                "No global pooling schemes were request, so cannot add global"
-                " variables after pooling."
-            )
-        self._add_global_variables_after_pooling = (
-            add_global_variables_after_pooling
-        )
-
-        # Base class constructor
-        super().__init__(nb_inputs, self._readout_layer_sizes[-1])
-
-        # Remaining member variables()
-        self._activation = torch.nn.LeakyReLU()
-        self._nb_inputs = nb_inputs
-        self._nb_global_variables = 5 + nb_inputs
-        self._nb_neighbours = nb_neighbours
-        self._features_subset = features_subset
-
-        self._construct_layers()
-
-    def _construct_layers(self) -> None:
-        """Construct layers (torch.nn.Modules)."""
-        # Convolutional operations
-        nb_input_features = self._nb_inputs
-        if not self._add_global_variables_after_pooling:
-            nb_input_features += self._nb_global_variables
-
-        self._conv_layers = torch.nn.ModuleList()
-        nb_latent_features = nb_input_features
-        for sizes in self._dynedge_layer_sizes:
-            layers = []
-            layer_sizes = [nb_latent_features] + list(sizes)
-            for ix, (nb_in, nb_out) in enumerate(
-                zip(layer_sizes[:-1], layer_sizes[1:])
-            ):
-                if ix == 0:
-                    nb_in *= 2
-                layers.append(torch.nn.Linear(nb_in, nb_out))
-                layers.append(self._activation)
-
-            conv_layer = DynEdgeConv(
-                torch.nn.Sequential(*layers),
-                aggr="add",
-                nb_neighbors=self._nb_neighbours,
-                features_subset=self._features_subset,
-            )
-            self._conv_layers.append(conv_layer)
-
-            nb_latent_features = nb_out
-
-        # Post-processing operations
-        nb_latent_features = (
-            sum(sizes[-1] for sizes in self._dynedge_layer_sizes)
-            + nb_input_features
-        )
-
-        post_processing_layers = []
-        layer_sizes = [nb_latent_features] + list(
-            self._post_processing_layer_sizes
-        )
-        for nb_in, nb_out in zip(layer_sizes[:-1], layer_sizes[1:]):
-            post_processing_layers.append(torch.nn.Linear(nb_in, nb_out))
-            post_processing_layers.append(self._activation)
-
-        self._post_processing = torch.nn.Sequential(*post_processing_layers)
-
-        # Read-out operations
-        nb_poolings = (
-            len(self._global_pooling_schemes)
-            if self._global_pooling_schemes
-            else 1
-        )
-        nb_latent_features = nb_out * nb_poolings
-        if self._add_global_variables_after_pooling:
-            nb_latent_features += self._nb_global_variables
-
-        readout_layers = []
-        layer_sizes = [nb_latent_features] + list(self._readout_layer_sizes)
-        for nb_in, nb_out in zip(layer_sizes[:-1], layer_sizes[1:]):
-            readout_layers.append(torch.nn.Linear(nb_in, nb_out))
-            readout_layers.append(self._activation)
-
-        self._readout = torch.nn.Sequential(*readout_layers)
-
-    def _global_pooling(self, x: Tensor, batch: LongTensor) -> Tensor:
-        """Perform global pooling."""
-        assert self._global_pooling_schemes
-        pooled = []
-        for pooling_scheme in self._global_pooling_schemes:
-            pooling_fn = GLOBAL_POOLINGS[pooling_scheme]
-            pooled_x = pooling_fn(x, index=batch, dim=0)
-            if isinstance(pooled_x, tuple) and len(pooled_x) == 2:
-                # `scatter_{min,max}`, which return also an argument, vs.
-                # `scatter_{mean,sum}`
-                pooled_x, _ = pooled_x
-            pooled.append(pooled_x)
-
-        return torch.cat(pooled, dim=1)
-
-    def _calculate_global_variables(
-        self,
-        x: Tensor,
-        edge_index: LongTensor,
-        batch: LongTensor,
-        *additional_attributes: Tensor,
-    ) -> Tensor:
-        """Calculate global variables."""
-        # Calculate homophily (scalar variables)
-        h_x, h_y, h_z, h_t = calculate_xyzt_homophily(x, edge_index, batch)
-
-        # Calculate mean features
-        global_means = scatter_mean(x, batch, dim=0)
-
-        # Add global variables
-        global_variables = torch.cat(
-            [
-                global_means,
-                h_x,
-                h_y,
-                h_z,
-                h_t,
-            ]
-            + [attr.unsqueeze(dim=1) for attr in additional_attributes],
-            dim=1,
-        )
-
-        return global_variables
-
-

-[docs]
-    def forward(self, data: Data) -> Tensor:
-        """Apply learnable forward pass."""
-        # Convenience variables
-        x, edge_index, batch = data.x, data.edge_index, data.batch
-
-        global_variables = self._calculate_global_variables(
-            x,
-            edge_index,
-            batch,
-            torch.log10(data.n_pulses),
-        )
-
-        # Distribute global variables out to each node
-        if not self._add_global_variables_after_pooling:
-            distribute = (
-                batch.unsqueeze(dim=1) == torch.unique(batch).unsqueeze(dim=0)
-            ).type(torch.float)
-
-            global_variables_distributed = torch.sum(
-                distribute.unsqueeze(dim=2)
-                * global_variables.unsqueeze(dim=0),
-                dim=1,
-            )
-
-            x = torch.cat((x, global_variables_distributed), dim=1)
-
-        # DynEdge-convolutions
-        skip_connections = [x]
-        for conv_layer in self._conv_layers:
-            x, edge_index = conv_layer(x, edge_index, batch)
-            skip_connections.append(x)
-
-        # Skip-cat
-        x = torch.cat(skip_connections, dim=1)
-
-        # Post-processing
-        x = self._post_processing(x)
-
-        # (Optional) Global pooling
-        if self._global_pooling_schemes:
-            x = self._global_pooling(x, batch=batch)
-            if self._add_global_variables_after_pooling:
-                x = torch.cat(
-                    [
-                        x,
-                        global_variables,
-                    ],
-                    dim=1,
-                )
-
-        # Read-out
-        x = self._readout(x)
-
-        return x

-

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Source code for graphnet.models.gnn.dynedge_jinst

-"""Implementation of the exact DynEdge architecture used in [2209.03042].
-
-Author: Rasmus Oersoe
-"""
-from typing import Optional
-
-import torch
-from torch import Tensor
-from torch_geometric.data import Data
-from torch_scatter import scatter_max, scatter_mean, scatter_min, scatter_sum
-
-from graphnet.models.components.layers import DynEdgeConv
-from graphnet.models.gnn.gnn import GNN
-from graphnet.models.utils import calculate_xyzt_homophily
-
-
-

-[docs]
-class DynEdgeJINST(GNN):
-    """DynEdge (dynamical edge convolutional) model used in [2209.03042]."""
-
-    def __init__(
-        self,
-        nb_inputs: int,
-        layer_size_scale: int = 4,
-    ):
-        """Construct `DynEdgeJINST`.
-
-        Args:
-            nb_inputs: Number of input features.
-            nb_outputs: Number of output features.
-            layer_size_scale: Integer that scales the size of hidden layers.
-        """
-        # Architecture configuration
-        c = layer_size_scale
-        l1, l2, l3, l4, l5, l6 = (
-            nb_inputs,
-            c * 16 * 2,
-            c * 32 * 2,
-            c * 42 * 2,
-            c * 32 * 2,
-            c * 16 * 2,
-        )
-
-        # Base class constructor
-        super().__init__(nb_inputs, l6)
-
-        # Graph convolutional operations
-        features_subset = slice(0, 3)
-        nb_neighbors = 8
-
-        self.conv_add1 = DynEdgeConv(
-            torch.nn.Sequential(
-                torch.nn.Linear(l1 * 2, l2),
-                torch.nn.LeakyReLU(),
-                torch.nn.Linear(l2, l3),
-                torch.nn.LeakyReLU(),
-            ),
-            aggr="add",
-            nb_neighbors=nb_neighbors,
-            features_subset=features_subset,
-        )
-
-        self.conv_add2 = DynEdgeConv(
-            torch.nn.Sequential(
-                torch.nn.Linear(l3 * 2, l4),
-                torch.nn.LeakyReLU(),
-                torch.nn.Linear(l4, l3),
-                torch.nn.LeakyReLU(),
-            ),
-            aggr="add",
-            nb_neighbors=nb_neighbors,
-            features_subset=features_subset,
-        )
-
-        self.conv_add3 = DynEdgeConv(
-            torch.nn.Sequential(
-                torch.nn.Linear(l3 * 2, l4),
-                torch.nn.LeakyReLU(),
-                torch.nn.Linear(l4, l3),
-                torch.nn.LeakyReLU(),
-            ),
-            aggr="add",
-            nb_neighbors=nb_neighbors,
-            features_subset=features_subset,
-        )
-
-        self.conv_add4 = DynEdgeConv(
-            torch.nn.Sequential(
-                torch.nn.Linear(l3 * 2, l4),
-                torch.nn.LeakyReLU(),
-                torch.nn.Linear(l4, l3),
-                torch.nn.LeakyReLU(),
-            ),
-            aggr="add",
-            nb_neighbors=nb_neighbors,
-            features_subset=features_subset,
-        )
-
-        # Post-processing operations
-        self.nn1 = torch.nn.Linear(l3 * 4 + l1, l4)
-        self.nn2 = torch.nn.Linear(l4, l5)
-        self.nn3 = torch.nn.Linear(4 * l5 + 5, l6)
-        self.lrelu = torch.nn.LeakyReLU()
-
-

-[docs]
-    def forward(self, data: Data) -> Tensor:
-        """Apply learnable forward pass."""
-        # Convenience variables
-        x, edge_index, batch = data.x, data.edge_index, data.batch
-
-        # Calculate homophily (scalar variables)
-        h_x, h_y, h_z, h_t = calculate_xyzt_homophily(x, edge_index, batch)
-
-        a, edge_index = self.conv_add1(x, edge_index, batch)
-        b, edge_index = self.conv_add2(a, edge_index, batch)
-        c, edge_index = self.conv_add3(b, edge_index, batch)
-        d, edge_index = self.conv_add4(c, edge_index, batch)
-
-        # Skip-cat
-        x = torch.cat((x, a, b, c, d), dim=1)
-
-        # Post-processing
-        x = self.nn1(x)
-        x = self.lrelu(x)
-        x = self.nn2(x)
-
-        # Aggregation across nodes
-        a, _ = scatter_max(x, batch, dim=0)
-        b, _ = scatter_min(x, batch, dim=0)
-        c = scatter_sum(x, batch, dim=0)
-        d = scatter_mean(x, batch, dim=0)
-
-        # Concatenate aggregations and scalar features
-        x = torch.cat(
-            (
-                a,
-                b,
-                c,
-                d,
-                h_t.reshape(-1, 1),
-                h_x.reshape(-1, 1),
-                h_y.reshape(-1, 1),
-                h_z.reshape(-1, 1),
-                data.n_pulses.reshape(-1, 1),
-            ),
-            dim=1,
-        )
-
-        # Read-out
-        x = self.lrelu(x)
-        x = self.nn3(x)
-
-        x = self.lrelu(x)
-
-        return x

-

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Source code for graphnet.models.gnn.dynedge_kaggle_tito

-"""Implementation of DynEdge architecture used in.
-
-                    IceCube - Neutrinos in Deep Ice
-Reconstruct the direction of neutrinos from the Universe to the South Pole
-
-Kaggle competition.
-
-Solution by TITO.
-"""
-
-from typing import List, Tuple, Optional, Union
-
-import torch
-from torch import Tensor, LongTensor
-
-from torch_geometric.data import Data
-from torch_scatter import scatter_max, scatter_mean, scatter_min, scatter_sum
-
-from graphnet.models.components.layers import DynTrans
-from graphnet.models.gnn.gnn import GNN
-from graphnet.models.utils import calculate_xyzt_homophily
-
-GLOBAL_POOLINGS = {
-    "min": scatter_min,
-    "max": scatter_max,
-    "sum": scatter_sum,
-    "mean": scatter_mean,
-}
-
-
-

-[docs]
-class DynEdgeTITO(GNN):
-    """DynEdgeTITO (dynamical edge convolutional with Transformer) model."""
-
-    def __init__(
-        self,
-        nb_inputs: int,
-        features_subset: List[int] = None,
-        dyntrans_layer_sizes: Optional[List[Tuple[int, ...]]] = None,
-        global_pooling_schemes: List[str] = ["max"],
-        use_global_features: bool = True,
-        use_post_processing_layers: bool = True,
-    ):
-        """Construct `DynEdgeTITO`.
-
-        Args:
-            nb_inputs: Number of input features on each node.
-            features_subset: 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].
-            dyntrans_layer_sizes: The layer sizes, or latent feature dimenions,
-                used in the `DynTrans` layer.
-                Defaults to [(256, 256), (256, 256), (256, 256), (256, 256)].
-            global_pooling_schemes: The list global pooling schemes to use.
-                Options are: "min", "max", "mean", and "sum".
-            use_global_features: Whether to use global features after pooling.
-            use_post_processing_layers: Whether to use post-processing layers
-                after the `DynTrans` layers.
-        """
-        # DynTrans layer sizes
-        if dyntrans_layer_sizes is None:
-            dyntrans_layer_sizes = [
-                (
-                    256,
-                    256,
-                ),
-                (
-                    256,
-                    256,
-                ),
-                (
-                    256,
-                    256,
-                ),
-                (
-                    256,
-                    256,
-                ),
-            ]
-
-        assert isinstance(dyntrans_layer_sizes, list)
-        assert len(dyntrans_layer_sizes)
-        assert all(isinstance(sizes, tuple) for sizes in dyntrans_layer_sizes)
-        assert all(len(sizes) > 0 for sizes in dyntrans_layer_sizes)
-        assert all(
-            all(size > 0 for size in sizes) for sizes in dyntrans_layer_sizes
-        )
-
-        self._dyntrans_layer_sizes = dyntrans_layer_sizes
-
-        # Post-processing layer sizes
-        post_processing_layer_sizes = [
-            336,
-            256,
-        ]
-
-        self._post_processing_layer_sizes = post_processing_layer_sizes
-
-        # Read-out layer sizes
-        readout_layer_sizes = [
-            256,
-            128,
-        ]
-
-        self._readout_layer_sizes = readout_layer_sizes
-
-        # Global pooling scheme(s)
-        if isinstance(global_pooling_schemes, str):
-            global_pooling_schemes = [global_pooling_schemes]
-
-        if isinstance(global_pooling_schemes, list):
-            for pooling_scheme in global_pooling_schemes:
-                assert (
-                    pooling_scheme in GLOBAL_POOLINGS
-                ), f"Global pooling scheme {pooling_scheme} not supported."
-        else:
-            assert global_pooling_schemes is None
-
-        self._global_pooling_schemes = global_pooling_schemes
-
-        assert self._global_pooling_schemes, (
-            "No global pooling schemes were request, so cannot add global"
-            " variables after pooling."
-        )
-
-        # Base class constructor
-        super().__init__(nb_inputs, self._readout_layer_sizes[-1])
-
-        # Remaining member variables()
-        self._activation = torch.nn.LeakyReLU()
-        self._nb_inputs = nb_inputs
-        self._nb_global_variables = 5 + nb_inputs
-        self._nb_neighbours = 8
-        self._features_subset = features_subset or [0, 1, 2, 3]
-        self._use_global_features = use_global_features
-        self._use_post_processing_layers = use_post_processing_layers
-        self._construct_layers()
-
-    def _construct_layers(self) -> None:
-        """Construct layers (torch.nn.Modules)."""
-        # Convolutional operations
-        nb_input_features = self._nb_inputs
-
-        self._conv_layers = torch.nn.ModuleList()
-        nb_latent_features = nb_input_features
-        for sizes in self._dyntrans_layer_sizes:
-            conv_layer = DynTrans(
-                [nb_latent_features] + list(sizes),
-                aggr="max",
-                features_subset=self._features_subset,
-                n_head=8,
-            )
-            self._conv_layers.append(conv_layer)
-            nb_latent_features = sizes[-1]
-
-        if self._use_post_processing_layers:
-            post_processing_layers = []
-            layer_sizes = [nb_latent_features] + list(
-                self._post_processing_layer_sizes
-            )
-            for nb_in, nb_out in zip(layer_sizes[:-1], layer_sizes[1:]):
-                post_processing_layers.append(torch.nn.Linear(nb_in, nb_out))
-                post_processing_layers.append(self._activation)
-            last_posting_layer_output_dim = nb_out
-
-            self._post_processing = torch.nn.Sequential(
-                *post_processing_layers
-            )
-        else:
-            last_posting_layer_output_dim = nb_latent_features
-
-        # Read-out operations
-        nb_poolings = (
-            len(self._global_pooling_schemes)
-            if self._global_pooling_schemes
-            else 1
-        )
-        nb_latent_features = last_posting_layer_output_dim * nb_poolings
-        if self._use_global_features:
-            nb_latent_features += self._nb_global_variables
-
-        readout_layers = []
-        layer_sizes = [nb_latent_features] + list(self._readout_layer_sizes)
-        for nb_in, nb_out in zip(layer_sizes[:-1], layer_sizes[1:]):
-            readout_layers.append(torch.nn.Linear(nb_in, nb_out))
-            readout_layers.append(self._activation)
-
-        self._readout = torch.nn.Sequential(*readout_layers)
-
-    def _global_pooling(self, x: Tensor, batch: LongTensor) -> Tensor:
-        """Perform global pooling."""
-        assert self._global_pooling_schemes
-        pooled = []
-        for pooling_scheme in self._global_pooling_schemes:
-            pooling_fn = GLOBAL_POOLINGS[pooling_scheme]
-            pooled_x = pooling_fn(x, index=batch, dim=0)
-            if isinstance(pooled_x, tuple) and len(pooled_x) == 2:
-                # `scatter_{min,max}`, which return also an argument, vs.
-                # `scatter_{mean,sum}`
-                pooled_x, _ = pooled_x
-            pooled.append(pooled_x)
-
-        return torch.cat(pooled, dim=1)
-
-    def _calculate_global_variables(
-        self,
-        x: Tensor,
-        edge_index: LongTensor,
-        batch: LongTensor,
-        *additional_attributes: Tensor,
-    ) -> Tensor:
-        """Calculate global variables."""
-        # Calculate homophily (scalar variables)
-        h_x, h_y, h_z, h_t = calculate_xyzt_homophily(x, edge_index, batch)
-
-        # Calculate mean features
-        global_means = scatter_mean(x, batch, dim=0)
-
-        # Add global variables
-        global_variables = torch.cat(
-            [
-                global_means,
-                h_x,
-                h_y,
-                h_z,
-                h_t,
-            ]
-            + [attr.unsqueeze(dim=1) for attr in additional_attributes],
-            dim=1,
-        )
-
-        return global_variables
-
-

-[docs]
-    def forward(self, data: Data) -> Tensor:
-        """Apply learnable forward pass."""
-        # Convenience variables
-        x, edge_index, batch = data.x, data.edge_index, data.batch
-
-        if self._use_global_features:
-            global_variables = self._calculate_global_variables(
-                x,
-                edge_index,
-                batch,
-                torch.log10(data.n_pulses),
-            )
-
-        # DynEdge-convolutions
-        for conv_layer in self._conv_layers:
-            x = conv_layer(x, edge_index, batch)
-
-        # Post-processing
-        if self._use_post_processing_layers:
-            x = self._post_processing(x)
-
-        x = self._global_pooling(x, batch=batch)
-        if self._use_global_features:
-            x = torch.cat(
-                [
-                    x,
-                    global_variables,
-                ],
-                dim=1,
-            )
-
-        # Read-out
-        x = self._readout(x)
-
-        return x

-

-
-
- -
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Source code for graphnet.models.gnn.gnn

-"""Base GNN-specific `Model` class(es)."""
-
-from abc import abstractmethod
-
-from torch import Tensor
-from torch_geometric.data import Data
-
-from graphnet.models import Model
-
-
-

-[docs]
-class GNN(Model):
-    """Base class for all core GNN models in graphnet."""
-
-    def __init__(self, nb_inputs: int, nb_outputs: int) -> None:
-        """Construct `GNN`."""
-        # Base class constructor
-        super().__init__()
-
-        # Member variables
-        self._nb_inputs = nb_inputs
-        self._nb_outputs = nb_outputs
-
-    @property
-    def nb_inputs(self) -> int:
-        """Return number of input features."""
-        return self._nb_inputs
-
-    @property
-    def nb_outputs(self) -> int:
-        """Return number of output features."""
-        return self._nb_outputs
-
-

-[docs]
-    @abstractmethod
-    def forward(self, data: Data) -> Tensor:
-        """Apply learnable forward pass in model."""

-

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Source code for graphnet.models.graphs.edges.edges

-"""Class(es) for building/connecting graphs."""
-
-from typing import List
-from abc import abstractmethod, ABC
-
-import torch
-from torch_geometric.nn import knn_graph, radius_graph
-from torch_geometric.data import Data
-
-from graphnet.models.utils import calculate_distance_matrix
-from graphnet.models import Model
-
-
-

-[docs]
-class EdgeDefinition(Model):  # pylint: disable=too-few-public-methods
-    """Base class for graph building."""
-
-

-[docs]
-    def forward(self, graph: Data) -> Data:
-        """Construct edges based on problem specific implementation of.
-
-        ´_construct_edges´
-
-        Args:
-            graph: a graph without edges
-
-        Returns:
-            graph: a graph with edges
-        """
-        if graph.edge_index is not None:
-            self.warning_once(
-                "GraphBuilder received graph with pre-existing "
-                "structure. Will overwrite."
-            )
-        return self._construct_edges(graph)

-
-
-    @abstractmethod
-    def _construct_edges(self, graph: Data) -> Data:
-        """Construct edges and assign them to graph. I.e. ´graph.edge_index = edge_index´.
-
-        Args:
-            graph: graph without edges
-
-        Returns:
-            graph: graph with edges assigned.
-        """

-
-
-
-

-[docs]
-class KNNEdges(EdgeDefinition):  # pylint: disable=too-few-public-methods
-    """Builds edges from the k-nearest neighbours."""
-
-    def __init__(
-        self,
-        nb_nearest_neighbours: int,
-        columns: List[int] = [0, 1, 2],
-    ):
-        """K-NN Edge definition.
-
-        Will connect nodes together with their ´nb_nearest_neighbours´
-        nearest neighbours in the feature space given by ´columns´.
-
-        Args:
-            nb_nearest_neighbours: number of neighbours.
-            columns: Node features to use for distance calculation.
-            Defaults to [0,1,2].
-        """
-        # Base class constructor
-        super().__init__(name=__name__, class_name=self.__class__.__name__)
-
-        # Member variable(s)
-        self._nb_nearest_neighbours = nb_nearest_neighbours
-        self._columns = columns
-
-    def _construct_edges(self, graph: Data) -> Data:
-        """Define K-NN edges."""
-        graph.edge_index = knn_graph(
-            graph.x[:, self._columns],
-            self._nb_nearest_neighbours,
-            graph.batch,
-        ).to(self.device)
-
-        return graph

-
-
-
-

-[docs]
-class RadialEdges(EdgeDefinition):
-    """Builds graph from a sphere of chosen radius centred at each node."""
-
-    def __init__(
-        self,
-        radius: float,
-        columns: List[int] = [0, 1, 2],
-    ):
-        """Radial edges.
-
-        Connects each node to other nodes that are within a sphere of
-        radius ´r´ centered at the node. The feature space of ´r´ is defined
-        by ´columns´
-
-        Args:
-            radius: radius of sphere
-            columns: columns of the node feature matrix used.
-            Defaults to [0,1,2].
-        """
-        # Base class constructor
-        super().__init__(name=__name__, class_name=self.__class__.__name__)
-
-        # Member variable(s)
-        self._radius = radius
-        self._columns = columns
-
-    def _construct_edges(self, graph: Data) -> Data:
-        """Define radial edges."""
-        graph.edge_index = radius_graph(
-            graph.x[:, self._columns],
-            self._radius,
-            graph.batch,
-        ).to(self.device)
-
-        return graph

-
-
-
-

-[docs]
-class EuclideanEdges(EdgeDefinition):  # pylint: disable=too-few-public-methods
-    """Builds edges according to Euclidean distance between nodes.
-
-    See https://arxiv.org/pdf/1809.06166.pdf.
-    """
-
-    def __init__(
-        self,
-        sigma: float,
-        threshold: float = 0.0,
-        columns: List[int] = None,
-    ):
-        """Construct `EuclideanEdges`."""
-        # Base class constructor
-        super().__init__(name=__name__, class_name=self.__class__.__name__)
-
-        # Check(s)
-        if columns is None:
-            columns = [0, 1, 2]
-
-        # Member variable(s)
-        self._sigma = sigma
-        self._threshold = threshold
-        self._columns = columns
-
-    def _construct_edges(self, graph: Data) -> Data:
-        """Forward pass."""
-        # Constructs the adjacency matrix from the raw, DOM-level data and
-        # returns this matrix
-        if graph.edge_index is not None:
-            self.info(
-                "WARNING: GraphBuilder received graph with pre-existing "
-                "structure. Will overwrite."
-            )
-
-        xyz_coords = graph.x[:, self._columns]
-
-        # Construct block-diagonal matrix indicating whether pulses belong to
-        # the same event in the batch
-        batch_mask = graph.batch.unsqueeze(dim=0) == graph.batch.unsqueeze(
-            dim=1
-        )
-
-        distance_matrix = calculate_distance_matrix(xyz_coords)
-        affinity_matrix = torch.exp(
-            -0.5 * distance_matrix**2 / self._sigma**2
-        )
-
-        # Use softmax to normalise all adjacencies to one for each node
-        exp_row_sums = torch.exp(affinity_matrix).sum(axis=1)
-        weighted_adj_matrix = torch.exp(
-            affinity_matrix
-        ) / exp_row_sums.unsqueeze(dim=1)
-
-        # Only include edges with weights that exceed the chosen threshold (and
-        # are part of the same event)
-        sources, targets = torch.where(
-            (weighted_adj_matrix > self._threshold) & (batch_mask)
-        )
-        edge_weights = weighted_adj_matrix[sources, targets]
-
-        graph.edge_index = torch.stack((sources, targets))
-        graph.edge_weight = edge_weights
-
-        return graph

-
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Source code for graphnet.models.graphs.edges.minkowski

-"""Module containing EdgeDefinitions based on the Minkowski Metric."""
-from typing import Optional, List
-
-import torch
-from torch_geometric.data import Data
-from torch_geometric.utils import to_dense_batch
-from graphnet.models.graphs.edges.edges import EdgeDefinition
-
-
-

-[docs]
-def compute_minkowski_distance_mat(
-    x: torch.Tensor,
-    y: torch.Tensor,
-    c: float,
-    space_coords: Optional[List[int]] = None,
-    time_coord: Optional[int] = 3,
-) -> torch.Tensor:
-    """Compute all pairwise Minkowski distances.
-
-    Args:
-        x: First tensor of shape (n, d).
-        y: Second tensor of shape (m, d).
-        c: Speed of light, in scaled units.
-        space_coords: Indices of space coordinates.
-        time_coord: Index of time coordinate.
-
-    Returns: Matrix of shape (n, m) of all pairwise Minkowski distances.
-    """
-    space_coords = space_coords or [0, 1, 2]
-    assert x.dim() == 2, "x must be 2-dimensional"
-    assert y.dim() == 2, "x must be 2-dimensional"
-    dist = x[:, None] - y[None, :]
-    pos = dist[:, :, space_coords]
-    time = dist[:, :, time_coord] * c
-    return (pos**2).sum(dim=-1) - time**2

-
-
-
-

-[docs]
-class MinkowskiKNNEdges(EdgeDefinition):
-    """Builds edges between most light-like separated."""
-
-    def __init__(
-        self,
-        nb_nearest_neighbours: int,
-        c: float,
-        time_like_weight: float = 1.0,
-        space_coords: Optional[List[int]] = None,
-        time_coord: Optional[int] = 3,
-    ):
-        """Initialize MinkowskiKNNEdges.
-
-        Args:
-            nb_nearest_neighbours: Number of neighbours to connect to.
-            c: Speed of light, in scaled units.
-            time_like_weight: Preference to time-like over space-like edges.
-                Scales time_like distances by this value, before finding
-                nearest neighbours.
-            space_coords: Coordinates of x, y, z.
-            time_coord: Coordinate of time.
-        """
-        super().__init__(name=__name__, class_name=self.__class__.__name__)
-        self.nb_nearest_neighbours = nb_nearest_neighbours
-        self.c = c
-        self.time_like_weight = time_like_weight
-        self.space_coords = space_coords or [0, 1, 2]
-        self.time_coord = time_coord
-
-    def _construct_edges(self, graph: Data) -> Data:
-        x, mask = to_dense_batch(graph.x, graph.batch)
-        count = 0
-        row = []
-        col = []
-        for batch in range(x.shape[0]):
-            distance_mat = compute_minkowski_distance_mat(
-                x_masked := x[batch][mask[batch]],
-                x_masked,
-                self.c,
-                self.space_coords,
-                self.time_coord,
-            )
-            num_points = x_masked.shape[0]
-            num_edges = min(self.nb_nearest_neighbours, num_points)
-            col += [
-                c
-                for c in range(num_points)
-                for _ in range(count, count + num_edges)
-            ]
-            distance_mat[distance_mat < 0] *= -self.time_like_weight
-            distance_mat += (
-                torch.eye(distance_mat.shape[0]) * 1e9
-            )  # self-loops
-            distance_sorted = distance_mat.argsort(dim=1)
-            distance_sorted += count  # offset by previous events
-            row += distance_sorted[:num_edges].flatten().tolist()
-            count += num_points
-
-        graph.edge_index = torch.tensor(
-            [row, col], dtype=torch.long, device=graph.x.device
-        )
-        return graph

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Source code for graphnet.models.graphs.graph_definition

-"""Modules for defining graphs.
-
-These are self-contained graph definitions that hold all the graph-altering
-code in graphnet. These modules define what the GNNs sees as input and can be
-passed to dataloaders during training and deployment.
-"""
-
-
-from typing import Any, List, Optional, Dict, Callable, Union
-import torch
-from torch_geometric.data import Data
-import numpy as np
-from numpy.random import default_rng, Generator
-
-from graphnet.models.detector import Detector
-from .edges import EdgeDefinition
-from .nodes import NodeDefinition, NodesAsPulses
-from graphnet.models import Model
-
-
-

-[docs]
-class GraphDefinition(Model):
-    """An Abstract class to create graph definitions from."""
-
-    def __init__(
-        self,
-        detector: Detector,
-        node_definition: NodeDefinition = NodesAsPulses(),
-        edge_definition: Optional[EdgeDefinition] = None,
-        input_feature_names: Optional[List[str]] = None,
-        dtype: Optional[torch.dtype] = torch.float,
-        perturbation_dict: Optional[Dict[str, float]] = None,
-        seed: Optional[Union[int, Generator]] = None,
-        add_inactive_sensors: bool = False,
-        sensor_mask: Optional[List[int]] = None,
-        string_mask: Optional[List[int]] = None,
-        sort_by: str = None,
-    ):
-        """Construct ´GraphDefinition´. The ´detector´ holds.
-
-        ´Detector´-specific code. E.g. scaling/standardization and geometry
-        tables.
-
-        ´node_definition´ defines the nodes in the graph.
-
-        ´edge_definition´ defines the connectivity of the nodes in the graph.
-
-        Args:
-            detector: The corresponding ´Detector´ representing the data.
-            node_definition: Definition of nodes. Defaults to NodesAsPulses.
-            edge_definition: Definition of edges. Defaults to None.
-            input_feature_names: Names of each column in expected input data
-                that will be built into a graph. If not provided,
-                it is automatically assumed that all features in `Detector` is
-                used.
-            dtype: data type used for node features. e.g. ´torch.float´
-            perturbation_dict: Dictionary mapping a feature name to a standard
-                               deviation according to which the values for this
-                               feature should be randomly perturbed. Defaults
-                               to None.
-            seed: seed or Generator used to randomly sample perturbations.
-                  Defaults to None.
-            add_inactive_sensors: If True, inactive sensors will be appended
-                to the graph with padded pulse information. Defaults to False.
-            sensor_mask: A list of sensor id's to be masked from the graph. Any
-                sensor listed here will be removed from the graph. Defaults to None.
-            string_mask: A list of string id's to be masked from the graph. Defaults to None.
-            sort_by: Name of node feature to sort by. Defaults to None.
-        """
-        # Base class constructor
-        super().__init__(name=__name__, class_name=self.__class__.__name__)
-
-        # Member Variables
-        self._detector = detector
-        self._edge_definition = edge_definition
-        self._node_definition = node_definition
-        self._perturbation_dict = perturbation_dict
-        self._sensor_mask = sensor_mask
-        self._string_mask = string_mask
-        self._add_inactive_sensors = add_inactive_sensors
-
-        self._resolve_masks()
-
-        if self._edge_definition is None:
-            self.warning_once(
-                """No EdgeDefinition given. Graphs will not have edges!"""
-            )
-
-        if input_feature_names is None:
-            # Assume all features in Detector is used.
-            input_feature_names = list(self._detector.feature_map().keys())  # type: ignore
-        self._input_feature_names = input_feature_names
-
-        # Set input data column names for node definition
-        self._node_definition.set_output_feature_names(
-            self._input_feature_names
-        )
-        self.output_feature_names = self._node_definition._output_feature_names
-
-        # Sorting
-        if sort_by is not None:
-            assert isinstance(sort_by, str)
-            try:
-                sort_by = self.output_feature_names.index(sort_by)  # type: ignore
-            except ValueError as e:
-                self.error(
-                    f"{sort_by} not in node features {self.output_feature_names}."
-                )
-                raise e
-        self._sort_by = sort_by
-        # Set data type
-        self.to(dtype)
-
-        # Set Input / Output dimensions
-        self._node_definition.set_number_of_inputs(
-            input_feature_names=input_feature_names
-        )
-        self.nb_inputs = len(self._input_feature_names)
-        self.nb_outputs = self._node_definition.nb_outputs
-
-        # Set perturbation_cols if needed
-        if isinstance(self._perturbation_dict, dict):
-            self._perturbation_cols = [
-                self._input_feature_names.index(key)
-                for key in self._perturbation_dict.keys()
-            ]
-        if seed is not None:
-            if isinstance(seed, int):
-                self.rng = default_rng(seed)
-            elif isinstance(seed, Generator):
-                self.rng = seed
-            else:
-                raise ValueError(
-                    "Invalid seed. Must be an int or a numpy Generator."
-                )
-        else:
-            self.rng = default_rng()
-
-

-[docs]
-    def forward(  # type: ignore
-        self,
-        input_features: np.ndarray,
-        input_feature_names: List[str],
-        truth_dicts: Optional[List[Dict[str, Any]]] = None,
-        custom_label_functions: Optional[Dict[str, Callable[..., Any]]] = None,
-        loss_weight_column: Optional[str] = None,
-        loss_weight: Optional[float] = None,
-        loss_weight_default_value: Optional[float] = None,
-        data_path: Optional[str] = None,
-    ) -> Data:
-        """Construct graph as ´Data´ object.
-
-        Args:
-            input_features: Input features for graph construction. Shape ´[num_rows, d]´
-            input_feature_names: name of each column. Shape ´[,d]´.
-            truth_dicts: Dictionary containing truth labels.
-            custom_label_functions: Custom label functions. See https://github.com/graphnet-team/graphnet/blob/main/GETTING_STARTED.md#adding-custom-truth-labels.
-            loss_weight_column: Name of column that holds loss weight.
-                                Defaults to None.
-            loss_weight: Loss weight associated with event. Defaults to None.
-            loss_weight_default_value: default value for loss weight.
-                    Used in instances where some events have
-                    no pre-defined loss weight. Defaults to None.
-            data_path: Path to dataset data files. Defaults to None.
-
-        Returns:
-            graph
-        """
-        # Checks
-        self._validate_input(
-            input_features=input_features,
-            input_feature_names=input_feature_names,
-        )
-
-        # Add inactive sensors if `add_inactive_sensors = True`
-        if self._add_inactive_sensors:
-            input_features = self._attach_inactive_sensors(
-                input_features, input_feature_names
-            )
-
-        # Mask out sensors if `sensor_mask` is given
-        if self._sensor_mask is not None:
-            input_features = self._mask_sensors(
-                input_features, input_feature_names
-            )
-
-        # Gaussian perturbation of each column if perturbation dict is given
-        input_features = self._perturb_input(input_features)
-
-        # Transform to pytorch tensor
-        input_features = torch.tensor(input_features, dtype=self.dtype)
-
-        # Standardize / Scale  node features
-        input_features = self._detector(input_features, input_feature_names)
-
-        # Create graph & get new node feature names
-        graph, node_feature_names = self._node_definition(input_features)
-        if self._sort_by is not None:
-            graph.x = graph.x[graph.x[:, self._sort_by].sort()[1]]
-
-        # Enforce dtype
-        graph.x = graph.x.type(self.dtype)
-
-        # Attach number of pulses as static attribute.
-        graph.n_pulses = torch.tensor(len(input_features), dtype=torch.int32)
-
-        # Assign edges
-        if self._edge_definition is not None:
-            graph = self._edge_definition(graph)
-
-        # Attach data path - useful for Ensemble datasets.
-        if data_path is not None:
-            graph["dataset_path"] = data_path
-
-        # Attach loss weights if they exist
-        graph = self._add_loss_weights(
-            graph=graph,
-            loss_weight=loss_weight,
-            loss_weight_column=loss_weight_column,
-            loss_weight_default_value=loss_weight_default_value,
-        )
-
-        # Attach default truth labels and node truths
-        if truth_dicts is not None:
-            graph = self._add_truth(graph=graph, truth_dicts=truth_dicts)
-
-        # Attach custom truth labels
-        if custom_label_functions is not None:
-            graph = self._add_custom_labels(
-                graph=graph, custom_label_functions=custom_label_functions
-            )
-
-        # Attach node features as seperate fields. MAY NOT CONTAIN 'x'
-        graph = self._add_features_individually(
-            graph=graph, node_feature_names=node_feature_names
-        )
-
-        # Add GraphDefinition Stamp
-        graph["graph_definition"] = self.__class__.__name__
-        return graph

-
-
-    def _resolve_masks(self) -> None:
-        """Handle cases with sensor/string masks."""
-        if self._sensor_mask is not None:
-            if self._string_mask is not None:
-                assert (
-                    1 == 2
-                ), """Got arguments for both `sensor_mask`and `string_mask`. Please specify only one. """
-
-        if (self._sensor_mask is None) & (self._string_mask is not None):
-            self._sensor_mask = self._convert_string_to_sensor_mask()
-
-        return
-
-    def _convert_string_to_sensor_mask(self) -> List[int]:
-        """Convert a string mask to a sensor mask."""
-        string_id_column = self._detector.string_id_column
-        sensor_id_column = self._detector.sensor_id_column
-        geometry_table = self._detector.geometry_table
-        idx = geometry_table[string_id_column].isin(self._string_mask)
-        return np.asarray(geometry_table.loc[idx, sensor_id_column]).tolist()
-
-    def _attach_inactive_sensors(
-        self, input_features: np.ndarray, input_feature_names: List[str]
-    ) -> np.ndarray:
-        """Attach inactive sensors to `input_features`.
-
-        This function will query the detector geometry table and add any sensor
-        in the geometry table that is not already present in `node_features`.
-        """
-        lookup = self._geometry_table_lookup(
-            input_features, input_feature_names
-        )
-        geometry_table = self._detector.geometry_table
-        unique_sensors = geometry_table.reset_index(drop=True)
-
-        # multiple lines to avoid long line:
-        inactive_idx = ~geometry_table.index.isin(lookup)
-        inactive_sensors = unique_sensors.loc[
-            inactive_idx, input_feature_names
-        ]
-        input_features = np.concatenate(
-            [input_features, inactive_sensors.to_numpy()], axis=0
-        )
-        return input_features
-
-    def _mask_sensors(
-        self, input_features: np.ndarray, input_feature_names: List[str]
-    ) -> np.ndarray:
-        """Mask sensors according to `sensor_mask`."""
-        sensor_id_column = self._detector.sensor_index_name
-        geometry_table = self._detector.geometry_table
-
-        lookup = self._geometry_table_lookup(
-            input_features=input_features,
-            input_feature_names=input_feature_names,
-        )
-        mask = ~geometry_table.loc[lookup, sensor_id_column].isin(
-            self._sensor_mask
-        )
-
-        return input_features[mask, :]
-
-    def _geometry_table_lookup(
-        self, input_features: np.ndarray, input_feature_names: List[str]
-    ) -> np.ndarray:
-        """Convert xyz in `input_features` into a set of sensor ids."""
-        lookup_columns = [
-            input_feature_names.index(feature)
-            for feature in self._detector.sensor_position_names
-        ]
-        idx = [*zip(*[tuple(input_features[:, k]) for k in lookup_columns])]
-        return self._detector.geometry_table.loc[idx, :].index
-
-    def _validate_input(
-        self, input_features: np.array, input_feature_names: List[str]
-    ) -> None:
-        # node feature matrix dimension check
-        assert input_features.shape[1] == len(input_feature_names)
-
-        # check that provided features for input is the same that the ´Graph´
-        # was instantiated with.
-        assert len(input_feature_names) == len(
-            self._input_feature_names
-        ), f"""Input features ({input_feature_names}) is not what 
-               {self.__class__.__name__} was instatiated
-               with ({self._input_feature_names})"""  # noqa
-        for idx in range(len(input_feature_names)):
-            assert (
-                input_feature_names[idx] == self._input_feature_names[idx]
-            ), f""" Order of node features in data
-                    are not the same as expected. Got {input_feature_names} 
-                    vs. {self._input_feature_names}"""  # noqa
-
-    def _perturb_input(self, input_features: np.ndarray) -> np.ndarray:
-        if isinstance(self._perturbation_dict, dict):
-            self.warning_once(
-                f"""Will randomly perturb
-                {list(self._perturbation_dict.keys())}
-                using stds {self._perturbation_dict.values()}"""  # noqa
-            )
-            perturbed_features = self.rng.normal(
-                loc=input_features[:, self._perturbation_cols],
-                scale=np.array(
-                    list(self._perturbation_dict.values()), dtype=float
-                ),
-            )
-            input_features[:, self._perturbation_cols] = perturbed_features
-        return input_features
-
-    def _add_loss_weights(
-        self,
-        graph: Data,
-        loss_weight_column: Optional[str] = None,
-        loss_weight: Optional[float] = None,
-        loss_weight_default_value: Optional[float] = None,
-    ) -> Data:
-        """Attempt to store a loss weight in the graph for use during training.
-
-        I.e. `graph[loss_weight_column] = loss_weight`
-
-        Args:
-            loss_weight: The non-negative weight to be stored.
-            graph: Data object representing the event.
-            loss_weight_column: The name under which the weight is stored in
-                                 the graph.
-            loss_weight_default_value: The default value used if
-                                        none was retrieved.
-
-        Returns:
-            A graph with loss weight added, if available.
-        """
-        # Add loss weight to graph.
-        if loss_weight is not None and loss_weight_column is not None:
-            # No loss weight was retrieved, i.e., it is missing for the current
-            # event.
-            if loss_weight < 0:
-                if loss_weight_default_value is None:
-                    raise ValueError(
-                        "At least one event is missing an entry in "
-                        f"{loss_weight_column} "
-                        "but loss_weight_default_value is None."
-                    )
-                graph[loss_weight_column] = torch.tensor(
-                    self._loss_weight_default_value, dtype=self.dtype
-                ).reshape(-1, 1)
-            else:
-                graph[loss_weight_column] = torch.tensor(
-                    loss_weight, dtype=self.dtype
-                ).reshape(-1, 1)
-        return graph
-
-    def _add_truth(
-        self, graph: Data, truth_dicts: List[Dict[str, Any]]
-    ) -> Data:
-        """Add truth labels from ´truth_dicts´ to ´graph´.
-
-        I.e. ´graph[key] = truth_dict[key]´
-
-
-        Args:
-            graph: graph where the label will be stored
-            truth_dicts: dictionary containing the labels
-
-        Returns:
-            graph with labels
-        """
-        # Write attributes, either target labels, truth info or original
-        # features.
-        for truth_dict in truth_dicts:
-            for key, value in truth_dict.items():
-                try:
-                    graph[key] = torch.tensor(value)
-                except TypeError:
-                    # Cannot convert `value` to Tensor due to its data type,
-                    # e.g. `str`.
-                    self.debug(
-                        (
-                            f"Could not assign `{key}` with type "
-                            f"'{type(value).__name__}' as attribute to graph."
-                        )
-                    )
-        return graph
-
-    def _add_features_individually(
-        self,
-        graph: Data,
-        node_feature_names: List[str],
-    ) -> Data:
-        # Additionally add original features as (static) attributes
-        graph.features = node_feature_names
-        for index, feature in enumerate(node_feature_names):
-            if feature not in ["x"]:  # reserved for node features.
-                graph[feature] = graph.x[:, index].detach()
-            else:
-                self.warning_once(
-                    """Cannot assign graph['x']. This field is reserved for
-                      node features. Please rename your input feature."""
-                )  # noqa
-
-        return graph
-
-    def _add_custom_labels(
-        self,
-        graph: Data,
-        custom_label_functions: Dict[str, Callable[..., Any]],
-    ) -> Data:
-        # Add custom labels to the graph
-        for key, fn in custom_label_functions.items():
-            graph[key] = fn(graph)
-        return graph

-
-
- -
-
-
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- - - - - \ No newline at end of file diff --git a/_modules/graphnet/models/graphs/graphs.html b/_modules/graphnet/models/graphs/graphs.html deleted file mode 100644 index 7e77b2ccc..000000000 --- a/_modules/graphnet/models/graphs/graphs.html +++ /dev/null @@ -1,419 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - graphnet.models.graphs.graphs — graphnet documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Skip to content -
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Source code for graphnet.models.graphs.graphs

-"""A module containing different graph representations in GraphNeT."""
-
-from typing import List, Optional, Dict, Union
-import torch
-from numpy.random import Generator
-
-from .graph_definition import GraphDefinition
-from graphnet.models.detector import Detector
-from graphnet.models.graphs.edges import EdgeDefinition, KNNEdges
-from graphnet.models.graphs.nodes import NodeDefinition, NodesAsPulses
-
-
-

-[docs]
-class KNNGraph(GraphDefinition):
-    """A Graph representation where Edges are drawn to nearest neighbours."""
-
-    def __init__(
-        self,
-        detector: Detector,
-        node_definition: NodeDefinition = None,
-        input_feature_names: Optional[List[str]] = None,
-        dtype: Optional[torch.dtype] = torch.float,
-        perturbation_dict: Optional[Dict[str, float]] = None,
-        seed: Optional[Union[int, Generator]] = None,
-        nb_nearest_neighbours: int = 8,
-        columns: List[int] = [0, 1, 2],
-    ) -> None:
-        """Construct k-nn graph representation.
-
-        Args:
-            detector: Detector that represents your data.
-            node_definition: Definition of nodes in the graph.
-            input_feature_names: Name of input feature columns.
-            dtype: data type for node features.
-            perturbation_dict: Dictionary mapping a feature name to a standard
-                               deviation according to which the values for this
-                               feature should be randomly perturbed. Defaults
-                               to None.
-            seed: seed or Generator used to randomly sample perturbations.
-                  Defaults to None.
-            nb_nearest_neighbours: Number of edges for each node. Defaults to 8.
-            columns: node feature columns used for distance calculation
-            . Defaults to [0, 1, 2].
-        """
-        # Base class constructor
-        super().__init__(
-            detector=detector,
-            node_definition=node_definition or NodesAsPulses(),
-            edge_definition=KNNEdges(
-                nb_nearest_neighbours=nb_nearest_neighbours,
-                columns=columns,
-            ),
-            dtype=dtype,
-            input_feature_names=input_feature_names,
-            perturbation_dict=perturbation_dict,
-            seed=seed,
-        )

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

-"""Class(es) for building/connecting graphs."""
-
-from typing import List, Tuple, Optional
-from abc import abstractmethod
-
-import torch
-from torch_geometric.data import Data
-
-from graphnet.utilities.decorators import final
-from graphnet.models import Model
-from graphnet.models.graphs.utils import (
-    cluster_summarize_with_percentiles,
-    identify_indices,
-)
-from copy import deepcopy
-
-
-

-[docs]
-class NodeDefinition(Model):  # pylint: disable=too-few-public-methods
-    """Base class for graph building."""
-
-    def __init__(
-        self, input_feature_names: Optional[List[str]] = None
-    ) -> None:
-        """Construct `Detector`."""
-        # Base class constructor
-        super().__init__(name=__name__, class_name=self.__class__.__name__)
-        if input_feature_names is not None:
-            self.set_output_feature_names(
-                input_feature_names=input_feature_names
-            )
-
-

-[docs]
-    @final
-    def forward(self, x: torch.tensor) -> Tuple[Data, List[str]]:
-        """Construct nodes from raw node features.
-
-        Args:
-            x: standardized node features with shape ´[num_pulses, d]´,
-            where ´d´ is the number of node features.
-            node_feature_names: list of names for each column in ´x´.
-
-        Returns:
-            graph: a graph without edges
-            new_features_name: List of new feature names.
-        """
-        graph = self._construct_nodes(x=x)
-        try:
-            self._output_feature_names
-        except AttributeError as e:
-            self.error(
-                f"""{self.__class__.__name__} was instantiated without
-                       `input_feature_names` and it was not set prior to this
-                       forward call. If you are using this class outside a
-                       `GraphDefinition`, please instatiate
-                       with `input_feature_names`."""
-            )  # noqa
-            raise e
-        return graph, self._output_feature_names

-
-
-    @property
-    def nb_outputs(self) -> int:
-        """Return number of output features.
-
-        This the default, but may be overridden by specific inheriting classes.
-        """
-        return len(self._output_feature_names)
-
-

-[docs]
-    @final
-    def set_number_of_inputs(self, input_feature_names: List[str]) -> None:
-        """Return number of inputs expected by node definition.
-
-        Args:
-            input_feature_names: name of each input feature column.
-        """
-        assert isinstance(input_feature_names, list)
-        self.nb_inputs = len(input_feature_names)

-
-
-

-[docs]
-    @final
-    def set_output_feature_names(self, input_feature_names: List[str]) -> None:
-        """Set output features names as a member variable.
-
-        Args:
-            input_feature_names: List of column names of the input to the
-            node definition.
-        """
-        self._output_feature_names = self._define_output_feature_names(
-            input_feature_names
-        )

-
-
-    @abstractmethod
-    def _define_output_feature_names(
-        self, input_feature_names: List[str]
-    ) -> List[str]:
-        """Construct names of output columns.
-
-        Args:
-            input_feature_names: List of column names for the input data.
-
-        Returns:
-            A list of column names for each column in
-            the node definition output.
-        """
-
-    @abstractmethod
-    def _construct_nodes(self, x: torch.tensor) -> Tuple[Data, List[str]]:
-        """Construct nodes from raw node features ´x´.
-
-        Args:
-            x: standardized node features with shape ´[num_pulses, d]´,
-            where ´d´ is the number of node features.
-            feature_names: List of names for reach column in `x`. Identical
-            order of appearance. Length `d`.
-
-        Returns:
-            graph: graph without edges.
-            new_node_features: A list of node features names.
-        """

-
-
-
-

-[docs]
-class NodesAsPulses(NodeDefinition):
-    """Represent each measured pulse of Cherenkov Radiation as a node."""
-
-    def _define_output_feature_names(
-        self, input_feature_names: List[str]
-    ) -> List[str]:
-        return input_feature_names
-
-    def _construct_nodes(self, x: torch.Tensor) -> Tuple[Data, List[str]]:
-        return Data(x=x)

-
-
-
-

-[docs]
-class PercentileClusters(NodeDefinition):
-    """Represent nodes as clusters with percentile summary node features.
-
-    If `cluster_on` is set to the xyz coordinates of DOMs
-    e.g. `cluster_on = ['dom_x', 'dom_y', 'dom_z']`, each node will be a
-    unique DOM and the pulse information (charge, time) is summarized using
-    percentiles.
-    """
-
-    def __init__(
-        self,
-        cluster_on: List[str],
-        percentiles: List[int],
-        add_counts: bool = True,
-        input_feature_names: Optional[List[str]] = None,
-    ) -> None:
-        """Construct `PercentileClusters`.
-
-        Args:
-            cluster_on: Names of features to create clusters from.
-            percentiles: List of percentiles. E.g. `[10, 50, 90]`.
-            add_counts: If True, number of duplicates is added to output array.
-            input_feature_names: (Optional) column names for input features.
-        """
-        self._cluster_on = cluster_on
-        self._percentiles = percentiles
-        self._add_counts = add_counts
-        # Base class constructor
-        super().__init__(input_feature_names=input_feature_names)
-
-    def _define_output_feature_names(
-        self, input_feature_names: List[str]
-    ) -> List[str]:
-        (
-            cluster_idx,
-            summ_idx,
-            new_feature_names,
-        ) = self._get_indices_and_feature_names(
-            input_feature_names, self._add_counts
-        )
-        self._cluster_indices = cluster_idx
-        self._summarization_indices = summ_idx
-        return new_feature_names
-
-    def _get_indices_and_feature_names(
-        self,
-        feature_names: List[str],
-        add_counts: bool,
-    ) -> Tuple[List[int], List[int], List[str]]:
-        cluster_idx, summ_idx, summ_names = identify_indices(
-            feature_names, self._cluster_on
-        )
-        new_feature_names = deepcopy(self._cluster_on)
-        for feature in summ_names:
-            for pct in self._percentiles:
-                new_feature_names.append(f"{feature}_pct{pct}")
-        if add_counts:
-            # add "counts" as the last feature
-            new_feature_names.append("counts")
-        return cluster_idx, summ_idx, new_feature_names
-
-    def _construct_nodes(self, x: torch.Tensor) -> Data:
-        # Cast to Numpy
-        x = x.numpy()
-        # Construct clusters with percentile-summarized features
-        if hasattr(self, "_summarization_indices"):
-            array = cluster_summarize_with_percentiles(
-                x=x,
-                summarization_indices=self._summarization_indices,
-                cluster_indices=self._cluster_indices,
-                percentiles=self._percentiles,
-                add_counts=self._add_counts,
-            )
-        else:
-            self.error(
-                f"""{self.__class__.__name__} was not instatiated with
-                `input_feature_names` and has not been set later.
-                Please instantiate this class with `input_feature_names`
-                if you're using it outside `GraphDefinition`."""
-            )  # noqa
-            raise AttributeError
-
-        return Data(x=torch.tensor(array))

-
-
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-
-
-
-
- - - - - \ No newline at end of file diff --git a/_modules/graphnet/models/graphs/utils.html b/_modules/graphnet/models/graphs/utils.html deleted file mode 100644 index 7081b3238..000000000 --- a/_modules/graphnet/models/graphs/utils.html +++ /dev/null @@ -1,532 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - graphnet.models.graphs.utils — graphnet documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Skip to content -
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Source code for graphnet.models.graphs.utils

-"""Utility functions for construction of graphs."""
-
-from typing import List, Tuple
-import numpy as np
-
-
-

-[docs]
-def lex_sort(x: np.array, cluster_columns: List[int]) -> np.ndarray:
-    """Sort numpy arrays according to columns on ´cluster_columns´.
-
-    Note that `x` is sorted along the dimensions in `cluster_columns`
-    backwards. I.e. `cluster_columns = [0,1,2]`
-    means `x` is sorted along `[2,1,0]`.
-
-    Args:
-        x: array to be sorted.
-        cluster_columns: Columns of `x` to be sorted along.
-
-    Returns:
-        A sorted version of `x`.
-    """
-    tmp_list = []
-    for cluster_column in cluster_columns:
-        tmp_list.append(x[:, cluster_column])
-    return x[np.lexsort(tuple(tmp_list)), :]

-
-
-
-

-[docs]
-def gather_cluster_sequence(
-    x: np.ndarray, feature_idx: int, cluster_columns: List[int]
-) -> Tuple[np.ndarray, np.ndarray, np.ndarray]:
-    """Turn `x` into rows of clusters with sequences along columns.
-
-    Sequences along columns are added which correspond to
-    gathered sequences of the feature in `x` specified by column index
-    `feature_idx` associated with each column. Sequences are padded with NaN to
-    be of same length. Dimension of clustered array is `[n_clusters, l +
-    len(cluster_columns)]`,where l is the largest sequence length.
-
-    **Example**:
-    Suppose `x` represents a neutrino event and we have chosen to cluster on
-    the PMT positions and that `feature_idx` correspond to pulse time.
-
-    The resulting array will have dimensions `[n_pmts, m + 3]` where `m` is the
-    maximum number of same-pmt pulses found in `x`, and `+3`for the three
-    spatial directions  defining each cluster.
-
-    Args:
-        x:  Array for clustering
-        feature_idx: Index of the feature in `x` to
-                     be gathered for each cluster.
-        cluster_columns: Index in `x` from which to build clusters.
-
-    Returns:
-        array: Array with dimensions  `[n_clusters, l + len(cluster_columns)]`
-        column_offset: Indices of the columns in `array` that defines clusters.
-    """
-    # sort pulses according to cluster columns
-    x = lex_sort(x=x, cluster_columns=cluster_columns)
-
-    # Calculate clusters and counts
-    unique_sensors, counts = np.unique(
-        x[:, cluster_columns], return_counts=True, axis=0
-    )
-    # sort DOMs and pulse-counts
-    sort_this = np.concatenate([unique_sensors, counts.reshape(-1, 1)], axis=1)
-    sort_this = lex_sort(x=sort_this, cluster_columns=cluster_columns)
-    unique_sensors = sort_this[:, 0 : unique_sensors.shape[1]]
-    counts = sort_this[:, unique_sensors.shape[1] :].flatten().astype(int)
-
-    # Pad unique sensor columns with NaN's up until the maximum number of
-    # Same pmt-pulses. Each of padded columns represents a pulse.
-    pad = np.empty((unique_sensors.shape[0], max(counts)))
-    pad[:] = np.nan
-    array = np.concatenate([unique_sensors, pad], axis=1)
-    column_offset = unique_sensors.shape[1]
-
-    # Construct indices for loop
-    cumsum = np.zeros(len(np.cumsum(counts)) + 1)
-    cumsum[0] = 0
-    cumsum[1:] = np.cumsum(counts)
-    cumsum = cumsum.astype(int)
-
-    # Insert pulse attribute in place of NaN.
-    for k in range(len(counts)):
-        array[k, column_offset : (column_offset + counts[k])] = x[
-            cumsum[k] : cumsum[k + 1], feature_idx
-        ]
-    return array, column_offset, counts

-
-
-
-

-[docs]
-def identify_indices(
-    feature_names: List[str], cluster_on: List[str]
-) -> Tuple[List[int], List[int], List[str]]:
-    """Identify indices for clustering and summarization."""
-    features_for_summarization = []
-    for feature in feature_names:
-        if feature not in cluster_on:
-            features_for_summarization.append(feature)
-    cluster_indices = [feature_names.index(column) for column in cluster_on]
-    summarization_indices = [
-        feature_names.index(column) for column in features_for_summarization
-    ]
-    return cluster_indices, summarization_indices, features_for_summarization

-
-
-
-

-[docs]
-def cluster_summarize_with_percentiles(
-    x: np.ndarray,
-    summarization_indices: List[int],
-    cluster_indices: List[int],
-    percentiles: List[int],
-    add_counts: bool,
-) -> np.ndarray:
-    """Turn `x` into clusters with percentile summary.
-
-    From variables specified by column indices `cluster_indices`, `x` is turned
-    into clusters. Information in columns of `x` specified by indices
-    `summarization_indices` with each cluster is summarized using percentiles.
-    It is assumed `x` represents a single event.
-
-    **Example use-case**:
-    Suppose `x` contains raw pulses from a neutrino event where some DOMs have
-    multiple measurements of Cherenkov radiation. If `cluster_indices` is set
-    to the columns corresponding to the xyz-position of the DOMs, and the
-    features specified in `summarization_indices` correspond to time, charge,
-    then each row in the returned array will correspond to a DOM,
-    and the time and charge for each DOM will be summarized by percentiles.
-    Returned output array has dimensions
-    `[n_clusters, len(percentiles)*len(summarization_indices) + len(cluster_indices)]`
-
-    Args:
-        x: Array to be clustered
-        summarization_indices: List of column indices that defines features
-                                that will be summarized with percentiles.
-        cluster_indices: List of column indices on which the clusters
-                        are constructed.
-        percentiles: percentiles used to summarize `x`. E.g. [10,50,90].
-
-    Returns:
-        Percentile-summarized array
-    """
-    pct_dict = {}
-    for feature_idx in summarization_indices:
-        summarized_array, column_offset, counts = gather_cluster_sequence(
-            x, feature_idx, cluster_indices
-        )
-        pct_dict[feature_idx] = np.nanpercentile(
-            summarized_array[:, column_offset:], percentiles, axis=1
-        ).T
-
-    for i, key in enumerate(pct_dict.keys()):
-        if i == 0:
-            array = summarized_array[:, 0:column_offset]
-
-        array = np.concatenate([array, pct_dict[key]], axis=1)
-
-    if add_counts:
-        array = np.concatenate(
-            [array, np.log10(counts).reshape(-1, 1)], axis=1
-        )
-
-    return array

-
-
- -
-
-
-
-
- - - - - \ No newline at end of file diff --git a/_modules/graphnet/models/standard_model.html b/_modules/graphnet/models/standard_model.html deleted file mode 100644 index 8d219a1e4..000000000 --- a/_modules/graphnet/models/standard_model.html +++ /dev/null @@ -1,912 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - graphnet.models.standard_model — graphnet documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Skip to content -
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Source code for graphnet.models.standard_model

-"""Standard model class(es)."""
-from collections import OrderedDict
-from typing import Any, Dict, List, Optional, Union, Type
-
-import numpy as np
-import torch
-from pytorch_lightning import Callback, Trainer
-from pytorch_lightning.callbacks import EarlyStopping, ModelCheckpoint
-from torch import Tensor
-from torch.nn import ModuleList
-from torch.optim import Adam
-from torch.utils.data import DataLoader, SequentialSampler
-from torch_geometric.data import Data
-import pandas as pd
-from pytorch_lightning.loggers import Logger as LightningLogger
-
-from graphnet.training.callbacks import ProgressBar
-from graphnet.models.graphs import GraphDefinition
-from graphnet.models.gnn.gnn import GNN
-from graphnet.models.model import Model
-from graphnet.models.task import StandardLearnedTask
-
-
-

-[docs]
-class StandardModel(Model):
-    """Main class for standard models in graphnet.
-
-    This class chains together the different elements of a complete GNN- based
-    model (detector read-in, GNN backbone, and task-specific read-outs).
-    """
-
-    def __init__(
-        self,
-        *,
-        graph_definition: GraphDefinition,
-        backbone: GNN = None,
-        gnn: Optional[GNN] = None,
-        tasks: Union[StandardLearnedTask, List[StandardLearnedTask]],
-        optimizer_class: Type[torch.optim.Optimizer] = Adam,
-        optimizer_kwargs: Optional[Dict] = None,
-        scheduler_class: Optional[type] = None,
-        scheduler_kwargs: Optional[Dict] = None,
-        scheduler_config: Optional[Dict] = None,
-    ) -> None:
-        """Construct `StandardModel`."""
-        # Base class constructor
-        super().__init__(name=__name__, class_name=self.__class__.__name__)
-
-        # Check(s)
-        if isinstance(tasks, StandardLearnedTask):
-            tasks = [tasks]
-        assert isinstance(tasks, (list, tuple))
-        assert all(isinstance(task, StandardLearnedTask) for task in tasks)
-        assert isinstance(graph_definition, GraphDefinition)
-
-        # deprecation warnings
-        if (backbone is None) & (gnn is not None):
-            backbone = gnn
-            # Code continues after warning
-            self.warning(
-                """DeprecationWarning: Argument `gnn` will be deprecated in GraphNeT 2.0. Please use `backbone` instead."""
-            )
-        elif (backbone is None) & (gnn is None):
-            # Code stops
-            raise TypeError(
-                "__init__() missing 1 required keyword-only argument: 'backbone'"
-            )
-        assert isinstance(backbone, GNN)
-
-        # Member variable(s)
-        self._graph_definition = graph_definition
-        self.backbone = backbone
-        self._tasks = ModuleList(tasks)
-        self._optimizer_class = optimizer_class
-        self._optimizer_kwargs = optimizer_kwargs or dict()
-        self._scheduler_class = scheduler_class
-        self._scheduler_kwargs = scheduler_kwargs or dict()
-        self._scheduler_config = scheduler_config or dict()
-
-        # set dtype of GNN from graph_definition
-        self.backbone.type(self._graph_definition._dtype)
-
-    @staticmethod
-    def _construct_trainer(
-        max_epochs: int = 10,
-        gpus: Optional[Union[List[int], int]] = None,
-        callbacks: Optional[List[Callback]] = None,
-        logger: Optional[LightningLogger] = None,
-        log_every_n_steps: int = 1,
-        gradient_clip_val: Optional[float] = None,
-        distribution_strategy: Optional[str] = "ddp",
-        **trainer_kwargs: Any,
-    ) -> Trainer:
-        if gpus:
-            accelerator = "gpu"
-            devices = gpus
-        else:
-            accelerator = "cpu"
-            devices = 1
-
-        trainer = Trainer(
-            accelerator=accelerator,
-            devices=devices,
-            max_epochs=max_epochs,
-            callbacks=callbacks,
-            log_every_n_steps=log_every_n_steps,
-            logger=logger,
-            gradient_clip_val=gradient_clip_val,
-            strategy=distribution_strategy,
-            **trainer_kwargs,
-        )
-
-        return trainer
-
-

-[docs]
-    def fit(
-        self,
-        train_dataloader: DataLoader,
-        val_dataloader: Optional[DataLoader] = None,
-        *,
-        max_epochs: int = 10,
-        early_stopping_patience: int = 5,
-        gpus: Optional[Union[List[int], int]] = None,
-        callbacks: Optional[List[Callback]] = None,
-        ckpt_path: Optional[str] = None,
-        logger: Optional[LightningLogger] = None,
-        log_every_n_steps: int = 1,
-        gradient_clip_val: Optional[float] = None,
-        distribution_strategy: Optional[str] = "ddp",
-        **trainer_kwargs: Any,
-    ) -> None:
-        """Fit `StandardModel` using `pytorch_lightning.Trainer`."""
-        # Checks
-        if callbacks is None:
-            # We create the bare-minimum callbacks for you.
-            callbacks = self._create_default_callbacks(
-                val_dataloader=val_dataloader,
-                early_stopping_patience=early_stopping_patience,
-            )
-            self.debug("No Callbacks specified. Default callbacks added.")
-        else:
-            # You are on your own!
-            self.debug("Initializing training with user-provided callbacks.")
-            pass
-        self._print_callbacks(callbacks)
-        has_early_stopping = self._contains_callback(callbacks, EarlyStopping)
-        has_model_checkpoint = self._contains_callback(
-            callbacks, ModelCheckpoint
-        )
-
-        if (has_early_stopping) & (has_model_checkpoint is False):
-            self.warning(
-                """No ModelCheckpoint found in callbacks. Best-fit model will not automatically be loaded after training!"""
-            )
-
-        self.train(mode=True)
-        trainer = self._construct_trainer(
-            max_epochs=max_epochs,
-            gpus=gpus,
-            callbacks=callbacks,
-            logger=logger,
-            log_every_n_steps=log_every_n_steps,
-            gradient_clip_val=gradient_clip_val,
-            distribution_strategy=distribution_strategy,
-            **trainer_kwargs,
-        )
-
-        try:
-            trainer.fit(
-                self, train_dataloader, val_dataloader, ckpt_path=ckpt_path
-            )
-        except KeyboardInterrupt:
-            self.warning("[ctrl+c] Exiting gracefully.")
-            pass
-
-        # Load weights from best-fit model after training if possible
-        if has_early_stopping & has_model_checkpoint:
-            for callback in callbacks:
-                if isinstance(callback, ModelCheckpoint):
-                    checkpoint_callback = callback
-            self.load_state_dict(
-                torch.load(checkpoint_callback.best_model_path)["state_dict"]
-            )
-            self.info("Best-fit weights from EarlyStopping loaded.")

-
-
-    def _print_callbacks(self, callbacks: List[Callback]) -> None:
-        callback_names = []
-        for cbck in callbacks:
-            callback_names.append(cbck.__class__.__name__)
-        self.info(
-            f"Training initiated with callbacks: {', '.join(callback_names)}"
-        )
-
-    def _contains_callback(
-        self, callbacks: List[Callback], callback: Callback
-    ) -> bool:
-        """Check if `callback` is in `callbacks`."""
-        for cbck in callbacks:
-            if isinstance(cbck, callback):
-                return True
-        return False
-
-    @property
-    def target_labels(self) -> List[str]:
-        """Return target label."""
-        return [label for task in self._tasks for label in task._target_labels]
-
-    @property
-    def prediction_labels(self) -> List[str]:
-        """Return prediction labels."""
-        return [
-            label for task in self._tasks for label in task._prediction_labels
-        ]
-
-

-[docs]
-    def configure_optimizers(self) -> Dict[str, Any]:
-        """Configure the model's optimizer(s)."""
-        optimizer = self._optimizer_class(
-            self.parameters(), **self._optimizer_kwargs
-        )
-        config = {
-            "optimizer": optimizer,
-        }
-        if self._scheduler_class is not None:
-            scheduler = self._scheduler_class(
-                optimizer, **self._scheduler_kwargs
-            )
-            config.update(
-                {
-                    "lr_scheduler": {
-                        "scheduler": scheduler,
-                        **self._scheduler_config,
-                    },
-                }
-            )
-        return config

-
-
-

-[docs]
-    def forward(
-        self, data: Union[Data, List[Data]]
-    ) -> List[Union[Tensor, Data]]:
-        """Forward pass, chaining model components."""
-        if isinstance(data, Data):
-            data = [data]
-        x_list = []
-        for d in data:
-            x = self.backbone(d)
-            x_list.append(x)
-        x = torch.cat(x_list, dim=0)
-
-        preds = [task(x) for task in self._tasks]
-        return preds

-
-
-

-[docs]
-    def shared_step(self, batch: List[Data], batch_idx: int) -> Tensor:
-        """Perform shared step.
-
-        Applies the forward pass and the following loss calculation, shared
-        between the training and validation step.
-        """
-        preds = self(batch)
-        loss = self.compute_loss(preds, batch)
-        return loss

-
-
-

-[docs]
-    def training_step(
-        self, train_batch: Union[Data, List[Data]], batch_idx: int
-    ) -> Tensor:
-        """Perform training step."""
-        if isinstance(train_batch, Data):
-            train_batch = [train_batch]
-        loss = self.shared_step(train_batch, batch_idx)
-        self.log(
-            "train_loss",
-            loss,
-            batch_size=self._get_batch_size(train_batch),
-            prog_bar=True,
-            on_epoch=True,
-            on_step=False,
-            sync_dist=True,
-        )
-        return loss

-
-
-

-[docs]
-    def validation_step(
-        self, val_batch: Union[Data, List[Data]], batch_idx: int
-    ) -> Tensor:
-        """Perform validation step."""
-        if isinstance(val_batch, Data):
-            val_batch = [val_batch]
-        loss = self.shared_step(val_batch, batch_idx)
-        self.log(
-            "val_loss",
-            loss,
-            batch_size=self._get_batch_size(val_batch),
-            prog_bar=True,
-            on_epoch=True,
-            on_step=False,
-            sync_dist=True,
-        )
-        return loss

-
-
-

-[docs]
-    def compute_loss(
-        self, preds: Tensor, data: List[Data], verbose: bool = False
-    ) -> Tensor:
-        """Compute and sum losses across tasks."""
-        data_merged = {}
-        target_labels_merged = list(set(self.target_labels))
-        for label in target_labels_merged:
-            data_merged[label] = torch.cat([d[label] for d in data], dim=0)
-        for task in self._tasks:
-            if task._loss_weight is not None:
-                data_merged[task._loss_weight] = torch.cat(
-                    [d[task._loss_weight] for d in data], dim=0
-                )
-
-        losses = [
-            task.compute_loss(pred, data_merged)
-            for task, pred in zip(self._tasks, preds)
-        ]
-        if verbose:
-            self.info(f"{losses}")
-        assert all(
-            loss.dim() == 0 for loss in losses
-        ), "Please reduce loss for each task separately"
-        return torch.sum(torch.stack(losses))

-
-
-

-[docs]
-    def inference(self) -> None:
-        """Activate inference mode."""
-        for task in self._tasks:
-            task.inference()

-
-
-

-[docs]
-    def train(self, mode: bool = True) -> "Model":
-        """Deactivate inference mode."""
-        super().train(mode)
-        if mode:
-            for task in self._tasks:
-                task.train_eval()
-        return self

-
-
-

-[docs]
-    def predict(
-        self,
-        dataloader: DataLoader,
-        gpus: Optional[Union[List[int], int]] = None,
-        distribution_strategy: Optional[str] = "auto",
-    ) -> List[Tensor]:
-        """Return predictions for `dataloader`."""
-        self.inference()
-        self.train(mode=False)
-
-        callbacks = self._create_default_callbacks(
-            val_dataloader=None,
-        )
-
-        inference_trainer = self._construct_trainer(
-            gpus=gpus,
-            distribution_strategy=distribution_strategy,
-            callbacks=callbacks,
-        )
-
-        predictions_list = inference_trainer.predict(self, dataloader)
-        assert len(predictions_list), "Got no predictions"
-
-        nb_outputs = len(predictions_list[0])
-        predictions: List[Tensor] = [
-            torch.cat([preds[ix] for preds in predictions_list], dim=0)
-            for ix in range(nb_outputs)
-        ]
-        return predictions

-
-
-

-[docs]
-    def predict_as_dataframe(
-        self,
-        dataloader: DataLoader,
-        prediction_columns: Optional[List[str]] = None,
-        *,
-        additional_attributes: Optional[List[str]] = None,
-        gpus: Optional[Union[List[int], int]] = None,
-        distribution_strategy: Optional[str] = "auto",
-    ) -> pd.DataFrame:
-        """Return predictions for `dataloader` as a DataFrame.
-
-        Include `additional_attributes` as additional columns in the output
-        DataFrame.
-        """
-        if prediction_columns is None:
-            prediction_columns = self.prediction_labels
-
-        if additional_attributes is None:
-            additional_attributes = []
-        assert isinstance(additional_attributes, list)
-
-        if (
-            not isinstance(dataloader.sampler, SequentialSampler)
-            and additional_attributes
-        ):
-            print(dataloader.sampler)
-            raise UserWarning(
-                "DataLoader has a `sampler` that is not `SequentialSampler`, "
-                "indicating that shuffling is enabled. Using "
-                "`predict_as_dataframe` with `additional_attributes` assumes "
-                "that the sequence of batches in `dataloader` are "
-                "deterministic. Either call this method a `dataloader` which "
-                "doesn't resample batches; or do not request "
-                "`additional_attributes`."
-            )
-        self.info(f"Column names for predictions are: \n {prediction_columns}")
-        predictions_torch = self.predict(
-            dataloader=dataloader,
-            gpus=gpus,
-            distribution_strategy=distribution_strategy,
-        )
-        predictions = (
-            torch.cat(predictions_torch, dim=1).detach().cpu().numpy()
-        )
-        assert len(prediction_columns) == predictions.shape[1], (
-            f"Number of provided column names ({len(prediction_columns)}) and "
-            f"number of output columns ({predictions.shape[1]}) don't match."
-        )
-
-        # Get additional attributes
-        attributes: Dict[str, List[np.ndarray]] = OrderedDict(
-            [(attr, []) for attr in additional_attributes]
-        )
-        for batch in dataloader:
-            for attr in attributes:
-                attribute = batch[attr]
-                if isinstance(attribute, torch.Tensor):
-                    attribute = attribute.detach().cpu().numpy()
-
-                # Check if node level predictions
-                # If true, additional attributes are repeated
-                # to make dimensions fit
-                if len(predictions) != len(dataloader.dataset):
-                    if len(attribute) < np.sum(
-                        batch.n_pulses.detach().cpu().numpy()
-                    ):
-                        attribute = np.repeat(
-                            attribute, batch.n_pulses.detach().cpu().numpy()
-                        )
-                        try:
-                            assert len(attribute) == len(batch.x)
-                        except AssertionError:
-                            self.warning_once(
-                                "Could not automatically adjust length"
-                                f"of additional attribute {attr} to match length of"
-                                f"predictions. Make sure {attr} is a graph-level or"
-                                "node-level attribute. Attribute skipped."
-                            )
-                            pass
-                attributes[attr].extend(attribute)
-
-        data = np.concatenate(
-            [predictions]
-            + [
-                np.asarray(values)[:, np.newaxis]
-                for values in attributes.values()
-            ],
-            axis=1,
-        )
-
-        results = pd.DataFrame(
-            data, columns=prediction_columns + additional_attributes
-        )
-        return results

-
-
-    def _create_default_callbacks(
-        self,
-        val_dataloader: DataLoader,
-        early_stopping_patience: Optional[int] = None,
-    ) -> List:
-        """Create default callbacks.
-
-        Used in cases where no callbacks are specified by the user in .fit
-        """
-        callbacks = [ProgressBar()]
-        if val_dataloader is not None:
-            assert early_stopping_patience is not None
-            # Add Early Stopping
-            callbacks.append(
-                EarlyStopping(
-                    monitor="val_loss",
-                    patience=early_stopping_patience,
-                )
-            )
-            # Add Model Check Point
-            callbacks.append(
-                ModelCheckpoint(
-                    save_top_k=1,
-                    monitor="val_loss",
-                    mode="min",
-                    filename=f"{self.backbone.__class__.__name__}"
-                    + "-{epoch}-{val_loss:.2f}-{train_loss:.2f}",
-                )
-            )
-            self.info(
-                f"EarlyStopping has been added with a patience of {early_stopping_patience}."
-            )
-        return callbacks
-
-    def _add_early_stopping(
-        self, val_dataloader: DataLoader, callbacks: List
-    ) -> List:
-        if val_dataloader is None:
-            return callbacks
-        has_early_stopping = False
-        assert isinstance(callbacks, list)
-        for callback in callbacks:
-            if isinstance(callback, EarlyStopping):
-                has_early_stopping = True
-
-        if not has_early_stopping:
-            callbacks.append(
-                EarlyStopping(
-                    monitor="val_loss",
-                    patience=5,
-                )
-            )
-            self.warning_once(
-                "Got validation dataloader but no EarlyStopping callback. An "
-                "EarlyStopping callback has been added automatically with "
-                "patience=5 and monitor = 'val_loss'."
-            )
-        return callbacks

-
-
- -
-
-
-
-
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Source code for graphnet.models.task.classification

-"""Classification-specific `Model` class(es)."""
-
-from typing import Any
-
-import torch
-from torch import Tensor
-
-from graphnet.models.task import IdentityTask, StandardLearnedTask
-
-
-

-[docs]
-class MulticlassClassificationTask(IdentityTask):
-    """General task for classifying any number of classes.
-
-    Requires the same number of input features as the number of classes being
-    predicted. Returns the untransformed latent features, which are interpreted
-    as the logits for each class being classified.
-    """

-
-
-
-

-[docs]
-class BinaryClassificationTask(StandardLearnedTask):
-    """Performs binary classification."""
-
-    # Requires one feature, logit for being signal class.
-    nb_inputs = 1
-    default_target_labels = ["target"]
-    default_prediction_labels = ["target_pred"]
-
-    def _forward(self, x: Tensor) -> Tensor:
-        # transform probability of being muon
-        return torch.sigmoid(x)

-
-
-
-

-[docs]
-class BinaryClassificationTaskLogits(StandardLearnedTask):
-    """Performs binary classification form logits."""
-
-    # Requires one feature, logit for being signal class.
-    nb_inputs = 1
-    default_target_labels = ["target"]
-    default_prediction_labels = ["target_pred"]
-
-    def _forward(self, x: Tensor) -> Tensor:
-        return x

-
-
- -
-
-
-
-
- - - - - \ No newline at end of file diff --git a/_modules/graphnet/models/task/reconstruction.html b/_modules/graphnet/models/task/reconstruction.html deleted file mode 100644 index 381966505..000000000 --- a/_modules/graphnet/models/task/reconstruction.html +++ /dev/null @@ -1,632 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - graphnet.models.task.reconstruction — graphnet documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Skip to content -
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- - -
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- -
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- -

Source code for graphnet.models.task.reconstruction

-"""Reconstruction-specific `Model` class(es)."""
-
-import numpy as np
-import torch
-from torch import Tensor
-
-from graphnet.models.task import StandardLearnedTask
-from graphnet.utilities.maths import eps_like
-
-
-

-[docs]
-class AzimuthReconstructionWithKappa(StandardLearnedTask):
-    """Reconstructs azimuthal angle and associated kappa (1/var)."""
-
-    # Requires two features: untransformed points in (x,y)-space.
-    default_target_labels = ["azimuth"]
-    default_prediction_labels = ["azimuth_pred", "azimuth_kappa"]
-    nb_inputs = 2
-
-    def _forward(self, x: Tensor) -> Tensor:
-        # Transform outputs to angle and prepare prediction
-        kappa = torch.linalg.vector_norm(x, dim=1) + eps_like(x)
-        angle = torch.atan2(x[:, 1], x[:, 0])
-        angle = torch.where(
-            angle < 0, angle + 2 * np.pi, angle
-        )  # atan(y,x) -> [-pi, pi]
-        return torch.stack((angle, kappa), dim=1)

-
-
-
-

-[docs]
-class AzimuthReconstruction(AzimuthReconstructionWithKappa):
-    """Reconstructs azimuthal angle."""
-
-    # Requires two features: untransformed points in (x,y)-space.
-    default_target_labels = ["azimuth"]
-    default_prediction_labels = ["azimuth_pred"]
-    nb_inputs = 2
-
-    def _forward(self, x: Tensor) -> Tensor:
-        # Transform outputs to angle and prepare prediction
-        res = super()._forward(x)
-        angle = res[:, 0].unsqueeze(1)
-        kappa = res[:, 1]
-        sigma = torch.sqrt(1.0 / kappa)
-        beta = 1e-3
-        kl_loss = torch.mean(sigma**2 - torch.log(sigma) - 1)
-        self._regularisation_loss += beta * kl_loss
-        return angle

-
-
-
-

-[docs]
-class DirectionReconstructionWithKappa(StandardLearnedTask):
-    """Reconstructs direction with kappa from the 3D-vMF distribution."""
-
-    # Requires three features: untransformed points in (x,y,z)-space.
-    default_target_labels = [
-        "direction"
-    ]  # contains dir_x, dir_y, dir_z see https://github.com/graphnet-team/graphnet/blob/95309556cfd46a4046bc4bd7609888aab649e295/src/graphnet/training/labels.py#L29
-    default_prediction_labels = [
-        "dir_x_pred",
-        "dir_y_pred",
-        "dir_z_pred",
-        "direction_kappa",
-    ]
-    nb_inputs = 3
-
-    def _forward(self, x: Tensor) -> Tensor:
-        # Transform outputs to angle and prepare prediction
-        kappa = torch.linalg.vector_norm(x, dim=1) + eps_like(x)
-        vec_x = x[:, 0] / kappa
-        vec_y = x[:, 1] / kappa
-        vec_z = x[:, 2] / kappa
-        return torch.stack((vec_x, vec_y, vec_z, kappa), dim=1)

-
-
-
-

-[docs]
-class ZenithReconstruction(StandardLearnedTask):
-    """Reconstructs zenith angle."""
-
-    # Requires two features: zenith angle itself.
-    default_target_labels = ["zenith"]
-    default_prediction_labels = ["zenith_pred"]
-    nb_inputs = 1
-
-    def _forward(self, x: Tensor) -> Tensor:
-        # Transform outputs to angle and prepare prediction
-        return torch.sigmoid(x[:, :1]) * np.pi

-
-
-
-

-[docs]
-class ZenithReconstructionWithKappa(ZenithReconstruction):
-    """Reconstructs zenith angle and associated kappa (1/var)."""
-
-    # Requires one feature in addition to `ZenithReconstruction`: kappa (unceratinty; 1/variance).
-    default_target_labels = ["zenith"]
-    default_prediction_labels = ["zenith_pred", "zenith_kappa"]
-    nb_inputs = 2
-
-    def _forward(self, x: Tensor) -> Tensor:
-        # Transform outputs to angle and prepare prediction
-        angle = super()._forward(x[:, :1]).squeeze(1)
-        kappa = torch.abs(x[:, 1]) + eps_like(x)
-        return torch.stack((angle, kappa), dim=1)

-
-
-
-

-[docs]
-class EnergyReconstruction(StandardLearnedTask):
-    """Reconstructs energy using stable method."""
-
-    # Requires one feature: untransformed energy
-    default_target_labels = ["energy"]
-    default_prediction_labels = ["energy_pred"]
-    nb_inputs = 1
-
-    def _forward(self, x: Tensor) -> Tensor:
-        # Transform to positive energy domain avoiding `-inf` in `log10`
-        # Transform, thereby preventing overflow and underflow error.
-        return torch.nn.functional.softplus(x, beta=0.05) + eps_like(x)

-
-
-
-

-[docs]
-class EnergyReconstructionWithPower(StandardLearnedTask):
-    """Reconstructs energy."""
-
-    # Requires one feature: untransformed energy
-    default_target_labels = ["energy"]
-    default_prediction_labels = ["energy_pred"]
-    nb_inputs = 1
-
-    def _forward(self, x: Tensor) -> Tensor:
-        # Transform energy
-        return torch.pow(10, x[:, 0] + 1.0).unsqueeze(1)

-
-
-
-

-[docs]
-class EnergyTCReconstruction(StandardLearnedTask):
-    """Reconstructs track and cascade energies using stable method."""
-
-    # Requires two features: untransformed energy for track and cascade
-    default_target_labels = ["energy_track", "energy_cascade"]
-    default_prediction_labels = ["energy_track_pred", "energy_cascade_pred"]
-    nb_inputs = 2
-
-    def _forward(self, x: Tensor) -> Tensor:
-        # Transform to positive energy domain avoiding `-inf` in `log10`
-        # Transform, thereby preventing overflow and underflow error.
-        x[:, 0] = torch.nn.functional.softplus(
-            x[:, 0].clone(), beta=0.05
-        ) + eps_like(x[:, 0].clone())
-        x[:, 1] = torch.nn.functional.softplus(
-            x[:, 1].clone(), beta=0.05
-        ) + eps_like(x[:, 1].clone())
-        return x

-
-
-
-

-[docs]
-class EnergyReconstructionWithUncertainty(EnergyReconstruction):
-    """Reconstructs energy and associated uncertainty (log(var))."""
-
-    # Requires one feature in addition to `EnergyReconstruction`: log-variance (uncertainty).
-    default_target_labels = ["energy"]
-    default_prediction_labels = ["energy_pred", "energy_sigma"]
-    nb_inputs = 2
-
-    def _forward(self, x: Tensor) -> Tensor:
-        # Transform energy
-        energy = super()._forward(x[:, :1]).squeeze(1)
-        log_var = x[:, 1]
-        pred = torch.stack((energy, log_var), dim=1)
-        return pred

-
-
-
-

-[docs]
-class VertexReconstruction(StandardLearnedTask):
-    """Reconstructs vertex position and time."""
-
-    # Requires four features, x, y, z, and t.
-    default_target_labels = ["vertex"]
-    default_prediction_labels = [
-        "position_x_pred",
-        "position_y_pred",
-        "position_z_pred",
-        "interaction_time_pred",
-    ]
-    nb_inputs = 4
-
-    def _forward(self, x: Tensor) -> Tensor:
-        # Scale xyz to roughly the right order of magnitude, leave time
-        x[:, 0] = x[:, 0] * 1e2
-        x[:, 1] = x[:, 1] * 1e2
-        x[:, 2] = x[:, 2] * 1e2
-
-        return x

-
-
-
-

-[docs]
-class PositionReconstruction(StandardLearnedTask):
-    """Reconstructs vertex position."""
-
-    # Requires three features, x, y, and z.
-    default_target_labels = ["position"]
-    default_prediction_labels = [
-        "position_x_pred",
-        "position_y_pred",
-        "position_z_pred",
-    ]
-    nb_inputs = 3
-
-    def _forward(self, x: Tensor) -> Tensor:
-        # Scale to roughly the right order of magnitude
-        x[:, 0] = x[:, 0] * 1e2
-        x[:, 1] = x[:, 1] * 1e2
-        x[:, 2] = x[:, 2] * 1e2
-
-        return x

-
-
-
-

-[docs]
-class TimeReconstruction(StandardLearnedTask):
-    """Reconstructs time."""
-
-    # Requires one feature, time.
-    default_target_labels = ["interaction_time"]
-    default_prediction_labels = ["interaction_time_pred"]
-    nb_inputs = 1
-
-    def _forward(self, x: Tensor) -> Tensor:
-        # Leave as it is
-        return x

-
-
-
-

-[docs]
-class InelasticityReconstruction(StandardLearnedTask):
-    """Reconstructs interaction inelasticity.
-
-    That is, 1-(track energy / hadronic energy).
-    """
-
-    # Requires one features: inelasticity itself
-    default_target_labels = ["inelasticity"]
-    default_prediction_labels = ["inelasticity_pred"]
-    nb_inputs = 1
-
-    def _forward(self, x: Tensor) -> Tensor:
-        # Transform output to unit range
-        return torch.sigmoid(x)

-
-
- -
-
-
-
-
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Source code for graphnet.models.task.task

-"""Base physics task-specific `Model` class(es)."""
-
-from abc import abstractmethod
-from typing import Any, TYPE_CHECKING, List, Tuple, Union
-from typing import Callable, Optional
-import numpy as np
-
-import torch
-from torch import Tensor
-from torch.nn import Linear
-from torch_geometric.data import Data
-
-if TYPE_CHECKING:
-    # Avoid cyclic dependency
-    from graphnet.training.loss_functions import LossFunction  # type: ignore[attr-defined]
-
-from graphnet.models import Model
-from graphnet.utilities.decorators import final
-
-
-

-[docs]
-class Task(Model):
-    """Base class for Tasks in GraphNeT."""
-
-    @property
-    @abstractmethod
-    def nb_inputs(self) -> int:
-        """Return number of inputs assumed by task."""
-
-    @property
-    def default_target_labels(self) -> List[str]:
-        """Return default target labels."""
-        return self._default_target_labels
-
-    @property
-    def default_prediction_labels(self) -> List[str]:
-        """Return default prediction labels."""
-        return self._default_prediction_labels
-
-    def __init__(
-        self,
-        *,
-        loss_function: "LossFunction",
-        target_labels: Optional[Union[str, List[str]]] = None,
-        prediction_labels: Optional[Union[str, List[str]]] = None,
-        transform_prediction_and_target: Optional[Callable] = None,
-        transform_target: Optional[Callable] = None,
-        transform_inference: Optional[Callable] = None,
-        transform_support: Optional[Tuple] = None,
-        loss_weight: Optional[str] = None,
-    ):
-        """Construct `Task`.
-
-        Args:
-            loss_function: Loss function appropriate to the task.
-            target_labels: Name(s) of the quantity/-ies being predicted, used
-                to extract the  target tensor(s) from the `Data` object in
-                `.compute_loss(...)`.
-            prediction_labels: The name(s) of each column that is predicted by
-                the model during inference. If not given, the name will auto
-                matically be set to `target_label + _pred`.
-            transform_prediction_and_target: Optional function to transform
-                both the predicted and target tensor before passing them to the
-                loss function. Useful e.g. for having the model predict
-                quantities on a physical scale, but transforming this scale to
-                O(1) for a numerically stable loss computation.
-            transform_target: Optional function to transform only the target
-                tensor before passing it, and the predicted tensor, to the loss
-                function. Useful e.g. for having the model predict a
-                transformed version of the target quantity, e.g. the log10-
-                scaled energy, rather than the physical quantity itself. Used
-                in conjunction with `transform_inference` to perform the
-                inverse transform on the predicted quantity to recover the
-                physical scale.
-            transform_inference: Optional function to inverse-transform the
-                model prediction to recover a physical scale. Used in
-                conjunction with `transform_target`.
-            transform_support: Optional tuple to specify minimum and maximum
-                of the range of validity for the inverse transforms
-                `transform_target` and `transform_inference` in case this is
-                restricted. By default the invertibility of `transform_target`
-                is tested on the range [-1e6, 1e6].
-            loss_weight: Name of the attribute in `data` containing per-event
-                loss weights.
-        """
-        # Base class constructor
-        super().__init__()
-        # Check(s)
-        if target_labels is None:
-            target_labels = self.default_target_labels
-        if isinstance(target_labels, str):
-            target_labels = [target_labels]
-
-        if prediction_labels is None:
-            prediction_labels = self.default_prediction_labels
-        if isinstance(prediction_labels, str):
-            prediction_labels = [prediction_labels]
-
-        assert isinstance(target_labels, List)  # mypy
-        assert isinstance(prediction_labels, List)  # mypy
-        # Member variables
-        self._regularisation_loss: Optional[float] = None
-        self._target_labels = target_labels
-        self._prediction_labels = prediction_labels
-        self._loss_function = loss_function
-        self._inference = False
-        self._loss_weight = loss_weight
-
-        self._transform_prediction_training: Callable[
-            [Tensor], Tensor
-        ] = lambda x: x
-        self._transform_prediction_inference: Callable[
-            [Tensor], Tensor
-        ] = lambda x: x
-        self._transform_target: Callable[[Tensor], Tensor] = lambda x: x
-        self._validate_and_set_transforms(
-            transform_prediction_and_target,
-            transform_target,
-            transform_inference,
-            transform_support,
-        )
-
-    @final
-    def _transform_prediction(
-        self, prediction: Union[Tensor, Data]
-    ) -> Union[Tensor, Data]:
-        if self._inference:
-            return self._transform_prediction_inference(prediction)
-        else:
-            return self._transform_prediction_training(prediction)
-
-

-[docs]
-    @final
-    def inference(self) -> None:
-        """Activate inference mode."""
-        self._inference = True

-
-
-

-[docs]
-    @final
-    def train_eval(self) -> None:
-        """Deactivate inference mode."""
-        self._inference = False

-
-
-    @final
-    def _validate_and_set_transforms(
-        self,
-        transform_prediction_and_target: Union[Callable, None],
-        transform_target: Union[Callable, None],
-        transform_inference: Union[Callable, None],
-        transform_support: Union[Tuple, None],
-    ) -> None:
-        """Validate and set transforms.
-
-        Assert that a valid combination of transformation arguments are passed
-        and update the corresponding functions.
-        """
-        # Checks
-        assert not (
-            (transform_prediction_and_target is not None)
-            and (transform_target is not None)
-        ), "Please specify at most one of `transform_prediction_and_target` and `transform_target`"
-        if (transform_target is not None) != (transform_inference is not None):
-            self.warning(
-                "Setting one of `transform_target` and `transform_inference`, but not "
-                "the other."
-            )
-
-        if transform_target is not None:
-            assert transform_target is not None
-            assert transform_inference is not None
-
-            if transform_support is not None:
-                assert transform_support is not None
-
-                assert (
-                    len(transform_support) == 2
-                ), "Please specify min and max for transformation support."
-                x_test = torch.from_numpy(
-                    np.linspace(transform_support[0], transform_support[1], 10)
-                )
-            else:
-                x_test = np.logspace(-6, 6, 12 + 1)
-                x_test = torch.from_numpy(
-                    np.concatenate([-x_test[::-1], [0], x_test])
-                )
-
-            # Add feature dimension before inference transformation to make it
-            # match the dimensions of a standard prediction. Remove it again
-            # before comparison. Temporary
-            try:
-                t_test = torch.unsqueeze(transform_target(x_test), -1)
-                t_test = torch.squeeze(transform_inference(t_test), -1)
-                valid = torch.isfinite(t_test)
-
-                assert torch.allclose(t_test[valid], x_test[valid]), (
-                    "The provided transforms for targets during training and "
-                    "predictions during inference are not inverse. Please "
-                    "adjust transformation functions or support."
-                )
-                del x_test, t_test, valid
-
-            except IndexError:
-                self.warning(
-                    "transform_target and/or transform_inference rely on "
-                    "indexing, which we won't validate. Please make sure that "
-                    "they are mutually inverse, i.e. that\n"
-                    "  x = transform_inference(transform_target(x))\n"
-                    "for all x that are within your target range."
-                )
-
-        # Set transforms
-        if transform_prediction_and_target is not None:
-            self._transform_prediction_training = (
-                transform_prediction_and_target
-            )
-            self._transform_target = transform_prediction_and_target
-        else:
-            if transform_target is not None:
-                self._transform_target = transform_target
-            if transform_inference is not None:
-                self._transform_prediction_inference = transform_inference

-
-
-
-

-[docs]
-class LearnedTask(Task):
-    """Task class with a learned mapping.
-
-    Applies a learned mapping between the last latent layer of `Model` and
-    target space. E.g. the `LearnedTask` contains learnable parameters that
-    acts like a prediction head.
-    """
-
-    def __init__(
-        self,
-        hidden_size: int,
-        **task_kwargs: Any,
-    ):
-        """Construct `LearnedTask`.
-
-        Args:
-            hidden_size: The number of columns in the output of
-                         the last latent layer of `Model` using this Task.
-                         Available through `Model.nb_outputs`
-        """
-        # Base class constructor
-        super().__init__(**task_kwargs)
-
-        # Mapping from last hidden layer to required size of input
-        self._affine = Linear(hidden_size, self.nb_inputs)
-
-    @abstractmethod
-    def _forward(  # type: ignore
-        self, x: Union[Tensor, Data]
-    ) -> Union[Tensor, Data]:
-        """Syntax like `.forward`, for implentation in inheriting classes."""
-        raise NotImplementedError
-
-

-[docs]
-    @abstractmethod
-    def compute_loss(self, pred: Union[Tensor, Data], data: Data) -> Tensor:
-        """Compute loss of `pred` wrt.
-
-        target labels in `data`.
-        """

-
-
-    @property
-    @abstractmethod
-    def nb_inputs(self) -> int:
-        """Return number of inputs assumed by task."""
-
-

-[docs]
-    @final
-    def forward(  # type: ignore
-        self, x: Union[Tensor, Data]
-    ) -> Union[Tensor, Data]:
-        """Forward call for `LearnedTask`.
-
-        The learned embedding transforms last latent layer of Model to meet
-        target dimensions.
-        """
-        self._regularisation_loss = 0  # Reset
-        x = self._affine(x)
-        x = self._forward(x=x)
-        return self._transform_prediction(x)

-

-
-
-
-

-[docs]
-class StandardLearnedTask(LearnedTask):
-    """Standard class for classification and reconstruction in GraphNeT.
-
-    This class comes with a definition of `compute_loss` that is compatible
-    with the vast majority of supervised learning tasks.
-    """
-
-    def __init__(
-        self,
-        hidden_size: int,
-        **task_kwargs: Any,
-    ):
-        """Construct `StandardLearnedTask`.
-
-        Args:
-            hidden_size: The number of columns in the output of
-                         the last latent layer of `Model` using this Task.
-                         Available through `Model.nb_outputs`
-        """
-        # Base class constructor
-        super().__init__(hidden_size=hidden_size, **task_kwargs)
-
-    @property
-    @abstractmethod
-    def nb_inputs(self) -> int:
-        """Return number of inputs assumed by task."""
-
-    @abstractmethod
-    def _forward(self, x: Union[Tensor, Data]) -> Union[Tensor, Data]:
-        """Syntax like `.forward`, for implentation in inheriting classes."""
-
-

-[docs]
-    @final
-    def compute_loss(self, pred: Union[Tensor, Data], data: Data) -> Tensor:
-        """Compute supervised learning loss.
-
-        Grabs truth labels in `data` and sends both `pred` and `target` to loss
-        function for evaluation. Suits most supervised learning `Task`s.
-        """
-        target = torch.stack(
-            [data[label] for label in self._target_labels], dim=1
-        )
-        target = self._transform_target(target)
-        if self._loss_weight is not None:
-            weights = data[self._loss_weight]
-        else:
-            weights = None
-        loss = (
-            self._loss_function(pred, target, weights=weights)
-            + self._regularisation_loss
-        )
-        return loss

-

-
-
-
-

-[docs]
-class IdentityTask(StandardLearnedTask):
-    """Identity, or trivial, task."""
-
-    def __init__(
-        self,
-        nb_outputs: int,
-        target_labels: Union[List[str], Any],
-        *args: Any,
-        **kwargs: Any,
-    ):
-        """Construct IdentityTask.
-
-        A task that does not apply a learned embedding to the input. It returns
-        the direct inputs from `Model`.
-        """
-        self._nb_inputs = nb_outputs
-        self._default_target_labels = (
-            target_labels
-            if isinstance(target_labels, list)
-            else [target_labels]
-        )
-        self._default_prediction_labels = [
-            f"target_{i}_pred" for i in range(len(self._default_target_labels))
-        ]
-
-        super().__init__(*args, **kwargs)
-        # Base class constructor
-
-    @property
-    def default_target_labels(self) -> List[str]:
-        """Return default target labels."""
-        return self._default_target_labels
-
-    @property
-    def default_prediction_labels(self) -> List[str]:
-        """Return default prediction labels."""
-        return self._default_prediction_labels
-
-    @property
-    def nb_inputs(self) -> int:
-        """Return number of inputs assumed by task."""
-        return self._nb_inputs
-
-    def _forward(self, x: Union[Tensor, Data]) -> Tensor:  # type: ignore
-        # Leave it as is.
-        return x

-
-
-
-

-[docs]
-class StandardFlowTask(Task):
-    """A `Task` for `NormalizingFlow`s in GraphNeT."""
-
-    def __init__(
-        self,
-        target_labels: List[str],
-        **task_kwargs: Any,
-    ):
-        """Construct `StandardLearnedTask`.
-
-        Args:
-            target_labels: A list of names for the targets of this Task.
-            hidden_size: The number of columns in the output of
-                         the last latent layer of `Model` using this Task.
-                         Available through `Model.nb_outputs`
-        """
-        # Base class constructor
-        super().__init__(target_labels=target_labels, **task_kwargs)
-
-

-[docs]
-    def nb_inputs(self) -> int:
-        """Return number of inputs assumed by task."""
-        return len(self._target_labels)

-
-
-    def _forward(self, x: Tensor, jacobian: Tensor) -> Tensor:  # type: ignore
-        # Leave it as is.
-        return x
-
-

-[docs]
-    @final
-    def forward(
-        self, x: Union[Tensor, Data], jacobian: Optional[Tensor]
-    ) -> Union[Tensor, Data]:
-        """Forward pass."""
-        self._regularisation_loss = 0  # Reset
-        x = self._forward(x, jacobian)
-        return self._transform_prediction(x)

-
-
-

-[docs]
-    @final
-    def compute_loss(
-        self, prediction: Tensor, jacobian: Tensor, data: Data
-    ) -> Tensor:
-        """Compute loss for normalizing flow tasks.
-
-        Args:
-            prediction: transformed sample in latent distribution space.
-            jacobian: the jacobian associated with the transformation.
-            data: the graph object.
-
-        Returns:
-            the loss associated with the transformation.
-        """
-        if self._loss_weight is not None:
-            weights = data[self._loss_weight]
-        else:
-            weights = None
-        loss = (
-            self._loss_function(
-                prediction=prediction,
-                jacobian=jacobian,
-                weights=weights,
-                target=None,
-            )
-            + self._regularisation_loss
-        )
-        return loss

-

-
-
- -
-
-
-
-
- - - - - \ No newline at end of file diff --git a/_modules/graphnet/models/utils.html b/_modules/graphnet/models/utils.html deleted file mode 100644 index 977a318ec..000000000 --- a/_modules/graphnet/models/utils.html +++ /dev/null @@ -1,430 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - graphnet.models.utils — graphnet documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Skip to content -
- -
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- -
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- -
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- - -
-
-
- -
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- -

Source code for graphnet.models.utils

-"""Utility functions for `graphnet.models`."""
-
-from typing import List, Tuple, Union
-from torch_geometric.nn import knn_graph
-from torch_geometric.data import Batch
-import torch
-from torch import Tensor, LongTensor
-
-from torch_geometric.utils.homophily import homophily
-
-
-

-[docs]
-def calculate_xyzt_homophily(
-    x: Tensor, edge_index: LongTensor, batch: Batch
-) -> Tuple[Tensor, Tensor, Tensor, Tensor]:
-    """Calculate xyzt-homophily from a batch of graphs.
-
-    Homophily is a graph scalar quantity that measures the likeness of
-    variables in nodes. Notice that this calculator assumes a special order of
-    input features in x.
-
-    Returns:
-        Tuple, each element with shape [batch_size,1].
-    """
-    hx = homophily(edge_index, x[:, 0], batch).reshape(-1, 1)
-    hy = homophily(edge_index, x[:, 1], batch).reshape(-1, 1)
-    hz = homophily(edge_index, x[:, 2], batch).reshape(-1, 1)
-    ht = homophily(edge_index, x[:, 3], batch).reshape(-1, 1)
-    return hx, hy, hz, ht

-
-
-
-

-[docs]
-def calculate_distance_matrix(xyz_coords: Tensor) -> Tensor:
-    """Calculate the matrix of pairwise distances between pulses.
-
-    Args:
-        xyz_coords: (x,y,z)-coordinates of pulses, of shape [nb_doms, 3].
-
-    Returns:
-        Matrix of pairwise distances, of shape [nb_doms, nb_doms]
-    """
-    diff = xyz_coords.unsqueeze(dim=2) - xyz_coords.T.unsqueeze(dim=0)
-    return torch.sqrt(torch.sum(diff**2, dim=1))

-
-
-
-

-[docs]
-def knn_graph_batch(batch: Batch, k: List[int], columns: List[int]) -> Batch:
-    """Calculate k-nearest-neighbours with individual k for each batch event.
-
-    Args:
-        batch: Batch of events.
-        k: A list of k's.
-        columns: The columns of Data.x used for computing the distances. E.g.,
-            Data.x[:,[0,1,2]]
-
-    Returns:
-        Returns the same batch of events, but with updated edges.
-    """
-    data_list = batch.to_data_list()
-    for i in range(len(data_list)):
-        data_list[i].edge_index = knn_graph(
-            x=data_list[i].x[:, columns], k=k[i]
-        )
-    return Batch.from_data_list(data_list)

-
-
- -
-
-
-
-
- - - - - \ No newline at end of file diff --git a/_modules/graphnet/training/utils.html b/_modules/graphnet/training/utils.html deleted file mode 100644 index 547bf5619..000000000 --- a/_modules/graphnet/training/utils.html +++ /dev/null @@ -1,697 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - graphnet.training.utils — graphnet documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Skip to content -
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- -
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- -
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-
-
- - -
-
-
- -
-
- -

Source code for graphnet.training.utils

-"""Utility functions for `graphnet.training`."""
-
-from collections import OrderedDict
-import os
-from typing import Dict, List, Optional, Tuple, Union, Callable
-
-import numpy as np
-import pandas as pd
-from pytorch_lightning import Trainer
-from sklearn.model_selection import train_test_split
-from torch.utils.data import DataLoader
-from torch_geometric.data import Batch, Data
-
-from graphnet.data.dataset import Dataset
-from graphnet.data.dataset import SQLiteDataset
-from graphnet.data.dataset import ParquetDataset
-from graphnet.models import Model
-from graphnet.utilities.logging import Logger
-from graphnet.models.graphs import GraphDefinition
-
-
-

-[docs]
-def collate_fn(graphs: List[Data]) -> Batch:
-    """Remove graphs with less than two DOM hits.
-
-    Should not occur in "production".
-    """
-    graphs = [g for g in graphs if g.n_pulses > 1]
-    return Batch.from_data_list(graphs)

-
-
-
-

-[docs]
-class collator_sequence_buckleting:
-    """Perform the sequence bucketing for the graphs in the batch."""
-
-    def __init__(self, batch_splits: List[float] = [0.8]):
-        """Set cutting points of the different mini-batches.
-
-        batch_splits: list of floats, each element is the fraction of the total
-        number of graphs. This list should not explicitly define the first and
-        last elements, which will always be 0 and 1 respectively.
-        """
-        self.batch_splits = batch_splits
-
-    def __call__(self, graphs: List[Data]) -> Batch:
-        """Execute sequence bucketing on the input list of graphs.
-
-        Args:
-            graphs: A list of Data objects representing the input graphs.
-
-        Returns:
-            A list of Batch objects, each containing a mini-batch of the input
-            graphs sorted by their number of pulses.
-        """
-        graphs = [g for g in graphs if g.n_pulses > 1]
-        graphs.sort(key=lambda x: x.n_pulses)
-        batch_list = []
-
-        for minp, maxp in zip(
-            [0] + self.batch_splits, self.batch_splits + [1]
-        ):
-            min_idx = int(minp * len(graphs))
-            max_idx = int(maxp * len(graphs))
-            this_graphs = graphs[min_idx:max_idx]
-            if len(this_graphs) > 0:
-                this_batch = Batch.from_data_list(this_graphs)
-                batch_list.append(this_batch)
-        return batch_list

-
-
-
-# @TODO: Remove in favour of DataLoader{,.from_dataset_config}
-

-[docs]
-def make_dataloader(
-    db: str,
-    pulsemaps: Union[str, List[str]],
-    graph_definition: GraphDefinition,
-    features: List[str],
-    truth: List[str],
-    *,
-    batch_size: int,
-    shuffle: bool,
-    selection: Optional[List[int]] = None,
-    num_workers: int = 10,
-    persistent_workers: bool = True,
-    node_truth: List[str] = None,
-    truth_table: str = "truth",
-    node_truth_table: Optional[str] = None,
-    string_selection: List[int] = None,
-    loss_weight_table: Optional[str] = None,
-    loss_weight_column: Optional[str] = None,
-    index_column: str = "event_no",
-    labels: Optional[Dict[str, Callable]] = None,
-) -> DataLoader:
-    """Construct `DataLoader` instance."""
-    # Check(s)
-    if isinstance(pulsemaps, str):
-        pulsemaps = [pulsemaps]
-
-    dataset = SQLiteDataset(
-        path=db,
-        pulsemaps=pulsemaps,
-        features=features,
-        truth=truth,
-        selection=selection,
-        node_truth=node_truth,
-        truth_table=truth_table,
-        node_truth_table=node_truth_table,
-        string_selection=string_selection,
-        loss_weight_table=loss_weight_table,
-        loss_weight_column=loss_weight_column,
-        index_column=index_column,
-        graph_definition=graph_definition,
-    )
-
-    # adds custom labels to dataset
-    if isinstance(labels, dict):
-        for label in labels.keys():
-            dataset.add_label(key=label, fn=labels[label])
-
-    dataloader = DataLoader(
-        dataset,
-        batch_size=batch_size,
-        shuffle=shuffle,
-        num_workers=num_workers,
-        collate_fn=collate_fn,
-        persistent_workers=persistent_workers,
-        prefetch_factor=2,
-    )
-
-    return dataloader

-
-
-
-# @TODO: Remove in favour of DataLoader{,.from_dataset_config}
-

-[docs]
-def make_train_validation_dataloader(
-    db: str,
-    graph_definition: GraphDefinition,
-    selection: Optional[List[int]],
-    pulsemaps: Union[str, List[str]],
-    features: List[str],
-    truth: List[str],
-    *,
-    batch_size: int,
-    database_indices: Optional[List[int]] = None,
-    seed: int = 42,
-    test_size: float = 0.33,
-    num_workers: int = 10,
-    persistent_workers: bool = True,
-    node_truth: Optional[str] = None,
-    truth_table: str = "truth",
-    node_truth_table: Optional[str] = None,
-    string_selection: Optional[List[int]] = None,
-    loss_weight_column: Optional[str] = None,
-    loss_weight_table: Optional[str] = None,
-    index_column: str = "event_no",
-    labels: Optional[Dict[str, Callable]] = None,
-) -> Tuple[DataLoader, DataLoader]:
-    """Construct train and test `DataLoader` instances."""
-    # Reproducibility
-    rng = np.random.default_rng(seed=seed)
-    # Checks(s)
-    if isinstance(pulsemaps, str):
-        pulsemaps = [pulsemaps]
-
-    if selection is None:
-        # If no selection is provided, use all events in dataset.
-        dataset: Dataset
-        if db.endswith(".db"):
-            dataset = SQLiteDataset(
-                path=db,
-                graph_definition=graph_definition,
-                pulsemaps=pulsemaps,
-                features=features,
-                truth=truth,
-                truth_table=truth_table,
-                index_column=index_column,
-            )
-        elif db.endswith(".parquet"):
-            dataset = ParquetDataset(
-                path=db,
-                graph_definition=graph_definition,
-                pulsemaps=pulsemaps,
-                features=features,
-                truth=truth,
-                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
-    if isinstance(db, list):
-        df_for_shuffle = pd.DataFrame(
-            {"event_no": selection, "db": database_indices}
-        )
-        shuffled_df = df_for_shuffle.sample(
-            frac=1, replace=False, random_state=rng
-        )
-        training_df, validation_df = train_test_split(
-            shuffled_df, test_size=test_size, random_state=seed
-        )
-        training_selection = training_df.values.tolist()
-        validation_selection = validation_df.values.tolist()
-    else:
-        training_selection, validation_selection = train_test_split(
-            selection, test_size=test_size, random_state=seed
-        )
-
-    # Create DataLoaders
-    common_kwargs = dict(
-        db=db,
-        pulsemaps=pulsemaps,
-        features=features,
-        truth=truth,
-        batch_size=batch_size,
-        num_workers=num_workers,
-        persistent_workers=persistent_workers,
-        node_truth=node_truth,
-        truth_table=truth_table,
-        node_truth_table=node_truth_table,
-        string_selection=string_selection,
-        loss_weight_column=loss_weight_column,
-        loss_weight_table=loss_weight_table,
-        index_column=index_column,
-        labels=labels,
-        graph_definition=graph_definition,
-    )
-
-    training_dataloader = make_dataloader(
-        shuffle=True,
-        selection=training_selection,
-        **common_kwargs,  # type: ignore[arg-type]
-    )
-
-    validation_dataloader = make_dataloader(
-        shuffle=False,
-        selection=validation_selection,
-        **common_kwargs,  # type: ignore[arg-type]
-    )
-
-    return (
-        training_dataloader,
-        validation_dataloader,
-    )

-
-
-
-# @TODO: Remove in favour of Model.predict{,_as_dataframe}
-

-[docs]
-def get_predictions(
-    trainer: Trainer,
-    model: Model,
-    dataloader: DataLoader,
-    prediction_columns: List[str],
-    *,
-    node_level: bool = False,
-    additional_attributes: Optional[List[str]] = None,
-) -> pd.DataFrame:
-    """Get `model` predictions on `dataloader`."""
-    # Gets predictions from model on the events in the dataloader.
-    # NOTE: dataloader must NOT have shuffle = True!
-
-    # Check(s)
-    if additional_attributes is None:
-        additional_attributes = []
-    assert isinstance(additional_attributes, list)
-
-    # Set model to inference mode
-    model.inference()
-
-    # Get predictions
-    predictions_torch = trainer.predict(model, dataloader)
-    predictions_list = [
-        p[0].detach().cpu().numpy() for p in predictions_torch
-    ]  # Assuming single task
-    predictions = np.concatenate(predictions_list, axis=0)
-    try:
-        assert len(prediction_columns) == predictions.shape[1]
-    except IndexError:
-        predictions = predictions.reshape((-1, 1))
-        assert len(prediction_columns) == predictions.shape[1]
-
-    # Get additional attributes
-    attributes: Dict[str, List[np.ndarray]] = OrderedDict(
-        [(attr, []) for attr in additional_attributes]
-    )
-    for batch in dataloader:
-        for attr in attributes:
-            attribute = batch[attr].detach().cpu().numpy()
-            if node_level:
-                if attr == "event_no":
-                    attribute = np.repeat(
-                        attribute, batch["n_pulses"].detach().cpu().numpy()
-                    )
-            attributes[attr].extend(attribute)
-
-    data = np.concatenate(
-        [predictions]
-        + [
-            np.asarray(values)[:, np.newaxis] for values in attributes.values()
-        ],
-        axis=1,
-    )
-
-    results = pd.DataFrame(
-        data, columns=prediction_columns + additional_attributes
-    )
-    return results

-
-
-
-# @TODO: Remove
-

-[docs]
-def save_results(
-    db: str, tag: str, results: pd.DataFrame, archive: str, model: Model
-) -> None:
-    """Save trained model and prediction `results` in `db`."""
-    db_name = db.split("/")[-1].split(".")[0]
-    path = archive + "/" + db_name + "/" + tag
-    os.makedirs(path, exist_ok=True)
-    results.to_csv(path + "/results.csv")
-    model.save_state_dict(path + "/" + tag + "_state_dict.pth")
-    model.save(path + "/" + tag + "_model.pth")
-    Logger().info("Results saved at: \n %s" % path)

-
-
- -
-
-
-
-
- - - - - \ No newline at end of file diff --git a/_modules/index.html b/_modules/index.html index b5d45ae22..0f4299580 100644 --- a/_modules/index.html +++ b/_modules/index.html @@ -323,10 +323,6 @@

All modules for which code is available

@@ -571,36 +465,7 @@
@@ -610,202 +475,8 @@
-
-

dataset

-

Base Dataset class(es) used in GraphNeT.

-
-
-exception graphnet.data.dataset.dataset.ColumnMissingException[source]
-

Bases: Exception

-

Exception to indicate a missing column in a dataset.

-
-
-
-graphnet.data.dataset.dataset.load_module(class_name)[source]
-

Load graphnet module from string name.

-
-
Parameters:
-

class_name (str) – name of class

-
-
Return type:
-

Type

-
-
Returns:
-

graphnet module.

-
-
-
-
-
-graphnet.data.dataset.dataset.parse_graph_definition(cfg)[source]
-

Construct GraphDefinition from DatasetConfig.

-
-
Return type:
-

GraphDefinition

-
-
Parameters:
-

cfg (dict) –

-
-
-
-
-
-class graphnet.data.dataset.dataset.Dataset(*args, **kwargs)[source]
-

Bases: Logger, Configurable, Dataset, ABC

-

Base Dataset class for reading from any intermediate file format.

-

Construct Dataset.

-
-
Parameters:
-
    -

  • path (Union[str, List[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 -different DOM types are stored in different maps.

    • -

  • features (List[str]) – List of columns in the input files that should be used as -node features on the graph objects.

    • -

  • truth (List[str]) – List of event-level columns in the input files that should -be used added as attributes on the graph objects.

    • -

  • node_truth (Optional[List[str]], default: None) – List of node-level columns in the input files that -should be used added as attributes on the graph objects.

    • -

  • index_column (str, default: 'event_no') – Name of the column in the input files that contains -unique indicies to identify and map events across tables.

    • -

  • truth_table (str, default: 'truth') – Name of the table containing event-level truth -information.

    • -

  • node_truth_table (Optional[str], default: None) – Name of the table containing node-level truth -information.

    • -

  • 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.

    • -

  • 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.

    • -

  • loss_weight_column (Optional[str], default: None) – 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 (Optional[float], default: None) – 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 (Optional[int], default: None) – 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 (GraphDefinition) – Method that defines the graph representation.

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • -
-
-
Return type:
-

object

-
-
-
-
-classmethod from_config(source)[source]
-

Construct Dataset instance from source configuration.

-
-
Return type:
-

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

-
-
Parameters:
-

source (DatasetConfig | str) –

-
-
-
-
-
-classmethod concatenate(datasets)[source]
-

Concatenate multiple `Dataset`s into one instance.

-
-
Return type:
-

EnsembleDataset

-
-
Parameters:
-

datasets (List[Dataset]) –

-
-
-
-
-
-property path: str | List[str]
-

Path to the file(s) from which this Dataset reads.

-
-
-
-property truth_table: str
-

Name of the table containing event-level truth information.

-
-
-
-abstract query_table(table, columns, sequential_index, selection)[source]
-

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

-
-
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:
-

List[Tuple[Any, ...]]

-
-
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.

-
-
-
-
-
-add_label(fn, key)[source]
-

Add custom graph label define using function fn.

-
-
Return type:
-

None

-
-
Parameters:
-
    -

  • fn (Callable[[Data], Any]) –

    • -

  • key (str | None) –

    • -
-
-
-
-
-
-
-class graphnet.data.dataset.dataset.EnsembleDataset(datasets)[source]
-

Bases: ConcatDataset

-

Construct a single dataset from a collection of datasets.

-

Construct a single dataset from a collection of datasets.

-
-
Parameters:
-

datasets (Iterable[Dataset]) – A collection of Datasets

-
-
-
+
+

dataset

diff --git a/api/graphnet.data.dataset.html b/api/graphnet.data.dataset.html index 4dc0f578f..60df5f0c1 100644 --- a/api/graphnet.data.dataset.html +++ b/api/graphnet.data.dataset.html @@ -474,9 +474,8 @@
-
-

dataset

-

Dataset classes for training in GraphNeT.

+
+

dataset

Subpackages

diff --git a/api/graphnet.data.dataset.parquet.html b/api/graphnet.data.dataset.parquet.html index d66b67d51..92b378c4d 100644 --- a/api/graphnet.data.dataset.parquet.html +++ b/api/graphnet.data.dataset.parquet.html @@ -482,16 +482,12 @@
-
-

parquet

-

Datasets using parquet backend.

+
+

parquet

Submodules

diff --git a/api/graphnet.data.dataset.parquet.parquet_dataset.html b/api/graphnet.data.dataset.parquet.parquet_dataset.html index 349f42c6b..82f085002 100644 --- a/api/graphnet.data.dataset.parquet.parquet_dataset.html +++ b/api/graphnet.data.dataset.parquet.parquet_dataset.html @@ -328,36 +328,11 @@ - - @@ -498,18 +473,7 @@
@@ -519,87 +483,8 @@
-
-

parquet_dataset

-

Dataset class(es) for reading from Parquet files.

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

Bases: Dataset

-

Pytorch dataset for reading from Parquet files.

-

Construct Dataset.

-
-
Parameters:
-
    -

  • path (Union[str, List[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 -different DOM types are stored in different maps.

    • -

  • features (List[str]) – List of columns in the input files that should be used as -node features on the graph objects.

    • -

  • truth (List[str]) – List of event-level columns in the input files that should -be used added as attributes on the graph objects.

    • -

  • node_truth (Optional[List[str]], default: None) – List of node-level columns in the input files that -should be used added as attributes on the graph objects.

    • -

  • index_column (str, default: 'event_no') – Name of the column in the input files that contains -unique indicies to identify and map events across tables.

    • -

  • truth_table (str, default: 'truth') – Name of the table containing event-level truth -information.

    • -

  • node_truth_table (Optional[str], default: None) – Name of the table containing node-level truth -information.

    • -

  • 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.

    • -

  • 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.

    • -

  • loss_weight_column (Optional[str], default: None) – 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 (Optional[float], default: None) – 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 (Optional[int], default: None) – 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 (GraphDefinition) – Method that defines the graph representation.

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • -
-
-
Return type:
-

object

-
-
-
-
-query_table(table, columns, sequential_index, selection)[source]
-

Query 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) –

    • -
-
-
-
-
+
+

parquet_dataset

diff --git a/api/graphnet.data.dataset.sqlite.html b/api/graphnet.data.dataset.sqlite.html index 8c8466a90..1564c771f 100644 --- a/api/graphnet.data.dataset.sqlite.html +++ b/api/graphnet.data.dataset.sqlite.html @@ -482,16 +482,12 @@
-
-

sqlite

-

Datasets using SQLite backend.

+
+

sqlite

Submodules

diff --git a/api/graphnet.data.dataset.sqlite.sqlite_dataset.html b/api/graphnet.data.dataset.sqlite.sqlite_dataset.html index e7c699424..41e7fac49 100644 --- a/api/graphnet.data.dataset.sqlite.sqlite_dataset.html +++ b/api/graphnet.data.dataset.sqlite.sqlite_dataset.html @@ -335,36 +335,11 @@ - - @@ -498,18 +473,7 @@
@@ -519,87 +483,8 @@
-
-

sqlite_dataset

-

Dataset class(es) for reading data from SQLite databases.

-
-
-class graphnet.data.dataset.sqlite.sqlite_dataset.SQLiteDataset(*args, **kwargs)[source]
-

Bases: Dataset

-

Pytorch dataset for reading data from SQLite databases.

-

Construct Dataset.

-
-
Parameters:
-
    -

  • path (Union[str, List[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 -different DOM types are stored in different maps.

    • -

  • features (List[str]) – List of columns in the input files that should be used as -node features on the graph objects.

    • -

  • truth (List[str]) – List of event-level columns in the input files that should -be used added as attributes on the graph objects.

    • -

  • node_truth (Optional[List[str]], default: None) – List of node-level columns in the input files that -should be used added as attributes on the graph objects.

    • -

  • index_column (str, default: 'event_no') – Name of the column in the input files that contains -unique indicies to identify and map events across tables.

    • -

  • truth_table (str, default: 'truth') – Name of the table containing event-level truth -information.

    • -

  • node_truth_table (Optional[str], default: None) – Name of the table containing node-level truth -information.

    • -

  • 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.

    • -

  • 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.

    • -

  • loss_weight_column (Optional[str], default: None) – 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 (Optional[float], default: None) – 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 (Optional[int], default: None) – 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 (GraphDefinition) – Method that defines the graph representation.

    • -

  • args (Any) –

    • -

  • kwargs (Any) –

    • -
-
-
Return type:
-

object

-
-
-
-
-query_table(table, columns, sequential_index, selection)[source]
-

Query 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) –

    • -
-
-
-
-
+
+

sqlite_dataset

diff --git a/api/graphnet.data.html b/api/graphnet.data.html index 5e2ae42f4..ecbcd0f4f 100644 --- a/api/graphnet.data.html +++ b/api/graphnet.data.html @@ -514,22 +514,14 @@
  • DataConverter
    • -
  • dataloader -
    • +
  • dataloader
  • filters
    • -
  • pipeline -
    • +
  • pipeline
    • diff --git a/api/graphnet.data.pipeline.html b/api/graphnet.data.pipeline.html index 4564c978d..f616b57ec 100644 --- a/api/graphnet.data.pipeline.html +++ b/api/graphnet.data.pipeline.html @@ -379,25 +379,11 @@ - - @@ -457,14 +443,7 @@
    @@ -474,36 +453,8 @@
    -
    -

    pipeline

    -

    Class(es) used for analysis in PISA.

    -
    -
    -class graphnet.data.pipeline.InSQLitePipeline(module_dict, features, truth, device, retro_table_name, outdir, batch_size, n_workers, pipeline_name)[source]
    -

    Bases: ABC, Logger

    -

    Create a SQLite database for PISA analysis.

    -

    The database will contain truth and GNN predictions and, if available, -RETRO reconstructions.

    -

    Initialise the pipeline.

    -
    -
    Parameters:
    -
      -

    • module_dict (Dict) – A dictionary with GNN modules from GraphNet. E.g. -{‘energy’: gnn_module_for_energy_regression}

      • -

    • features (List[str]) – List of input features for the GNN modules.

      • -

    • truth (List[str]) – List of truth for the GNN ModuleList.

      • -

    • device (device) – The device used for computation.

      • -

    • retro_table_name (str, default: 'retro') – Name of the retro table for.

      • -

    • outdir (Optional[str], default: None) – the directory in which the pipeline database will be -stored.

      • -

    • batch_size (int, default: 100) – Batch size for inference.

      • -

    • n_workers (int, default: 10) – Number of workers used in dataloading.

      • -

    • pipeline_name (str, default: 'pipeline') – Name of the pipeline. If such a pipeline already -exists, an error will be prompted to avoid overwriting.

      • -
    -
    -
    -
    +
    +

    pipeline

    diff --git a/api/graphnet.data.utilities.string_selection_resolver.html b/api/graphnet.data.utilities.string_selection_resolver.html index 2abdce906..b404e94d3 100644 --- a/api/graphnet.data.utilities.string_selection_resolver.html +++ b/api/graphnet.data.utilities.string_selection_resolver.html @@ -559,7 +559,7 @@
    Parameters:
    @@ -427,18 +395,7 @@
    @@ -448,94 +405,8 @@
    -
    -

    graphnet_module

    -

    Class(es) for deploying GraphNeT models in icetray as I3Modules.

    -
    -
    -class graphnet.deployment.i3modules.graphnet_module.GraphNeTI3Module(graph_definition, pulsemap, features, pulsemap_extractor, gcd_file)[source]
    -

    Bases: object

    -

    Base I3 Module for GraphNeT.

    -

    Contains methods for extracting pulsemaps, producing graphs and writing to -frames.

    -

    I3Module Constructor.

    -
    -
    Parameters:
    -
      -

    • graph_definition (GraphDefinition) – An instance of GraphDefinition. E.g. KNNGraph.

      • -

    • pulsemap (str) – the pulse map on which the module functions

      • -

    • features (List[str]) – the features that is used from the pulse map. -E.g. [dom_x, dom_y, dom_z, charge]

      • -

    • pulsemap_extractor (Union[List[I3FeatureExtractor], I3FeatureExtractor]) – The I3FeatureExtractor used to extract the -pulsemap from the I3Frames

      • -

    • gcd_file (str) – Path to the associated gcd-file.

      • -
    -
    -
    -
    -
    -
    -class graphnet.deployment.i3modules.graphnet_module.I3InferenceModule(pulsemap, features, pulsemap_extractor, model_config, state_dict, model_name, gcd_file, prediction_columns)[source]
    -

    Bases: GraphNeTI3Module

    -

    General class for inference on i3 frames.

    -

    General class for inference on I3Frames (physics).

    -
    -
    Parameters:
    -
      -

    • pulsemap (str) – the pulsmap that the model is expecting as input.

      • -

    • features (List[str]) – the features of the pulsemap that the model is expecting.

      • -

    • pulsemap_extractor (Union[List[I3FeatureExtractor], I3FeatureExtractor]) – The extractor used to extract the pulsemap.

      • -

    • model_config (Union[ModelConfig, str]) – The ModelConfig (or path to it) that summarizes the -model used for inference.

      • -

    • state_dict (str) – Path to state_dict containing the learned weights.

      • -

    • model_name (str) – The name used for the model. Will help define the -named entry in the I3Frame. E.g. “dynedge”.

      • -

    • gcd_file (str) – path to associated gcd file.

      • -

    • prediction_columns (Union[str, List[str], None], default: None) –

      column names for the predictions of the model. -Will help define the named entry in the I3Frame.

      -
      -

      E.g. [‘energy_reco’]. Optional.

      -
      -

      • -
    -
    -
    -
    -
    -
    -class graphnet.deployment.i3modules.graphnet_module.I3PulseCleanerModule(pulsemap, features, pulsemap_extractor, model_config, state_dict, model_name, *, gcd_file, threshold, discard_empty_events, prediction_columns)[source]
    -

    Bases: I3InferenceModule

    -

    A specialized module for pulse cleaning.

    -

    It is assumed that the model provided has been trained for this.

    -

    General class for inference on I3Frames (physics).

    -
    -
    Parameters:
    -
      -

    • pulsemap (str) – the pulsmap that the model is expecting as input -(the one that is being cleaned).

      • -

    • features (List[str]) – the features of the pulsemap that the model is expecting.

      • -

    • pulsemap_extractor (Union[List[I3FeatureExtractor], I3FeatureExtractor]) – The extractor used to extract the pulsemap.

      • -

    • model_config (str) – The ModelConfig (or path to it) that summarizes the -model used for inference.

      • -

    • state_dict (str) – Path to state_dict containing the learned weights.

      • -

    • model_name (str) – The name used for the model. Will help define the named -entry in the I3Frame. E.g. “dynedge”.

      • -

    • gcd_file (str) – path to associated gcd file.

      • -

    • threshold (float, default: 0.7) – the threshold for being considered a positive case. -E.g., predictions >= threshold will be considered -to be signal, all else noise.

      • -

    • discard_empty_events (bool, default: False) – When true, this flag will eliminate events -whose cleaned pulse series are empty. Can be used -to speed up processing especially for noise -simulation, since it will not do any writing or -further calculations.

      • -

    • prediction_columns (Union[str, List[str], None], default: None) – column names for the predictions of the model. -Will help define the named entry in the I3Frame. -E.g. [‘energy_reco’]. Optional.

      • -
    -
    -
    -
    +
    +

    graphnet_module

    diff --git a/api/graphnet.deployment.i3modules.html b/api/graphnet.deployment.i3modules.html index 434164c3f..6a247ab6a 100644 --- a/api/graphnet.deployment.i3modules.html +++ b/api/graphnet.deployment.i3modules.html @@ -410,12 +410,7 @@

    i3modules

    diff --git a/api/graphnet.models.coarsening.html b/api/graphnet.models.coarsening.html index 602eed114..369288274 100644 --- a/api/graphnet.models.coarsening.html +++ b/api/graphnet.models.coarsening.html @@ -125,7 +125,6 @@ - @@ -366,90 +365,11 @@ - -
  • @@ -516,30 +436,7 @@
    @@ -549,134 +446,8 @@
    -
    -

    coarsening

    -

    Class(es) for coarsening operations (i.e., clustering, or local pooling).

    -
    -
    -graphnet.models.coarsening.unbatch_edge_index(edge_index, batch)[source]
    -

    Splits the edge_index according to a batch vector.

    -
    -
    Parameters:
    -
      -

    • edge_index (Tensor) – The edge_index tensor. Must be ordered.

      • -

    • batch (LongTensor) – The batch vector -\(\mathbf{b} \in {\{ 0, \ldots, B-1\}}^N\), which assigns each -node to a specific example. Must be ordered.

      • -
    -
    -
    Return type:
    -

    List[Tensor]

    -
    -
    -
    -
    -
    -class graphnet.models.coarsening.Coarsening(*args, **kwargs)[source]
    -

    Bases: Model

    -

    Base class for coarsening operations.

    -

    Construct Coarsening.

    -
    -
    Parameters:
    -
      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -reduce_options = {'avg': (<function avg_pool>, <function avg_pool_x>), 'max': (<function max_pool>, <function max_pool_x>), 'min': (<function min_pool>, <function min_pool_x>), 'sum': (<function sum_pool>, <function sum_pool_x>)}
    -
    -
    -
    -forward(data)[source]
    -

    Perform coarsening operation.

    -
    -
    Return type:
    -

    Union[Data, Batch]

    -
    -
    Parameters:
    -

    data (Data | Batch) –

    -
    -
    -
    -
    -
    -
    -class graphnet.models.coarsening.AttributeCoarsening(*args, **kwargs)[source]
    -

    Bases: Coarsening

    -

    Coarsen pulses based on specified attributes.

    -

    Construct SimpleCoarsening.

    -
    -
    Parameters:
    -
      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -
    -class graphnet.models.coarsening.DOMCoarsening(*args, **kwargs)[source]
    -

    Bases: Coarsening

    -

    Coarsen pulses to DOM-level.

    -

    Cluster pulses on the same DOM.

    -
    -
    Parameters:
    -
      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -
    -class graphnet.models.coarsening.CustomDOMCoarsening(*args, **kwargs)[source]
    -

    Bases: DOMCoarsening

    -

    Coarsen pulses to DOM-level with additional attributes.

    -

    Cluster pulses on the same DOM.

    -
    -
    Parameters:
    -
      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -
    -class graphnet.models.coarsening.DOMAndTimeWindowCoarsening(*args, **kwargs)[source]
    -

    Bases: Coarsening

    -

    Coarsen pulses to DOM-level, with additional time-window clustering.

    -

    Cluster pulses on the same DOM within time_window.

    -
    -
    Parameters:
    -
      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    +
    +

    coarsening

    diff --git a/api/graphnet.models.components.html b/api/graphnet.models.components.html index 073301a16..e72fdd239 100644 --- a/api/graphnet.models.components.html +++ b/api/graphnet.models.components.html @@ -460,31 +460,13 @@
    -
    -

    components

    -

    Components for constructing models.

    +
    +

    components

    Submodules

    diff --git a/api/graphnet.models.components.layers.html b/api/graphnet.models.components.layers.html index f7cebd134..2e3ad6d0b 100644 --- a/api/graphnet.models.components.layers.html +++ b/api/graphnet.models.components.layers.html @@ -336,94 +336,11 @@ - -
  • @@ -534,34 +451,7 @@
    @@ -571,145 +461,8 @@
    -
    -

    layers

    -

    Class(es) implementing layers to be used in graphnet models.

    -
    -
    -class graphnet.models.components.layers.DynEdgeConv(nn, aggr, nb_neighbors, features_subset, **kwargs)[source]
    -

    Bases: EdgeConv, LightningModule

    -

    Dynamical edge convolution layer.

    -

    Construct DynEdgeConv.

    -
    -
    Parameters:
    -
      -

    • nn (Callable) – The MLP/torch.Module to be used within the EdgeConv.

      • -

    • aggr (str, default: 'max') – Aggregation method to be used with EdgeConv.

      • -

    • nb_neighbors (int, default: 8) – Number of neighbours to be clustered after the -EdgeConv operation.

      • -

    • features_subset (Union[Sequence[int], slice, None], default: None) – Subset of features in Data.x that should be used -when dynamically performing the new graph clustering after the -EdgeConv operation. Defaults to all features.

      • -

    • **kwargs (Any) – Additional features to be passed to EdgeConv.

      • -
    -
    -
    -
    -
    -forward(x, edge_index, batch)[source]
    -

    Forward pass.

    -
    -
    Return type:
    -

    Tensor

    -
    -
    Parameters:
    -
      -

    • x (Tensor) –

      • -

    • edge_index (Tensor | SparseTensor) –

      • -

    • batch (Tensor | None) –

      • -
    -
    -
    -
    -
    -
    -
    -class graphnet.models.components.layers.EdgeConvTito(nn, aggr, **kwargs)[source]
    -

    Bases: MessagePassing, LightningModule

    -

    Implementation of EdgeConvTito layer used in TITO solution for.

    -

    ‘IceCube - Neutrinos in Deep’ kaggle competition.

    -

    Construct EdgeConvTito.

    -
    -
    Parameters:
    -
      -

    • nn (Callable) – The MLP/torch.Module to be used within the EdgeConvTito.

      • -

    • aggr (str, default: 'max') – Aggregation method to be used with EdgeConvTito.

      • -

    • **kwargs (Any) – Additional features to be passed to EdgeConvTito.

      • -
    -
    -
    -
    -
    -reset_parameters()[source]
    -

    Reset all learnable parameters of the module.

    -
    -
    Return type:
    -

    None

    -
    -
    -
    -
    -
    -forward(x, edge_index)[source]
    -

    Forward pass.

    -
    -
    Return type:
    -

    Tensor

    -
    -
    Parameters:
    -
      -

    • x (Tensor | Tuple[Tensor, Tensor]) –

      • -

    • edge_index (Tensor | SparseTensor) –

      • -
    -
    -
    -
    -
    -
    -message(x_i, x_j)[source]
    -

    Edgeconvtito message passing.

    -
    -
    Return type:
    -

    Tensor

    -
    -
    Parameters:
    -
      -

    • x_i (Tensor) –

      • -

    • x_j (Tensor) –

      • -
    -
    -
    -
    -
    -
    -
    -class graphnet.models.components.layers.DynTrans(layer_sizes, aggr, features_subset, n_head, **kwargs)[source]
    -

    Bases: EdgeConvTito, LightningModule

    -

    Implementation of dynTrans1 layer used in TITO solution for.

    -

    ‘IceCube - Neutrinos in Deep’ kaggle competition.

    -

    Construct DynTrans.

    -
    -
    Parameters:
    -
      -

    • nn – The MLP/torch.Module to be used within the DynTrans.

      • -

    • layer_sizes (Optional[List[int]], default: None) – List of layer sizes to be used in DynTrans.

      • -

    • aggr (str, default: 'max') – Aggregation method to be used with DynTrans.

      • -

    • features_subset (Union[Sequence[int], slice, None], default: None) – Subset of features in Data.x that should be used -when dynamically performing the new graph clustering after the -EdgeConv operation. Defaults to all features.

      • -

    • n_head (int, default: 8) – Number of heads to be used in the multiheadattention models.

      • -

    • **kwargs (Any) – Additional features to be passed to DynTrans.

      • -
    -
    -
    -
    -
    -forward(x, edge_index, batch)[source]
    -

    Forward pass.

    -
    -
    Return type:
    -

    Tensor

    -
    -
    Parameters:
    -
      -

    • x (Tensor) –

      • -

    • edge_index (Tensor | SparseTensor) –

      • -

    • batch (Tensor | None) –

      • -
    -
    -
    -
    -
    +
    +

    layers

    diff --git a/api/graphnet.models.components.pool.html b/api/graphnet.models.components.pool.html index 00ca61435..5cd8d2b76 100644 --- a/api/graphnet.models.components.pool.html +++ b/api/graphnet.models.components.pool.html @@ -125,7 +125,6 @@ - @@ -344,106 +343,11 @@ - -
    • @@ -547,32 +451,7 @@
    @@ -582,220 +461,8 @@
    -
    -

    pool

    -

    Functions for performing pooling/clustering/coarsening.

    -
    -
    -graphnet.models.components.pool.min_pool(cluster, data, transform)[source]
    -

    Perform min-pooling of Data.

    -

    Like max_pool, just negating `data.x.

    -
    -
    Return type:
    -

    Data

    -
    -
    Parameters:
    -
      -

    • cluster (LongTensor) –

      • -

    • data (Data) –

      • -

    • transform (Any | None) –

      • -
    -
    -
    -
    -
    -
    -graphnet.models.components.pool.min_pool_x(cluster, x, batch, size)[source]
    -

    Perform min-pooling of Tensor.

    -

    Like max_pool_x, just negating `x.

    -
    -
    Return type:
    -

    Tensor

    -
    -
    Parameters:
    -
      -

    • cluster (LongTensor) –

      • -

    • x (Tensor) –

      • -

    • batch (LongTensor) –

      • -

    • size (int | None) –

      • -
    -
    -
    -
    -
    -
    -graphnet.models.components.pool.sum_pool_and_distribute(tensor, cluster_index, batch)[source]
    -

    Sum-pool values and distribute result to the individual nodes.

    -
    -
    Return type:
    -

    Tensor

    -
    -
    Parameters:
    -
      -

    • tensor (Tensor) –

      • -

    • cluster_index (LongTensor) –

      • -

    • batch (LongTensor | None) –

      • -
    -
    -
    -
    -
    -
    -graphnet.models.components.pool.group_by(data, keys)[source]
    -

    Group nodes in data that have identical values of keys.

    -

    This grouping is done with in each event in case of batching. This allows -for, e.g., assigning the same index to all pulses on the same PMT or DOM in -the same event. This can be used for coarsening graphs, e.g., from pulse- -level to DOM-level by aggregating feature across each group returned by this -method.

    -
    -
    Return type:
    -

    LongTensor

    -
    -
    Parameters:
    -
      -

    • data (Data | Batch) –

      • -

    • keys (List[str]) –

      • -
    -
    -
    -

    Example

    -
    -
    Given:

    data.f1 = [1,1,2,2,2] -data.f2 = [6,7,7,7,8]

    -
    -
    Calls:

    groupby(data, [‘f1’]) -> [0, 0, 1, 1, 1] -groupby(data, [‘f2’]) -> [0, 1, 1, 1, 2] -groupby(data, [‘f1’, ‘f2’]) -> [0, 1, 2, 2, 3]

    -
    -
    -
    -
    -
    -graphnet.models.components.pool.group_pulses_to_dom(data)[source]
    -

    Group pulses on the same DOM, using DOM and string number.

    -
    -
    Return type:
    -

    Data

    -
    -
    Parameters:
    -

    data (Data) –

    -
    -
    -
    -
    -
    -graphnet.models.components.pool.group_pulses_to_pmt(data)[source]
    -

    Group pulses on the same PMT, using PMT, DOM, and string number.

    -
    -
    Return type:
    -

    Data

    -
    -
    Parameters:
    -

    data (Data) –

    -
    -
    -
    -
    -
    -graphnet.models.components.pool.sum_pool_x(cluster, x, batch, size)[source]
    -

    Sum-pool node features according to the clustering defined in cluster.

    -
    -
    Parameters:
    -
      -

    • cluster (LongTensor) – Cluster vector \(\mathbf{c} \in \{ 0, -\ldots, N - 1 \}^N\), which assigns each node to a specific cluster.

      • -

    • x (Tensor) – Node feature matrix -\(\mathbf{X} \in \mathbb{R}^{(N_1 + \ldots + N_B) \times F}\).

      • -

    • batch (LongTensor) – Batch vector \(\mathbf{b} \in {\{ 0, \ldots, -B-1\}}^N\), which assigns each node to a specific example.

      • -

    • size (Optional[int], default: None) – The maximum number of clusters in a single -example. This property is useful to obtain a batch-wise dense -representation, e.g. for applying FC layers, but should only be -used if the size of the maximum number of clusters per example is -known in advance.

      • -
    -
    -
    Return type:
    -

    Tensor

    -
    -
    -
    -
    -
    -graphnet.models.components.pool.std_pool_x(cluster, x, batch, size)[source]
    -

    Std-pool node features according to the clustering defined in cluster.

    -
    -
    Parameters:
    -
      -

    • cluster (LongTensor) – Cluster vector \(\mathbf{c} \in \{ 0, -\ldots, N - 1 \}^N\), which assigns each node to a specific cluster.

      • -

    • x (Tensor) – Node feature matrix -\(\mathbf{X} \in \mathbb{R}^{(N_1 + \ldots + N_B) \times F}\).

      • -

    • batch (LongTensor) – Batch vector \(\mathbf{b} \in {\{ 0, \ldots, -B-1\}}^N\), which assigns each node to a specific example.

      • -

    • size (Optional[int], default: None) – The maximum number of clusters in a single -example. This property is useful to obtain a batch-wise dense -representation, e.g. for applying FC layers, but should only be -used if the size of the maximum number of clusters per example is -known in advance.

      • -
    -
    -
    Return type:
    -

    Tensor

    -
    -
    -
    -
    -
    -graphnet.models.components.pool.sum_pool(cluster, data, transform)[source]
    -

    Pool and coarsen graph according to the clustering defined in cluster.

    -

    All nodes within the same cluster will be represented as one node. -Final node features are defined by the sum of features of all nodes -within the same cluster, node positions are averaged and edge indices are -defined to be the union of the edge indices of all nodes within the same -cluster.

    -
    -
    Parameters:
    -
      -

    • cluster (LongTensor) – Cluster vector \(\mathbf{c} \in \{ 0, -\ldots, N - 1 \}^N\), which assigns each node to a specific cluster.

      • -

    • data (Data) – Graph data object.

      • -

    • transform (Optional[Callable], default: None) – A function/transform that takes in the -coarsened and pooled torch_geometric.data.Data object and -returns a transformed version.

      • -
    -
    -
    Return type:
    -

    Data

    -
    -
    -
    -
    -
    -graphnet.models.components.pool.std_pool(cluster, data, transform)[source]
    -

    Pool and coarsen graph according to the clustering defined in cluster.

    -

    All nodes within the same cluster will be represented as one node. -Final node features are defined by the std of features of all nodes -within the same cluster, node positions are averaged and edge indices are -defined to be the union of the edge indices of all nodes within the same -cluster.

    -
    -
    Parameters:
    -
      -

    • cluster (LongTensor) – Cluster vector \(\mathbf{c} \in \{ 0, -\ldots, N - 1 \}^N\), which assigns each node to a specific cluster.

      • -

    • data (Data) – Graph data object.

      • -

    • transform (Optional[Callable], default: None) – A function/transform that takes in the -coarsened and pooled torch_geometric.data.Data object and -returns a transformed version.

      • -
    -
    -
    Return type:
    -

    Data

    -
    -
    -
    +
    +

    pool

    diff --git a/api/graphnet.models.gnn.convnet.html b/api/graphnet.models.gnn.convnet.html index 6b11359f2..333d51552 100644 --- a/api/graphnet.models.gnn.convnet.html +++ b/api/graphnet.models.gnn.convnet.html @@ -350,36 +350,11 @@ - -
  • @@ -497,18 +472,7 @@
    @@ -518,47 +482,8 @@
    -
    -

    convnet

    -

    Implementation of the ConvNet GNN model architecture.

    -

    Author: Martin Ha Minh

    -
    -
    -class graphnet.models.gnn.convnet.ConvNet(*args, **kwargs)[source]
    -

    Bases: GNN

    -

    ConvNet (convolutional network) model.

    -

    Construct ConvNet.

    -
    -
    Parameters:
    -
      -

    • nb_inputs (int) – Number of input features, i.e. dimension of input -layer.

      • -

    • nb_outputs (int) – Number of prediction labels, i.e. dimension of -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) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -forward(data)[source]
    -

    Apply learnable forward pass.

    -
    -
    Return type:
    -

    Tensor

    -
    -
    Parameters:
    -

    data (Data) –

    -
    -
    -
    -
    +
    +

    convnet

    diff --git a/api/graphnet.models.gnn.dynedge.html b/api/graphnet.models.gnn.dynedge.html index ec76a893b..8b6a25eb0 100644 --- a/api/graphnet.models.gnn.dynedge.html +++ b/api/graphnet.models.gnn.dynedge.html @@ -357,36 +357,11 @@ - -
  • @@ -497,18 +472,7 @@
    @@ -518,69 +482,8 @@
    -
    -

    dynedge

    -

    Implementation of the DynEdge GNN model architecture.

    -
    -
    -class graphnet.models.gnn.dynedge.DynEdge(*args, **kwargs)[source]
    -

    Bases: GNN

    -

    DynEdge (dynamical edge convolutional) model.

    -

    Construct DynEdge.

    -
    -
    Parameters:
    -
      -

    • nb_inputs (int) – Number of input features on each node.

      • -

    • nb_neighbours (int, default: 8) – Number of neighbours to used in the k-nearest -neighbour clustering which is performed after each (dynamical) -edge convolution.

      • -

    • features_subset (Union[List[int], slice, None], 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].

      • -

    • dynedge_layer_sizes (Optional[List[Tuple[int, ...]]], default: None) – The layer sizes, or latent feature dimenions, -used in the DynEdgeConv layer. Each entry in -dynedge_layer_sizes corresponds to a single DynEdgeConv -layer; the integers in the corresponding tuple corresponds to -the layer sizes in the multi-layer perceptron (MLP) that is -applied within each DynEdgeConv layer. That is, a list of -size-two tuples means that all DynEdgeConv layers contain a -two-layer MLP. -Defaults to [(128, 256), (336, 256), (336, 256), (336, 256)].

      • -

    • post_processing_layer_sizes (Optional[List[int]], default: None) – Hidden layer sizes in the MLP -following the skip-concatenation of the outputs of each -DynEdgeConv layer. Defaults to [336, 256].

      • -

    • readout_layer_sizes (Optional[List[int]], default: None) – Hidden layer sizes in the MLP following the -post-processing _and_ optional global pooling. As this is the -last layer(s) in the model, the last layer in the read-out -yields the output of the DynEdge model. Defaults to [128,].

      • -

    • global_pooling_schemes (Union[str, List[str], None], default: None) – The list global pooling schemes to use. -Options are: “min”, “max”, “mean”, and “sum”.

      • -

    • add_global_variables_after_pooling (bool, default: False) – Whether to add global variables -after global pooling. The alternative is to added (distribute) -them to the individual nodes before any convolutional -operations.

      • -

    • args (Any) –

      • -

    • kwargs (Any) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -forward(data)[source]
    -

    Apply learnable forward pass.

    -
    -
    Return type:
    -

    Tensor

    -
    -
    Parameters:
    -

    data (Data) –

    -
    -
    -
    -
    +
    +

    dynedge

    diff --git a/api/graphnet.models.gnn.dynedge_jinst.html b/api/graphnet.models.gnn.dynedge_jinst.html index 562835544..a006285ec 100644 --- a/api/graphnet.models.gnn.dynedge_jinst.html +++ b/api/graphnet.models.gnn.dynedge_jinst.html @@ -364,36 +364,11 @@ - -
  • @@ -497,18 +472,7 @@
    @@ -518,44 +482,8 @@
    -
    -

    dynedge_jinst

    -

    Implementation of the exact DynEdge architecture used in [2209.03042].

    -

    Author: Rasmus Oersoe

    -
    -
    -class graphnet.models.gnn.dynedge_jinst.DynEdgeJINST(*args, **kwargs)[source]
    -

    Bases: GNN

    -

    DynEdge (dynamical edge convolutional) model used in [2209.03042].

    -

    Construct DynEdgeJINST.

    -
    -
    Parameters:
    -
      -

    • 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) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -forward(data)[source]
    -

    Apply learnable forward pass.

    -
    -
    Return type:
    -

    Tensor

    -
    -
    Parameters:
    -

    data (Data) –

    -
    -
    -
    -
    +
    +

    dynedge_jinst

    diff --git a/api/graphnet.models.gnn.dynedge_kaggle_tito.html b/api/graphnet.models.gnn.dynedge_kaggle_tito.html index bf31a35ba..7231ceb1c 100644 --- a/api/graphnet.models.gnn.dynedge_kaggle_tito.html +++ b/api/graphnet.models.gnn.dynedge_kaggle_tito.html @@ -371,36 +371,11 @@ - -
  • @@ -497,18 +472,7 @@
    @@ -518,58 +482,8 @@
    -
    -

    dynedge_kaggle_tito

    -

    Implementation of DynEdge architecture used in.

    -
    -

    IceCube - Neutrinos in Deep Ice

    -
    -

    Reconstruct the direction of neutrinos from the Universe to the South Pole

    -

    Kaggle competition.

    -

    Solution by TITO.

    -
    -
    -class graphnet.models.gnn.dynedge_kaggle_tito.DynEdgeTITO(*args, **kwargs)[source]
    -

    Bases: GNN

    -

    DynEdgeTITO (dynamical edge convolutional with Transformer) model.

    -

    Construct DynEdgeTITO.

    -
    -
    Parameters:
    -
      -

    • nb_inputs (int) – Number of input features on each node.

      • -

    • 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].

      • -

    • dyntrans_layer_sizes (Optional[List[Tuple[int, ...]]], default: None) – The layer sizes, or latent feature dimenions, -used in the DynTrans layer. -Defaults to [(256, 256), (256, 256), (256, 256), (256, 256)].

      • -

    • global_pooling_schemes (List[str], default: ['max']) – The list global pooling schemes to use. -Options are: “min”, “max”, “mean”, and “sum”.

      • -

    • use_global_features (bool, default: True) – Whether to use global features after pooling.

      • -

    • use_post_processing_layers (bool, default: True) – Whether to use post-processing layers -after the DynTrans layers.

      • -

    • args (Any) –

      • -

    • kwargs (Any) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -forward(data)[source]
    -

    Apply learnable forward pass.

    -
    -
    Return type:
    -

    Tensor

    -
    -
    Parameters:
    -

    data (Data) –

    -
    -
    -
    -
    +
    +

    dynedge_kaggle_tito

    diff --git a/api/graphnet.models.gnn.gnn.html b/api/graphnet.models.gnn.gnn.html index 4d1518d3a..9391893f5 100644 --- a/api/graphnet.models.gnn.gnn.html +++ b/api/graphnet.models.gnn.gnn.html @@ -378,54 +378,11 @@ - -
    • @@ -515,22 +472,7 @@
    @@ -540,50 +482,8 @@
    -
    -

    gnn

    -

    Base GNN-specific Model class(es).

    -
    -
    -class graphnet.models.gnn.gnn.GNN(*args, **kwargs)[source]
    -

    Bases: Model

    -

    Base class for all core GNN models in graphnet.

    -

    Construct GNN.

    -
    -
    Parameters:
    -
      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -property nb_inputs: int
    -

    Return number of input features.

    -
    -
    -
    -property nb_outputs: int
    -

    Return number of output features.

    -
    -
    -
    -abstract forward(data)[source]
    -

    Apply learnable forward pass in model.

    -
    -
    Return type:
    -

    Tensor

    -
    -
    Parameters:
    -

    data (Data) –

    -
    -
    -
    -
    +
    +

    gnn

    diff --git a/api/graphnet.models.gnn.html b/api/graphnet.models.gnn.html index b84087b08..c92088621 100644 --- a/api/graphnet.models.gnn.html +++ b/api/graphnet.models.gnn.html @@ -481,32 +481,16 @@
    -
    -

    gnn

    -

    GNN-specific modules, for performing the main learnable operations.

    +
    +

    gnn

    Submodules

    diff --git a/api/graphnet.models.graphs.edges.edges.html b/api/graphnet.models.graphs.edges.edges.html index c638b906f..b752b8a91 100644 --- a/api/graphnet.models.graphs.edges.edges.html +++ b/api/graphnet.models.graphs.edges.edges.html @@ -363,63 +363,11 @@ - -
  • @@ -539,24 +487,7 @@
    @@ -566,114 +497,8 @@
    -
    -

    edges

    -

    Class(es) for building/connecting graphs.

    -
    -
    -class graphnet.models.graphs.edges.edges.EdgeDefinition(*args, **kwargs)[source]
    -

    Bases: Model

    -

    Base class for graph building.

    -

    Construct Logger.

    -
    -
    Parameters:
    -
      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -forward(graph)[source]
    -

    Construct edges based on problem specific implementation of.

    -

    ´_construct_edges´

    -
    -
    Parameters:
    -

    graph (Data) – a graph without edges

    -
    -
    Returns:
    -

    a graph with edges

    -
    -
    Return type:
    -

    graph

    -
    -
    -
    -
    -
    -
    -class graphnet.models.graphs.edges.edges.KNNEdges(*args, **kwargs)[source]
    -

    Bases: EdgeDefinition

    -

    Builds edges from the k-nearest neighbours.

    -

    K-NN Edge definition.

    -

    Will connect nodes together with their ´nb_nearest_neighbours´ -nearest neighbours in the feature space given by ´columns´.

    -
    -
    Parameters:
    -
      -

    • 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) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -
    -class graphnet.models.graphs.edges.edges.RadialEdges(*args, **kwargs)[source]
    -

    Bases: EdgeDefinition

    -

    Builds graph from a sphere of chosen radius centred at each node.

    -

    Radial edges.

    -

    Connects each node to other nodes that are within a sphere of -radius ´r´ centered at the node. The feature space of ´r´ is defined -by ´columns´

    -
    -
    Parameters:
    -
      -

    • 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) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -
    -class graphnet.models.graphs.edges.edges.EuclideanEdges(*args, **kwargs)[source]
    -

    Bases: EdgeDefinition

    -

    Builds edges according to Euclidean distance between nodes.

    -

    See https://arxiv.org/pdf/1809.06166.pdf.

    -

    Construct EuclideanEdges.

    -
    -
    Parameters:
    -
      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    +
    +

    edges

    diff --git a/api/graphnet.models.graphs.edges.html b/api/graphnet.models.graphs.edges.html index 55df9498a..cd05a6814 100644 --- a/api/graphnet.models.graphs.edges.html +++ b/api/graphnet.models.graphs.edges.html @@ -496,27 +496,13 @@
    -
    -

    edges

    -

    Modules for constructing graphs.

    -

    ´GraphDefinition´ defines the nodes and their features, and contains general -graph-manipulation.´EdgeDefinition´ defines how edges are drawn between nodes -and their features.

    +
    +

    edges

    Submodules

    diff --git a/api/graphnet.models.graphs.edges.minkowski.html b/api/graphnet.models.graphs.edges.minkowski.html index b94c54396..1e75d8cc6 100644 --- a/api/graphnet.models.graphs.edges.minkowski.html +++ b/api/graphnet.models.graphs.edges.minkowski.html @@ -370,34 +370,11 @@ - -
    • @@ -510,16 +487,7 @@
    @@ -529,54 +497,8 @@
    -
    -

    minkowski

    -

    Module containing EdgeDefinitions based on the Minkowski Metric.

    -
    -
    -graphnet.models.graphs.edges.minkowski.compute_minkowski_distance_mat(x, y, c, space_coords, time_coord)[source]
    -

    Compute all pairwise Minkowski distances.

    -
    -
    Parameters:
    -
      -

    • x (Tensor) – First tensor of shape (n, d).

      • -

    • y (Tensor) – Second tensor of shape (m, d).

      • -

    • c (float) – Speed of light, in scaled units.

      • -

    • space_coords (Optional[List[int]], default: None) – Indices of space coordinates.

      • -

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

      • -
    -
    -
    Return type:
    -

    Tensor

    -
    -
    -

    Returns: Matrix of shape (n, m) of all pairwise Minkowski distances.

    -
    -
    -
    -class graphnet.models.graphs.edges.minkowski.MinkowskiKNNEdges(*args, **kwargs)[source]
    -

    Bases: EdgeDefinition

    -

    Builds edges between most light-like separated.

    -

    Initialize MinkowskiKNNEdges.

    -
    -
    Parameters:
    -
      -

    • nb_nearest_neighbours (int) – Number of neighbours to connect to.

      • -

    • c (float) – Speed of light, in scaled units.

      • -

    • time_like_weight (float, default: 1.0) – Preference to time-like over space-like edges. -Scales time_like distances by this value, before finding -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) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    +
    +

    minkowski

    diff --git a/api/graphnet.models.graphs.graph_definition.html b/api/graphnet.models.graphs.graph_definition.html index 85be967ee..3d62ee917 100644 --- a/api/graphnet.models.graphs.graph_definition.html +++ b/api/graphnet.models.graphs.graph_definition.html @@ -371,36 +371,11 @@ - -
  • @@ -497,18 +472,7 @@
    @@ -518,82 +482,8 @@
    -
    -

    graph_definition

    -

    Modules for defining graphs.

    -

    These are self-contained graph definitions that hold all the graph-altering -code in graphnet. These modules define what the GNNs sees as input and can be -passed to dataloaders during training and deployment.

    -
    -
    -class graphnet.models.graphs.graph_definition.GraphDefinition(*args, **kwargs)[source]
    -

    Bases: Model

    -

    An Abstract class to create graph definitions from.

    -

    Construct ´GraphDefinition´. The ´detector´ holds.

    -

    ´Detector´-specific code. E.g. scaling/standardization and geometry -tables.

    -

    ´node_definition´ defines the nodes in the graph.

    -

    ´edge_definition´ defines the connectivity of the nodes in the graph.

    -
    -
    Parameters:
    -
      -

    • detector (Detector) – The corresponding ´Detector´ representing the data.

      • -

    • node_definition (NodeDefinition, default: NodesAsPulses()) – Definition of nodes. Defaults to NodesAsPulses.

      • -

    • edge_definition (Optional[EdgeDefinition], default: None) – Definition of edges. Defaults to None.

      • -

    • input_feature_names (Optional[List[str]], default: None) – Names of each column in expected input data -that will be built into a graph. If not provided, -it is automatically assumed that all features in Detector is -used.

      • -

    • dtype (Optional[dtype], default: torch.float32) – data type used for node features. e.g. ´torch.float´

      • -

    • perturbation_dict (Optional[Dict[str, float]], default: None) – Dictionary mapping a feature name to a standard -deviation according to which the values for this -feature should be randomly perturbed. Defaults -to None.

      • -

    • seed (Union[int, Generator, None], default: None) – seed or Generator used to randomly sample perturbations. -Defaults to None.

      • -

    • add_inactive_sensors (bool, default: False) – If True, inactive sensors will be appended -to the graph with padded pulse information. Defaults to False.

      • -

    • sensor_mask (Optional[List[int]], default: None) – A list of sensor id’s to be masked from the graph. Any -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) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -forward(input_features, input_feature_names, truth_dicts, custom_label_functions, loss_weight_column, loss_weight, loss_weight_default_value, data_path)[source]
    -

    Construct graph as ´Data´ object.

    -
    -
    Parameters:
    -
      -

    • input_features (ndarray) – Input features for graph construction. Shape ´[num_rows, d]´

      • -

    • input_feature_names (List[str]) – name of each column. Shape ´[,d]´.

      • -

    • truth_dicts (Optional[List[Dict[str, Any]]], default: None) – Dictionary containing truth labels.

      • -

    • custom_label_functions (Optional[Dict[str, Callable[..., Any]]], default: None) – Custom label functions. See https://github.com/graphnet-team/graphnet/blob/main/GETTING_STARTED.md#adding-custom-truth-labels.

      • -

    • loss_weight_column (Optional[str], default: None) – Name of column that holds loss weight. -Defaults to None.

      • -

    • loss_weight (Optional[float], default: None) – Loss weight associated with event. Defaults to None.

      • -

    • loss_weight_default_value (Optional[float], default: None) – default value for loss weight. -Used in instances where some events have -no pre-defined loss weight. Defaults to None.

      • -

    • data_path (Optional[str], default: None) – Path to dataset data files. Defaults to None.

      • -
    -
    -
    Return type:
    -

    Data

    -
    -
    Returns:
    -

    graph

    -
    -
    -
    -
    +
    +

    graph_definition

    diff --git a/api/graphnet.models.graphs.graphs.html b/api/graphnet.models.graphs.graphs.html index 81c36ff78..c42c6b03e 100644 --- a/api/graphnet.models.graphs.graphs.html +++ b/api/graphnet.models.graphs.graphs.html @@ -378,25 +378,11 @@ - -
  • @@ -486,14 +472,7 @@
    @@ -503,42 +482,8 @@
    -
    -

    graphs

    -

    A module containing different graph representations in GraphNeT.

    -
    -
    -class graphnet.models.graphs.graphs.KNNGraph(*args, **kwargs)[source]
    -

    Bases: GraphDefinition

    -

    A Graph representation where Edges are drawn to nearest neighbours.

    -

    Construct k-nn graph representation.

    -
    -
    Parameters:
    -
      -

    • detector (Detector) – Detector that represents your data.

      • -

    • node_definition (Optional[NodeDefinition], default: None) – Definition of nodes in the graph.

      • -

    • input_feature_names (Optional[List[str]], default: None) – Name of input feature columns.

      • -

    • dtype (Optional[dtype], default: torch.float32) – data type for node features.

      • -

    • perturbation_dict (Optional[Dict[str, float]], default: None) – Dictionary mapping a feature name to a standard -deviation according to which the values for this -feature should be randomly perturbed. Defaults -to None.

      • -

    • seed (Union[int, Generator, None], default: None) – seed or Generator used to randomly sample perturbations. -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) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    +
    +

    graphs

    diff --git a/api/graphnet.models.graphs.html b/api/graphnet.models.graphs.html index 8e26eaac0..dcaf44d79 100644 --- a/api/graphnet.models.graphs.html +++ b/api/graphnet.models.graphs.html @@ -481,12 +481,8 @@
    -
    -

    graphs

    -

    Modules for constructing graphs.

    -

    ´GraphDefinition´ defines the nodes and their features, and contains general -graph-manipulation.´EdgeDefinition´ defines how edges are drawn between nodes -and their features.

    +
    +

    graphs

    Subpackages

    diff --git a/api/graphnet.models.graphs.nodes.html b/api/graphnet.models.graphs.nodes.html index 3796f586d..392dc3d0e 100644 --- a/api/graphnet.models.graphs.nodes.html +++ b/api/graphnet.models.graphs.nodes.html @@ -489,21 +489,12 @@
    -
    -

    nodes

    -

    Modules for constructing graphs.

    -

    ´GraphDefinition´ defines the nodes and their features, and contains general -graph-manipulation.´EdgeDefinition´ defines how edges are drawn between nodes -and their features.

    +
    +

    nodes

    Submodules

    diff --git a/api/graphnet.models.graphs.nodes.nodes.html b/api/graphnet.models.graphs.nodes.nodes.html index 69cbf1385..f3a2d6e1c 100644 --- a/api/graphnet.models.graphs.nodes.nodes.html +++ b/api/graphnet.models.graphs.nodes.nodes.html @@ -370,81 +370,11 @@ - -
    • @@ -550,28 +480,7 @@
    @@ -581,127 +490,8 @@
    -
    -

    nodes

    -

    Class(es) for building/connecting graphs.

    -
    -
    -class graphnet.models.graphs.nodes.nodes.NodeDefinition(*args, **kwargs)[source]
    -

    Bases: Model

    -

    Base class for graph building.

    -

    Construct Detector.

    -
    -
    Parameters:
    -
      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -forward(x)[source]
    -

    Construct nodes from raw node features.

    -
    -
    Parameters:
    -
      -

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

      • -

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

      • -

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

      • -
    -
    -
    Returns:
    -

    a graph without edges -new_features_name: List of new feature names.

    -
    -
    Return type:
    -

    graph

    -
    -
    -
    -
    -
    -property nb_outputs: int
    -

    Return number of output features.

    -

    This the default, but may be overridden by specific inheriting classes.

    -
    -
    -
    -set_number_of_inputs(input_feature_names)[source]
    -

    Return number of inputs expected by node definition.

    -
    -
    Parameters:
    -

    input_feature_names (List[str]) – name of each input feature column.

    -
    -
    Return type:
    -

    None

    -
    -
    -
    -
    -
    -set_output_feature_names(input_feature_names)[source]
    -

    Set output features names as a member variable.

    -
    -
    Parameters:
    -
      -

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

      • -

    • definition. (node) –

      • -
    -
    -
    Return type:
    -

    None

    -
    -
    -
    -
    -
    -
    -class graphnet.models.graphs.nodes.nodes.NodesAsPulses(*args, **kwargs)[source]
    -

    Bases: NodeDefinition

    -

    Represent each measured pulse of Cherenkov Radiation as a node.

    -

    Construct Detector.

    -
    -
    Parameters:
    -
      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -
    -class graphnet.models.graphs.nodes.nodes.PercentileClusters(*args, **kwargs)[source]
    -

    Bases: NodeDefinition

    -

    Represent nodes as clusters with percentile summary node features.

    -

    If cluster_on is set to the xyz coordinates of DOMs -e.g. cluster_on = [‘dom_x’, ‘dom_y’, ‘dom_z’], each node will be a -unique DOM and the pulse information (charge, time) is summarized using -percentiles.

    -

    Construct PercentileClusters.

    -
    -
    Parameters:
    -
      -

    • cluster_on (List[str]) – Names of features to create clusters from.

      • -

    • 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) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    +
    +

    nodes

    diff --git a/api/graphnet.models.graphs.utils.html b/api/graphnet.models.graphs.utils.html index 779b94300..cd741c019 100644 --- a/api/graphnet.models.graphs.utils.html +++ b/api/graphnet.models.graphs.utils.html @@ -385,52 +385,11 @@ - - @@ -513,20 +472,7 @@
    @@ -536,117 +482,8 @@
    -
    -

    utils

    -

    Utility functions for construction of graphs.

    -
    -
    -graphnet.models.graphs.utils.lex_sort(x, cluster_columns)[source]
    -

    Sort numpy arrays according to columns on ´cluster_columns´.

    -

    Note that x is sorted along the dimensions in cluster_columns -backwards. I.e. cluster_columns = [0,1,2] -means x is sorted along [2,1,0].

    -
    -
    Parameters:
    -
      -

    • x (array) – array to be sorted.

      • -

    • cluster_columns (List[int]) – Columns of x to be sorted along.

      • -
    -
    -
    Return type:
    -

    ndarray

    -
    -
    Returns:
    -

    A sorted version of x.

    -
    -
    -
    -
    -
    -graphnet.models.graphs.utils.gather_cluster_sequence(x, feature_idx, cluster_columns)[source]
    -

    Turn x into rows of clusters with sequences along columns.

    -

    Sequences along columns are added which correspond to -gathered sequences of the feature in x specified by column index -feature_idx associated with each column. Sequences are padded with NaN to -be of same length. Dimension of clustered array is [n_clusters, l + -len(cluster_columns)],where l is the largest sequence length.

    -

    Example: -Suppose x represents a neutrino event and we have chosen to cluster on -the PMT positions and that feature_idx correspond to pulse time.

    -

    The resulting array will have dimensions [n_pmts, m + 3] where m is the -maximum number of same-pmt pulses found in x, and `+3`for the three -spatial directions defining each cluster.

    -
    -
    Parameters:
    -
      -

    • x (ndarray) – Array for clustering

      • -

    • feature_idx (int) – Index of the feature in x to -be gathered for each cluster.

      • -

    • cluster_columns (List[int]) – Index in x from which to build clusters.

      • -
    -
    -
    Returns:
    -

    Array with dimensions [n_clusters, l + len(cluster_columns)] -column_offset: Indices of the columns in array that defines clusters.

    -
    -
    Return type:
    -

    array

    -
    -
    -
    -
    -
    -graphnet.models.graphs.utils.identify_indices(feature_names, cluster_on)[source]
    -

    Identify indices for clustering and summarization.

    -
    -
    Return type:
    -

    Tuple[List[int], List[int], List[str]]

    -
    -
    Parameters:
    -
      -

    • feature_names (List[str]) –

      • -

    • cluster_on (List[str]) –

      • -
    -
    -
    -
    -
    -
    -graphnet.models.graphs.utils.cluster_summarize_with_percentiles(x, summarization_indices, cluster_indices, percentiles, add_counts)[source]
    -

    Turn x into clusters with percentile summary.

    -

    From variables specified by column indices cluster_indices, x is turned -into clusters. Information in columns of x specified by indices -summarization_indices with each cluster is summarized using percentiles. -It is assumed x represents a single event.

    -

    Example use-case: -Suppose x contains raw pulses from a neutrino event where some DOMs have -multiple measurements of Cherenkov radiation. If cluster_indices is set -to the columns corresponding to the xyz-position of the DOMs, and the -features specified in summarization_indices correspond to time, charge, -then each row in the returned array will correspond to a DOM, -and the time and charge for each DOM will be summarized by percentiles. -Returned output array has dimensions -[n_clusters, len(percentiles)*len(summarization_indices) + len(cluster_indices)]

    -
    -
    Parameters:
    -
      -

    • x (ndarray) – Array to be clustered

      • -

    • summarization_indices (List[int]) – List of column indices that defines features -that will be summarized with percentiles.

      • -

    • 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) –

      • -
    -
    -
    Return type:
    -

    ndarray

    -
    -
    Returns:
    -

    Percentile-summarized array

    -
    -
    -
    +
    +

    utils

    diff --git a/api/graphnet.models.html b/api/graphnet.models.html index 6ef893d4d..473d93200 100644 --- a/api/graphnet.models.html +++ b/api/graphnet.models.html @@ -445,14 +445,8 @@
    -
    -

    models

    -

    Modules for configuring and building models.

    -

    graphnet.models allows for configuring and building complex GNN models using -simple, physics-oriented components. This module provides modular components -subclassing torch.nn.Module, meaning that users only need to import a few, -existing, purpose-built components and chain them together to form a complete -GNN

    +
    +

    models

    Subpackages

    diff --git a/api/graphnet.models.standard_model.html b/api/graphnet.models.standard_model.html index ed04dde69..a0e813fe9 100644 --- a/api/graphnet.models.standard_model.html +++ b/api/graphnet.models.standard_model.html @@ -379,144 +379,11 @@ - -
  • @@ -569,42 +436,7 @@
    @@ -614,216 +446,8 @@
    -
    -

    standard_model

    -

    Standard model class(es).

    -
    -
    -class graphnet.models.standard_model.StandardModel(*args, **kwargs)[source]
    -

    Bases: Model

    -

    Main class for standard models in graphnet.

    -

    This class chains together the different elements of a complete GNN- based -model (detector read-in, GNN backbone, and task-specific read-outs).

    -

    Construct StandardModel.

    -
    -
    Parameters:
    -
      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -fit(train_dataloader, val_dataloader, *, max_epochs, early_stopping_patience, gpus, callbacks, ckpt_path, logger, log_every_n_steps, gradient_clip_val, distribution_strategy, **trainer_kwargs)[source]
    -

    Fit StandardModel using pytorch_lightning.Trainer.

    -
    -
    Return type:
    -

    None

    -
    -
    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) –

      • -
    -
    -
    -
    -
    -
    -property target_labels: List[str]
    -

    Return target label.

    -
    -
    -
    -property prediction_labels: List[str]
    -

    Return prediction labels.

    -
    -
    -
    -configure_optimizers()[source]
    -

    Configure the model’s optimizer(s).

    -
    -
    Return type:
    -

    Dict[str, Any]

    -
    -
    -
    -
    -
    -forward(data)[source]
    -

    Forward pass, chaining model components.

    -
    -
    Return type:
    -

    List[Union[Tensor, Data]]

    -
    -
    Parameters:
    -

    data (Data | List[Data]) –

    -
    -
    -
    -
    -
    -shared_step(batch, batch_idx)[source]
    -

    Perform shared step.

    -

    Applies the forward pass and the following loss calculation, shared -between the training and validation step.

    -
    -
    Return type:
    -

    Tensor

    -
    -
    Parameters:
    -
      -

    • batch (List[Data]) –

      • -

    • batch_idx (int) –

      • -
    -
    -
    -
    -
    -
    -training_step(train_batch, batch_idx)[source]
    -

    Perform training step.

    -
    -
    Return type:
    -

    Tensor

    -
    -
    Parameters:
    -
      -

    • train_batch (Data | List[Data]) –

      • -

    • batch_idx (int) –

      • -
    -
    -
    -
    -
    -
    -validation_step(val_batch, batch_idx)[source]
    -

    Perform validation step.

    -
    -
    Return type:
    -

    Tensor

    -
    -
    Parameters:
    -
      -

    • val_batch (Data | List[Data]) –

      • -

    • batch_idx (int) –

      • -
    -
    -
    -
    -
    -
    -compute_loss(preds, data, verbose)[source]
    -

    Compute and sum losses across tasks.

    -
    -
    Return type:
    -

    Tensor

    -
    -
    Parameters:
    -
      -

    • preds (Tensor) –

      • -

    • data (List[Data]) –

      • -

    • verbose (bool) –

      • -
    -
    -
    -
    -
    -
    -inference()[source]
    -

    Activate inference mode.

    -
    -
    Return type:
    -

    None

    -
    -
    -
    -
    -
    -train(mode)[source]
    -

    Deactivate inference mode.

    -
    -
    Return type:
    -

    Model

    -
    -
    Parameters:
    -

    mode (bool) –

    -
    -
    -
    -
    -
    -predict(dataloader, gpus, distribution_strategy)[source]
    -

    Return predictions for dataloader.

    -
    -
    Return type:
    -

    List[Tensor]

    -
    -
    Parameters:
    -
      -

    • dataloader (DataLoader) –

      • -

    • gpus (List[int] | int | None) –

      • -

    • distribution_strategy (str | None) –

      • -
    -
    -
    -
    -
    -
    -predict_as_dataframe(dataloader, prediction_columns, *, additional_attributes, gpus, distribution_strategy)[source]
    -

    Return predictions for dataloader as a DataFrame.

    -

    Include additional_attributes as additional columns in the output -DataFrame.

    -
    -
    Return type:
    -

    DataFrame

    -
    -
    Parameters:
    -
      -

    • dataloader (DataLoader) –

      • -

    • prediction_columns (List[str] | None) –

      • -

    • additional_attributes (List[str] | None) –

      • -

    • gpus (List[int] | int | None) –

      • -

    • distribution_strategy (str | None) –

      • -
    -
    -
    -
    -
    +
    +

    standard_model

    diff --git a/api/graphnet.models.task.classification.html b/api/graphnet.models.task.classification.html index 7692bc6e2..09c86ff7d 100644 --- a/api/graphnet.models.task.classification.html +++ b/api/graphnet.models.task.classification.html @@ -364,101 +364,11 @@ - -
  • @@ -548,34 +458,7 @@
    @@ -585,98 +468,8 @@
    -
    -

    classification

    -

    Classification-specific Model class(es).

    -
    -
    -class graphnet.models.task.classification.MulticlassClassificationTask(*args, **kwargs)[source]
    -

    Bases: IdentityTask

    -

    General task for classifying any number of classes.

    -

    Requires the same number of input features as the number of classes being -predicted. Returns the untransformed latent features, which are interpreted -as the logits for each class being classified.

    -

    Construct IdentityTask.

    -

    A task that does not apply a learned embedding to the input. It returns -the direct inputs from Model.

    -
    -
    Parameters:
    -
      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -
    -class graphnet.models.task.classification.BinaryClassificationTask(*args, **kwargs)[source]
    -

    Bases: StandardLearnedTask

    -

    Performs binary classification.

    -

    Construct StandardLearnedTask.

    -
    -
    Parameters:
    -
      -

    • 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) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -nb_inputs = 1
    -
    -
    -
    -default_target_labels = ['target']
    -
    -
    -
    -default_prediction_labels = ['target_pred']
    -
    -
    -
    -
    -class graphnet.models.task.classification.BinaryClassificationTaskLogits(*args, **kwargs)[source]
    -

    Bases: StandardLearnedTask

    -

    Performs binary classification form logits.

    -

    Construct StandardLearnedTask.

    -
    -
    Parameters:
    -
      -

    • 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) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -nb_inputs = 1
    -
    -
    -
    -default_target_labels = ['target']
    -
    -
    -
    -default_prediction_labels = ['target_pred']
    -
    -
    +
    +

    classification

    diff --git a/api/graphnet.models.task.html b/api/graphnet.models.task.html index d5d882f9e..3ac7f9967 100644 --- a/api/graphnet.models.task.html +++ b/api/graphnet.models.task.html @@ -467,42 +467,14 @@
    -
    -

    task

    -

    Physics task-specific modules to be used as model “read-outs”.

    +
    +

    task

    Submodules

    diff --git a/api/graphnet.models.task.reconstruction.html b/api/graphnet.models.task.reconstruction.html index 8b5c8d1d6..2b4943ac1 100644 --- a/api/graphnet.models.task.reconstruction.html +++ b/api/graphnet.models.task.reconstruction.html @@ -371,510 +371,11 @@ - -
  • @@ -957,142 +458,7 @@
    @@ -1102,439 +468,8 @@
    -
    -

    reconstruction

    -

    Reconstruction-specific Model class(es).

    -
    -
    -class graphnet.models.task.reconstruction.AzimuthReconstructionWithKappa(*args, **kwargs)[source]
    -

    Bases: StandardLearnedTask

    -

    Reconstructs azimuthal angle and associated kappa (1/var).

    -

    Construct StandardLearnedTask.

    -
    -
    Parameters:
    -
      -

    • 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) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -default_target_labels = ['azimuth']
    -
    -
    -
    -default_prediction_labels = ['azimuth_pred', 'azimuth_kappa']
    -
    -
    -
    -nb_inputs = 2
    -
    -
    -
    -
    -class graphnet.models.task.reconstruction.AzimuthReconstruction(*args, **kwargs)[source]
    -

    Bases: AzimuthReconstructionWithKappa

    -

    Reconstructs azimuthal angle.

    -

    Construct StandardLearnedTask.

    -
    -
    Parameters:
    -
      -

    • 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) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -default_target_labels = ['azimuth']
    -
    -
    -
    -default_prediction_labels = ['azimuth_pred']
    -
    -
    -
    -nb_inputs = 2
    -
    -
    -
    -
    -class graphnet.models.task.reconstruction.DirectionReconstructionWithKappa(*args, **kwargs)[source]
    -

    Bases: StandardLearnedTask

    -

    Reconstructs direction with kappa from the 3D-vMF distribution.

    -

    Construct StandardLearnedTask.

    -
    -
    Parameters:
    -
      -

    • 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) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -default_target_labels = ['direction']
    -
    -
    -
    -default_prediction_labels = ['dir_x_pred', 'dir_y_pred', 'dir_z_pred', 'direction_kappa']
    -
    -
    -
    -nb_inputs = 3
    -
    -
    -
    -
    -class graphnet.models.task.reconstruction.ZenithReconstruction(*args, **kwargs)[source]
    -

    Bases: StandardLearnedTask

    -

    Reconstructs zenith angle.

    -

    Construct StandardLearnedTask.

    -
    -
    Parameters:
    -
      -

    • 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) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -default_target_labels = ['zenith']
    -
    -
    -
    -default_prediction_labels = ['zenith_pred']
    -
    -
    -
    -nb_inputs = 1
    -
    -
    -
    -
    -class graphnet.models.task.reconstruction.ZenithReconstructionWithKappa(*args, **kwargs)[source]
    -

    Bases: ZenithReconstruction

    -

    Reconstructs zenith angle and associated kappa (1/var).

    -

    Construct StandardLearnedTask.

    -
    -
    Parameters:
    -
      -

    • 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) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -default_target_labels = ['zenith']
    -
    -
    -
    -default_prediction_labels = ['zenith_pred', 'zenith_kappa']
    -
    -
    -
    -nb_inputs = 2
    -
    -
    -
    -
    -class graphnet.models.task.reconstruction.EnergyReconstruction(*args, **kwargs)[source]
    -

    Bases: StandardLearnedTask

    -

    Reconstructs energy using stable method.

    -

    Construct StandardLearnedTask.

    -
    -
    Parameters:
    -
      -

    • 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) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -default_target_labels = ['energy']
    -
    -
    -
    -default_prediction_labels = ['energy_pred']
    -
    -
    -
    -nb_inputs = 1
    -
    -
    -
    -
    -class graphnet.models.task.reconstruction.EnergyReconstructionWithPower(*args, **kwargs)[source]
    -

    Bases: StandardLearnedTask

    -

    Reconstructs energy.

    -

    Construct StandardLearnedTask.

    -
    -
    Parameters:
    -
      -

    • 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) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -default_target_labels = ['energy']
    -
    -
    -
    -default_prediction_labels = ['energy_pred']
    -
    -
    -
    -nb_inputs = 1
    -
    -
    -
    -
    -class graphnet.models.task.reconstruction.EnergyTCReconstruction(*args, **kwargs)[source]
    -

    Bases: StandardLearnedTask

    -

    Reconstructs track and cascade energies using stable method.

    -

    Construct StandardLearnedTask.

    -
    -
    Parameters:
    -
      -

    • 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) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -default_target_labels = ['energy_track', 'energy_cascade']
    -
    -
    -
    -default_prediction_labels = ['energy_track_pred', 'energy_cascade_pred']
    -
    -
    -
    -nb_inputs = 2
    -
    -
    -
    -
    -class graphnet.models.task.reconstruction.EnergyReconstructionWithUncertainty(*args, **kwargs)[source]
    -

    Bases: EnergyReconstruction

    -

    Reconstructs energy and associated uncertainty (log(var)).

    -

    Construct StandardLearnedTask.

    -
    -
    Parameters:
    -
      -

    • 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) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -default_target_labels = ['energy']
    -
    -
    -
    -default_prediction_labels = ['energy_pred', 'energy_sigma']
    -
    -
    -
    -nb_inputs = 2
    -
    -
    -
    -
    -class graphnet.models.task.reconstruction.VertexReconstruction(*args, **kwargs)[source]
    -

    Bases: StandardLearnedTask

    -

    Reconstructs vertex position and time.

    -

    Construct StandardLearnedTask.

    -
    -
    Parameters:
    -
      -

    • 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) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -default_target_labels = ['vertex']
    -
    -
    -
    -default_prediction_labels = ['position_x_pred', 'position_y_pred', 'position_z_pred', 'interaction_time_pred']
    -
    -
    -
    -nb_inputs = 4
    -
    -
    -
    -
    -class graphnet.models.task.reconstruction.PositionReconstruction(*args, **kwargs)[source]
    -

    Bases: StandardLearnedTask

    -

    Reconstructs vertex position.

    -

    Construct StandardLearnedTask.

    -
    -
    Parameters:
    -
      -

    • 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) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -default_target_labels = ['position']
    -
    -
    -
    -default_prediction_labels = ['position_x_pred', 'position_y_pred', 'position_z_pred']
    -
    -
    -
    -nb_inputs = 3
    -
    -
    -
    -
    -class graphnet.models.task.reconstruction.TimeReconstruction(*args, **kwargs)[source]
    -

    Bases: StandardLearnedTask

    -

    Reconstructs time.

    -

    Construct StandardLearnedTask.

    -
    -
    Parameters:
    -
      -

    • 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) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -default_target_labels = ['interaction_time']
    -
    -
    -
    -default_prediction_labels = ['interaction_time_pred']
    -
    -
    -
    -nb_inputs = 1
    -
    -
    -
    -
    -class graphnet.models.task.reconstruction.InelasticityReconstruction(*args, **kwargs)[source]
    -

    Bases: StandardLearnedTask

    -

    Reconstructs interaction inelasticity.

    -

    That is, 1-(track energy / hadronic energy).

    -

    Construct StandardLearnedTask.

    -
    -
    Parameters:
    -
      -

    • 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) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -default_target_labels = ['inelasticity']
    -
    -
    -
    -default_prediction_labels = ['inelasticity_pred']
    -
    -
    -
    -nb_inputs = 1
    -
    -
    +
    +

    reconstruction

    diff --git a/api/graphnet.models.task.task.html b/api/graphnet.models.task.task.html index 1c6b88a25..c6347337d 100644 --- a/api/graphnet.models.task.task.html +++ b/api/graphnet.models.task.task.html @@ -378,215 +378,11 @@ - -
    • @@ -662,64 +458,7 @@
    @@ -729,302 +468,8 @@
    -
    -

    task

    -

    Base physics task-specific Model class(es).

    -
    -
    -class graphnet.models.task.task.Task(*args, **kwargs)[source]
    -

    Bases: Model

    -

    Base class for Tasks in GraphNeT.

    -

    Construct Task.

    -
    -
    Parameters:
    -
      -

    • loss_function (LossFunction) – Loss function appropriate to the task.

      • -

    • target_labels (Union[str, List[str], None], default: None) – Name(s) of the quantity/-ies being predicted, used -to extract the target tensor(s) from the Data object in -.compute_loss(…).

      • -

    • prediction_labels (Union[str, List[str], None], default: None) – The name(s) of each column that is predicted by -the model during inference. If not given, the name will auto -matically be set to target_label + _pred.

      • -

    • transform_prediction_and_target (Optional[Callable], default: None) – Optional function to transform -both the predicted and target tensor before passing them to the -loss function. Useful e.g. for having the model predict -quantities on a physical scale, but transforming this scale to -O(1) for a numerically stable loss computation.

      • -

    • transform_target (Optional[Callable], default: None) – Optional function to transform only the target -tensor before passing it, and the predicted tensor, to the loss -function. Useful e.g. for having the model predict a -transformed version of the target quantity, e.g. the log10- -scaled energy, rather than the physical quantity itself. Used -in conjunction with transform_inference to perform the -inverse transform on the predicted quantity to recover the -physical scale.

      • -

    • transform_inference (Optional[Callable], default: None) – Optional function to inverse-transform the -model prediction to recover a physical scale. Used in -conjunction with transform_target.

      • -

    • transform_support (Optional[Tuple], default: None) – Optional tuple to specify minimum and maximum -of the range of validity for the inverse transforms -transform_target and transform_inference in case this is -restricted. By default the invertibility of transform_target -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) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -abstract property nb_inputs: int
    -

    Return number of inputs assumed by task.

    -
    -
    -
    -property default_target_labels: List[str]
    -

    Return default target labels.

    -
    -
    -
    -property default_prediction_labels: List[str]
    -

    Return default prediction labels.

    -
    -
    -
    -inference()[source]
    -

    Activate inference mode.

    -
    -
    Return type:
    -

    None

    -
    -
    -
    -
    -
    -train_eval()[source]
    -

    Deactivate inference mode.

    -
    -
    Return type:
    -

    None

    -
    -
    -
    -
    -
    -
    -class graphnet.models.task.task.LearnedTask(*args, **kwargs)[source]
    -

    Bases: Task

    -

    Task class with a learned mapping.

    -

    Applies a learned mapping between the last latent layer of Model and -target space. E.g. the LearnedTask contains learnable parameters that -acts like a prediction head.

    -

    Construct LearnedTask.

    -
    -
    Parameters:
    -
      -

    • 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) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -abstract compute_loss(pred, data)[source]
    -

    Compute loss of pred wrt.

    -

    target labels in data.

    -
    -
    Return type:
    -

    Tensor

    -
    -
    Parameters:
    -
      -

    • pred (Tensor | Data) –

      • -

    • data (Data) –

      • -
    -
    -
    -
    -
    -
    -abstract property nb_inputs: int
    -

    Return number of inputs assumed by task.

    -
    -
    -
    -forward(x)[source]
    -

    Forward call for LearnedTask.

    -

    The learned embedding transforms last latent layer of Model to meet -target dimensions.

    -
    -
    Return type:
    -

    Union[Tensor, Data]

    -
    -
    Parameters:
    -

    x (Tensor | Data) –

    -
    -
    -
    -
    -
    -
    -class graphnet.models.task.task.StandardLearnedTask(*args, **kwargs)[source]
    -

    Bases: LearnedTask

    -

    Standard class for classification and reconstruction in GraphNeT.

    -

    This class comes with a definition of compute_loss that is compatible -with the vast majority of supervised learning tasks.

    -

    Construct StandardLearnedTask.

    -
    -
    Parameters:
    -
      -

    • 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) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -abstract property nb_inputs: int
    -

    Return number of inputs assumed by task.

    -
    -
    -
    -compute_loss(pred, data)[source]
    -

    Compute supervised learning loss.

    -
    -
    Return type:
    -

    Tensor

    -
    -
    Parameters:
    -
      -

    • pred (Tensor | Data) –

      • -

    • data (Data) –

      • -
    -
    -
    -

    Grabs truth labels in data and sends both pred and target to loss -function for evaluation. Suits most supervised learning `Task`s.

    -
    -
    -
    -
    -class graphnet.models.task.task.IdentityTask(*args, **kwargs)[source]
    -

    Bases: StandardLearnedTask

    -

    Identity, or trivial, task.

    -

    Construct IdentityTask.

    -

    A task that does not apply a learned embedding to the input. It returns -the direct inputs from Model.

    -
    -
    Parameters:
    -
      -

    • args (Any) –

      • -

    • kwargs (Any) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -property default_target_labels: List[str]
    -

    Return default target labels.

    -
    -
    -
    -property default_prediction_labels: List[str]
    -

    Return default prediction labels.

    -
    -
    -
    -property nb_inputs: int
    -

    Return number of inputs assumed by task.

    -
    -
    -
    -
    -class graphnet.models.task.task.StandardFlowTask(*args, **kwargs)[source]
    -

    Bases: Task

    -

    A Task for `NormalizingFlow`s in GraphNeT.

    -

    Construct StandardLearnedTask.

    -
    -
    Parameters:
    -
      -

    • target_labels (List[str]) – A list of names for the targets of this Task.

      • -

    • 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) –

      • -
    -
    -
    Return type:
    -

    object

    -
    -
    -
    -
    -nb_inputs()[source]
    -

    Return number of inputs assumed by task.

    -
    -
    Return type:
    -

    int

    -
    -
    -
    -
    -
    -forward(x, jacobian)[source]
    -

    Forward pass.

    -
    -
    Return type:
    -

    Union[Tensor, Data]

    -
    -
    Parameters:
    -
      -

    • x (Tensor | Data) –

      • -

    • jacobian (Tensor | None) –

      • -
    -
    -
    -
    -
    -
    -compute_loss(prediction, jacobian, data)[source]
    -

    Compute loss for normalizing flow tasks.

    -
    -
    Parameters:
    -
      -

    • prediction (Tensor) – transformed sample in latent distribution space.

      • -

    • jacobian (Tensor) – the jacobian associated with the transformation.

      • -

    • data (Data) – the graph object.

      • -
    -
    -
    Return type:
    -

    Tensor

    -
    -
    Returns:
    -

    the loss associated with the transformation.

    -
    -
    -
    -
    +
    +

    task

    diff --git a/api/graphnet.models.utils.html b/api/graphnet.models.utils.html index 1499ab427..58f115973 100644 --- a/api/graphnet.models.utils.html +++ b/api/graphnet.models.utils.html @@ -386,43 +386,11 @@ - - @@ -468,18 +436,7 @@
    @@ -489,69 +446,8 @@
    -
    -

    utils

    -

    Utility functions for graphnet.models.

    -
    -
    -graphnet.models.utils.calculate_xyzt_homophily(x, edge_index, batch)[source]
    -

    Calculate xyzt-homophily from a batch of graphs.

    -

    Homophily is a graph scalar quantity that measures the likeness of -variables in nodes. Notice that this calculator assumes a special order of -input features in x.

    -
    -
    Return type:
    -

    Tuple[Tensor, Tensor, Tensor, Tensor]

    -
    -
    Returns:
    -

    Tuple, each element with shape [batch_size,1].

    -
    -
    Parameters:
    -
      -

    • x (Tensor) –

      • -

    • edge_index (LongTensor) –

      • -

    • batch (Batch) –

      • -
    -
    -
    -
    -
    -
    -graphnet.models.utils.calculate_distance_matrix(xyz_coords)[source]
    -

    Calculate the matrix of pairwise distances between pulses.

    -
    -
    Parameters:
    -

    xyz_coords (Tensor) – (x,y,z)-coordinates of pulses, of shape [nb_doms, 3].

    -
    -
    Return type:
    -

    Tensor

    -
    -
    Returns:
    -

    Matrix of pairwise distances, of shape [nb_doms, nb_doms]

    -
    -
    -
    -
    -
    -graphnet.models.utils.knn_graph_batch(batch, k, columns)[source]
    -

    Calculate k-nearest-neighbours with individual k for each batch event.

    -
    -
    Parameters:
    -
      -

    • batch (Batch) – Batch of events.

      • -

    • k (List[int]) – A list of k’s.

      • -

    • columns (List[int]) – The columns of Data.x used for computing the distances. E.g., -Data.x[:,[0,1,2]]

      • -
    -
    -
    Return type:
    -

    Batch

    -
    -
    Returns:
    -

    Returns the same batch of events, but with updated edges.

    -
    -
    -
    +
    +

    utils

    diff --git a/api/graphnet.training.callbacks.html b/api/graphnet.training.callbacks.html index 30f76fb50..64fa5e7e2 100644 --- a/api/graphnet.training.callbacks.html +++ b/api/graphnet.training.callbacks.html @@ -772,8 +772,8 @@
    Parameters:
      -

    • trainer (Trainer) – The trainer.

      • -

    • graphnet_model (Model) – The model.

      • +

    • trainer (pl.Trainer) – The trainer.

      • +

    • graphnet_model (Model) – The model.

    • stage (Optional[str], default: None) – The stage of training.

    @@ -789,8 +789,8 @@
    Parameters:
      -

    • trainer (Trainer) – Trainer object.

      • -

    • graphnet_model (Model) – Graphnet Model.

      • +

    • trainer (pl.Trainer) – Trainer object.

      • +

    • graphnet_model (Model) – Graphnet Model.

    Return type:
    @@ -806,8 +806,8 @@
    Parameters:
      -

    • trainer (Trainer) – Trainer object.

      • -

    • graphnet_model (Model) – Graphnet Model.

      • +

    • trainer (pl.Trainer) – Trainer object.

      • +

    • graphnet_model (Model) – Graphnet Model.

    Return type:
    @@ -823,8 +823,8 @@
    Parameters:
      -

    • trainer (Trainer) – Trainer object.

      • -

    • graphnet_model (Model) – Graphnet Model.

      • +

    • trainer (pl.Trainer) – Trainer object.

      • +

    • graphnet_model (Model) – Graphnet Model.

    Return type:
    diff --git a/api/graphnet.training.html b/api/graphnet.training.html index d33bd01fc..add559a4a 100644 --- a/api/graphnet.training.html +++ b/api/graphnet.training.html @@ -449,15 +449,7 @@
  • VonMisesFisher3DLoss
    • -
  • utils -
    • +
  • utils
  • weight_fitting
    • WeightFitter
    • Uniform
      • diff --git a/api/graphnet.training.utils.html b/api/graphnet.training.utils.html index a2ddce336..cd1922ff0 100644 --- a/api/graphnet.training.utils.html +++ b/api/graphnet.training.utils.html @@ -365,70 +365,11 @@ - -
    • @@ -467,24 +408,7 @@
      @@ -494,143 +418,8 @@
      -
      -

      utils

      -

      Utility functions for graphnet.training.

      -
      -
      -graphnet.training.utils.collate_fn(graphs)[source]
      -

      Remove graphs with less than two DOM hits.

      -

      Should not occur in “production”.

      -
      -
      Return type:
      -

      Batch

      -
      -
      Parameters:
      -

      graphs (List[Data]) –

      -
      -
      -
      -
      -
      -class graphnet.training.utils.collator_sequence_buckleting(batch_splits=[0.8])[source]
      -

      Bases: object

      -

      Perform the sequence bucketing for the graphs in the batch.

      -

      Set cutting points of the different mini-batches.

      -

      batch_splits: list of floats, each element is the fraction of the total -number of graphs. This list should not explicitly define the first and -last elements, which will always be 0 and 1 respectively.

      -
      -
      Parameters:
      -

      batch_splits (List[float]) –

      -
      -
      -
      -
      -
      -graphnet.training.utils.make_dataloader(db, pulsemaps, graph_definition, features, truth, *, batch_size, shuffle, selection, num_workers, persistent_workers, node_truth, truth_table, node_truth_table, string_selection, loss_weight_table, loss_weight_column, index_column, labels)[source]
      -

      Construct DataLoader instance.

      -
      -
      Return type:
      -

      DataLoader

      -
      -
      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) –

        • -
      -
      -
      -
      -
      -
      -graphnet.training.utils.make_train_validation_dataloader(db, graph_definition, selection, pulsemaps, features, truth, *, batch_size, database_indices, seed, test_size, num_workers, persistent_workers, node_truth, truth_table, node_truth_table, string_selection, loss_weight_column, loss_weight_table, index_column, labels)[source]
      -

      Construct train and test DataLoader instances.

      -
      -
      Return type:
      -

      Tuple[DataLoader, DataLoader]

      -
      -
      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) –

        • -
      -
      -
      -
      -
      -
      -graphnet.training.utils.get_predictions(trainer, model, dataloader, prediction_columns, *, node_level, additional_attributes)[source]
      -

      Get model predictions on dataloader.

      -
      -
      Return type:
      -

      DataFrame

      -
      -
      Parameters:
      -
        -

      • trainer (Trainer) –

        • -

      • model (Model) –

        • -

      • dataloader (DataLoader) –

        • -

      • prediction_columns (List[str]) –

        • -

      • node_level (bool) –

        • -

      • additional_attributes (List[str] | None) –

        • -
      -
      -
      -
      -
      -
      -graphnet.training.utils.save_results(db, tag, results, archive, model)[source]
      -

      Save trained model and prediction results in db.

      -
      -
      Return type:
      -

      None

      -
      -
      Parameters:
      -
        -

      • db (str) –

        • -

      • tag (str) –

        • -

      • results (DataFrame) –

        • -

      • archive (str) –

        • -

      • model (Model) –

        • -
      -
      -
      -
      +
      +

      utils

      diff --git a/api/graphnet.utilities.config.base_config.html b/api/graphnet.utilities.config.base_config.html index fe7430500..a43d9ac48 100644 --- a/api/graphnet.utilities.config.base_config.html +++ b/api/graphnet.utilities.config.base_config.html @@ -369,6 +369,8 @@
    • as_dict()
      • +
    • model_computed_fields +
    • model_config
    • model_fields @@ -407,6 +409,13 @@ as_dict() +
      • +
    • + + + model_computed_fields + +
    • @@ -554,6 +563,8 @@
    • as_dict()
      • +
    • model_computed_fields +
    • model_config
    • model_fields @@ -584,8 +595,7 @@

      Create a new model by parsing and validating input data from keyword arguments.

      Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

      -

      __init__ uses __pydantic_self__ instead of the more common self for the first arg to -allow self as a field name.

      +

      self is explicitly positional-only to allow self as a field name.

      @@ -626,6 +636,11 @@
    • +
    +model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}
    +

    A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

    +
    +
    model_config: ClassVar[ConfigDict] = {}

    Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

    diff --git a/api/graphnet.utilities.config.dataset_config.html b/api/graphnet.utilities.config.dataset_config.html index 80a4de048..524f74d53 100644 --- a/api/graphnet.utilities.config.dataset_config.html +++ b/api/graphnet.utilities.config.dataset_config.html @@ -409,6 +409,8 @@
  • as_dict()
    • +
  • model_computed_fields +
  • model_config
  • model_fields @@ -542,6 +544,13 @@ as_dict() +
    • +
  • + + + model_computed_fields + +
  • @@ -715,6 +724,8 @@
  • as_dict()
    • +
  • model_computed_fields +
  • model_config
  • model_fields @@ -913,6 +924,11 @@
    • +
    +model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}
    +

    A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

    +
    +
    model_config: ClassVar[ConfigDict] = {}

    Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

    diff --git a/api/graphnet.utilities.config.model_config.html b/api/graphnet.utilities.config.model_config.html index b49f3c48e..39894fd70 100644 --- a/api/graphnet.utilities.config.model_config.html +++ b/api/graphnet.utilities.config.model_config.html @@ -390,6 +390,8 @@
  • as_dict()
    • +
  • model_computed_fields +
  • model_config
  • model_fields @@ -432,6 +434,13 @@ as_dict() +
    • +
  • + + + model_computed_fields + +
  • @@ -572,6 +581,8 @@
  • as_dict()
    • +
  • model_computed_fields +
  • model_config
  • model_fields @@ -652,6 +663,11 @@
    • +
    +model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}
    +

    A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

    +
    +
    model_config: ClassVar[ConfigDict] = {}

    Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

    diff --git a/api/graphnet.utilities.config.training_config.html b/api/graphnet.utilities.config.training_config.html index 319a33188..fb1647bf3 100644 --- a/api/graphnet.utilities.config.training_config.html +++ b/api/graphnet.utilities.config.training_config.html @@ -406,6 +406,8 @@
  • dataloader
    • +
  • model_computed_fields +
  • model_config
  • model_fields @@ -449,6 +451,13 @@ dataloader +
    • +
  • + + + model_computed_fields + +
  • @@ -556,6 +565,8 @@
  • dataloader
    • +
  • model_computed_fields +
  • model_config
  • model_fields @@ -584,8 +595,7 @@

    Create a new model by parsing and validating input data from keyword arguments.

    Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

    -

    __init__ uses __pydantic_self__ instead of the more common self for the first arg to -allow self as a field name.

    +

    self is explicitly positional-only to allow self as a field name.

    Parameters:
      @@ -613,6 +623,11 @@ dataloader: Dict[str, Any]
    +
    +model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}
    +

    A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

    +
    +
    model_config: ClassVar[ConfigDict] = {}

    Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

    diff --git a/genindex.html b/genindex.html index 7cb4459cb..e743f2336 100644 --- a/genindex.html +++ b/genindex.html @@ -339,7 +339,6 @@

    Index

    | N | O | P - | Q | R | S | T @@ -347,20 +346,19 @@

    Index

    | V | W | X - | Z

    • A

    + -
    @@ -388,13 +378,9 @@

    B

  • backward() (graphnet.training.loss_functions.LogCMK static method)
  • BaseConfig (class in graphnet.utilities.config.base_config) -
    • -
  • BinaryClassificationTask (class in graphnet.models.task.classification)
    • + - @@ -613,29 +467,13 @@

    E

    + -

    G

    + -
    +
    • graphnet.data.sqlite.sqlite_utilities @@ -1078,50 +816,6 @@

      G

      • -
    • - graphnet.deployment.i3modules.graphnet_module - -
      • -
    • - graphnet.models - -
      • -
    • - graphnet.models.coarsening - -
      • -
    • - graphnet.models.components - -
      • -
      -
    • - graphnet.models.components.layers - -
      • -
    • - graphnet.models.components.pool - -
    • @@ -1150,111 +844,6 @@

      G

      • -
    • - graphnet.models.gnn - -
      • -
    • - graphnet.models.gnn.convnet - -
      • -
    • - graphnet.models.gnn.dynedge - -
      • -
    • - graphnet.models.gnn.dynedge_jinst - -
      • -
    • - graphnet.models.gnn.dynedge_kaggle_tito - -
      • -
    • - graphnet.models.gnn.gnn - -
      • -
    • - graphnet.models.graphs - -
      • -
    • - graphnet.models.graphs.edges - -
      • -
    • - graphnet.models.graphs.edges.edges - -
      • -
    • - graphnet.models.graphs.edges.minkowski - -
      • -
    • - graphnet.models.graphs.graph_definition - -
      • -
    • - graphnet.models.graphs.graphs - -
      • -
    • - graphnet.models.graphs.nodes - -
      • -
    • - graphnet.models.graphs.nodes.nodes - -
      • -
    • - graphnet.models.graphs.utils - -
    • @@ -1262,48 +851,6 @@

      G

      • -
    • - graphnet.models.standard_model - -
      • -
    • - graphnet.models.task - -
      • -
    • - graphnet.models.task.classification - -
      • -
    • - graphnet.models.task.reconstruction - -
      • -
    • - graphnet.models.task.task - -
      • -
    • - graphnet.models.utils - -
    • @@ -1353,13 +900,6 @@

      G

      • -
    • - graphnet.training.utils - -
    • @@ -1475,14 +1015,6 @@

      G

  • GraphnetEarlyStopping (class in graphnet.training.callbacks) -
    • -
  • GraphNeTI3Module (class in graphnet.deployment.i3modules.graphnet_module) -
    • -
  • group_by() (in module graphnet.models.components.pool) -
    • -
  • group_pulses_to_dom() (in module graphnet.models.components.pool) -
    • -
  • group_pulses_to_pmt() (in module graphnet.models.components.pool)
    • @@ -1529,16 +1061,12 @@

    I

  • I3GalacticPlaneHybridRecoExtractor (class in graphnet.data.extractors.i3hybridrecoextractor)
  • I3GenericExtractor (class in graphnet.data.extractors.i3genericextractor) -
    • -
  • I3InferenceModule (class in graphnet.deployment.i3modules.graphnet_module)
  • I3NTMuonLabelExtractor (class in graphnet.data.extractors.i3ntmuonlabelsextractor)
  • I3ParticleExtractor (class in graphnet.data.extractors.i3particleextractor)
  • I3PISAExtractor (class in graphnet.data.extractors.i3pisaextractor) -
    • -
  • I3PulseCleanerModule (class in graphnet.deployment.i3modules.graphnet_module)
  • I3PulseNoiseTruthFlagIceCubeUpgrade (class in graphnet.data.extractors.i3featureextractor)
    • @@ -1560,28 +1088,16 @@

    I

  • (graphnet.data.constants.TRUTH attribute)
    • -
  • IceCubeDeepCore (class in graphnet.models.detector.icecube) -
    • -
  • key (graphnet.training.labels.Label property) -
    • @@ -1647,10 +1155,6 @@

    L

    - +
    -
  • load_module() (in module graphnet.data.dataset.dataset) -
  • load_state_dict() (graphnet.models.model.Model method)
  • log_cmk() (graphnet.training.loss_functions.VonMisesFisherLoss class method)
    • -
    -

    Q

    - - -
    -

    R

    - + + -
  • sensor_index_name (graphnet.models.detector.detector.Detector property)
    • +     		-
  • set_number_of_inputs() (graphnet.models.graphs.nodes.nodes.NodeDefinition method) -
    • -
    @@ -2249,44 +1557,26 @@

    T

    - +

    U

    @@ -2303,14 +1593,10 @@

    U

    V

    -

    Z

    - - - -
    -
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    Python Module Index

        graphnet.data.dataconverter - - -     - graphnet.data.dataloader - - - -     - graphnet.data.dataset - - - -     - graphnet.data.dataset.dataset - - - -     - graphnet.data.dataset.parquet - - - -     - graphnet.data.dataset.parquet.parquet_dataset - - - -     - graphnet.data.dataset.sqlite - - - -     - graphnet.data.dataset.sqlite.sqlite_dataset -     @@ -495,11 +460,6 @@

    Python Module Index

        graphnet.data.parquet.parquet_dataconverter - - -     - graphnet.data.pipeline -     @@ -540,36 +500,6 @@

    Python Module Index

        graphnet.deployment - - -     - graphnet.deployment.i3modules.graphnet_module - - - -     - graphnet.models - - - -     - graphnet.models.coarsening - - - -     - graphnet.models.components - - - -     - graphnet.models.components.layers - - - -     - graphnet.models.components.pool -     @@ -590,116 +520,11 @@

    Python Module Index

        graphnet.models.detector.prometheus - - -     - graphnet.models.gnn - - - -     - graphnet.models.gnn.convnet - - - -     - graphnet.models.gnn.dynedge - - - -     - graphnet.models.gnn.dynedge_jinst - - - -     - graphnet.models.gnn.dynedge_kaggle_tito - - - -     - graphnet.models.gnn.gnn - - - -     - graphnet.models.graphs - - - -     - graphnet.models.graphs.edges - - - -     - graphnet.models.graphs.edges.edges - - - -     - graphnet.models.graphs.edges.minkowski - - - -     - graphnet.models.graphs.graph_definition - - - -     - graphnet.models.graphs.graphs - - - -     - graphnet.models.graphs.nodes - - - -     - graphnet.models.graphs.nodes.nodes - - - -     - graphnet.models.graphs.utils -     graphnet.models.model - - -     - graphnet.models.standard_model - - - -     - graphnet.models.task - - - -     - graphnet.models.task.classification - - - -     - graphnet.models.task.reconstruction - - - -     - graphnet.models.task.task - - - -     - graphnet.models.utils -     @@ -735,11 +560,6 @@

    Python Module Index

        graphnet.training.loss_functions - - -     - graphnet.training.utils -     diff --git a/searchindex.js b/searchindex.js index 228159cba..d349ad633 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["about", "api/graphnet", "api/graphnet.constants", "api/graphnet.data", "api/graphnet.data.constants", "api/graphnet.data.dataconverter", "api/graphnet.data.dataloader", "api/graphnet.data.dataset", "api/graphnet.data.dataset.dataset", "api/graphnet.data.dataset.parquet", "api/graphnet.data.dataset.parquet.parquet_dataset", "api/graphnet.data.dataset.sqlite", "api/graphnet.data.dataset.sqlite.sqlite_dataset", "api/graphnet.data.extractors", "api/graphnet.data.extractors.i3extractor", "api/graphnet.data.extractors.i3featureextractor", "api/graphnet.data.extractors.i3genericextractor", "api/graphnet.data.extractors.i3hybridrecoextractor", "api/graphnet.data.extractors.i3ntmuonlabelsextractor", "api/graphnet.data.extractors.i3particleextractor", "api/graphnet.data.extractors.i3pisaextractor", "api/graphnet.data.extractors.i3quesoextractor", "api/graphnet.data.extractors.i3retroextractor", "api/graphnet.data.extractors.i3splinempeextractor", "api/graphnet.data.extractors.i3truthextractor", "api/graphnet.data.extractors.i3tumextractor", "api/graphnet.data.extractors.utilities", "api/graphnet.data.extractors.utilities.collections", "api/graphnet.data.extractors.utilities.frames", "api/graphnet.data.extractors.utilities.types", "api/graphnet.data.filters", "api/graphnet.data.parquet", "api/graphnet.data.parquet.parquet_dataconverter", "api/graphnet.data.pipeline", "api/graphnet.data.sqlite", "api/graphnet.data.sqlite.sqlite_dataconverter", "api/graphnet.data.sqlite.sqlite_utilities", "api/graphnet.data.utilities", "api/graphnet.data.utilities.parquet_to_sqlite", "api/graphnet.data.utilities.random", "api/graphnet.data.utilities.string_selection_resolver", "api/graphnet.deployment", "api/graphnet.deployment.i3modules", "api/graphnet.deployment.i3modules.deployer", "api/graphnet.deployment.i3modules.graphnet_module", "api/graphnet.models", "api/graphnet.models.coarsening", "api/graphnet.models.components", "api/graphnet.models.components.layers", "api/graphnet.models.components.pool", "api/graphnet.models.detector", "api/graphnet.models.detector.detector", "api/graphnet.models.detector.icecube", "api/graphnet.models.detector.prometheus", "api/graphnet.models.gnn", "api/graphnet.models.gnn.convnet", "api/graphnet.models.gnn.dynedge", "api/graphnet.models.gnn.dynedge_jinst", "api/graphnet.models.gnn.dynedge_kaggle_tito", "api/graphnet.models.gnn.gnn", "api/graphnet.models.graphs", "api/graphnet.models.graphs.edges", "api/graphnet.models.graphs.edges.edges", "api/graphnet.models.graphs.edges.minkowski", "api/graphnet.models.graphs.graph_definition", "api/graphnet.models.graphs.graphs", "api/graphnet.models.graphs.nodes", "api/graphnet.models.graphs.nodes.nodes", "api/graphnet.models.graphs.utils", "api/graphnet.models.model", "api/graphnet.models.standard_model", "api/graphnet.models.task", "api/graphnet.models.task.classification", "api/graphnet.models.task.reconstruction", "api/graphnet.models.task.task", "api/graphnet.models.utils", "api/graphnet.pisa", "api/graphnet.pisa.fitting", "api/graphnet.pisa.plotting", "api/graphnet.training", "api/graphnet.training.callbacks", "api/graphnet.training.labels", "api/graphnet.training.loss_functions", "api/graphnet.training.utils", "api/graphnet.training.weight_fitting", "api/graphnet.utilities", "api/graphnet.utilities.argparse", "api/graphnet.utilities.config", "api/graphnet.utilities.config.base_config", "api/graphnet.utilities.config.configurable", "api/graphnet.utilities.config.dataset_config", "api/graphnet.utilities.config.model_config", "api/graphnet.utilities.config.parsing", "api/graphnet.utilities.config.training_config", "api/graphnet.utilities.decorators", "api/graphnet.utilities.deprecation_tools", "api/graphnet.utilities.filesys", "api/graphnet.utilities.imports", "api/graphnet.utilities.logging", "api/graphnet.utilities.maths", "api/modules", "contribute", "index", "install"], "filenames": ["about.md", "api/graphnet.rst", "api/graphnet.constants.rst", "api/graphnet.data.rst", "api/graphnet.data.constants.rst", "api/graphnet.data.dataconverter.rst", "api/graphnet.data.dataloader.rst", "api/graphnet.data.dataset.rst", "api/graphnet.data.dataset.dataset.rst", "api/graphnet.data.dataset.parquet.rst", "api/graphnet.data.dataset.parquet.parquet_dataset.rst", "api/graphnet.data.dataset.sqlite.rst", "api/graphnet.data.dataset.sqlite.sqlite_dataset.rst", "api/graphnet.data.extractors.rst", "api/graphnet.data.extractors.i3extractor.rst", "api/graphnet.data.extractors.i3featureextractor.rst", "api/graphnet.data.extractors.i3genericextractor.rst", "api/graphnet.data.extractors.i3hybridrecoextractor.rst", "api/graphnet.data.extractors.i3ntmuonlabelsextractor.rst", "api/graphnet.data.extractors.i3particleextractor.rst", "api/graphnet.data.extractors.i3pisaextractor.rst", "api/graphnet.data.extractors.i3quesoextractor.rst", "api/graphnet.data.extractors.i3retroextractor.rst", "api/graphnet.data.extractors.i3splinempeextractor.rst", "api/graphnet.data.extractors.i3truthextractor.rst", "api/graphnet.data.extractors.i3tumextractor.rst", "api/graphnet.data.extractors.utilities.rst", "api/graphnet.data.extractors.utilities.collections.rst", "api/graphnet.data.extractors.utilities.frames.rst", "api/graphnet.data.extractors.utilities.types.rst", "api/graphnet.data.filters.rst", "api/graphnet.data.parquet.rst", "api/graphnet.data.parquet.parquet_dataconverter.rst", "api/graphnet.data.pipeline.rst", "api/graphnet.data.sqlite.rst", "api/graphnet.data.sqlite.sqlite_dataconverter.rst", "api/graphnet.data.sqlite.sqlite_utilities.rst", "api/graphnet.data.utilities.rst", "api/graphnet.data.utilities.parquet_to_sqlite.rst", "api/graphnet.data.utilities.random.rst", "api/graphnet.data.utilities.string_selection_resolver.rst", "api/graphnet.deployment.rst", "api/graphnet.deployment.i3modules.rst", "api/graphnet.deployment.i3modules.deployer.rst", "api/graphnet.deployment.i3modules.graphnet_module.rst", "api/graphnet.models.rst", "api/graphnet.models.coarsening.rst", "api/graphnet.models.components.rst", "api/graphnet.models.components.layers.rst", "api/graphnet.models.components.pool.rst", "api/graphnet.models.detector.rst", "api/graphnet.models.detector.detector.rst", "api/graphnet.models.detector.icecube.rst", "api/graphnet.models.detector.prometheus.rst", "api/graphnet.models.gnn.rst", "api/graphnet.models.gnn.convnet.rst", "api/graphnet.models.gnn.dynedge.rst", "api/graphnet.models.gnn.dynedge_jinst.rst", "api/graphnet.models.gnn.dynedge_kaggle_tito.rst", "api/graphnet.models.gnn.gnn.rst", "api/graphnet.models.graphs.rst", "api/graphnet.models.graphs.edges.rst", "api/graphnet.models.graphs.edges.edges.rst", "api/graphnet.models.graphs.edges.minkowski.rst", "api/graphnet.models.graphs.graph_definition.rst", "api/graphnet.models.graphs.graphs.rst", "api/graphnet.models.graphs.nodes.rst", "api/graphnet.models.graphs.nodes.nodes.rst", "api/graphnet.models.graphs.utils.rst", "api/graphnet.models.model.rst", "api/graphnet.models.standard_model.rst", "api/graphnet.models.task.rst", "api/graphnet.models.task.classification.rst", "api/graphnet.models.task.reconstruction.rst", "api/graphnet.models.task.task.rst", "api/graphnet.models.utils.rst", "api/graphnet.pisa.rst", "api/graphnet.pisa.fitting.rst", "api/graphnet.pisa.plotting.rst", "api/graphnet.training.rst", "api/graphnet.training.callbacks.rst", "api/graphnet.training.labels.rst", "api/graphnet.training.loss_functions.rst", "api/graphnet.training.utils.rst", "api/graphnet.training.weight_fitting.rst", "api/graphnet.utilities.rst", "api/graphnet.utilities.argparse.rst", "api/graphnet.utilities.config.rst", "api/graphnet.utilities.config.base_config.rst", "api/graphnet.utilities.config.configurable.rst", "api/graphnet.utilities.config.dataset_config.rst", "api/graphnet.utilities.config.model_config.rst", "api/graphnet.utilities.config.parsing.rst", "api/graphnet.utilities.config.training_config.rst", "api/graphnet.utilities.decorators.rst", "api/graphnet.utilities.deprecation_tools.rst", "api/graphnet.utilities.filesys.rst", "api/graphnet.utilities.imports.rst", "api/graphnet.utilities.logging.rst", "api/graphnet.utilities.maths.rst", "api/modules.rst", "contribute.md", "index.rst", "install.md"], "titles": ["About", "API", "constants", "data", "constants", "dataconverter", "dataloader", "dataset", "dataset", "parquet", "parquet_dataset", "sqlite", "sqlite_dataset", "extractors", "i3extractor", "i3featureextractor", "i3genericextractor", "i3hybridrecoextractor", "i3ntmuonlabelsextractor", "i3particleextractor", "i3pisaextractor", "i3quesoextractor", "i3retroextractor", "i3splinempeextractor", "i3truthextractor", "i3tumextractor", "utilities", "collections", "frames", "types", "filters", "parquet", "parquet_dataconverter", "pipeline", "sqlite", "sqlite_dataconverter", "sqlite_utilities", "utilities", "parquet_to_sqlite", "random", "string_selection_resolver", "deployment", "i3modules", "deployer", "graphnet_module", "models", "coarsening", "components", "layers", "pool", "detector", "detector", "icecube", "prometheus", "gnn", "convnet", "dynedge", "dynedge_jinst", "dynedge_kaggle_tito", "gnn", "graphs", "edges", "edges", "minkowski", "graph_definition", "graphs", "nodes", "nodes", "utils", "model", "standard_model", "task", "classification", "reconstruction", "task", "utils", "pisa", "fitting", "plotting", "training", "callbacks", "labels", "loss_functions", "utils", "weight_fitting", "utilities", "argparse", "config", "base_config", "configurable", "dataset_config", "model_config", "parsing", "training_config", "decorators", "deprecation_tools", "filesys", "imports", "logging", "maths", "src", "Contribute", "About", "Install"], "terms": {"graphnet": [0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 48, 49, 51, 52, 53, 55, 56, 57, 58, 59, 62, 63, 64, 65, 67, 68, 69, 70, 72, 73, 74, 75, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 95, 96, 97, 98, 99, 101, 102, 103], "i": [0, 1, 8, 10, 12, 14, 16, 27, 28, 29, 30, 35, 36, 39, 40, 44, 46, 49, 55, 56, 62, 64, 67, 68, 73, 74, 75, 78, 80, 81, 82, 83, 84, 86, 91, 92, 95, 96, 97, 98, 101, 102, 103], "an": [0, 5, 29, 32, 33, 35, 40, 44, 64, 82, 96, 98, 101, 102, 103], "open": [0, 101, 102], "sourc": [0, 4, 5, 6, 8, 10, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 32, 33, 35, 36, 38, 39, 40, 44, 46, 48, 49, 51, 52, 53, 55, 56, 57, 58, 59, 62, 63, 64, 65, 67, 68, 69, 70, 72, 73, 74, 75, 77, 78, 80, 81, 82, 83, 84, 86, 88, 89, 90, 91, 92, 93, 95, 96, 97, 98, 99, 101, 102], "python": [0, 1, 5, 13, 14, 16, 27, 29, 101, 102, 103], "framework": [0, 102], "aim": [0, 1, 101, 102], "provid": [0, 1, 8, 10, 12, 44, 45, 64, 82, 101, 102, 103], "high": [0, 102], "qualiti": [0, 102], "user": [0, 45, 80, 102, 103], "friendli": [0, 102], "end": [0, 1, 5, 32, 35, 80, 102], "function": [0, 5, 6, 8, 29, 36, 39, 44, 46, 49, 52, 53, 64, 68, 69, 74, 75, 77, 78, 82, 83, 85, 90, 91, 92, 95, 96, 97, 99, 102], "perform": [0, 46, 48, 49, 54, 56, 58, 70, 72, 74, 83, 102], "reconstruct": [0, 1, 15, 17, 18, 22, 23, 25, 33, 41, 45, 58, 71, 74, 102], "task": [0, 1, 45, 70, 72, 73, 82, 101, 102], "neutrino": [0, 1, 48, 58, 68, 77, 102], "telescop": [0, 1, 102], "us": [0, 1, 2, 4, 5, 6, 8, 9, 10, 11, 12, 14, 19, 24, 26, 27, 32, 33, 35, 36, 37, 38, 40, 41, 44, 45, 48, 49, 51, 56, 57, 58, 62, 64, 65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 77, 80, 81, 82, 84, 85, 86, 87, 88, 90, 91, 92, 93, 97, 98, 101, 102, 103], "graph": [0, 1, 6, 8, 10, 12, 44, 45, 48, 49, 51, 61, 62, 63, 64, 66, 67, 68, 74, 75, 81, 83, 101, 102], "neural": [0, 1, 102], "network": [0, 1, 55, 102], "gnn": [0, 1, 33, 45, 55, 56, 57, 58, 64, 70, 102, 103], "make": [0, 5, 84, 90, 91, 101, 102, 103], "fast": [0, 102, 103], "easi": [0, 102], "train": [0, 1, 7, 40, 41, 44, 64, 70, 80, 81, 82, 83, 84, 86, 90, 91, 93, 100, 102, 103], "complex": [0, 45, 102], "model": [0, 1, 41, 44, 46, 47, 48, 49, 51, 52, 53, 55, 56, 57, 58, 59, 62, 63, 64, 65, 67, 68, 70, 71, 72, 73, 74, 75, 78, 79, 80, 82, 83, 86, 88, 90, 91, 93, 100, 102, 103], "can": [0, 1, 8, 10, 12, 14, 16, 19, 38, 44, 49, 64, 77, 78, 84, 86, 88, 90, 91, 101, 102, 103], "event": [0, 1, 8, 10, 12, 21, 36, 38, 40, 44, 49, 64, 68, 74, 75, 77, 82, 84, 90, 102], "state": [0, 95, 102], "art": [0, 102], "arbitrari": [0, 102], "detector": [0, 1, 24, 45, 52, 53, 64, 65, 67, 70, 102], "configur": [0, 1, 8, 45, 69, 70, 77, 85, 87, 88, 90, 91, 93, 98, 102], "infer": [0, 1, 33, 41, 44, 70, 74, 102, 103], "time": [0, 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101, 102, 103], "build": [0, 1, 45, 51, 62, 63, 67, 68, 69, 88, 90, 91, 102], "gener": [0, 5, 8, 10, 12, 16, 30, 44, 60, 61, 64, 65, 66, 72, 82, 102], "reusabl": [0, 102], "softwar": [0, 82, 102], "packag": [0, 1, 39, 92, 96, 97, 101, 102, 103], "base": [0, 4, 5, 6, 8, 10, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 32, 33, 35, 38, 40, 44, 46, 48, 51, 52, 53, 55, 56, 57, 58, 59, 62, 63, 64, 65, 67, 69, 70, 72, 73, 74, 77, 80, 81, 82, 83, 84, 86, 88, 89, 90, 91, 93, 97, 98, 102], "engin": [0, 102], "best": [0, 80, 101, 102], "practic": [0, 101, 102], "lower": [0, 78, 102], "technic": [0, 102], "threshold": [0, 44, 102], "most": [0, 1, 40, 63, 74, 102, 103], "scientif": [0, 1, 102], "problem": [0, 62, 101, 102], "The": [0, 5, 8, 10, 12, 27, 29, 33, 35, 36, 44, 46, 48, 49, 56, 58, 62, 64, 68, 72, 73, 74, 75, 77, 78, 80, 81, 82, 95, 102], "improv": [0, 1, 86, 102], "classif": [0, 1, 45, 71, 74, 82, 102], "yield": [0, 56, 77, 82, 102], "veri": [0, 40, 102], "accur": [0, 102], "e": [0, 1, 5, 6, 8, 10, 12, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 27, 29, 32, 33, 35, 36, 40, 44, 46, 48, 49, 51, 52, 53, 55, 59, 62, 64, 67, 68, 69, 70, 72, 73, 74, 75, 80, 81, 82, 84, 88, 98, 101, 102, 103], "g": [0, 1, 5, 8, 10, 12, 24, 27, 29, 32, 33, 35, 36, 40, 44, 49, 64, 67, 68, 74, 75, 84, 98, 101, 102, 103], "low": [0, 102], "energi": [0, 4, 33, 73, 74, 84, 102], "observ": [0, 102], "icecub": [0, 1, 15, 28, 29, 45, 48, 50, 58, 97, 102, 103], "here": [0, 64, 101, 102, 103], "implement": [0, 1, 5, 14, 31, 32, 34, 35, 48, 55, 56, 57, 58, 62, 82, 101, 102], "wa": [0, 102], "appli": [0, 8, 10, 12, 14, 49, 55, 56, 57, 58, 59, 70, 72, 74, 92, 102], "oscil": [0, 76, 102], "lead": [0, 102], "signific": [0, 102], "angular": [0, 102], "rang": [0, 74, 102], "relev": [0, 1, 29, 39, 96, 101, 102], "studi": [0, 102], "furthermor": [0, 102], "shown": [0, 102], "could": [0, 101, 102], "muon": [0, 18, 102], "v": [0, 102], "therebi": [0, 1, 90, 91, 102], "effici": [0, 102], "puriti": [0, 102], "sampl": [0, 40, 64, 65, 74, 102], "analysi": [0, 33, 102, 103], "similarli": [0, 29, 102], "ha": [0, 5, 29, 32, 35, 36, 44, 55, 68, 82, 96, 102, 103], "great": [0, 102], "point": [0, 23, 81, 82, 83, 102], "analys": [0, 41, 76, 102], "final": [0, 49, 80, 90, 102], "millisecond": [0, 102], "allow": [0, 41, 45, 49, 80, 88, 93, 102, 103], "whole": [0, 102], "new": [0, 1, 35, 48, 67, 88, 93, 101, 102], "type": [0, 5, 6, 8, 10, 12, 13, 14, 26, 27, 28, 32, 35, 36, 38, 39, 40, 46, 48, 49, 51, 52, 53, 55, 56, 57, 58, 59, 62, 63, 64, 65, 67, 68, 69, 70, 72, 73, 74, 75, 77, 78, 80, 82, 83, 84, 86, 88, 89, 90, 91, 92, 95, 96, 97, 98, 99, 101, 102], "cosmic": [0, 102], "alert": [0, 102], "which": [0, 8, 10, 12, 14, 15, 24, 28, 33, 40, 44, 46, 49, 56, 64, 65, 68, 69, 72, 77, 82, 83, 86, 102, 103], "were": [0, 102], "previous": [0, 102], "unfeas": [0, 102], "possibl": [0, 27, 101, 102], "identifi": [0, 5, 8, 10, 12, 24, 68, 90, 91, 102], "10": [0, 33, 52, 53, 67, 68, 86, 102], "tev": [0, 102], 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"kaggle (graphnet.data.constants.features attribute)": [[4, "graphnet.data.constants.FEATURES.KAGGLE"]], "kaggle (graphnet.data.constants.truth attribute)": [[4, "graphnet.data.constants.TRUTH.KAGGLE"]], "prometheus (graphnet.data.constants.features attribute)": [[4, "graphnet.data.constants.FEATURES.PROMETHEUS"]], "prometheus (graphnet.data.constants.truth attribute)": [[4, "graphnet.data.constants.TRUTH.PROMETHEUS"]], "truth (class in graphnet.data.constants)": [[4, "graphnet.data.constants.TRUTH"]], "upgrade (graphnet.data.constants.features attribute)": [[4, "graphnet.data.constants.FEATURES.UPGRADE"]], "upgrade (graphnet.data.constants.truth attribute)": [[4, "graphnet.data.constants.TRUTH.UPGRADE"]], "graphnet.data.constants": [[4, "module-graphnet.data.constants"]], "dataconverter (class in graphnet.data.dataconverter)": [[5, "graphnet.data.dataconverter.DataConverter"]], "fileset (class in graphnet.data.dataconverter)": [[5, "graphnet.data.dataconverter.FileSet"]], "cache_output_files() (in module graphnet.data.dataconverter)": [[5, "graphnet.data.dataconverter.cache_output_files"]], "execute() (graphnet.data.dataconverter.dataconverter method)": [[5, "graphnet.data.dataconverter.DataConverter.execute"]], "file_suffix (graphnet.data.dataconverter.dataconverter property)": [[5, "graphnet.data.dataconverter.DataConverter.file_suffix"]], "gcd_file (graphnet.data.dataconverter.fileset attribute)": [[5, "graphnet.data.dataconverter.FileSet.gcd_file"]], "get_map_function() (graphnet.data.dataconverter.dataconverter method)": [[5, "graphnet.data.dataconverter.DataConverter.get_map_function"]], "graphnet.data.dataconverter": [[5, "module-graphnet.data.dataconverter"]], "i3_file (graphnet.data.dataconverter.fileset attribute)": [[5, "graphnet.data.dataconverter.FileSet.i3_file"]], "init_global_index() (in module graphnet.data.dataconverter)": [[5, "graphnet.data.dataconverter.init_global_index"]], "merge_files() (graphnet.data.dataconverter.dataconverter method)": [[5, "graphnet.data.dataconverter.DataConverter.merge_files"]], "save_data() (graphnet.data.dataconverter.dataconverter method)": [[5, "graphnet.data.dataconverter.DataConverter.save_data"]], "dataloader (class in graphnet.data.dataloader)": [[6, "graphnet.data.dataloader.DataLoader"]], "collate_fn() (in module graphnet.data.dataloader)": [[6, "graphnet.data.dataloader.collate_fn"]], "do_shuffle() (in module graphnet.data.dataloader)": [[6, "graphnet.data.dataloader.do_shuffle"]], "from_dataset_config() (graphnet.data.dataloader.dataloader class method)": [[6, "graphnet.data.dataloader.DataLoader.from_dataset_config"]], "graphnet.data.dataloader": [[6, "module-graphnet.data.dataloader"]], "graphnet.data.dataset": [[7, "module-graphnet.data.dataset"]], "columnmissingexception": [[8, "graphnet.data.dataset.dataset.ColumnMissingException"]], "dataset (class in graphnet.data.dataset.dataset)": [[8, "graphnet.data.dataset.dataset.Dataset"]], "ensembledataset (class in graphnet.data.dataset.dataset)": [[8, "graphnet.data.dataset.dataset.EnsembleDataset"]], "add_label() (graphnet.data.dataset.dataset.dataset method)": [[8, "graphnet.data.dataset.dataset.Dataset.add_label"]], "concatenate() (graphnet.data.dataset.dataset.dataset class method)": [[8, "graphnet.data.dataset.dataset.Dataset.concatenate"]], "from_config() (graphnet.data.dataset.dataset.dataset class method)": [[8, "graphnet.data.dataset.dataset.Dataset.from_config"]], "graphnet.data.dataset.dataset": [[8, "module-graphnet.data.dataset.dataset"]], "load_module() (in module graphnet.data.dataset.dataset)": [[8, "graphnet.data.dataset.dataset.load_module"]], "parse_graph_definition() (in module graphnet.data.dataset.dataset)": [[8, "graphnet.data.dataset.dataset.parse_graph_definition"]], "path (graphnet.data.dataset.dataset.dataset property)": [[8, "graphnet.data.dataset.dataset.Dataset.path"]], "query_table() (graphnet.data.dataset.dataset.dataset method)": [[8, "graphnet.data.dataset.dataset.Dataset.query_table"]], "truth_table (graphnet.data.dataset.dataset.dataset property)": [[8, "graphnet.data.dataset.dataset.Dataset.truth_table"]], "graphnet.data.dataset.parquet": [[9, "module-graphnet.data.dataset.parquet"]], "parquetdataset (class in graphnet.data.dataset.parquet.parquet_dataset)": [[10, "graphnet.data.dataset.parquet.parquet_dataset.ParquetDataset"]], "graphnet.data.dataset.parquet.parquet_dataset": [[10, "module-graphnet.data.dataset.parquet.parquet_dataset"]], "query_table() (graphnet.data.dataset.parquet.parquet_dataset.parquetdataset method)": [[10, "graphnet.data.dataset.parquet.parquet_dataset.ParquetDataset.query_table"]], "graphnet.data.dataset.sqlite": [[11, "module-graphnet.data.dataset.sqlite"]], "sqlitedataset (class in graphnet.data.dataset.sqlite.sqlite_dataset)": [[12, "graphnet.data.dataset.sqlite.sqlite_dataset.SQLiteDataset"]], "graphnet.data.dataset.sqlite.sqlite_dataset": [[12, "module-graphnet.data.dataset.sqlite.sqlite_dataset"]], "query_table() (graphnet.data.dataset.sqlite.sqlite_dataset.sqlitedataset method)": [[12, "graphnet.data.dataset.sqlite.sqlite_dataset.SQLiteDataset.query_table"]], "graphnet.data.extractors": [[13, "module-graphnet.data.extractors"]], "i3extractor (class in graphnet.data.extractors.i3extractor)": [[14, "graphnet.data.extractors.i3extractor.I3Extractor"]], "i3extractorcollection (class in graphnet.data.extractors.i3extractor)": [[14, "graphnet.data.extractors.i3extractor.I3ExtractorCollection"]], "graphnet.data.extractors.i3extractor": [[14, "module-graphnet.data.extractors.i3extractor"]], "name (graphnet.data.extractors.i3extractor.i3extractor property)": [[14, "graphnet.data.extractors.i3extractor.I3Extractor.name"]], "set_files() (graphnet.data.extractors.i3extractor.i3extractor method)": [[14, "graphnet.data.extractors.i3extractor.I3Extractor.set_files"]], "set_files() (graphnet.data.extractors.i3extractor.i3extractorcollection method)": [[14, "graphnet.data.extractors.i3extractor.I3ExtractorCollection.set_files"]], "i3featureextractor (class in graphnet.data.extractors.i3featureextractor)": [[15, "graphnet.data.extractors.i3featureextractor.I3FeatureExtractor"]], "i3featureextractoricecube86 (class in graphnet.data.extractors.i3featureextractor)": [[15, "graphnet.data.extractors.i3featureextractor.I3FeatureExtractorIceCube86"]], "i3featureextractoricecubedeepcore (class in graphnet.data.extractors.i3featureextractor)": [[15, "graphnet.data.extractors.i3featureextractor.I3FeatureExtractorIceCubeDeepCore"]], "i3featureextractoricecubeupgrade (class in graphnet.data.extractors.i3featureextractor)": [[15, "graphnet.data.extractors.i3featureextractor.I3FeatureExtractorIceCubeUpgrade"]], "i3pulsenoisetruthflagicecubeupgrade (class in graphnet.data.extractors.i3featureextractor)": [[15, "graphnet.data.extractors.i3featureextractor.I3PulseNoiseTruthFlagIceCubeUpgrade"]], "graphnet.data.extractors.i3featureextractor": [[15, "module-graphnet.data.extractors.i3featureextractor"]], "i3genericextractor (class in graphnet.data.extractors.i3genericextractor)": [[16, "graphnet.data.extractors.i3genericextractor.I3GenericExtractor"]], "graphnet.data.extractors.i3genericextractor": [[16, "module-graphnet.data.extractors.i3genericextractor"]], "i3galacticplanehybridrecoextractor (class in graphnet.data.extractors.i3hybridrecoextractor)": [[17, "graphnet.data.extractors.i3hybridrecoextractor.I3GalacticPlaneHybridRecoExtractor"]], "graphnet.data.extractors.i3hybridrecoextractor": [[17, "module-graphnet.data.extractors.i3hybridrecoextractor"]], "i3ntmuonlabelextractor (class in graphnet.data.extractors.i3ntmuonlabelsextractor)": [[18, "graphnet.data.extractors.i3ntmuonlabelsextractor.I3NTMuonLabelExtractor"]], "graphnet.data.extractors.i3ntmuonlabelsextractor": [[18, "module-graphnet.data.extractors.i3ntmuonlabelsextractor"]], "i3particleextractor (class in graphnet.data.extractors.i3particleextractor)": [[19, "graphnet.data.extractors.i3particleextractor.I3ParticleExtractor"]], "graphnet.data.extractors.i3particleextractor": [[19, "module-graphnet.data.extractors.i3particleextractor"]], "i3pisaextractor (class in graphnet.data.extractors.i3pisaextractor)": [[20, "graphnet.data.extractors.i3pisaextractor.I3PISAExtractor"]], "graphnet.data.extractors.i3pisaextractor": [[20, "module-graphnet.data.extractors.i3pisaextractor"]], "i3quesoextractor (class in graphnet.data.extractors.i3quesoextractor)": [[21, "graphnet.data.extractors.i3quesoextractor.I3QUESOExtractor"]], "graphnet.data.extractors.i3quesoextractor": [[21, "module-graphnet.data.extractors.i3quesoextractor"]], "i3retroextractor (class in graphnet.data.extractors.i3retroextractor)": [[22, "graphnet.data.extractors.i3retroextractor.I3RetroExtractor"]], "graphnet.data.extractors.i3retroextractor": [[22, "module-graphnet.data.extractors.i3retroextractor"]], "i3splinempeicextractor (class in graphnet.data.extractors.i3splinempeextractor)": [[23, "graphnet.data.extractors.i3splinempeextractor.I3SplineMPEICExtractor"]], "graphnet.data.extractors.i3splinempeextractor": [[23, "module-graphnet.data.extractors.i3splinempeextractor"]], "i3truthextractor (class in graphnet.data.extractors.i3truthextractor)": [[24, "graphnet.data.extractors.i3truthextractor.I3TruthExtractor"]], "graphnet.data.extractors.i3truthextractor": [[24, "module-graphnet.data.extractors.i3truthextractor"]], "i3tumextractor (class in graphnet.data.extractors.i3tumextractor)": [[25, "graphnet.data.extractors.i3tumextractor.I3TUMExtractor"]], "graphnet.data.extractors.i3tumextractor": [[25, "module-graphnet.data.extractors.i3tumextractor"]], "graphnet.data.extractors.utilities": [[26, "module-graphnet.data.extractors.utilities"]], "flatten_nested_dictionary() (in module graphnet.data.extractors.utilities.collections)": [[27, "graphnet.data.extractors.utilities.collections.flatten_nested_dictionary"]], "graphnet.data.extractors.utilities.collections": [[27, "module-graphnet.data.extractors.utilities.collections"]], "serialise() (in module graphnet.data.extractors.utilities.collections)": [[27, "graphnet.data.extractors.utilities.collections.serialise"]], "transpose_list_of_dicts() (in module graphnet.data.extractors.utilities.collections)": [[27, "graphnet.data.extractors.utilities.collections.transpose_list_of_dicts"]], "frame_is_montecarlo() (in module graphnet.data.extractors.utilities.frames)": [[28, "graphnet.data.extractors.utilities.frames.frame_is_montecarlo"]], "frame_is_noise() (in module graphnet.data.extractors.utilities.frames)": [[28, "graphnet.data.extractors.utilities.frames.frame_is_noise"]], "get_om_keys_and_pulseseries() (in module graphnet.data.extractors.utilities.frames)": [[28, "graphnet.data.extractors.utilities.frames.get_om_keys_and_pulseseries"]], "graphnet.data.extractors.utilities.frames": [[28, "module-graphnet.data.extractors.utilities.frames"]], "break_cyclic_recursion() (in module graphnet.data.extractors.utilities.types)": [[29, "graphnet.data.extractors.utilities.types.break_cyclic_recursion"]], "cast_object_to_pure_python() (in module graphnet.data.extractors.utilities.types)": [[29, "graphnet.data.extractors.utilities.types.cast_object_to_pure_python"]], "cast_pulse_series_to_pure_python() (in module graphnet.data.extractors.utilities.types)": [[29, "graphnet.data.extractors.utilities.types.cast_pulse_series_to_pure_python"]], "get_member_variables() (in module graphnet.data.extractors.utilities.types)": [[29, "graphnet.data.extractors.utilities.types.get_member_variables"]], "graphnet.data.extractors.utilities.types": [[29, "module-graphnet.data.extractors.utilities.types"]], "is_boost_class() (in module graphnet.data.extractors.utilities.types)": [[29, "graphnet.data.extractors.utilities.types.is_boost_class"]], "is_boost_enum() (in module graphnet.data.extractors.utilities.types)": [[29, "graphnet.data.extractors.utilities.types.is_boost_enum"]], "is_icecube_class() (in module graphnet.data.extractors.utilities.types)": [[29, "graphnet.data.extractors.utilities.types.is_icecube_class"]], "is_method() (in module graphnet.data.extractors.utilities.types)": [[29, "graphnet.data.extractors.utilities.types.is_method"]], "is_type() (in module graphnet.data.extractors.utilities.types)": [[29, "graphnet.data.extractors.utilities.types.is_type"]], "i3filter (class in graphnet.data.filters)": [[30, "graphnet.data.filters.I3Filter"]], "i3filtermask (class in graphnet.data.filters)": [[30, "graphnet.data.filters.I3FilterMask"]], "nullspliti3filter (class in graphnet.data.filters)": [[30, "graphnet.data.filters.NullSplitI3Filter"]], "graphnet.data.filters": [[30, "module-graphnet.data.filters"]], "graphnet.data.parquet": [[31, "module-graphnet.data.parquet"]], "parquetdataconverter (class in graphnet.data.parquet.parquet_dataconverter)": [[32, "graphnet.data.parquet.parquet_dataconverter.ParquetDataConverter"]], "file_suffix (graphnet.data.parquet.parquet_dataconverter.parquetdataconverter attribute)": [[32, "graphnet.data.parquet.parquet_dataconverter.ParquetDataConverter.file_suffix"]], "graphnet.data.parquet.parquet_dataconverter": [[32, "module-graphnet.data.parquet.parquet_dataconverter"]], "merge_files() (graphnet.data.parquet.parquet_dataconverter.parquetdataconverter method)": [[32, "graphnet.data.parquet.parquet_dataconverter.ParquetDataConverter.merge_files"]], "save_data() (graphnet.data.parquet.parquet_dataconverter.parquetdataconverter method)": [[32, "graphnet.data.parquet.parquet_dataconverter.ParquetDataConverter.save_data"]], "insqlitepipeline (class in graphnet.data.pipeline)": [[33, "graphnet.data.pipeline.InSQLitePipeline"]], "graphnet.data.pipeline": [[33, "module-graphnet.data.pipeline"]], "graphnet.data.sqlite": [[34, "module-graphnet.data.sqlite"]], "sqlitedataconverter (class in graphnet.data.sqlite.sqlite_dataconverter)": [[35, "graphnet.data.sqlite.sqlite_dataconverter.SQLiteDataConverter"]], "any_pulsemap_is_non_empty() (graphnet.data.sqlite.sqlite_dataconverter.sqlitedataconverter method)": [[35, "graphnet.data.sqlite.sqlite_dataconverter.SQLiteDataConverter.any_pulsemap_is_non_empty"]], "construct_dataframe() (in module graphnet.data.sqlite.sqlite_dataconverter)": [[35, "graphnet.data.sqlite.sqlite_dataconverter.construct_dataframe"]], "file_suffix (graphnet.data.sqlite.sqlite_dataconverter.sqlitedataconverter attribute)": [[35, "graphnet.data.sqlite.sqlite_dataconverter.SQLiteDataConverter.file_suffix"]], "graphnet.data.sqlite.sqlite_dataconverter": [[35, "module-graphnet.data.sqlite.sqlite_dataconverter"]], "is_mc_tree() (in module graphnet.data.sqlite.sqlite_dataconverter)": [[35, "graphnet.data.sqlite.sqlite_dataconverter.is_mc_tree"]], "is_pulse_map() (in module graphnet.data.sqlite.sqlite_dataconverter)": [[35, "graphnet.data.sqlite.sqlite_dataconverter.is_pulse_map"]], "merge_files() (graphnet.data.sqlite.sqlite_dataconverter.sqlitedataconverter method)": [[35, "graphnet.data.sqlite.sqlite_dataconverter.SQLiteDataConverter.merge_files"]], "save_data() (graphnet.data.sqlite.sqlite_dataconverter.sqlitedataconverter method)": [[35, "graphnet.data.sqlite.sqlite_dataconverter.SQLiteDataConverter.save_data"]], "attach_index() (in module graphnet.data.sqlite.sqlite_utilities)": [[36, "graphnet.data.sqlite.sqlite_utilities.attach_index"]], "create_table() (in module graphnet.data.sqlite.sqlite_utilities)": [[36, "graphnet.data.sqlite.sqlite_utilities.create_table"]], "create_table_and_save_to_sql() (in module graphnet.data.sqlite.sqlite_utilities)": [[36, "graphnet.data.sqlite.sqlite_utilities.create_table_and_save_to_sql"]], "database_exists() (in module graphnet.data.sqlite.sqlite_utilities)": [[36, "graphnet.data.sqlite.sqlite_utilities.database_exists"]], "database_table_exists() (in module graphnet.data.sqlite.sqlite_utilities)": [[36, "graphnet.data.sqlite.sqlite_utilities.database_table_exists"]], "graphnet.data.sqlite.sqlite_utilities": [[36, "module-graphnet.data.sqlite.sqlite_utilities"]], "run_sql_code() (in module graphnet.data.sqlite.sqlite_utilities)": [[36, "graphnet.data.sqlite.sqlite_utilities.run_sql_code"]], "save_to_sql() (in module graphnet.data.sqlite.sqlite_utilities)": [[36, "graphnet.data.sqlite.sqlite_utilities.save_to_sql"]], "graphnet.data.utilities": [[37, "module-graphnet.data.utilities"]], "parquettosqliteconverter (class in graphnet.data.utilities.parquet_to_sqlite)": [[38, "graphnet.data.utilities.parquet_to_sqlite.ParquetToSQLiteConverter"]], "graphnet.data.utilities.parquet_to_sqlite": [[38, "module-graphnet.data.utilities.parquet_to_sqlite"]], "run() (graphnet.data.utilities.parquet_to_sqlite.parquettosqliteconverter method)": [[38, "graphnet.data.utilities.parquet_to_sqlite.ParquetToSQLiteConverter.run"]], "graphnet.data.utilities.random": [[39, "module-graphnet.data.utilities.random"]], "pairwise_shuffle() (in module graphnet.data.utilities.random)": [[39, "graphnet.data.utilities.random.pairwise_shuffle"]], "stringselectionresolver (class in graphnet.data.utilities.string_selection_resolver)": [[40, "graphnet.data.utilities.string_selection_resolver.StringSelectionResolver"]], "graphnet.data.utilities.string_selection_resolver": [[40, "module-graphnet.data.utilities.string_selection_resolver"]], "resolve() (graphnet.data.utilities.string_selection_resolver.stringselectionresolver method)": [[40, "graphnet.data.utilities.string_selection_resolver.StringSelectionResolver.resolve"]], "graphnet.deployment": [[41, "module-graphnet.deployment"]], "graphneti3module (class in graphnet.deployment.i3modules.graphnet_module)": [[44, "graphnet.deployment.i3modules.graphnet_module.GraphNeTI3Module"]], "i3inferencemodule (class in graphnet.deployment.i3modules.graphnet_module)": [[44, "graphnet.deployment.i3modules.graphnet_module.I3InferenceModule"]], "i3pulsecleanermodule (class in graphnet.deployment.i3modules.graphnet_module)": [[44, "graphnet.deployment.i3modules.graphnet_module.I3PulseCleanerModule"]], "graphnet.deployment.i3modules.graphnet_module": [[44, "module-graphnet.deployment.i3modules.graphnet_module"]], "graphnet.models": [[45, "module-graphnet.models"]], "attributecoarsening (class in graphnet.models.coarsening)": [[46, "graphnet.models.coarsening.AttributeCoarsening"]], "coarsening (class in graphnet.models.coarsening)": [[46, "graphnet.models.coarsening.Coarsening"]], "customdomcoarsening (class in graphnet.models.coarsening)": [[46, "graphnet.models.coarsening.CustomDOMCoarsening"]], "domandtimewindowcoarsening (class in graphnet.models.coarsening)": [[46, "graphnet.models.coarsening.DOMAndTimeWindowCoarsening"]], "domcoarsening (class in graphnet.models.coarsening)": [[46, "graphnet.models.coarsening.DOMCoarsening"]], "forward() (graphnet.models.coarsening.coarsening method)": [[46, "graphnet.models.coarsening.Coarsening.forward"]], "graphnet.models.coarsening": [[46, "module-graphnet.models.coarsening"]], "reduce_options (graphnet.models.coarsening.coarsening attribute)": [[46, "graphnet.models.coarsening.Coarsening.reduce_options"]], "unbatch_edge_index() (in module graphnet.models.coarsening)": [[46, "graphnet.models.coarsening.unbatch_edge_index"]], "graphnet.models.components": [[47, "module-graphnet.models.components"]], "dynedgeconv (class in graphnet.models.components.layers)": [[48, "graphnet.models.components.layers.DynEdgeConv"]], "dyntrans (class in graphnet.models.components.layers)": [[48, "graphnet.models.components.layers.DynTrans"]], "edgeconvtito (class in graphnet.models.components.layers)": [[48, 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graphnet.data.extractors.i3extractor)": [[14, "graphnet.data.extractors.i3extractor.I3Extractor"]], "i3extractorcollection (class in graphnet.data.extractors.i3extractor)": [[14, "graphnet.data.extractors.i3extractor.I3ExtractorCollection"]], "graphnet.data.extractors.i3extractor": [[14, "module-graphnet.data.extractors.i3extractor"]], "name (graphnet.data.extractors.i3extractor.i3extractor property)": [[14, "graphnet.data.extractors.i3extractor.I3Extractor.name"]], "set_files() (graphnet.data.extractors.i3extractor.i3extractor method)": [[14, "graphnet.data.extractors.i3extractor.I3Extractor.set_files"]], "set_files() (graphnet.data.extractors.i3extractor.i3extractorcollection method)": [[14, "graphnet.data.extractors.i3extractor.I3ExtractorCollection.set_files"]], "i3featureextractor (class in graphnet.data.extractors.i3featureextractor)": [[15, "graphnet.data.extractors.i3featureextractor.I3FeatureExtractor"]], "i3featureextractoricecube86 (class in 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"transpose_list_of_dicts() (in module graphnet.data.extractors.utilities.collections)": [[27, "graphnet.data.extractors.utilities.collections.transpose_list_of_dicts"]], "frame_is_montecarlo() (in module graphnet.data.extractors.utilities.frames)": [[28, "graphnet.data.extractors.utilities.frames.frame_is_montecarlo"]], "frame_is_noise() (in module graphnet.data.extractors.utilities.frames)": [[28, "graphnet.data.extractors.utilities.frames.frame_is_noise"]], "get_om_keys_and_pulseseries() (in module graphnet.data.extractors.utilities.frames)": [[28, "graphnet.data.extractors.utilities.frames.get_om_keys_and_pulseseries"]], "graphnet.data.extractors.utilities.frames": [[28, "module-graphnet.data.extractors.utilities.frames"]], "break_cyclic_recursion() (in module graphnet.data.extractors.utilities.types)": [[29, "graphnet.data.extractors.utilities.types.break_cyclic_recursion"]], "cast_object_to_pure_python() (in module graphnet.data.extractors.utilities.types)": [[29, 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