From 2ae3df8c2a511665019762cbd389f613bef6a32b Mon Sep 17 00:00:00 2001 From: David Nicholson Date: Sat, 12 Oct 2024 09:51:08 -0400 Subject: [PATCH] ENH: Several features/fixes for version 5.1 (#280) * CLN: Fix line break in formats/seq/simple.py * Import format classes at package level, fix #273 * Have SimpleSeq only map column names in `column_map`, fix #272 Inside `SimpleSeq.from_file`, when someone specifies a `column_map` argument, we only do the mapping if a column name in the loaded csv file is a key in `column_map`. Otherwise we leave the column as-is, and if it's not one of the columns we need for the annotations ("onset_s", "offset_s", "label"), it gets thrown away. * Make SimpleSeq work with csv that doesn't have labels, fix #271 Adds `default_label` argument to `from_file` method, a string that defaults to `'-'` and if the `pandas.DataFrame` loaded from the csv file does not already have a 'label' column, adds that column with the `default_label` value as the label in every row. This makes it possible to load segmentations saved in csv files that do not have labels, just start and stop times of the segments. * Add validation logic for `columns_map` to SimpleSeq * Fix SimpleSeq to handle empty csv file, fixes #264 * Fixup add validation of columns_map to SimpleSeq.from_file * Add fixture `jourjine_et_al_2023_csv_path` to fixtures/simple.py * Write unit tests for new features added to SimpleSeq * Fixup import format classes at package level * Rewrite crowsetta.data as crowsetta.examples, fix #278 As described in issue, and also: Add example data files to dir Remove crowsetta.data Rewrite tests/test_data.py as tests/test_example.py * Add csv from Jourjine et al 2023 dataset in tests + examples, fix #274 * Add helpful error message in SimpleSeq.from_file for when columns don't have expected names. * Fix examples in docstrings of format classes after changing data -> example * Apply linting * Squelch flake8 line-length warnings for examples * Add how-to on how to work with unlabeled segmentations * Use crowsetta.example not crowsetta.data in doc/index.md * Use crowsetta.example not crowsetta.data in doc/api/core.md * Fixup empty SimpleSeq unit test * Add __len__ to Sequence, fix #276 * Fix unit test for empty SimpleSeq to just use pytest tempdir, not tempfile * Add unit tests for Sequence.__len__ * Add assert in unit test for empty SimpleSeq that we can call to_seq and get a Sequence of length 0 * Fixup usage of in index.md -- fix example names * Put all of API onto one page in docs, fix how we show crowsetta.examples.show and crowsetta.example --- doc/api/core.md | 129 -- doc/api/formats.md | 20 - doc/api/index.md | 195 +- doc/api/interface.md | 42 - .../work-with-unlabeled-segmentations.md | 82 + doc/index.md | 43 +- src/crowsetta/__init__.py | 17 +- src/crowsetta/annotation.py | 1 + src/crowsetta/bbox.py | 1 + src/crowsetta/data/__init__.py | 19 - src/crowsetta/data/audbbox/__init__.py | 0 src/crowsetta/data/audseq/__init__.py | 0 src/crowsetta/data/birdsongrec/__init__.py | 0 src/crowsetta/data/data.py | 291 --- src/crowsetta/data/generic/__init__.py | 0 src/crowsetta/data/generic/citation.txt | 1 - src/crowsetta/data/notmat/__init__.py | 0 src/crowsetta/data/raven/__init__.py | 0 src/crowsetta/data/simple/__init__.py | 0 src/crowsetta/data/textgrid/__init__.py | 0 src/crowsetta/data/timit/__init__.py | 0 ...14_2016_69640887.audacity-description.txt} | 2 + ...marron1_June_14_2016_69640887.audacity.txt | 0 .../AVO-maea-basic.TextGrid | 0 .../AVO-maea-basic.TextGrid-description.txt} | 1 + .../birdsongrec => examples}/Annotation.xml | 0 .../Annotation.xml-description.txt} | 1 + ...fr1_p9_2021-10-02_12-35-01-description.txt | 5 + ...0_m_337_295_fr1_p9_2021-10-02_12-35-01.csv | 1563 +++++++++++++++++ ...ent_02.Table.1.selections-description.txt} | 2 + ...ording_1_Segment_02.Table.1.selections.txt | 0 src/crowsetta/examples/__init__.py | 3 + src/crowsetta/examples/_examples.py | 228 +++ .../bird1.csv} | 0 src/crowsetta/examples/bird1.txt | 3 + ...12_0721.20144_annotations-description.txt} | 2 + ...bl26lb16_190412_0721.20144_annotations.csv | 0 src/crowsetta/examples/example-metadata.json | 74 + ..._230312_0808.138.cbin.not-description.txt} | 2 + ...6or6_baseline_230312_0808.138.cbin.not.mat | Bin .../sa1-description.txt} | 0 .../{data/timit => examples}/sa1.phn | 0 .../spinetail-description.txt} | 5 +- .../{data/audbbox => examples}/spinetail.txt | 0 src/crowsetta/formats/bbox/audbbox.py | 74 +- src/crowsetta/formats/bbox/raven.py | 43 +- src/crowsetta/formats/seq/audseq.py | 101 +- src/crowsetta/formats/seq/birdsongrec.py | 14 +- src/crowsetta/formats/seq/generic.py | 26 +- src/crowsetta/formats/seq/notmat.py | 15 +- src/crowsetta/formats/seq/simple.py | 67 +- src/crowsetta/formats/seq/textgrid/classes.py | 1 + src/crowsetta/formats/seq/textgrid/parse.py | 1 + .../formats/seq/textgrid/textgrid.py | 37 +- src/crowsetta/formats/seq/timit.py | 29 +- src/crowsetta/formats/seq/yarden.py | 1 + src/crowsetta/interface/__init__.py | 1 + src/crowsetta/interface/bbox/base.py | 1 + src/crowsetta/interface/seq/base.py | 1 + src/crowsetta/segment.py | 1 + src/crowsetta/sequence.py | 4 + src/crowsetta/transcriber.py | 8 +- src/crowsetta/typing.py | 1 + src/crowsetta/validation.py | 1 + ...0_m_337_295_fr1_p9_2021-10-02_12-35-01.csv | 1563 +++++++++++++++++ tests/fixtures/simple.py | 8 + tests/test_data.py | 236 --- tests/test_example.py | 30 + tests/test_formats/test_seq/test_simple.py | 89 + tests/test_sequence.py | 11 + 70 files changed, 4196 insertions(+), 900 deletions(-) delete mode 100644 doc/api/core.md delete mode 100644 doc/api/formats.md delete mode 100644 doc/api/interface.md create mode 100644 doc/howto/work-with-unlabeled-segmentations.md delete mode 100644 src/crowsetta/data/__init__.py delete mode 100644 src/crowsetta/data/audbbox/__init__.py delete mode 100644 src/crowsetta/data/audseq/__init__.py delete mode 100644 src/crowsetta/data/birdsongrec/__init__.py delete mode 100644 src/crowsetta/data/data.py delete mode 100644 src/crowsetta/data/generic/__init__.py delete mode 100644 src/crowsetta/data/generic/citation.txt delete mode 100644 src/crowsetta/data/notmat/__init__.py delete mode 100644 src/crowsetta/data/raven/__init__.py delete mode 100644 src/crowsetta/data/simple/__init__.py delete mode 100644 src/crowsetta/data/textgrid/__init__.py delete mode 100644 src/crowsetta/data/timit/__init__.py rename src/crowsetta/{data/audseq/citation.txt => examples/405_marron1_June_14_2016_69640887.audacity-description.txt} (72%) rename src/crowsetta/{data/audseq => examples}/405_marron1_June_14_2016_69640887.audacity.txt (100%) rename src/crowsetta/{data/textgrid => examples}/AVO-maea-basic.TextGrid (100%) rename src/crowsetta/{data/textgrid/citation.txt => examples/AVO-maea-basic.TextGrid-description.txt} (89%) rename src/crowsetta/{data/birdsongrec => examples}/Annotation.xml (100%) rename src/crowsetta/{data/birdsongrec/citation.txt => examples/Annotation.xml-description.txt} (73%) create mode 100644 src/crowsetta/examples/GO_24860x23748_ltr2_pup3_ch4_4800_m_337_295_fr1_p9_2021-10-02_12-35-01-description.txt create mode 100644 src/crowsetta/examples/GO_24860x23748_ltr2_pup3_ch4_4800_m_337_295_fr1_p9_2021-10-02_12-35-01.csv rename src/crowsetta/{data/raven/citation.txt => examples/Recording_1_Segment_02.Table.1.selections-description.txt} (82%) rename src/crowsetta/{data/raven => examples}/Recording_1_Segment_02.Table.1.selections.txt (100%) create mode 100644 src/crowsetta/examples/__init__.py create mode 100644 src/crowsetta/examples/_examples.py rename src/crowsetta/{data/generic/example_custom_format.csv => examples/bird1.csv} (100%) create mode 100644 src/crowsetta/examples/bird1.txt rename src/crowsetta/{data/simple/citation.txt => examples/bl26lb16_190412_0721.20144_annotations-description.txt} (73%) rename src/crowsetta/{data/simple => examples}/bl26lb16_190412_0721.20144_annotations.csv (100%) create mode 100644 src/crowsetta/examples/example-metadata.json rename src/crowsetta/{data/notmat/citation.txt => examples/gy6or6_baseline_230312_0808.138.cbin.not-description.txt} (65%) rename src/crowsetta/{data/notmat => examples}/gy6or6_baseline_230312_0808.138.cbin.not.mat (100%) rename src/crowsetta/{data/timit/citation.txt => examples/sa1-description.txt} (100%) rename src/crowsetta/{data/timit => examples}/sa1.phn (100%) rename src/crowsetta/{data/audbbox/citation.txt => examples/spinetail-description.txt} (54%) rename src/crowsetta/{data/audbbox => examples}/spinetail.txt (100%) create mode 100644 tests/data_for_tests/simple-csv/jourjine-et-al-2023/GO_24860x23748_ltr2_pup3_ch4_4800_m_337_295_fr1_p9_2021-10-02_12-35-01.csv delete mode 100644 tests/test_data.py create mode 100644 tests/test_example.py diff --git a/doc/api/core.md b/doc/api/core.md deleted file mode 100644 index 566b5efc..00000000 --- a/doc/api/core.md +++ /dev/null @@ -1,129 +0,0 @@ -(api-core)= - -# Core - -This page documents the core API of crowsetta, -including data types, other classes, and modules. - -## Data types - -### Annotation - -```{eval-rst} -.. autosummary:: - :toctree: generated - :template: class.rst - - crowsetta.Annotation -``` - -### Sequence - -```{eval-rst} -.. autosummary:: - :toctree: generated - :template: class.rst - - crowsetta.Sequence -``` - -### Segment - -```{eval-rst} -.. autosummary:: - :toctree: generated - :template: class.rst - - crowsetta.Segment -``` - -### BBox - -```{eval-rst} -.. autosummary:: - :toctree: generated - :template: class.rst - - crowsetta.BBox -``` - -## Classes - -### Transcriber - -```{eval-rst} -.. autosummary:: - :toctree: generated - :template: class.rst - - crowsetta.Transcriber -``` - -## Modules - -### `crowsetta.data` - -```{eval-rst} -.. autosummary:: - :toctree: generated - :template: module.rst - :recursive: - - crowsetta.data.data -``` - -```{note} -Modules in `crowsetta.data` besides `crowsetta.data.data` -contain example data files and a citation, -e.g., `crowsetta.data.birdsongrec` contains an example -file `Annotation.xml` and `citation.txt`. -For that reason just `crowsetta.data.data` is shown. -``` - -### `crowsetta.interface` - -For complete documentation of the interface, -please see {ref}`this page `. - -```{eval-rst} -.. autosummary:: - :toctree: generated - :template: module.rst - - crowsetta.interface -``` - - -### typing - -```{eval-rst} -.. autosummary:: - :toctree: generated - :template: module.rst - :recursive: - - crowsetta.typing -``` - - -### validation - -```{eval-rst} -.. autosummary:: - :toctree: generated - :template: module.rst - :recursive: - - crowsetta.validation -``` - -## Decorators - -### `crowsetta.register_format` - -```{eval-rst} -.. autosummary:: - :toctree: generated - - crowsetta.register_format -``` diff --git a/doc/api/formats.md b/doc/api/formats.md deleted file mode 100644 index 69fe2eff..00000000 --- a/doc/api/formats.md +++ /dev/null @@ -1,20 +0,0 @@ -(api-formats)= - -# Formats - -This page documents the API of the `crowsetta.formats` module. -It is generated automatically. -If you are a crowsetta user looking for -more detail about the built-in formats, -please see: {ref}`formats-index`. - -```{eval-rst} -.. autosummary:: - :toctree: generated - :template: module.rst - :recursive: - - crowsetta.formats - crowsetta.formats.bbox - crowsetta.formats.seq -``` diff --git a/doc/api/index.md b/doc/api/index.md index b119c6cd..ec5498f5 100644 --- a/doc/api/index.md +++ b/doc/api/index.md @@ -8,22 +8,189 @@ This section documents the [API](https://en.wikipedia.org/wiki/API) of crowsetta. -```{list-table} -:widths: 30 70 +(api-core)= -* - {ref}`Core ` - - The core data types, classes and modules of crowsetta -* - {ref}`Interface ` - - Defines an interface for classes that represent annotation formats -* - {ref}`Formats ` - - Modules with the classes representing annotation formats, - and functions for conveniently accessing them. +# Core + +This section documents the core API of crowsetta, +including data types, other classes, and modules. + +## Data types + +### Annotation + +```{eval-rst} +.. autosummary:: + :toctree: generated + :template: class.rst + + crowsetta.Annotation +``` + +### Sequence + +```{eval-rst} +.. autosummary:: + :toctree: generated + :template: class.rst + + crowsetta.Sequence +``` + +### Segment + +```{eval-rst} +.. autosummary:: + :toctree: generated + :template: class.rst + + crowsetta.Segment +``` + +### BBox + +```{eval-rst} +.. autosummary:: + :toctree: generated + :template: class.rst + + crowsetta.BBox +``` + +## Classes + +### Transcriber + +```{eval-rst} +.. autosummary:: + :toctree: generated + :template: class.rst + + crowsetta.Transcriber +``` + +## Modules + +### `crowsetta.interface` + +For complete documentation of the interface, +please see {ref}`this page `. + +```{eval-rst} +.. autosummary:: + :toctree: generated + :template: module.rst + + crowsetta.interface ``` -```{toctree} -:hidden: true -core -interface -formats +### typing + +```{eval-rst} +.. autosummary:: + :toctree: generated + :template: module.rst + :recursive: + + crowsetta.typing +``` + + +### validation + +```{eval-rst} +.. autosummary:: + :toctree: generated + :template: module.rst + :recursive: + + crowsetta.validation +``` + +## Decorators + +### `crowsetta.register_format` + +```{eval-rst} +.. autosummary:: + :toctree: generated + + crowsetta.register_format +``` + +## Example data + +```{eval-rst} +.. autosummary:: + :toctree: generated + + crowsetta.example + crowsetta.examples.show +``` + +(api-formats)= + +# Formats + +This section documents the API of the :mod:`crowsetta.formats` module. +It is generated automatically. +If you are a crowsetta user looking for +more detail about the built-in formats, +please see: {ref}`formats-index`. + +```{eval-rst} +.. autosummary:: + :toctree: generated + :template: module.rst + :recursive: + + crowsetta.formats + crowsetta.formats.bbox + crowsetta.formats.seq +``` + +(api-interface)= + +# Interface + +The section documents the API of the :mod:`crowsetta.interface` module. + +```{eval-rst} +.. autosummary:: + :toctree: generated + :template: module.rst + :recursive: + + crowsetta.interface +``` + +## Base + +```{eval-rst} +.. autosummary:: + :toctree: generated + :template: class.rst + + crowsetta.interface.base.BaseFormat +``` + +## Sequence-Like + +```{eval-rst} +.. autosummary:: + :toctree: generated + :template: class.rst + + crowsetta.interface.seq.SeqLike +``` + +## Bounding Box-Like + +```{eval-rst} +.. autosummary:: + :toctree: generated + :template: class.rst + + crowsetta.interface.bbox.BBoxLike ``` diff --git a/doc/api/interface.md b/doc/api/interface.md deleted file mode 100644 index 26ce7126..00000000 --- a/doc/api/interface.md +++ /dev/null @@ -1,42 +0,0 @@ -(api-interface)= - -# Interface - -```{eval-rst} -.. autosummary:: - :toctree: generated - :template: module.rst - :recursive: - - crowsetta.interface -``` - -## Base - -```{eval-rst} -.. autosummary:: - :toctree: generated - :template: class.rst - - crowsetta.interface.base.BaseFormat -``` - -## Sequence-Like - -```{eval-rst} -.. autosummary:: - :toctree: generated - :template: class.rst - - crowsetta.interface.seq.SeqLike -``` - -## Bounding Box-Like - -```{eval-rst} -.. autosummary:: - :toctree: generated - :template: class.rst - - crowsetta.interface.bbox.BBoxLike -``` diff --git a/doc/howto/work-with-unlabeled-segmentations.md b/doc/howto/work-with-unlabeled-segmentations.md new file mode 100644 index 00000000..e6dca260 --- /dev/null +++ b/doc/howto/work-with-unlabeled-segmentations.md @@ -0,0 +1,82 @@ +--- +jupytext: + formats: md:myst + text_representation: + extension: .md + format_name: myst + format_version: 0.13 + jupytext_version: 1.16.4 +kernelspec: + display_name: Python 3 (ipykernel) + language: python + name: python3 +--- + +# How to work with unlabeled segmentations using `crowsetta.SimpleSeq` + ++++ + +Sometimes, instead of animal sounds that have been annotated by a human, we have a "raw" segmentation of sounds, that is the output of some algorithm. For example, the signal processing-based algorithms in the [`vocalpy.segment`](https://vocalpy.readthedocs.io/en/latest/api/generated/vocalpy.segment.html) module. + +crowsetta tries to make it easy for you to work with these segmentations, without needing all the machinery of VocalPy. The way to do this is with the `"simple-seq"` format, represented by the `crowsetta.SimpleSeq` class. This page gives you a brief example of how it's done. + ++++ + +We use an example annotation file from [this dataset](https://datadryad.org/stash/dataset/doi:10.5061/dryad.g79cnp5ts) of mouse pup calls. + +```{code-cell} ipython3 +import crowsetta + +go_path = crowsetta.example("GO", return_path=True) +print(go_path) +``` + +We can see that we have a csv file. + +If, instead of loading it with crowsetta, we first load the csv file with pandas, we can get an idea of what it looks like. + +```{code-cell} ipython3 +import pandas as pd + +df = pd.read_csv(go_path) +df.head() +``` + +Notice that we have the start and stop times of the segments, in seconds. We also have a column with the source file for the segmentation, and the duration of the segment, neither of which we need for our current purposes. What we *don't* have are labels for the segments -- something that crowsetta typically expects. + ++++ + +Let's see what we get if we load this example directly (instead of setting `return_path=True` to get the path to the annotation file as we did above). + +```{code-cell} ipython3 +go = crowsetta.example("GO") +print(go) +``` + +Hmm, so we can see that we have the same start and stop times from above, but they are now called `onsets_s` and `offsets_s`. And somehow we suddenly have `labels` for the segments, but it looks like they are all dashes (`"-"`). Notice that the `"source_file"` and `"duration"` columns have disappeared. + +How did that happen? + +Notice also that the annotation format is `SimpleSeq`, as stated at the top of this page. If we try to make an instance of `crowsetta.SimpleSeq` ourselves, though, using the `from_file` method, we will get an error. + +```{code-cell} ipython3 +crowsetta.SimpleSeq.from_file(go_path) +``` + +What crowsetta is telling us with is that the columns in the csv file don't have the expected names. + +The secret is to use two arguments to the `from_file` method of the `crowsetta.SimpleSeq` class: `columns_map` and `default_label`, which is what the `crowsetta.example` function is doing under the hood. + +```{code-cell} ipython3 +crowsetta.SimpleSeq.from_file( + go_path, + columns_map={"start_seconds": "onset_s", "stop_seconds": "offset_s"}, + default_label="x", +) +``` + +What's happening here is that the `crowsetta.SimpleSeq` class loads the csv file into a `pandas.DataFrame`, just as we did above, and then uses `columns_map` to rename the columns `start_seconds` and `stop_seconds` to the names that the class expects, `onset_s` and `offset_s`. (These columns become attributes of an instance of the class called `onsets_s`, where `onsets` is pluralized, and `offsets_s`, also pluralized.) The other columns (`"source_file"` and `"duration"`) are not used. + +You can also see that we got default labels that are all `"x"`s this time. That's because the *default value* for `default_label` is `"-"`, but as we're showing here, you can change it to something else as suits your needs. + +Hopefully this makes it easier for you to work with different datasets! diff --git a/doc/index.md b/doc/index.md index 6dff52dd..edf2bd47 100644 --- a/doc/index.md +++ b/doc/index.md @@ -4,7 +4,7 @@ jupytext: extension: .md format_name: myst format_version: 0.13 - jupytext_version: 1.14.5 + jupytext_version: 1.16.4 kernelspec: display_name: Python 3 (ipykernel) language: python @@ -159,20 +159,10 @@ and {ref}`Raven .txt files `. Here is an example of loading an example {ref}`Praat .TextGrid ` file: -```{code-cell} ipython3 -:tags: [remove-cell] - -# We make the `user_data_dir` directory ahead of time -# to avoid triggering a call to `input` prompting the user if it's ok -# to make that directory -import crowsetta -crowsetta.data.extract_data_files() -``` - ```{code-cell} ipython3 import crowsetta -example = crowsetta.data.get('textgrid') -a_textgrid = crowsetta.formats.seq.TextGrid.from_file(example.annot_path) +path = crowsetta.example('AVO-maea-basic', return_path=True) +a_textgrid = crowsetta.formats.seq.TextGrid.from_file(path) print( f"`a_textgrid` is a {type(a_textgrid)}" ) @@ -187,8 +177,8 @@ each format can also be referred to by a shorthand string name: ```{code-cell} ipython3 import crowsetta -example = crowsetta.data.get('textgrid') -a_textgrid = crowsetta.formats.by_name('textgrid').from_file(example.annot_path) +path = crowsetta.example('AVO-maea-basic', return_path=True) +a_textgrid = crowsetta.formats.by_name('textgrid').from_file(path) print(f"`a_textgrid` is a {type(a_textgrid)} (even when we load it with `formats.by_name`)") ``` @@ -261,9 +251,9 @@ import numpy as np import crowsetta # load an example annotation file -example = crowsetta.data.get('birdsong-recognition-dataset') +path = crowsetta.example('Annotation.xml', return_path=True) # in the next line we use the class, to make it absolutely clear which format we are working with -birdsongrec = crowsetta.formats.seq.BirdsongRec.from_file(example.annot_path) +birdsongrec = crowsetta.formats.seq.BirdsongRec.from_file(path) annots = birdsongrec.to_annot() # returns a list of `crowsetta.Annotation`s syllables_spects = [] @@ -297,23 +287,26 @@ a csv file. ```{code-cell} ipython3 import crowsetta -example = crowsetta.data.get('birdsong-recognition-dataset') -birdsongrec = crowsetta.formats.by_name('birdsong-recognition-dataset').from_file(example.annot_path) +path = crowsetta.example('Annotation.xml', return_path=True) +birdsongrec = crowsetta.formats.by_name('birdsong-recognition-dataset').from_file(path) annots = birdsongrec.to_annot(samplerate=32000) # returns a list of `crowsetta.Annotation`s # the 'generic-seq' format can write csv files from `Annotation`s with `Sequence`s. generic_seq = crowsetta.formats.by_name('generic-seq')(annots=annots) generic_seq.to_file(annot_path='./data/birdsong-rec.csv') ``` -Here are the first few lines of the .csv created by the snippet above: +We load the csv into a pandas `DataFrame` to inspect the first few lines. + +```{code-cell} ipython3 +import pandas as pd +df = pd.read_csv("./data/birdsong-rec.csv") -```{literalinclude} ./data/birdsong-rec.csv -:language: none -:lines: 1-5 +from IPython.display import display +display(df.head(10)) ``` -Now that you have that, you can load it into a [pandas](https://pandas.pydata.org/) dataframe -or an Excel spreadsheet or an SQL database, or whatever you want. +Now that you have that csv file, you can load it into a pandas `DataFrame` +or an Excel spreadsheet or an SQLite database, or whatever you want. You might find this useful in any situation where you want to share audio files of song and some associated annotations, but you don't want to require the user to diff --git a/src/crowsetta/__init__.py b/src/crowsetta/__init__.py index ee653288..86e14901 100644 --- a/src/crowsetta/__init__.py +++ b/src/crowsetta/__init__.py @@ -1,4 +1,4 @@ -from . import data, interface, typing, validation +from . import examples, interface, typing, validation from .__about__ import ( __author__, __commit__, @@ -12,6 +12,7 @@ ) from .annotation import Annotation from .bbox import BBox +from .examples._examples import example from .segment import Segment from .sequence import Sequence from .transcriber import Transcriber @@ -20,6 +21,8 @@ # isort: off from . import formats from .formats import register_format +from .formats.seq import AudSeq, BirdsongRec, GenericSeq, NotMat, SimpleSeq, Timit, SongAnnotationGUI +from .formats.bbox import AudBBox, Raven # isort: on @@ -34,8 +37,18 @@ "__uri__", "__version__", "Annotation", + "AudBBox", + "AudSeq", "BBox", - "data", + "BirdsongRec", + "GenericSeq", + "NotMat", + "Raven", + "SimpleSeq", + "Timit", + "SongAnnotationGUI", + "example", + "examples", "formats", "interface", "register_format", diff --git a/src/crowsetta/annotation.py b/src/crowsetta/annotation.py index 62e55d4a..8e0146e6 100644 --- a/src/crowsetta/annotation.py +++ b/src/crowsetta/annotation.py @@ -1,4 +1,5 @@ """A class to represent annotations for a single file.""" + from __future__ import annotations import reprlib diff --git a/src/crowsetta/bbox.py b/src/crowsetta/bbox.py index 900c2218..9f507d8e 100644 --- a/src/crowsetta/bbox.py +++ b/src/crowsetta/bbox.py @@ -1,6 +1,7 @@ """A class that represents a bounding box on a spectrogram, drawn around animal communication or other sounds. """ + import attrs from attrs import field diff --git a/src/crowsetta/data/__init__.py b/src/crowsetta/data/__init__.py deleted file mode 100644 index 00730293..00000000 --- a/src/crowsetta/data/__init__.py +++ /dev/null @@ -1,19 +0,0 @@ -"""Module that handles example data built into ``crowsetta``""" -from . import audbbox, audseq, birdsongrec, generic, notmat, raven, simple, textgrid, timit -from .data import ExampleAnnotFile, available_formats, extract_data_files, get - -__all__ = [ - "audbbox", - "audseq", - "available_formats", - "birdsongrec", - "ExampleAnnotFile", - "extract_data_files", - "generic", - "get", - "notmat", - "raven", - "simple", - "textgrid", - "timit", -] diff --git a/src/crowsetta/data/audbbox/__init__.py b/src/crowsetta/data/audbbox/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/src/crowsetta/data/audseq/__init__.py b/src/crowsetta/data/audseq/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/src/crowsetta/data/birdsongrec/__init__.py b/src/crowsetta/data/birdsongrec/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/src/crowsetta/data/data.py b/src/crowsetta/data/data.py deleted file mode 100644 index 2260033d..00000000 --- a/src/crowsetta/data/data.py +++ /dev/null @@ -1,291 +0,0 @@ -from __future__ import annotations - -import contextlib - -try: - from importlib.resources import as_file, files, open_text -except ImportError: - from importlib_resources import as_file, files, open_text - -import pathlib -import shutil -from typing import Union - -import appdirs -import attr - -from ..__about__ import __version__ as version -from ..typing import PathLike - -APP_DIRS = appdirs.AppDirs(appname="crowsetta", appauthor="vocalpy", version=version) - - -@attr.define -class FormatPathArgs: - """arguments that should be - passed into - ``importlib.resources.path`` - when loading resources - for each annotation format - """ - - package: str - resource: str - - -@attr.define -class ExampleAnnotFile: - """Class representing - an example annotation file. - Returned by ``crowsetta.data.get``. - - Attributes - ---------- - annot_path : pathlib.Path, contextlib._GeneratorContextManager - Path to annotation file, - can be used to load. - If annotation files are not been extracted to - the local file system using the function - ``crowsetta.data.extract_data_files``, - then ``crowsetta.data.get`` will return - ``annot_path`` as a context manager - that will provide a path to a temporary file. - citation : str - Citation for dataset - from which example is taken - """ - - annot_path: Union[PathLike, contextlib._GeneratorContextManager] - citation: str - - -DATA = { - "aud-bbox": FormatPathArgs(package="crowsetta.data.audbbox", resource="spinetail.txt"), - "aud-seq": FormatPathArgs( - package="crowsetta.data.audseq", resource="405_marron1_June_14_2016_69640887.audacity.txt" - ), - "birdsong-recognition-dataset": FormatPathArgs(package="crowsetta.data.birdsongrec", resource="Annotation.xml"), - "generic-seq": FormatPathArgs(package="crowsetta.data.generic", resource="example_custom_format.csv"), - "notmat": FormatPathArgs(package="crowsetta.data.notmat", resource="gy6or6_baseline_230312_0808.138.cbin.not.mat"), - "raven": FormatPathArgs(package="crowsetta.data.raven", resource="Recording_1_Segment_02.Table.1.selections.txt"), - "simple-seq": FormatPathArgs( - package="crowsetta.data.simple", resource="bl26lb16_190412_0721.20144_annotations.csv" - ), - "textgrid": FormatPathArgs(package="crowsetta.data.textgrid", resource="AVO-maea-basic.TextGrid"), - "timit": FormatPathArgs(package="crowsetta.data.timit", resource="sa1.phn"), -} - - -def extract_data_files(user_data_dir: PathLike | None = None): - """Extract example annotation files from ``crowsetta.data`` - to a local directory on the file system. - - Parameters - ---------- - user_data_dir : str, pathlib.Path - Location where example annotation files should be extracted to. - If none is given, defaults to the value of - ``crowsetta.data.data.APP_DIRS.user_data_dir`` - """ - if user_data_dir is None: - user_data_dir = APP_DIRS.user_data_dir - user_data_dir = pathlib.Path(user_data_dir) - user_data_dir.mkdir(parents=True, exist_ok=True) - for _, path_args in DATA.items(): - # don't use full name `importlib.resources` here - # because we need to use backport package, not stdlib, on Python 3.8 - source = files(path_args.package).joinpath(path_args.resource) - annot_path = as_file(source) - dst_annot_dir = user_data_dir / path_args.package.split(".")[-1] - dst_annot_dir.mkdir(exist_ok=True) - dst_annot_path = dst_annot_dir / path_args.resource - # don't bother copying if we already did this - if not dst_annot_path.exists(): - with annot_path as annot_path: - shutil.copy(annot_path, dst_annot_path) - dst_citation_txt_path = dst_annot_dir / "citation.txt" - if not dst_citation_txt_path.exists(): - with as_file(files(path_args.package).joinpath("citation.txt")) as citation_txt_path: - shutil.copy(citation_txt_path, dst_citation_txt_path) - - -def _get_example_from_user_data_dir(format: str, user_data_dir: PathLike | None = None) -> ExampleAnnotFile: - """Returns example from ``user_data_dir``. - - Assumes that example data has already been copied to - ``user_data_dir`` by calling ``_extract_data_files``. - Helper function used by ``crowsetta.data.get``. - - Parameters - ---------- - format : str - Name of annotation format. - Should be the shorthand string name, - as listed by ``crowsetta.formats.as_list``. - user_data_dir : str, pathlib.Path - Location where example annotation files have been extracted to, - by calling ``crowsetta.data.extract_data_files``. - If none is given, defaults to the value of - ``crowsetta.data.data.APP_DIRS.user_data_dir`` - - Returns - ------- - example : ExampleAnnotFile - with ``annot_path`` and ``citation`` attributes. - """ - try: - path_args = DATA[format] - except KeyError as e: - raise ValueError(f"format not recognized: {format}") from e - - if user_data_dir is None: - user_data_dir = APP_DIRS.user_data_dir - - format_pkg = path_args.package.split(".")[-1] - annot_path = user_data_dir / format_pkg / path_args.resource - citation_txt = user_data_dir / format_pkg / "citation.txt" - with citation_txt.open("r") as fp: - citation = fp.read().replace("\n", "") - - return ExampleAnnotFile(annot_path=annot_path, citation=citation) - - -def _get_example_as_context_manager(format: str) -> ExampleAnnotFile: - """Gets an example annotation file - as a context manager, that can be used - as shown in the example below. - - Helper function used by ``crowsetta.data.get``. - - Parameters - ---------- - format : str - Name of annotation format. - Should be the shorthand string name, - as listed by ``crowsetta.formats.as_list``. - - Returns - ------- - example_annot_file : crowsetta.data.ExampleAnnotFile - class instance with attributes ``annot_path`` - and ``citation``. The ``annot_path`` - attribute should be used as part of a ``with`` - statement to open the file; see Examples below - or examples in the docstrings. - """ - try: - path_args = DATA[format] - except KeyError as e: - raise ValueError(f"format not recognized: {format}") from e - - # don't use full name `importlib.resources` here - # because we need to use backport package, not stdlib, on Python 3.8 - source = files(path_args.package).joinpath(path_args.resource) - annot_path = as_file(source) - - with open_text(package=path_args.package, resource="citation.txt") as fp: - citation = fp.read().replace("\n", "") - - return ExampleAnnotFile(annot_path=annot_path, citation=citation) - - -def get(format: str, user_data_dir: PathLike | None = None) -> ExampleAnnotFile: - """Get an example annotation files. - - Parameters - ---------- - format : str - Name of annotation format. - Should be the shorthand string name, - as listed by ``crowsetta.formats.as_list``. - user_data_dir : str, pathlib.Path - Location where example annotation files - are stored. - If none is given, defaults to the value of - ``crowsetta.data.data.APP_DIRS.user_data_dir`` - This default can be changed, but will require - passing the same path in every time - this function is called to avoid - being prompted about extracting the example files - to the default location. - - Returns - ------- - example_annot_file : ExampleAnnotFile - class instance with attributes ``annot_path`` - and ``citation``. - If the annotation files have been - extracted to the local file system, - then ``annot_path`` will be a path - to a file. - Otherwise, ``annot_path`` will be - a context manager that should be - used as part of a ``with`` - statement to open the file; see Examples below - or examples in the docstrings. - - Examples - -------- - >>> # example of a context manager - >>> example = crowsetta.data.get('textgrid') - >>> with example.annot_path as annot_path: - ... textgrid = crowsetta.formats.seq.TextGrid.from_file(annot_path) - """ - if format not in DATA: - raise ValueError(f"format not recognized: {format}") - - if user_data_dir is None: - user_data_dir = APP_DIRS.user_data_dir - - user_data_dir = pathlib.Path(user_data_dir) - if not user_data_dir.exists(): - y_or_n = input( - f"``user_data_dir`` does not exist at default location:\n{user_data_dir}\n" - "(To choose a location besides the default, call this function with that location " - "as the argument for ``user_data_dir``.)\n\n" - "Do you want to create this ``user_data_dir`` and extract example annotation files into it?\n" - "[yes]/no >>>" - ) - if y_or_n.lower().startswith("y") or y_or_n == "": - extract_data_files(user_data_dir) - return _get_example_from_user_data_dir(format, user_data_dir) - else: - print( - """Not extracting data. Will return a context manager.\n - Use the context manager to get a path to a temporary path - like in the following example:\n - - >>> example = crowsetta.data.get('timit') - >>> with example.annot_path as annot_path: - ... timit = crowsetta.formats.seq.Timit.from_file(annot_path=annot_path) - >>> annot = timit.to_annot() - """ - ) - return _get_example_as_context_manager(format) - else: - return _get_example_from_user_data_dir(format, user_data_dir) - - -def available_formats() -> list: - """Return list of string names - of annotation formats - that have built-in sample data - available. - - Any of the names in the returned list - can be passed into ``crowsetta.data.get`` - to get a path to an annotation file - in that format. - - Returns - ------- - data_list : list - List of names of formats - that have built-in sample data available. - - Examples - -------- - >>> crowsetta.data.available_formats() - ['aud-bbox', 'aud-seq', 'birdsong-recognition-dataset', 'generic-seq', 'notmat', 'raven', 'simple-seq', 'textgrid', 'timit'] # noqa - """ - return list(DATA.keys()) diff --git a/src/crowsetta/data/generic/__init__.py b/src/crowsetta/data/generic/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/src/crowsetta/data/generic/citation.txt b/src/crowsetta/data/generic/citation.txt deleted file mode 100644 index b0047fa4..00000000 --- a/src/crowsetta/data/generic/citation.txt +++ /dev/null @@ -1 +0,0 @@ -None diff --git a/src/crowsetta/data/notmat/__init__.py b/src/crowsetta/data/notmat/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/src/crowsetta/data/raven/__init__.py b/src/crowsetta/data/raven/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/src/crowsetta/data/simple/__init__.py b/src/crowsetta/data/simple/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/src/crowsetta/data/textgrid/__init__.py b/src/crowsetta/data/textgrid/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/src/crowsetta/data/timit/__init__.py b/src/crowsetta/data/timit/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/src/crowsetta/data/audseq/citation.txt b/src/crowsetta/examples/405_marron1_June_14_2016_69640887.audacity-description.txt similarity index 72% rename from src/crowsetta/data/audseq/citation.txt rename to src/crowsetta/examples/405_marron1_June_14_2016_69640887.audacity-description.txt index 413277f2..8fa45305 100644 --- a/src/crowsetta/data/audseq/citation.txt +++ b/src/crowsetta/examples/405_marron1_June_14_2016_69640887.audacity-description.txt @@ -1,3 +1,5 @@ +Canary song annotation in Audacity default LabelTrack format. +From the following dataset: Giraudon, Juliette, Trouvain, Nathan, Cazala, Aurore, Del Negro, Catherine, & Hinaut, Xavier. (2021). Labeled songs of domestic canary M1-2016-spring (Serinus canaria) (0.0.2) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.6521932 diff --git a/src/crowsetta/data/audseq/405_marron1_June_14_2016_69640887.audacity.txt b/src/crowsetta/examples/405_marron1_June_14_2016_69640887.audacity.txt similarity index 100% rename from src/crowsetta/data/audseq/405_marron1_June_14_2016_69640887.audacity.txt rename to src/crowsetta/examples/405_marron1_June_14_2016_69640887.audacity.txt diff --git a/src/crowsetta/data/textgrid/AVO-maea-basic.TextGrid b/src/crowsetta/examples/AVO-maea-basic.TextGrid similarity index 100% rename from src/crowsetta/data/textgrid/AVO-maea-basic.TextGrid rename to src/crowsetta/examples/AVO-maea-basic.TextGrid diff --git a/src/crowsetta/data/textgrid/citation.txt b/src/crowsetta/examples/AVO-maea-basic.TextGrid-description.txt similarity index 89% rename from src/crowsetta/data/textgrid/citation.txt rename to src/crowsetta/examples/AVO-maea-basic.TextGrid-description.txt index de884475..c9acffd7 100644 --- a/src/crowsetta/data/textgrid/citation.txt +++ b/src/crowsetta/examples/AVO-maea-basic.TextGrid-description.txt @@ -1,3 +1,4 @@ +TextGrid annotation file from dataset: Sound files and Praat TextGrids accompanying Sasha Calhoun, Corinne Seals, Toaga Alefosio and Niusila Faamanatu-Eteuati, 'Phrasal Prosody of Heritage Speakers of Samoan in Aotearoa New Zealand', diff --git a/src/crowsetta/data/birdsongrec/Annotation.xml b/src/crowsetta/examples/Annotation.xml similarity index 100% rename from src/crowsetta/data/birdsongrec/Annotation.xml rename to src/crowsetta/examples/Annotation.xml diff --git a/src/crowsetta/data/birdsongrec/citation.txt b/src/crowsetta/examples/Annotation.xml-description.txt similarity index 73% rename from src/crowsetta/data/birdsongrec/citation.txt rename to src/crowsetta/examples/Annotation.xml-description.txt index 1ec41cb2..699f94fc 100644 --- a/src/crowsetta/data/birdsongrec/citation.txt +++ b/src/crowsetta/examples/Annotation.xml-description.txt @@ -1,3 +1,4 @@ +Example set of annotations from BirdsongRecognition dataset. Koumura, T. (2016). BirdsongRecognition (Version 1). figshare. https://doi.org/10.6084/m9.figshare.3470165.v1. https://figshare.com/articles/BirdsongRecognition/3470165. diff --git a/src/crowsetta/examples/GO_24860x23748_ltr2_pup3_ch4_4800_m_337_295_fr1_p9_2021-10-02_12-35-01-description.txt b/src/crowsetta/examples/GO_24860x23748_ltr2_pup3_ch4_4800_m_337_295_fr1_p9_2021-10-02_12-35-01-description.txt new file mode 100644 index 00000000..94f30aa2 --- /dev/null +++ b/src/crowsetta/examples/GO_24860x23748_ltr2_pup3_ch4_4800_m_337_295_fr1_p9_2021-10-02_12-35-01-description.txt @@ -0,0 +1,5 @@ +Segmentation of cotton mouse (Peromyscus gossypinus) pup calls in a csv file. +From the dataset: +Jourjine, Nicholas et al. (2023). +Two pup vocalization types are genetically and functionally separable in deer mice [Dataset]. +Dryad. https://doi.org/10.5061/dryad.g79cnp5ts \ No newline at end of file diff --git a/src/crowsetta/examples/GO_24860x23748_ltr2_pup3_ch4_4800_m_337_295_fr1_p9_2021-10-02_12-35-01.csv b/src/crowsetta/examples/GO_24860x23748_ltr2_pup3_ch4_4800_m_337_295_fr1_p9_2021-10-02_12-35-01.csv new file mode 100644 index 00000000..7b159fb3 --- /dev/null +++ b/src/crowsetta/examples/GO_24860x23748_ltr2_pup3_ch4_4800_m_337_295_fr1_p9_2021-10-02_12-35-01.csv @@ -0,0 +1,1563 @@ +start_seconds,stop_seconds,source_file,duration +0.526336,0.688128,/n/hoekstra_lab_tier1/Users/njourjine/manuscript/audio/tests_20240503/GO_test/audio/GO_24860x23748_ltr2_pup3_ch4_4800_m_337_295_fr1_p9_2021-10-02_12-35-01.wav,0.16179199999999994 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+598.583296,598.695936,/n/hoekstra_lab_tier1/Users/njourjine/manuscript/audio/tests_20240503/GO_test/audio/GO_24860x23748_ltr2_pup3_ch4_4800_m_337_295_fr1_p9_2021-10-02_12-35-01.wav,0.11263999999994212 +598.806528,598.925312,/n/hoekstra_lab_tier1/Users/njourjine/manuscript/audio/tests_20240503/GO_test/audio/GO_24860x23748_ltr2_pup3_ch4_4800_m_337_295_fr1_p9_2021-10-02_12-35-01.wav,0.11878400000000511 +599.068672,599.1690239999999,/n/hoekstra_lab_tier1/Users/njourjine/manuscript/audio/tests_20240503/GO_test/audio/GO_24860x23748_ltr2_pup3_ch4_4800_m_337_295_fr1_p9_2021-10-02_12-35-01.wav,0.10035199999992983 diff --git a/src/crowsetta/data/raven/citation.txt b/src/crowsetta/examples/Recording_1_Segment_02.Table.1.selections-description.txt similarity index 82% rename from src/crowsetta/data/raven/citation.txt rename to src/crowsetta/examples/Recording_1_Segment_02.Table.1.selections-description.txt index 214bae17..ccf0c098 100644 --- a/src/crowsetta/data/raven/citation.txt +++ b/src/crowsetta/examples/Recording_1_Segment_02.Table.1.selections-description.txt @@ -1,3 +1,5 @@ +Selection table exported from Raven. +From the dataset: Chronister, L. M., Rhinehart, T. A., Place, A., & Kitzes, J. (2021). An annotated set of audio recordings of Eastern North American birds containing frequency, time, and species information. diff --git a/src/crowsetta/data/raven/Recording_1_Segment_02.Table.1.selections.txt b/src/crowsetta/examples/Recording_1_Segment_02.Table.1.selections.txt similarity index 100% rename from src/crowsetta/data/raven/Recording_1_Segment_02.Table.1.selections.txt rename to src/crowsetta/examples/Recording_1_Segment_02.Table.1.selections.txt diff --git a/src/crowsetta/examples/__init__.py b/src/crowsetta/examples/__init__.py new file mode 100644 index 00000000..fa116638 --- /dev/null +++ b/src/crowsetta/examples/__init__.py @@ -0,0 +1,3 @@ +from ._examples import show + +__all__ = ["show"] diff --git a/src/crowsetta/examples/_examples.py b/src/crowsetta/examples/_examples.py new file mode 100644 index 00000000..1274efe9 --- /dev/null +++ b/src/crowsetta/examples/_examples.py @@ -0,0 +1,228 @@ +"""Functions that provide example data""" + +import importlib.resources +import json +import pathlib + +from attr import define + + +@define +class Example: + """Dataclass that represents an example annotation file. + + Attributes + ---------- + filename : str + Name of annotation file. + description_filename: str + Name of text file that contains description of + annotation file, including any relevant citations. + format: str + Annotation file format. + name: str, optional + A human-readable name for the annotation file. + Can be specified if the filename is not convenient to type. + If None, defaults to filename. + from_file_kwargs : dict, optional + Keyword arguments to pass into + :meth:`crowsetta.Transcriber.from_file` + when loading the annotation file. + Optional, default is None. + + Notes + ----- + This dataclass is used to load metadata from + `vocalpy/examples/example-metadata.json`. + """ + + filename: str + path: pathlib.Path + description: str + format: str + name: str | None = None + from_file_kwargs: dict | None = None + + @classmethod + def from_metadata( + cls, filename, description_filename, format: str, name: str | None = None, from_file_kwargs: dict | None = None + ): + """Create a :class:`Example` instance from metadata. + + Parameters + ---------- + filename : str + Name of annotation file. + description_filename: str + Name of text file that contains description of + annotation file, including any relevant citations. + format: str + Annotation file format. + name: str, optional + A human-readable name for the annotation file. + Can be specified if the filename is not convenient to type. + If None, defaults to filename. + from_file_kwargs : dict, optional + Keyword arguments to pass into + :meth:`crowsetta.Transcriber.from_file` + when loading the annotation file. + Optional, default is None. + + Returns + ------- + example : Example + Instance of :class:`Example` dataclass + """ + path = importlib.resources.files("crowsetta.examples").joinpath(filename) + + description_path = importlib.resources.files("crowsetta.examples").joinpath(description_filename) + description = description_path.read_text() + + if name is None: + name = filename + + if from_file_kwargs is None: + from_file_kwargs = {} + + return cls(filename, path, description, format, name, from_file_kwargs) + + def load(self): + import crowsetta + + scribe = crowsetta.Transcriber(format=self.format) + return scribe.from_file(self.path, **self.from_file_kwargs) + + +EXAMPLE_METADATA_JSON_PATH = pathlib.Path( + importlib.resources.files("crowsetta.examples").joinpath("example-metadata.json") +) +with EXAMPLE_METADATA_JSON_PATH.open("r") as fp: + ALL_EXAMPLE_METADATA = json.load(fp) + +EXAMPLES = [Example.from_metadata(**example_metadata) for example_metadata in ALL_EXAMPLE_METADATA] + +REGISTRY = {example_.name: example_ for example_ in EXAMPLES} + + +def example(name: str, return_path: bool = False): + """Get an example annotation file. + + Parameter + --------- + name : str + Human-readable name that refers to annotation file. + For a list pf names, call :func:`crowsetta.examples.show`. + return_path : bool + If ``True``, return the path to the annotation file. + Default is ``False``. + When ``False``, an instance of the class that represents + a set of annotations in the format used by the example + is returned. + + Examples + -------- + + >>> marron1 = crowsetta.example("marron1") + >>> print(marron1) + AudSeq(start_times=array([ 0. , 0.76981817, 1.13127401, 2.21840074, 2.55502374, + 3.09030949, 3.69457537, 3.81322118, 4.05603121, 4.86171904, + 4.87551507, 5.52392822, 6.55587085, 6.59449972, 7.0883974 , + 7.18772877, 7.23463526, 7.94375092, 9.01984083, 9.06950652, + 9.18263392, 10.06282028, 10.07661631, 10.9705987 , 10.98715393, + 11.80663778, 11.86458109, 12.19016727, 13.24142433, 13.277294 , + 14.49686257, 14.60723076, 15.22805186, 15.31082801, 16.22136563, + 17.25606747, 18.16660509, 18.20247475, 19.65381653, 19.75590711, + 20.71059201, 20.78509054, 20.96719806, 21.02514137, 21.35624596, + 21.45005892, 21.66527691, 21.67355452, 22.73860761, 22.82966137, + 23.63534921, 24.59831172, 24.60383013, 24.67281025, 24.77214163, + 25.68267925, 25.70751209, 26.65943778, 27.7410461 , 27.76036054, + 28.34531198]), end_times=array([ 0.76981817, 1.13127401, 2.21840074, 2.55502374, 3.09030949, + 3.69457537, 3.81322118, 4.05603121, 4.86171904, 4.87551507, + 5.53496504, 6.55587085, 6.59449972, 7.0883974 , 7.18772877, + 7.23463526, 7.94375092, 9.01984083, 9.06950652, 9.18263392, + 10.06282028, 10.07661631, 10.9705987 , 10.98715393, 11.80663778, + 11.86458109, 12.20396329, 13.24142433, 13.277294 , 14.49686257, + 14.60723076, 15.22805186, 15.31082801, 16.22136563, 17.25606747, + 18.16660509, 18.20247475, 19.65381653, 19.75590711, 20.71059201, + 20.78509054, 20.96719806, 21.02514137, 21.35624596, 21.45005892, + 21.66527691, 21.67355452, 22.73860761, 22.82966137, 23.63534921, + 24.59831172, 24.60383013, 24.67281025, 24.77214163, 25.68267925, + 25.70751209, 26.65943778, 27.7410461 , 27.76036054, 28.359108 , + 29.10133412]), labels= + [ 'SIL', 'call', 'SIL', 'call', 'SIL', 'Z', 'SIL', 'Ci', 'C', + 'SIL', 'H', 'E', 'SIL', 'R', 'SIL', 'J1', 'J1', 'J2', + 'J2', 'SIL', 'B1', 'SIL', 'B2', 'SIL', 'Q', 'SIL', 'H', + 'E', 'SIL', 'R', 'SIL', 'O', 'SIL', 'J1', 'J2', 'L', + 'SIL', 'N', 'SIL', 'A', 'SIL', 'O', 'SIL', 'P', 'SIL', + 'K', 'SIL', 'V', 'SIL', 'J1', 'J2', 'SIL', 'J2', 'SIL', + 'B1', 'SIL', 'B2', 'Q', 'SIL', 'H', 'E'] + Length: 61, dtype: string, annot_path=PosixPath('/Users/davidnicholson/Documents/repos/vocalpy/crowsetta/src/crowsetta/examples/405_marron1_June_14_2016_69640887.audacity.txt'), notated_path=None) # noqa: E501 + + You can specify ``return_path=True`` to get a ``pathlib.Path`` + instance that points to the file. + This can be used with the ``from_file`` method of the + format classes. + + >>> patg = crowsetta.example("marron1", return_path=True) + >>> marron1 = crowsetta.AudSeq.from_file(path) + >>> print(marron1) + AudSeq(start_times=array([ 0. , 0.76981817, 1.13127401, 2.21840074, 2.55502374, + 3.09030949, 3.69457537, 3.81322118, 4.05603121, 4.86171904, + 4.87551507, 5.52392822, 6.55587085, 6.59449972, 7.0883974 , + 7.18772877, 7.23463526, 7.94375092, 9.01984083, 9.06950652, + 9.18263392, 10.06282028, 10.07661631, 10.9705987 , 10.98715393, + 11.80663778, 11.86458109, 12.19016727, 13.24142433, 13.277294 , + 14.49686257, 14.60723076, 15.22805186, 15.31082801, 16.22136563, + 17.25606747, 18.16660509, 18.20247475, 19.65381653, 19.75590711, + 20.71059201, 20.78509054, 20.96719806, 21.02514137, 21.35624596, + 21.45005892, 21.66527691, 21.67355452, 22.73860761, 22.82966137, + 23.63534921, 24.59831172, 24.60383013, 24.67281025, 24.77214163, + 25.68267925, 25.70751209, 26.65943778, 27.7410461 , 27.76036054, + 28.34531198]), end_times=array([ 0.76981817, 1.13127401, 2.21840074, 2.55502374, 3.09030949, + 3.69457537, 3.81322118, 4.05603121, 4.86171904, 4.87551507, + 5.53496504, 6.55587085, 6.59449972, 7.0883974 , 7.18772877, + 7.23463526, 7.94375092, 9.01984083, 9.06950652, 9.18263392, + 10.06282028, 10.07661631, 10.9705987 , 10.98715393, 11.80663778, + 11.86458109, 12.20396329, 13.24142433, 13.277294 , 14.49686257, + 14.60723076, 15.22805186, 15.31082801, 16.22136563, 17.25606747, + 18.16660509, 18.20247475, 19.65381653, 19.75590711, 20.71059201, + 20.78509054, 20.96719806, 21.02514137, 21.35624596, 21.45005892, + 21.66527691, 21.67355452, 22.73860761, 22.82966137, 23.63534921, + 24.59831172, 24.60383013, 24.67281025, 24.77214163, 25.68267925, + 25.70751209, 26.65943778, 27.7410461 , 27.76036054, 28.359108 , + 29.10133412]), labels= + [ 'SIL', 'call', 'SIL', 'call', 'SIL', 'Z', 'SIL', 'Ci', 'C', + 'SIL', 'H', 'E', 'SIL', 'R', 'SIL', 'J1', 'J1', 'J2', + 'J2', 'SIL', 'B1', 'SIL', 'B2', 'SIL', 'Q', 'SIL', 'H', + 'E', 'SIL', 'R', 'SIL', 'O', 'SIL', 'J1', 'J2', 'L', + 'SIL', 'N', 'SIL', 'A', 'SIL', 'O', 'SIL', 'P', 'SIL', + 'K', 'SIL', 'V', 'SIL', 'J1', 'J2', 'SIL', 'J2', 'SIL', + 'B1', 'SIL', 'B2', 'Q', 'SIL', 'H', 'E'] + Length: 61, dtype: string, annot_path=PosixPath('/Users/davidnicholson/Documents/repos/vocalpy/crowsetta/src/crowsetta/examples/405_marron1_June_14_2016_69640887.audacity.txt'), notated_path=None) # noqa: E501 + """ + try: + example_ = REGISTRY[name] + except KeyError as e: + raise ValueError( + f"The `name` is not recongized as an example annotation file: {name}.\n" + "Please call `crowsetta.examples.show()` to see the list of example annotation files." + ) from e + + if return_path: + return example_.path + else: + return example_.load() + + +def show(): + """Print the names and descriptions of all + example annotation files built into :mod:`crowsetta`""" + print("Example annotation files built into crowsetta") + print("=" * 72) + for example_ in EXAMPLES: + print( + f"Name: {example_.name}\n" + f"Format name in `crowsetta`: {example_.format}\n" + "Description:\n" + f"{example_.description}\n" + ) diff --git a/src/crowsetta/data/generic/example_custom_format.csv b/src/crowsetta/examples/bird1.csv similarity index 100% rename from src/crowsetta/data/generic/example_custom_format.csv rename to src/crowsetta/examples/bird1.csv diff --git a/src/crowsetta/examples/bird1.txt b/src/crowsetta/examples/bird1.txt new file mode 100644 index 00000000..4f3f5382 --- /dev/null +++ b/src/crowsetta/examples/bird1.txt @@ -0,0 +1,3 @@ +Example of a custom format converted to the GenericSeq format, +from the crowsetta docs: +https://crowsetta.readthedocs.io/en/latest/howto/howto-user-format.html \ No newline at end of file diff --git a/src/crowsetta/data/simple/citation.txt b/src/crowsetta/examples/bl26lb16_190412_0721.20144_annotations-description.txt similarity index 73% rename from src/crowsetta/data/simple/citation.txt rename to src/crowsetta/examples/bl26lb16_190412_0721.20144_annotations-description.txt index cbc7fbee..690be96c 100644 --- a/src/crowsetta/data/simple/citation.txt +++ b/src/crowsetta/examples/bl26lb16_190412_0721.20144_annotations-description.txt @@ -1,3 +1,5 @@ +Annotation in DAS format, +that can be loaded with the SimpleSeq class. Clemens, Jan, 2021, "Bengalese finch - train and test data", https://doi.org/10.25625/ENKMJS, diff --git a/src/crowsetta/data/simple/bl26lb16_190412_0721.20144_annotations.csv b/src/crowsetta/examples/bl26lb16_190412_0721.20144_annotations.csv similarity index 100% rename from src/crowsetta/data/simple/bl26lb16_190412_0721.20144_annotations.csv rename to src/crowsetta/examples/bl26lb16_190412_0721.20144_annotations.csv diff --git a/src/crowsetta/examples/example-metadata.json b/src/crowsetta/examples/example-metadata.json new file mode 100644 index 00000000..c17edb98 --- /dev/null +++ b/src/crowsetta/examples/example-metadata.json @@ -0,0 +1,74 @@ +[ + { + "filename": "spinetail.txt", + "description_filename": "spinetail-description.txt", + "format": "aud-bbox" + }, + { + "filename": "405_marron1_June_14_2016_69640887.audacity.txt", + "description_filename": "405_marron1_June_14_2016_69640887.audacity-description.txt", + "format": "aud-seq", + "name": "marron1" + }, + { + "filename": "Annotation.xml", + "description_filename": "Annotation.xml-description.txt", + "format": "birdsong-recognition-dataset" + }, + { + "filename": "bird1.csv", + "description_filename": "bird1.txt", + "format": "generic-seq" + }, + { + "filename": "gy6or6_baseline_230312_0808.138.cbin.not.mat", + "description_filename": "gy6or6_baseline_230312_0808.138.cbin.not-description.txt", + "format": "notmat", + "name": "gy6or6" + }, + { + "filename": "Recording_1_Segment_02.Table.1.selections.txt", + "description_filename": "Recording_1_Segment_02.Table.1.selections-description.txt", + "format": "raven", + "name": "Recording1", + "from_file_kwargs": { + "annot_col": "Species" + } + }, + { + "filename": "bl26lb16_190412_0721.20144_annotations.csv", + "description_filename": "bl26lb16_190412_0721.20144_annotations-description.txt", + "format": "simple-seq", + "name": "bl26lb16", + "from_file_kwargs": { + "columns_map": { + "name": "label", + "start_seconds": "onset_s", + "stop_seconds": "offset_s" + } + } + }, + { + "filename": "GO_24860x23748_ltr2_pup3_ch4_4800_m_337_295_fr1_p9_2021-10-02_12-35-01.csv", + "description_filename": "GO_24860x23748_ltr2_pup3_ch4_4800_m_337_295_fr1_p9_2021-10-02_12-35-01-description.txt", + "format": "simple-seq", + "name": "GO", + "from_file_kwargs": { + "columns_map": { + "start_seconds": "onset_s", + "stop_seconds": "offset_s" + } + } + }, + { + "filename": "AVO-maea-basic.TextGrid", + "description_filename": "AVO-maea-basic.TextGrid-description.txt", + "format": "textgrid", + "name": "AVO-maea-basic" + }, + { + "filename": "sa1.phn", + "description_filename": "sa1-description.txt", + "format": "timit" + } +] diff --git a/src/crowsetta/data/notmat/citation.txt b/src/crowsetta/examples/gy6or6_baseline_230312_0808.138.cbin.not-description.txt similarity index 65% rename from src/crowsetta/data/notmat/citation.txt rename to src/crowsetta/examples/gy6or6_baseline_230312_0808.138.cbin.not-description.txt index 29d82e9d..9c48d697 100644 --- a/src/crowsetta/data/notmat/citation.txt +++ b/src/crowsetta/examples/gy6or6_baseline_230312_0808.138.cbin.not-description.txt @@ -1,3 +1,5 @@ +Annotation file in the format used by the MatLab GUI evsonganaly. +From the dataset: Nicholson, David; Queen, Jonah E.; J. Sober, Samuel (2017): Bengalese Finch song repository. figshare. Dataset. https://doi.org/10.6084/m9.figshare.4805749.v6 diff --git a/src/crowsetta/data/notmat/gy6or6_baseline_230312_0808.138.cbin.not.mat b/src/crowsetta/examples/gy6or6_baseline_230312_0808.138.cbin.not.mat similarity index 100% rename from src/crowsetta/data/notmat/gy6or6_baseline_230312_0808.138.cbin.not.mat rename to src/crowsetta/examples/gy6or6_baseline_230312_0808.138.cbin.not.mat diff --git a/src/crowsetta/data/timit/citation.txt b/src/crowsetta/examples/sa1-description.txt similarity index 100% rename from src/crowsetta/data/timit/citation.txt rename to src/crowsetta/examples/sa1-description.txt diff --git a/src/crowsetta/data/timit/sa1.phn b/src/crowsetta/examples/sa1.phn similarity index 100% rename from src/crowsetta/data/timit/sa1.phn rename to src/crowsetta/examples/sa1.phn diff --git a/src/crowsetta/data/audbbox/citation.txt b/src/crowsetta/examples/spinetail-description.txt similarity index 54% rename from src/crowsetta/data/audbbox/citation.txt rename to src/crowsetta/examples/spinetail-description.txt index 07854601..a970b6e7 100644 --- a/src/crowsetta/data/audbbox/citation.txt +++ b/src/crowsetta/examples/spinetail-description.txt @@ -1,3 +1,4 @@ -scikit-maad developers. (2018-present). -Example data file. +Annotation file for spinetail in Audacity extended LabelTrack format. +Data file used by scikit-maad for testing. Adapted under BSD License: https://github.com/scikit-maad/scikit-maad/blob/production/LICENSE +scikit-maad developers. (2018-present). diff --git a/src/crowsetta/data/audbbox/spinetail.txt b/src/crowsetta/examples/spinetail.txt similarity index 100% rename from src/crowsetta/data/audbbox/spinetail.txt rename to src/crowsetta/examples/spinetail.txt diff --git a/src/crowsetta/formats/bbox/audbbox.py b/src/crowsetta/formats/bbox/audbbox.py index 7a1aab2e..f7168c90 100644 --- a/src/crowsetta/formats/bbox/audbbox.py +++ b/src/crowsetta/formats/bbox/audbbox.py @@ -2,6 +2,7 @@ in extended format, exported to txt files https://manual.audacityteam.org/man/importing_and_exporting_labels.html#Extended_format_with_frequency_ranges """ + from __future__ import annotations import pathlib @@ -96,16 +97,14 @@ def df_to_lines(df: pd.DataFrame) -> list[str]: return lines -class AudBBoxSchema(pandera.DataFrameModel - -): +class AudBBoxSchema(pandera.DataFrameModel): """A :class:`pandera.DataFrameModel -` that - validates :mod:`pandas` dataframes - loaded from Audacity label tracks - in extended format, exported to txt files - https://manual.audacityteam.org/man/importing_and_exporting_labels.html#Extended_format_with_frequency_ranges + ` that + validates :mod:`pandas` dataframes + loaded from Audacity label tracks + in extended format, exported to txt files + https://manual.audacityteam.org/man/importing_and_exporting_labels.html#Extended_format_with_frequency_ranges """ begin_time_s: Series[float] = pandera.Field(coerce=True) @@ -138,6 +137,31 @@ class AudBBox: Path to Audacity txt file from which annotations were loaded. audio_path : str. pathlib.Path Path to audio file that the Audacity txt file annotates. + + + Examples + -------- + >>> audbbox = crowsetta.example('spinetail.txt') + >>> print(audbbox) + AudBBox(df= begin_time_s end_time_s label low_freq_hz high_freq_hz + 0 0.101385 0.367520 SP 6441.064453 12296.577148 + 1 0.506924 3.041545 CRER 2593.156006 8866.920898 + 2 1.203945 1.482753 SP 6608.365234 11543.726562 + 3 2.724718 3.218969 SP 4851.710938 12631.178711 + 4 5.221319 7.869998 CRER 2509.505615 8699.620117 + 5 6.260514 6.666053 SP 5939.163574 12798.478516 + 6 7.946037 8.288210 SP 4600.760254 13049.430664 + 7 8.896519 9.302059 SP 5827.929351 12513.294481 + 8 9.973733 10.353927 SP 4851.710938 13969.581055 + 9 11.329756 13.750319 CRER 2091.254639 9117.871094 + 10 11.773314 12.077469 SP 6106.464355 12296.577148 + 11 12.660432 12.939240 SP 5604.562500 12296.577148 + 12 15.435842 15.879400 SP 4015.209229 13216.730469 + 13 16.170882 16.563748 SP 4098.859375 12463.878906 + 14 16.437017 18.730849 CRER 2676.806152 8699.620117 + 15 17.159384 17.514231 SP 5688.213379 12714.829102 + 16 18.198578 18.502733 SP 5353.612305 12463.878906 + 17 19.073023 19.465889 SP 4349.810059 12296.577148, annot_path=PosixPath('/Users/davidnicholson/Documents/repos/vocalpy/crowsetta/src/crowsetta/examples/spinetail.txt'), audio_path=None) # noqa: E501 """ COLUMNS_MAP: ClassVar[dict] = { @@ -170,8 +194,28 @@ def from_file(cls, annot_path: PathLike, audio_path: Optional[PathLike] = None) Examples -------- - >>> example = crowsetta.data.get('aud-bbox') - >>> audbbox = crowsetta.formats.bbox.AudBBox.from_file(example.annot_path) + >>> path = crowsetta.example('spinetail.txt', return_path=True) + >>> audbbox = crowsetta.formats.bbox.AudBBox.from_file(path) + >>> print(audbbox) + AudBBox(df= begin_time_s end_time_s label low_freq_hz high_freq_hz + 0 0.101385 0.367520 SP 6441.064453 12296.577148 + 1 0.506924 3.041545 CRER 2593.156006 8866.920898 + 2 1.203945 1.482753 SP 6608.365234 11543.726562 + 3 2.724718 3.218969 SP 4851.710938 12631.178711 + 4 5.221319 7.869998 CRER 2509.505615 8699.620117 + 5 6.260514 6.666053 SP 5939.163574 12798.478516 + 6 7.946037 8.288210 SP 4600.760254 13049.430664 + 7 8.896519 9.302059 SP 5827.929351 12513.294481 + 8 9.973733 10.353927 SP 4851.710938 13969.581055 + 9 11.329756 13.750319 CRER 2091.254639 9117.871094 + 10 11.773314 12.077469 SP 6106.464355 12296.577148 + 11 12.660432 12.939240 SP 5604.562500 12296.577148 + 12 15.435842 15.879400 SP 4015.209229 13216.730469 + 13 16.170882 16.563748 SP 4098.859375 12463.878906 + 14 16.437017 18.730849 CRER 2676.806152 8699.620117 + 15 17.159384 17.514231 SP 5688.213379 12714.829102 + 16 18.198578 18.502733 SP 5353.612305 12463.878906 + 17 19.073023 19.465889 SP 4349.810059 12296.577148, annot_path=PosixPath('/Users/davidnicholson/Documents/repos/vocalpy/crowsetta/src/crowsetta/examples/spinetail.txt'), audio_path=None) # noqa: E501 """ annot_path = pathlib.Path(annot_path) crowsetta.validation.validate_ext(annot_path, extension=cls.ext) @@ -198,8 +242,8 @@ def to_bbox(self) -> List[crowsetta.BBox]: Examples -------- - >>> example = crowsetta.data.get('aud-bbox') - >>> audbbox = crowsetta.formats.bbox.AudBBox.from_file(example.annot_path) + >>> path = crowsetta.example('spinetail.txt', return_path=True) + >>> audbbox = crowsetta.formats.bbox.AudBBox.from_file(path) >>> bboxes = audbbox.to_bbox() """ bboxes = [] @@ -225,9 +269,9 @@ def to_annot(self) -> crowsetta.Annotation: Examples -------- - >>> example = crowsetta.data.get('aud-bbox') - >>> audacitybbox = crowsetta.formats.bbox.AudBBox.from_file(example.annot_path) - >>> annot = audacitybbox.to_annot() + >>> path = crowsetta.example('spinetail.txt', return_path=True) + >>> audbbox = crowsetta.formats.bbox.AudBBox.from_file(path) + >>> annot = audbbox.to_annot() """ bboxes = self.to_bbox() return crowsetta.Annotation(annot_path=self.annot_path, notated_path=self.audio_path, bboxes=bboxes) diff --git a/src/crowsetta/formats/bbox/raven.py b/src/crowsetta/formats/bbox/raven.py index 274e2019..d01ca5c9 100644 --- a/src/crowsetta/formats/bbox/raven.py +++ b/src/crowsetta/formats/bbox/raven.py @@ -5,6 +5,7 @@ https://github.com/kitzeslab/opensoundscape/blob/master/opensoundscape/annotations.py under MIT license """ + import pathlib from typing import ClassVar, List, Optional @@ -17,14 +18,12 @@ from crowsetta.typing import PathLike -class RavenSchema(pandera.DataFrameModel - -): +class RavenSchema(pandera.DataFrameModel): """A :class:`pandera.DataFrameModel -` that validates :type:`pandas.DataFrame`s - loaded from a txt file, created by exporting a Selection Table - from Raven. + ` that validates :type:`pandas.DataFrame`s + loaded from a txt file, created by exporting a Selection Table + from Raven. """ begin_time_s: Series[float] = pandera.Field() @@ -60,6 +59,18 @@ class Raven: Path to Raven txt file from which annotations were loaded. audio_path : str. pathlib.Path Path to audio file that the Raven txt file annotates. + + Examples + -------- + >>> raven = crowsetta.example('Recording1') + >>> print(raven) + Raven(df= Selection View Channel begin_time_s end_time_s low_freq_hz high_freq_hz annotation + 0 1 Spectrogram 1 1 154.387793 154.911598 2878.2 4049.0 EATO + 1 2 Spectrogram 1 1 167.526598 168.173020 2731.9 3902.7 EATO + 2 3 Spectrogram 1 1 183.609637 184.097752 2878.2 3975.8 EATO + 3 4 Spectrogram 1 1 250.527481 251.160711 2756.2 3951.4 EATO + 4 5 Spectrogram 1 1 277.887243 278.480896 2707.5 3975.8 EATO + 5 6 Spectrogram 1 1 295.529708 296.110168 2951.4 3975.8 EATO, annot_path=PosixPath('/Users/davidnicholson/Documents/repos/vocalpy/crowsetta/src/crowsetta/examples/Recording_1_Segment_02.Table.1.selections.txt'), annot_col='Species', audio_path=None) # noqa: E501 """ name: ClassVar[str] = "raven" @@ -95,8 +106,16 @@ def from_file( Examples -------- - >>> example = crowsetta.data.get('raven') - >>> raven = crowsetta.formats.bbox.Raven.from_file(example.annot_path) + >>> path = crowsetta.example('Recording1', return_path=True) + >>> raven = crowsetta.formats.bbox.Raven.from_file(path, annot_col="Species") + >>> print(raven) + Raven(df= Selection View Channel begin_time_s end_time_s low_freq_hz high_freq_hz annotation + 0 1 Spectrogram 1 1 154.387793 154.911598 2878.2 4049.0 EATO + 1 2 Spectrogram 1 1 167.526598 168.173020 2731.9 3902.7 EATO + 2 3 Spectrogram 1 1 183.609637 184.097752 2878.2 3975.8 EATO + 3 4 Spectrogram 1 1 250.527481 251.160711 2756.2 3951.4 EATO + 4 5 Spectrogram 1 1 277.887243 278.480896 2707.5 3975.8 EATO + 5 6 Spectrogram 1 1 295.529708 296.110168 2951.4 3975.8 EATO, annot_path=PosixPath('/Users/davidnicholson/Documents/repos/vocalpy/crowsetta/src/crowsetta/examples/Recording_1_Segment_02.Table.1.selections.txt'), annot_col='Species', audio_path=None) # noqa: E501 """ annot_path = pathlib.Path(annot_path) crowsetta.validation.validate_ext(annot_path, extension=cls.ext) @@ -128,8 +147,8 @@ def to_bbox(self) -> List[crowsetta.BBox]: Examples -------- - >>> example = crowsetta.data.get('raven') - >>> raven = crowsetta.formats.bbox.Raven.from_file(example.annot_path) + >>> path = crowsetta.example('Recording1') + >>> raven = crowsetta.formats.bbox.Raven.from_file(path) >>> bboxes = raven.to_bbox() """ bboxes = [] @@ -155,8 +174,8 @@ def to_annot(self) -> crowsetta.Annotation: Examples -------- - >>> example = crowsetta.data.get('raven') - >>> raven = crowsetta.formats.bbox.Raven.from_file(example.annot_path) + >>> path = crowsetta.example('Recording1') + >>> raven = crowsetta.formats.bbox.Raven.from_file(path) >>> annot = raven.to_annot() """ bboxes = self.to_bbox() diff --git a/src/crowsetta/formats/seq/audseq.py b/src/crowsetta/formats/seq/audseq.py index 15418476..fd2782b7 100644 --- a/src/crowsetta/formats/seq/audseq.py +++ b/src/crowsetta/formats/seq/audseq.py @@ -2,6 +2,7 @@ in standard/default format exported to txt files https://manual.audacityteam.org/man/importing_and_exporting_labels.html#Standard_.28default.29_format """ + import pathlib from typing import ClassVar, Optional @@ -15,18 +16,16 @@ from crowsetta.typing import PathLike -class AudSeqSchema(pandera.DataFrameModel - -): +class AudSeqSchema(pandera.DataFrameModel): """A :class:`pandera.DataFrameModel -` - that validates :type:`pandas.DataFrame`s - loaded from Audacity Labeltrack annotations - exported to txt files in the standard format. + ` + that validates :type:`pandas.DataFrame`s + loaded from Audacity Labeltrack annotations + exported to txt files in the standard format. - The standard format is described here: - https://manual.audacityteam.org/man/importing_and_exporting_labels.html#Standard_.28default.29_format + The standard format is described here: + https://manual.audacityteam.org/man/importing_and_exporting_labels.html#Standard_.28default.29_format """ start_time: Optional[Series[float]] = pandera.Field() @@ -73,6 +72,44 @@ class AudSeq: that contains a spectrogram generated from audio. Optional, default is None. + Examples + -------- + >>> audseq = crowsetta.example('marron1') + >>> print(audseq) + AudSeq(start_times=array([ 0. , 0.76981817, 1.13127401, 2.21840074, 2.55502374, + 3.09030949, 3.69457537, 3.81322118, 4.05603121, 4.86171904, + 4.87551507, 5.52392822, 6.55587085, 6.59449972, 7.0883974 , + 7.18772877, 7.23463526, 7.94375092, 9.01984083, 9.06950652, + 9.18263392, 10.06282028, 10.07661631, 10.9705987 , 10.98715393, + 11.80663778, 11.86458109, 12.19016727, 13.24142433, 13.277294 , + 14.49686257, 14.60723076, 15.22805186, 15.31082801, 16.22136563, + 17.25606747, 18.16660509, 18.20247475, 19.65381653, 19.75590711, + 20.71059201, 20.78509054, 20.96719806, 21.02514137, 21.35624596, + 21.45005892, 21.66527691, 21.67355452, 22.73860761, 22.82966137, + 23.63534921, 24.59831172, 24.60383013, 24.67281025, 24.77214163, + 25.68267925, 25.70751209, 26.65943778, 27.7410461 , 27.76036054, + 28.34531198]), end_times=array([ 0.76981817, 1.13127401, 2.21840074, 2.55502374, 3.09030949, + 3.69457537, 3.81322118, 4.05603121, 4.86171904, 4.87551507, + 5.53496504, 6.55587085, 6.59449972, 7.0883974 , 7.18772877, + 7.23463526, 7.94375092, 9.01984083, 9.06950652, 9.18263392, + 10.06282028, 10.07661631, 10.9705987 , 10.98715393, 11.80663778, + 11.86458109, 12.20396329, 13.24142433, 13.277294 , 14.49686257, + 14.60723076, 15.22805186, 15.31082801, 16.22136563, 17.25606747, + 18.16660509, 18.20247475, 19.65381653, 19.75590711, 20.71059201, + 20.78509054, 20.96719806, 21.02514137, 21.35624596, 21.45005892, + 21.66527691, 21.67355452, 22.73860761, 22.82966137, 23.63534921, + 24.59831172, 24.60383013, 24.67281025, 24.77214163, 25.68267925, + 25.70751209, 26.65943778, 27.7410461 , 27.76036054, 28.359108 , + 29.10133412]), labels= + [ 'SIL', 'call', 'SIL', 'call', 'SIL', 'Z', 'SIL', 'Ci', 'C', + 'SIL', 'H', 'E', 'SIL', 'R', 'SIL', 'J1', 'J1', 'J2', + 'J2', 'SIL', 'B1', 'SIL', 'B2', 'SIL', 'Q', 'SIL', 'H', + 'E', 'SIL', 'R', 'SIL', 'O', 'SIL', 'J1', 'J2', 'L', + 'SIL', 'N', 'SIL', 'A', 'SIL', 'O', 'SIL', 'P', 'SIL', + 'K', 'SIL', 'V', 'SIL', 'J1', 'J2', 'SIL', 'J2', 'SIL', + 'B1', 'SIL', 'B2', 'Q', 'SIL', 'H', 'E'] + Length: 61, dtype: string, annot_path=PosixPath('/Users/davidnicholson/Documents/repos/vocalpy/crowsetta/src/crowsetta/examples/405_marron1_June_14_2016_69640887.audacity.txt'), notated_path=None) # noqa: E501 + References ---------- .. [1^] https://manual.audacityteam.org/man/importing_and_exporting_labels.html#Standard_.28default.29_format @@ -108,8 +145,42 @@ def from_file( Examples -------- - >>> example = crowsetta.data.get('aud-seq') - >>> audseq = crowsetta.formats.seq.AudSeq.from_file(example.annot_path) + >>> path = crowsetta.example('marron1', return_path=True) + >>> audseq = crowsetta.formats.seq.AudSeq.from_file(path) + >>> print(audseq) + AudSeq(start_times=array([ 0. , 0.76981817, 1.13127401, 2.21840074, 2.55502374, + 3.09030949, 3.69457537, 3.81322118, 4.05603121, 4.86171904, + 4.87551507, 5.52392822, 6.55587085, 6.59449972, 7.0883974 , + 7.18772877, 7.23463526, 7.94375092, 9.01984083, 9.06950652, + 9.18263392, 10.06282028, 10.07661631, 10.9705987 , 10.98715393, + 11.80663778, 11.86458109, 12.19016727, 13.24142433, 13.277294 , + 14.49686257, 14.60723076, 15.22805186, 15.31082801, 16.22136563, + 17.25606747, 18.16660509, 18.20247475, 19.65381653, 19.75590711, + 20.71059201, 20.78509054, 20.96719806, 21.02514137, 21.35624596, + 21.45005892, 21.66527691, 21.67355452, 22.73860761, 22.82966137, + 23.63534921, 24.59831172, 24.60383013, 24.67281025, 24.77214163, + 25.68267925, 25.70751209, 26.65943778, 27.7410461 , 27.76036054, + 28.34531198]), end_times=array([ 0.76981817, 1.13127401, 2.21840074, 2.55502374, 3.09030949, + 3.69457537, 3.81322118, 4.05603121, 4.86171904, 4.87551507, + 5.53496504, 6.55587085, 6.59449972, 7.0883974 , 7.18772877, + 7.23463526, 7.94375092, 9.01984083, 9.06950652, 9.18263392, + 10.06282028, 10.07661631, 10.9705987 , 10.98715393, 11.80663778, + 11.86458109, 12.20396329, 13.24142433, 13.277294 , 14.49686257, + 14.60723076, 15.22805186, 15.31082801, 16.22136563, 17.25606747, + 18.16660509, 18.20247475, 19.65381653, 19.75590711, 20.71059201, + 20.78509054, 20.96719806, 21.02514137, 21.35624596, 21.45005892, + 21.66527691, 21.67355452, 22.73860761, 22.82966137, 23.63534921, + 24.59831172, 24.60383013, 24.67281025, 24.77214163, 25.68267925, + 25.70751209, 26.65943778, 27.7410461 , 27.76036054, 28.359108 , + 29.10133412]), labels= + [ 'SIL', 'call', 'SIL', 'call', 'SIL', 'Z', 'SIL', 'Ci', 'C', + 'SIL', 'H', 'E', 'SIL', 'R', 'SIL', 'J1', 'J1', 'J2', + 'J2', 'SIL', 'B1', 'SIL', 'B2', 'SIL', 'Q', 'SIL', 'H', + 'E', 'SIL', 'R', 'SIL', 'O', 'SIL', 'J1', 'J2', 'L', + 'SIL', 'N', 'SIL', 'A', 'SIL', 'O', 'SIL', 'P', 'SIL', + 'K', 'SIL', 'V', 'SIL', 'J1', 'J2', 'SIL', 'J2', 'SIL', + 'B1', 'SIL', 'B2', 'Q', 'SIL', 'H', 'E'] + Length: 61, dtype: string, annot_path=PosixPath('/Users/davidnicholson/Documents/repos/vocalpy/crowsetta/src/crowsetta/examples/405_marron1_June_14_2016_69640887.audacity.txt'), notated_path=None) # noqa: E501 """ annot_path = pathlib.Path(annot_path) crowsetta.validation.validate_ext(annot_path, extension=cls.ext) @@ -144,8 +215,8 @@ def to_seq(self, round_times: bool = True, decimals: int = 3) -> crowsetta.Seque Examples -------- - >>> example = crowsetta.data.get('aud-seq') - >>> audseq = crowsetta.formats.seq.AudSeq.from_file(example.annot_path) + >>> path = crowsetta.example('marron1') + >>> audseq = crowsetta.formats.seq.AudSeq.from_file(path) >>> seq = audseq.to_seq() Notes @@ -185,8 +256,8 @@ def to_annot(self, round_times: bool = True, decimals: int = 3) -> crowsetta.Ann Examples -------- - >>> example = crowsetta.data.get('aud-seq') - >>> audseq = crowsetta.formats.seq.AudSeq.from_file(example.annot_path) + >>> path = crowsetta.example('marron1') + >>> audseq = crowsetta.formats.seq.AudSeq.from_file(path) >>> annot = audseq.to_annot() Notes diff --git a/src/crowsetta/formats/seq/birdsongrec.py b/src/crowsetta/formats/seq/birdsongrec.py index 2da229cb..f4640a73 100644 --- a/src/crowsetta/formats/seq/birdsongrec.py +++ b/src/crowsetta/formats/seq/birdsongrec.py @@ -8,6 +8,7 @@ Boundaries in the Birdsong with Variable Sequences. PLoS ONE 11(7): e0159188. doi:10.1371/journal.pone.0159188 """ + from __future__ import annotations import os @@ -241,6 +242,11 @@ class BirdsongRec: to convert onset and offset times from sample number to seconds, when converting annotations to ``crowsetta.Sequence``. + + Examples + -------- + >>> birdsongrec = crowsetta.example('Annotation.xml') + Notes ----- This class uses the Python package ``birdsong-recognition-dataset`` @@ -303,8 +309,8 @@ def from_file( Examples -------- - >>> example = crowsetta.data.get('birdsong-recognition-dataset') - >>> birdsongrec = crowsetta.formats.seq.BirdsongRec.from_file(example.annot_path) + >>> path = crowsetta.example('Annotation.xml', return_path=True) + >>> birdsongrec = crowsetta.formats.seq.BirdsongRec.from_file(path) .. [1] Koumura, T. (2016). BirdsongRecognition (Version 1). figshare. https://doi.org/10.6084/m9.figshare.3470165.v1 @@ -357,7 +363,7 @@ def to_seq( Examples -------- - >>> example = crowsetta.data.get('birdsong-recognition-dataset') + >>> example = crowsetta.example('birdsong-recognition-dataset') >>> birdsongrec = crowsetta.formats.seq.BirdsongRec.from_file(example.annot_path) >>> seqs = birdsongrec.to_seq() @@ -458,7 +464,7 @@ def to_annot( Examples -------- - >>> example = crowsetta.data.get('birdsong-recognition-dataset') + >>> example = crowsetta.example('birdsong-recognition-dataset') >>> birdsongrec = crowsetta.formats.seq.BirdsongRec.from_file(example.annot_path) >>> annots = birdsongrec.to_annot() diff --git a/src/crowsetta/formats/seq/generic.py b/src/crowsetta/formats/seq/generic.py index c8560388..4065930f 100644 --- a/src/crowsetta/formats/seq/generic.py +++ b/src/crowsetta/formats/seq/generic.py @@ -15,6 +15,7 @@ with :class:`~crowsetta.Sequence`s can be converted to this format. """ + import os from collections import OrderedDict from typing import ClassVar, List, Optional, Union @@ -35,15 +36,13 @@ """ -class GenericSeqSchema(pandera.DataFrameModel - -): +class GenericSeqSchema(pandera.DataFrameModel): """A :class: `pandera.DataFrameModel -` that validates - :type:`pandas.DataFrame`s - loaded from a csv file in the ``'generic-seq'`` annotation - format. + ` that validates + :type:`pandas.DataFrame`s + loaded from a csv file in the ``'generic-seq'`` annotation + format. """ label: Series[pd.StringDtype] = pandera.Field(coerce=True) @@ -327,8 +326,9 @@ def from_file(cls, annot_path: PathLike) -> "Self": # noqa: F821 Examples -------- - >>> example = crowsetta.data.get('generic-seq') - >>> generic = crowsetta.formats.seq.GenericSeq.from_file(example.annot_path)""" + >>> path = crowsetta.example('bird1.csv', return_path=True) + >>> generic = crowsetta.formats.seq.GenericSeq.from_file(path) + """ annots = csv2annot(csv_path=annot_path) return cls(annots=annots) @@ -338,8 +338,8 @@ def to_seq(self) -> List[crowsetta.Sequence]: Examples -------- - >>> example = crowsetta.data.get('generic-seq') - >>> generic = crowsetta.formats.seq.GenericSeq.from_file(example.annot_path) + >>> path = crowsetta.example('bird1.csv', return_path=True) + >>> generic = crowsetta.formats.seq.GenericSeq.from_file(path) >>> seqs = generic.to_seq() """ return [annot.seq for annot in self.annots] @@ -354,8 +354,8 @@ def to_annot(self) -> List[crowsetta.Annotation]: Examples -------- - >>> example = crowsetta.data.get('generic-seq') - >>> generic = crowsetta.formats.seq.GenericSeq.from_file(example.annot_path) + >>> path = crowsetta.example('bird1.csv', return_path=True) + >>> generic = crowsetta.formats.seq.GenericSeq.from_file(path) >>> annots = generic.to_annot() """ return self.annots diff --git a/src/crowsetta/formats/seq/notmat.py b/src/crowsetta/formats/seq/notmat.py index 4e0cf140..93b82e56 100644 --- a/src/crowsetta/formats/seq/notmat.py +++ b/src/crowsetta/formats/seq/notmat.py @@ -1,6 +1,7 @@ """Module with functions that handle .not.mat annotation files produced by evsonganaly GUI. """ + from __future__ import annotations import pathlib @@ -91,7 +92,7 @@ class NotMat: Notes ----- - This class uses the Python package ``evfuncs`` + This class uses code adapted from the Python package ``evfuncs`` to load the annotations. https://github.com/NickleDave/evfuncs """ @@ -116,8 +117,8 @@ def from_file(cls, annot_path: PathLike) -> "Self": # noqa: F821 Examples -------- - >>> example = crowsetta.data.get('notmat') - >>> notmat = crowsetta.formats.seq.NotMat.from_file(example.annot_path) + >>> path = crowsetta.example('notmat', return_path=True) + >>> notmat = crowsetta.formats.seq.NotMat.from_file(path) """ annot_path = pathlib.Path(annot_path) crowsetta.validation.validate_ext(annot_path, extension=cls.ext) @@ -150,8 +151,8 @@ def to_seq(self, round_times: bool = True, decimals: int = 3) -> crowsetta.Seque Examples -------- - >>> example = crowsetta.data.get('notmat') - >>> notmat = crowsetta.formats.seq.NotMat.from_file(example.annot_path) + >>> path = crowsetta.example('notmat', return_path=True) + >>> notmat = crowsetta.formats.seq.NotMat.from_file(path) >>> seq = notmat.to_seq() Notes @@ -191,8 +192,8 @@ def to_annot(self, round_times: bool = True, decimals: int = 3) -> crowsetta.Ann Examples -------- - >>> example = crowsetta.data.get('notmat') - >>> notmat = crowsetta.formats.seq.NotMat.from_file(example.annot_path) + >>> path = crowsetta.example('notmat', return_path=True) + >>> notmat = crowsetta.formats.seq.NotMat.from_file(path) >>> annot = notmat.to_annot() Notes diff --git a/src/crowsetta/formats/seq/simple.py b/src/crowsetta/formats/seq/simple.py index c45a3edb..cf0c471f 100644 --- a/src/crowsetta/formats/seq/simple.py +++ b/src/crowsetta/formats/seq/simple.py @@ -17,6 +17,7 @@ corresponds to one annotated source file, i.e. a single audio or spectrogram file. """ + import pathlib from typing import ClassVar, Mapping, Optional @@ -31,9 +32,7 @@ class SimpleSeqSchema(pandera.DataFrameModel): - """A :class:`pandera.DataFrameModel - -` + """A :class:`pandera.DataFrameModel` that validates :type:`pandas.DataFrame`s loaded from a csv or txt file in a 'simple-seq' format. @@ -51,6 +50,9 @@ class Config: strict = True +SIMPLESEQ_COLUMNS = ("onset_s", "offset_s", "label") + + @crowsetta.interface.SeqLike.register @attr.define class SimpleSeq: @@ -112,6 +114,7 @@ def from_file( notated_path: Optional[PathLike] = None, columns_map: Optional[Mapping] = None, read_csv_kwargs: Optional[Mapping] = None, + default_label: str = "-", ) -> "Self": # noqa: F821 """Load annotations from a file in the 'simple-seq' format. @@ -157,8 +160,8 @@ def from_file( Examples -------- - >>> example = crowsetta.data.get('simple-seq') - >>> simple = crowsetta.formats.seq.SimpleSeq.from_file(example.annot_path, + >>> path = crowsetta.example('bl26lb16', return_path=True) + >>> simple = crowsetta.formats.seq.SimpleSeq.from_file(path, >>> columns_map={'start_seconds': 'onset_s', >>> 'stop_seconds': 'offset_s', >>> 'name': 'label'}, @@ -172,9 +175,49 @@ def from_file( else: df = pd.read_csv(annot_path) - if columns_map: - df.columns = [columns_map[column_name] for column_name in df.columns] - df = df[["onset_s", "offset_s", "label"]] # put in correct order + if len(df) == 0: + # handle empty csv file, fixes https://github.com/vocalpy/crowsetta/issues/264 + return cls( + onsets_s=[], + offsets_s=[], + labels=[], + annot_path=annot_path, + notated_path=notated_path, + ) + + if columns_map is not None: + if not isinstance(columns_map, dict): + raise TypeError(f"The `columns_map` argument must be a `dict` but type was: {type(dict)}") + if not all((isinstance(k, str) and isinstance(v, str) for k, v in columns_map.items())): + raise ValueError( + "The `columns_map` argument must be a dict that maps string keys to string values, " + "but not all keys and values were strings." + ) + if not all(v in SIMPLESEQ_COLUMNS for v in columns_map.values()): + invalid_values = [v for v in columns_map.values() if v not in SIMPLESEQ_COLUMNS] + raise ValueError( + f"The `columns_map` argument must map keys (column names in the csv) " + 'to these values: ("onset_s", "offset_s", "label"). ' + f"The following values are invalid: {invalid_values}" + ) + df.columns = [ + columns_map[column_name] if column_name in columns_map else column_name for column_name in df.columns + ] + + if "label" not in df.columns: + df["label"] = default_label + + if not all([col_name in df.columns for col_name in SIMPLESEQ_COLUMNS]): + raise ValueError( + "Annotations loaded from path did not have expected column names. " + f"Column names from loaded csv file were: {df.columns.to_list()}\n" + f"Expected column names are: {SIMPLESEQ_COLUMNS}\n" + f"Please either re-map the column names using the `columns_map` argument, " + "or if needed modify the csv file directly. " + "Note that you only need to remap the column names that correspond to onset " + "times, offset times, and labels; other columns will be ignored." + ) + df = df[list(SIMPLESEQ_COLUMNS)] # put in correct order df = SimpleSeqSchema.validate(df) return cls( @@ -204,8 +247,8 @@ def to_seq(self, round_times: bool = True, decimals: int = 3) -> crowsetta.Seque Examples -------- - >>> example = crowsetta.data.get('simple-seq') - >>> simple = crowsetta.formats.seq.SimpleSeq.from_file(example.annot_path, + >>> path = crowsetta.example('bl26lb16', return_path=True) + >>> simple = crowsetta.formats.seq.SimpleSeq.from_file(path, >>> columns_map={'start_seconds': 'onset_s', >>> 'stop_seconds': 'offset_s', >>> 'name': 'label'}, @@ -249,8 +292,8 @@ def to_annot(self, round_times: bool = True, decimals: int = 3) -> crowsetta.Ann Examples -------- - >>> example = crowsetta.data.get('simple-seq') - >>> simple = crowsetta.formats.seq.SimpleSeq.from_file(example.annot_path, + >>> path = crowsetta.example('bl26lb1b', return_path=True) + >>> simple = crowsetta.formats.seq.SimpleSeq.from_file(path, >>> columns_map={'start_seconds': 'onset_s', >>> 'stop_seconds': 'offset_s', >>> 'name': 'label'}, diff --git a/src/crowsetta/formats/seq/textgrid/classes.py b/src/crowsetta/formats/seq/textgrid/classes.py index e4968730..15b5c98e 100644 --- a/src/crowsetta/formats/seq/textgrid/classes.py +++ b/src/crowsetta/formats/seq/textgrid/classes.py @@ -1,5 +1,6 @@ """Data classes used to represent components of TextGrids. """ + from __future__ import annotations import numpy as np diff --git a/src/crowsetta/formats/seq/textgrid/parse.py b/src/crowsetta/formats/seq/textgrid/parse.py index a0f93b81..1fe51ae9 100644 --- a/src/crowsetta/formats/seq/textgrid/parse.py +++ b/src/crowsetta/formats/seq/textgrid/parse.py @@ -18,6 +18,7 @@ https://github.com/hbuschme/TextGridTools but note that both of these have a GPL license. """ + from __future__ import annotations import pathlib diff --git a/src/crowsetta/formats/seq/textgrid/textgrid.py b/src/crowsetta/formats/seq/textgrid/textgrid.py index 821e5b2f..05f6ce4b 100644 --- a/src/crowsetta/formats/seq/textgrid/textgrid.py +++ b/src/crowsetta/formats/seq/textgrid/textgrid.py @@ -1,4 +1,5 @@ """Module with functions for working with Praat TextGrid annotation files""" + from __future__ import annotations import pathlib @@ -69,36 +70,31 @@ class TextGrid: -------- Loading the example textgrid - >>> example = crowsetta.data.get('textgrid') - >>> textgrid = crowsetta.formats.seq.TextGrid.from_file(example.annot_path) + >>> textgrid = crowsetta.example('AVO-maea-basic') >>> print(textgrid) TextGrid(tiers=[PointTier(nam...ark='L+!H-')]), IntervalTier(...aleila\\-^')]), IntervalTier(...t='earlier')])], xmin=0.0, xmax=2.4360509767904546, annot_path=PosixPath('/home/pimienta/.local/share/crowsetta/5.0.0rc2/textgrid/AVO-maea-basic.TextGrid'), audio_path=None) # noqa: E501 Determining the number of tiers in the textgrid - >>> example = crowsetta.data.get('textgrid') - >>> textgrid = crowsetta.formats.seq.TextGrid.from_file(example.annot_path) + >>> textgrid = crowsetta.example('AVO-maea-basic') >>> len(textgrid) 3 Getting the names of the tiers in the textgrid - >>> example = crowsetta.data.get('textgrid') - >>> textgrid = crowsetta.formats.seq.TextGrid.from_file(example.annot_path) + >>> textgrid = crowsetta.example('AVO-maea-basic') >>> textgrid.tier_names ['Tones', 'Samoan', 'Gloss'] Getting a tier from the TextGrid by name - >>> example = crowsetta.data.get('textgrid') - >>> textgrid = crowsetta.formats.seq.TextGrid.from_file(example.annot_path) + >>> textgrid = crowsetta.example('AVO-maea-basic') >>> textgrid['Gloss'] IntervalTier(name='Gloss', xmin=0.0, xmax=2.4360509767904546, intervals=[Interval(xmin=0.0, xmax=0.051451575248407266, text='PRES'), Interval(xmin=0.051451575248407266, xmax=0.6407379583230295, text='Sione'), Interval(xmin=0.6407379583230295, xmax=0.7544662733943284, text='PAST'), Interval(xmin=0.7544662733943284, xmax=1.244041566788134, text='pull-ES'), Interval(xmin=1.244041566788134, xmax=1.3481058803597676, text='DET'), Interval(xmin=1.3481058803597676, xmax=1.70760078178904, text='rope'), Interval(xmin=1.70760078178904, xmax=2.4360509767904546, text='earlier')]) # noqa: E501 Getting a tier from the TextGrid by index - >>> example = crowsetta.data.get('textgrid') - >>> textgrid = crowsetta.formats.seq.TextGrid.from_file(example.annot_path) + >>> textgrid = crowsetta.example('AVO-maea-basic') >>> textgrid[2] # same tier we just got by name IntervalTier(name='Gloss', xmin=0.0, xmax=2.4360509767904546, intervals=[Interval(xmin=0.0, xmax=0.051451575248407266, text='PRES'), Interval(xmin=0.051451575248407266, xmax=0.6407379583230295, text='Sione'), Interval(xmin=0.6407379583230295, xmax=0.7544662733943284, text='PAST'), Interval(xmin=0.7544662733943284, xmax=1.244041566788134, text='pull-ES'), Interval(xmin=1.244041566788134, xmax=1.3481058803597676, text='DET'), Interval(xmin=1.3481058803597676, xmax=1.70760078178904, text='rope'), Interval(xmin=1.70760078178904, xmax=2.4360509767904546, text='earlier')]) # noqa: E501 @@ -107,8 +103,7 @@ class TextGrid: :class:`~crowsetta.Sequence` instances, in the order they appear in the TextGrid. - >>> example = crowsetta.data.get('textgrid') - >>> textgrid = crowsetta.formats.seq.TextGrid.from_file(example.annot_path) + >>> textgrid = crowsetta.example('AVO-maea-basic') >>> textgrid.to_seq() [, ] @@ -117,8 +112,7 @@ class TextGrid: :class:`~crowsetta.formats.seq.textgrid.classes.IntervalTier`s to a single :class:`~crowsetta.Sequence` instance. - >>> example = crowsetta.data.get('textgrid') - >>> textgrid = crowsetta.formats.seq.TextGrid.from_file(example.annot_path) + >>> textgrid = crowsetta.example('AVO-maea-basic') >>> textgrid.to_seq(tier=2) [] @@ -128,8 +122,7 @@ class TextGrid: I.e., this parameter works the same way as square bracket access to a TextGrid as shown above. - >>> example = crowsetta.data.get('textgrid') - >>> textgrid = crowsetta.formats.seq.TextGrid.from_file(example.annot_path) + >>> textgrid = crowsetta.example('AVO-maea-basic') >>> seq1 = textgrid.to_seq(tier=2) >>> seq2 = textgrid.to_seq(tier="Gloss") >>> seq1 == seq2 @@ -200,8 +193,8 @@ def from_file( Examples -------- - >>> example = crowsetta.data.get('textgrid') - >>> textgrid = crowsetta.formats.seq.TextGrid.from_file(example.annot_path) + >>> path = crowsetta.example('AVO-maea-basic', return_path=True) + >>> textgrid = crowsetta.formats.seq.TextGrid.from_file(path) >>> print(textgrid) TextGrid(tiers=[PointTier(nam...ark='L+!H-')]), IntervalTier(...aleila\\-^')]), IntervalTier(...t='earlier')])], xmin=0.0, xmax=2.4360509767904546, annot_path=PosixPath('/home/pimienta/.local/share/crowsetta/5.0.0rc2/textgrid/AVO-maea-basic.TextGrid'), audio_path=None) # noqa: E501 @@ -313,7 +306,7 @@ def to_seq( :class:`~crowsetta.Sequence` instances, in the order they appear in the TextGrid. - >>> example = crowsetta.data.get('textgrid') + >>> example = crowsetta.example('textgrid') >>> textgrid = crowsetta.formats.seq.TextGrid.from_file(example.annot_path) >>> textgrid.to_seq() [, ] @@ -323,7 +316,7 @@ def to_seq( :class:`~crowsetta.formats.seq.textgrid.classes.IntervalTier` to a single :class:`~crowsetta.Sequence`. - >>> example = crowsetta.data.get('textgrid') + >>> example = crowsetta.example('textgrid') >>> textgrid = crowsetta.formats.seq.TextGrid.from_file(example.annot_path) >>> textgrid.to_seq(tier=2) [] @@ -334,7 +327,7 @@ def to_seq( I.e., this parameter works the same way as square bracket access to a TextGrid as shown above. - >>> example = crowsetta.data.get('textgrid') + >>> example = crowsetta.example('textgrid') >>> textgrid = crowsetta.formats.seq.TextGrid.from_file(example.annot_path) >>> seq1 = textgrid.to_seq(tier=2) >>> seq2 = textgrid.to_seq(tier="Gloss") @@ -395,7 +388,7 @@ def to_annot( Examples -------- - >>> example = crowsetta.data.get('textgrid') + >>> example = crowsetta.example('textgrid') >>> textgrid = crowsetta.formats.seq.TextGrid.from_file(example.annot_path) >>> annot = textgrid.to_annot() diff --git a/src/crowsetta/formats/seq/timit.py b/src/crowsetta/formats/seq/timit.py index 90085ff2..68383c13 100644 --- a/src/crowsetta/formats/seq/timit.py +++ b/src/crowsetta/formats/seq/timit.py @@ -4,6 +4,7 @@ .. [1] Garofolo, John S., et al. TIMIT Acoustic-Phonetic Continuous Speech Corpus LDC93S1. Web Download. Philadelphia: Linguistic Data Consortium, 1993. """ + import pathlib import warnings from typing import ClassVar, Optional @@ -19,18 +20,16 @@ from crowsetta.typing import PathLike -class TimitTranscriptSchema(pandera.DataFrameModel - -): +class TimitTranscriptSchema(pandera.DataFrameModel): """A :class:`pandera.DataFrameModel -` that validates :type:`pandas.DataFrame`s - loaded from a phn or wrd file in the TIMIT[1]_ transcription format. + ` that validates :type:`pandas.DataFrame`s + loaded from a phn or wrd file in the TIMIT[1]_ transcription format. - References - ---------- - .. [1] Garofolo, John S., et al. TIMIT Acoustic-Phonetic Continuous Speech Corpus LDC93S1. - Web Download. Philadelphia: Linguistic Data Consortium, 1993. + References + ---------- + .. [1] Garofolo, John S., et al. TIMIT Acoustic-Phonetic Continuous Speech Corpus LDC93S1. + Web Download. Philadelphia: Linguistic Data Consortium, 1993. """ begin_sample: Optional[Series[int]] = pandera.Field() @@ -102,8 +101,8 @@ def from_file(cls, annot_path: PathLike, audio_path: Optional[PathLike] = None) Examples -------- - >>> example = crowsetta.data.get('timit') - >>> timit = crowsetta.formats.seq.Timit.from_file(example.annot_path) + >>> path = crowsetta.example('timit', return_path=True) + >>> timit = crowsetta.formats.seq.Timit.from_file(path) Notes ----- @@ -168,8 +167,8 @@ def to_seq( Examples -------- - >>> example = crowsetta.data.get('timit') - >>> timit = crowsetta.formats.seq.Timit.from_file(example.annot_path) + >>> path = crowsetta.example('timit', return_path=True) + >>> timit = crowsetta.formats.seq.Timit.from_file(path) >>> seq = timit.to_seq() Returns @@ -244,8 +243,8 @@ def to_annot( Examples -------- - >>> example = crowsetta.data.get('timit') - >>> timit = crowsetta.formats.seq.Timit.from_file(example.annot_path) + >>> path = crowsetta.example('timit', return_path=True) + >>> timit = crowsetta.formats.seq.Timit.from_file(path) >>> annot = timit.to_annot() Returns diff --git a/src/crowsetta/formats/seq/yarden.py b/src/crowsetta/formats/seq/yarden.py index e4d4615e..9d8fb198 100644 --- a/src/crowsetta/formats/seq/yarden.py +++ b/src/crowsetta/formats/seq/yarden.py @@ -2,6 +2,7 @@ created by SongAnnotationGUI: https://github.com/yardencsGitHub/BirdSongBout/tree/master/helpers/GUI """ + import os import pathlib from typing import ClassVar, List diff --git a/src/crowsetta/interface/__init__.py b/src/crowsetta/interface/__init__.py index cefa63ef..4084919f 100644 --- a/src/crowsetta/interface/__init__.py +++ b/src/crowsetta/interface/__init__.py @@ -1,6 +1,7 @@ """This module declares the interface for any class that represents annotations for animal communication sounds loaded from a file in a specific format.""" + from .base import BaseFormat from .bbox import BBoxLike from .seq import SeqLike diff --git a/src/crowsetta/interface/bbox/base.py b/src/crowsetta/interface/bbox/base.py index 4cc038fa..3d6e4c06 100644 --- a/src/crowsetta/interface/bbox/base.py +++ b/src/crowsetta/interface/bbox/base.py @@ -1,6 +1,7 @@ """An abstract base class defining the interface for any annotation format that can be represented as a set of bounding boxes""" + import abc from typing import Sequence, Union diff --git a/src/crowsetta/interface/seq/base.py b/src/crowsetta/interface/seq/base.py index 40191960..440f4541 100644 --- a/src/crowsetta/interface/seq/base.py +++ b/src/crowsetta/interface/seq/base.py @@ -1,4 +1,5 @@ """An abstract base class for sequence-like annotation formats""" + import abc from typing import Sequence, Union diff --git a/src/crowsetta/segment.py b/src/crowsetta/segment.py index b20fefed..351fc3e9 100644 --- a/src/crowsetta/segment.py +++ b/src/crowsetta/segment.py @@ -1,5 +1,6 @@ """A class that represents a segment of a time series, used to annotate animal communication.""" + import attr import numpy as np from attr.validators import instance_of diff --git a/src/crowsetta/sequence.py b/src/crowsetta/sequence.py index 57bc9186..f9fcadd2 100644 --- a/src/crowsetta/sequence.py +++ b/src/crowsetta/sequence.py @@ -1,5 +1,6 @@ """A class that represents a sequence of segments, used to annotate animal acoustic communication.""" + from __future__ import annotations import numpy as np @@ -179,6 +180,9 @@ def __gt__(self, other): def __ge__(self, other): raise NotImplementedError + def __len__(self): + return self.onsets_s.shape[-1] + @staticmethod def _convert_labels(labels): if isinstance(labels, str): diff --git a/src/crowsetta/transcriber.py b/src/crowsetta/transcriber.py index 124f3fb2..7b5e0c63 100644 --- a/src/crowsetta/transcriber.py +++ b/src/crowsetta/transcriber.py @@ -54,7 +54,7 @@ class Transcriber: >>> import crowsetta >>> scribe = crowsetta.Transcriber(format='aud-seq') - >>> example = crowsetta.data.get('aud-seq') + >>> example = crowsetta.example('aud-seq') >>> audseq = scribe.from_file(example.annot_path) >>> annot = audseq.to_annot() >>> annot @@ -68,7 +68,7 @@ class Transcriber: >>> import crowsetta >>> scribe = crowsetta.Transcriber(format='raven') - >>> example = crowsetta.data.get('raven') + >>> example = crowsetta.example('raven') >>> raven = scribe.from_file(example.annot_path, annot_col='Species') >>> annot = raven.to_annot() >>> annot @@ -164,7 +164,7 @@ def from_file( >>> import crowsetta >>> scribe = crowsetta.Transcriber(format='aud-seq') - >>> example = crowsetta.data.get('aud-seq') + >>> example = crowsetta.example('aud-seq') >>> audseq = scribe.from_file(example.annot_path) >>> annot = audseq.to_annot() >>> annot @@ -180,7 +180,7 @@ def from_file( >>> import crowsetta >>> scribe = crowsetta.Transcriber(format='raven') - >>> example = crowsetta.data.get('raven') + >>> example = crowsetta.example('raven') >>> raven = scribe.from_file(example.annot_path, annot_col='Species') >>> annot = raven.to_annot() >>> annot diff --git a/src/crowsetta/typing.py b/src/crowsetta/typing.py index 1b85ec47..e1a37437 100644 --- a/src/crowsetta/typing.py +++ b/src/crowsetta/typing.py @@ -1,4 +1,5 @@ """Module for type hinting that is specific to ``crowsetta``""" + import os import pathlib import typing diff --git a/src/crowsetta/validation.py b/src/crowsetta/validation.py index 2d5277c8..67b10137 100644 --- a/src/crowsetta/validation.py +++ b/src/crowsetta/validation.py @@ -3,6 +3,7 @@ Some utilities adapted from scikit-learn under BSD 3 License https://github.com/scikit-learn/scikit-learn/blob/master/sklearn/utils/validation.py """ + import numbers from pathlib import PurePath from typing import Sequence, Union diff --git a/tests/data_for_tests/simple-csv/jourjine-et-al-2023/GO_24860x23748_ltr2_pup3_ch4_4800_m_337_295_fr1_p9_2021-10-02_12-35-01.csv b/tests/data_for_tests/simple-csv/jourjine-et-al-2023/GO_24860x23748_ltr2_pup3_ch4_4800_m_337_295_fr1_p9_2021-10-02_12-35-01.csv new file mode 100644 index 00000000..7b159fb3 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"jourjine-et-al-2023" / + "GO_24860x23748_ltr2_pup3_ch4_4800_m_337_295_fr1_p9_2021-10-02_12-35-01.csv" + ) \ No newline at end of file diff --git a/tests/test_data.py b/tests/test_data.py deleted file mode 100644 index f30f4dec..00000000 --- a/tests/test_data.py +++ /dev/null @@ -1,236 +0,0 @@ -import contextlib - -try: - from importlib.resources import as_file, files, open_text -except ImportError: - from importlib_resources import as_file, files, open_text - -import pathlib -import shutil - -import pytest - -import crowsetta - -DEFAULT_USER_DATA_DIR = pathlib.Path(crowsetta.data.data.APP_DIRS.user_data_dir) - - -@pytest.fixture -def default_user_data_dir() -> pathlib.Path: - return DEFAULT_USER_DATA_DIR - - -def delete_default_user_data_dir() -> None: - if DEFAULT_USER_DATA_DIR.exists(): - shutil.rmtree(DEFAULT_USER_DATA_DIR) - - -def all_data_files_exist_in_dst_dir(dst_dir): - exist = [] - - for format_name, path_args in crowsetta.data.data.DATA.items(): - # don't use full name `importlib.resources` here - # because we need to use backport package, not stdlib, on Python 3.8 - source = files(path_args.package).joinpath(path_args.resource) - annot_path = as_file(source) - dst_annot_dir = dst_dir / path_args.package.split(".")[-1] - dst_annot_path = dst_annot_dir / path_args.resource - dst_citation_txt_path = dst_annot_dir / "citation.txt" - exist.append((dst_annot_path.exists() and dst_citation_txt_path.exists())) - - return all(exist) - - -def test_extract_data_files_default_dir(default_user_data_dir): - delete_default_user_data_dir() - crowsetta.data.extract_data_files(user_data_dir=default_user_data_dir) - assert all_data_files_exist_in_dst_dir(dst_dir=default_user_data_dir) - - -def test_extract_data_files_user_specified(tmp_path): - user_specified_data_dir = tmp_path / "crowsetta-data" - crowsetta.data.extract_data_files(user_data_dir=user_specified_data_dir) - assert all_data_files_exist_in_dst_dir(dst_dir=user_specified_data_dir) - - -FORMATS_PARAMETRIZE_ARGNAMES = "format, format_class" -FORMATS_PARAMETRIZE_ARGVALUES = [ - ("aud-seq", crowsetta.formats.seq.AudSeq), - ("birdsong-recognition-dataset", crowsetta.formats.seq.BirdsongRec), - ("generic-seq", crowsetta.formats.seq.GenericSeq), - ("notmat", crowsetta.formats.seq.NotMat), - ("raven", crowsetta.formats.bbox.Raven), - ("simple-seq", crowsetta.formats.seq.SimpleSeq), - ("textgrid", crowsetta.formats.seq.TextGrid), - ("timit", crowsetta.formats.seq.Timit), -] - - -@pytest.mark.parametrize(FORMATS_PARAMETRIZE_ARGNAMES, FORMATS_PARAMETRIZE_ARGVALUES) -def test__get_example_as_context_manager(format, format_class): - """test helper function ``_get_example_as_context_manager``""" - example = crowsetta.data.data._get_example_as_context_manager(format) - - assert isinstance(example, crowsetta.data.ExampleAnnotFile) - assert hasattr(example, "annot_path") - assert isinstance(example.annot_path, contextlib._GeneratorContextManager) - assert hasattr(example, "citation") - assert isinstance(example.citation, str) - - if format_class is crowsetta.formats.bbox.Raven: - with example.annot_path as annot_path: - annot_instance = format_class.from_file(annot_path, annot_col="Species") - elif format_class is crowsetta.formats.seq.SimpleSeq: - with example.annot_path as annot_path: - annot_instance = format_class.from_file( - annot_path, - columns_map={"start_seconds": "onset_s", "stop_seconds": "offset_s", "name": "label"}, - read_csv_kwargs={"index_col": 0}, - ) - else: - with example.annot_path as annot_path: - annot_instance = format_class.from_file(annot_path) - assert isinstance(annot_instance, format_class) - - -@pytest.mark.parametrize(FORMATS_PARAMETRIZE_ARGNAMES, FORMATS_PARAMETRIZE_ARGVALUES) -def test__get_example_from_user_data_dir(format, format_class, default_user_data_dir): - delete_default_user_data_dir() - crowsetta.data.extract_data_files(user_data_dir=default_user_data_dir) - - example = crowsetta.data.data._get_example_from_user_data_dir(format, default_user_data_dir) - - assert isinstance(example, crowsetta.data.ExampleAnnotFile) - assert hasattr(example, "annot_path") - assert isinstance(example.annot_path, pathlib.Path) - assert hasattr(example, "citation") - assert isinstance(example.citation, str) - - if format_class is crowsetta.formats.bbox.Raven: - annot_instance = format_class.from_file(example.annot_path, annot_col="Species") - elif format_class is crowsetta.formats.seq.SimpleSeq: - annot_instance = format_class.from_file( - example.annot_path, - columns_map={"start_seconds": "onset_s", "stop_seconds": "offset_s", "name": "label"}, - read_csv_kwargs={"index_col": 0}, - ) - else: - annot_instance = format_class.from_file(example.annot_path) - assert isinstance(annot_instance, format_class) - - -@pytest.mark.parametrize(FORMATS_PARAMETRIZE_ARGNAMES, FORMATS_PARAMETRIZE_ARGVALUES) -def test_get_with_extract(format, format_class, monkeypatch): - """test that ``crowsetta.data.get`` works - when we **do** extract annotation files - to the local file system - - Added as a regression test, - to make sure #186 stays fixed: - https://github.com/vocalpy/crowsetta/issues/186 - """ - # set up - delete_default_user_data_dir() - - # this will cause the call to ``input`` in ``crowsetta.data.get`` - # to return ``Yes``, so that data is extracted - monkeypatch.setattr("builtins.input", lambda _: "Yes") - - example = crowsetta.data.get(format) - - assert isinstance(example, crowsetta.data.ExampleAnnotFile) - assert hasattr(example, "annot_path") - assert isinstance(example.annot_path, pathlib.Path) - assert hasattr(example, "citation") - assert isinstance(example.citation, str) - - if format_class is crowsetta.formats.bbox.Raven: - annot_instance = format_class.from_file(example.annot_path, annot_col="Species") - elif format_class is crowsetta.formats.seq.SimpleSeq: - annot_instance = format_class.from_file( - example.annot_path, - columns_map={"start_seconds": "onset_s", "stop_seconds": "offset_s", "name": "label"}, - read_csv_kwargs={"index_col": 0}, - ) - else: - annot_instance = format_class.from_file(example.annot_path) - assert isinstance(annot_instance, format_class) - - -@pytest.mark.parametrize(FORMATS_PARAMETRIZE_ARGNAMES, FORMATS_PARAMETRIZE_ARGVALUES) -def test_get_with_extracted_already(format, format_class): - """test that ``crowsetta.data.get`` works - when annotation files are **already** extracted - to the local file system""" - # set up - delete_default_user_data_dir() - # this assumes a function we test here will work - # but I can't think of a better way to test it. - # re-write the function as a test in this file? - # Seems redundant and error-prone. - # So the trade-off is that here if ``extract_data_files`` fails - # then this unit test will probably fail too. - crowsetta.data.extract_data_files() # to default user data dir - - example = crowsetta.data.get(format) - - assert isinstance(example, crowsetta.data.ExampleAnnotFile) - assert hasattr(example, "annot_path") - assert isinstance(example.annot_path, pathlib.Path) - assert hasattr(example, "citation") - assert isinstance(example.citation, str) - - if format_class is crowsetta.formats.bbox.Raven: - annot_instance = format_class.from_file(example.annot_path, annot_col="Species") - elif format_class is crowsetta.formats.seq.SimpleSeq: - annot_instance = format_class.from_file( - example.annot_path, - columns_map={"start_seconds": "onset_s", "stop_seconds": "offset_s", "name": "label"}, - read_csv_kwargs={"index_col": 0}, - ) - else: - annot_instance = format_class.from_file(example.annot_path) - assert isinstance(annot_instance, format_class) - - -@pytest.mark.parametrize(FORMATS_PARAMETRIZE_ARGNAMES, FORMATS_PARAMETRIZE_ARGVALUES) -def test_get_with_no_extract(format, format_class, monkeypatch): - """test that ``crowsetta.data.get`` works - even if we do not extract annotation files - from package to local file system - """ - # set up - delete_default_user_data_dir() - # this will cause the call to ``input`` in ``crowsetta.data.get`` - # to return ``No``, so that data is not extracted - monkeypatch.setattr("builtins.input", lambda _: "No") - - example = crowsetta.data.get(format) - - assert isinstance(example, crowsetta.data.ExampleAnnotFile) - assert hasattr(example, "annot_path") - assert isinstance(example.annot_path, contextlib._GeneratorContextManager) - assert hasattr(example, "citation") - assert isinstance(example.citation, str) - - if format_class is crowsetta.formats.bbox.Raven: - with example.annot_path as annot_path: - annot_instance = format_class.from_file(annot_path, annot_col="Species") - elif format_class is crowsetta.formats.seq.SimpleSeq: - with example.annot_path as annot_path: - annot_instance = format_class.from_file( - annot_path, - columns_map={"start_seconds": "onset_s", "stop_seconds": "offset_s", "name": "label"}, - read_csv_kwargs={"index_col": 0}, - ) - else: - with example.annot_path as annot_path: - annot_instance = format_class.from_file(annot_path) - assert isinstance(annot_instance, format_class) - - -def test_available_formats(): - formats_with_example_data_list = crowsetta.data.available_formats() - assert isinstance(formats_with_example_data_list, list) - for format in formats_with_example_data_list: - assert format in crowsetta.formats.as_list() diff --git a/tests/test_example.py b/tests/test_example.py new file mode 100644 index 00000000..33c2e20a --- /dev/null +++ b/tests/test_example.py @@ -0,0 +1,30 @@ +import pathlib + +import pytest + +import crowsetta + +@pytest.fixture(params=[False, True, None]) +def return_path(request): + return request.param + +@pytest.mark.parametrize( + 'example', + crowsetta.examples._examples.EXAMPLES +) +def test_example(example, return_path): + # this is basically a smoke test, + # that tests whether we can iterate through all examples + # without an error + if return_path is not None: + out = crowsetta.example(example.name, return_path=return_path) + else: + out = crowsetta.example(example.name) + + if return_path is True: + assert isinstance(out, pathlib.Path) + else: + assert isinstance( + out, + crowsetta.formats.FORMATS[example.format] + ) diff --git a/tests/test_formats/test_seq/test_simple.py b/tests/test_formats/test_seq/test_simple.py index e00fe95e..ca3c07fa 100644 --- a/tests/test_formats/test_seq/test_simple.py +++ b/tests/test_formats/test_seq/test_simple.py @@ -1,4 +1,6 @@ import filecmp +import inspect +import tempfile import numpy as np import pandas as pd @@ -112,3 +114,90 @@ def test_to_file(a_simple_csv_path, tmp_path): csv_path = tmp_path / a_simple_csv_path.name simple.to_file(annot_path=csv_path) assert filecmp.cmp(a_simple_csv_path, csv_path) + + +@pytest.fixture +def empty_csv_file_path(tmpdir): + empty_df = pd.DataFrame.from_records([]) + empty_csv_file_path = tmpdir / "empty.csv" + empty_df.to_csv(empty_csv_file_path) + return empty_csv_file_path + + +def test_empty_annotations(empty_csv_file_path): + # test fix for https://github.com/vocalpy/crowsetta/issues/264 + simple = crowsetta.formats.seq.SimpleSeq.from_file(annot_path=empty_csv_file_path) + assert isinstance(simple, crowsetta.formats.seq.SimpleSeq) + for attr in ("onsets_s", "offsets_s", "labels"): + assert np.array_equal( + getattr(simple, attr), np.array([]) + ) + seq = simple.to_seq() + assert len(seq) == 0 + + +def test_columns_map_only_maps_columns(jourjine_et_al_2023_csv_path): + # test fixes for https://github.com/vocalpy/crowsetta/issues/272 + simple = crowsetta.formats.seq.SimpleSeq.from_file( + annot_path=jourjine_et_al_2023_csv_path, + columns_map={"start_seconds": "onset_s", "stop_seconds": "offset_s"} + ) + assert isinstance(simple, crowsetta.formats.seq.SimpleSeq) + + +@pytest.mark.parametrize( + 'columns_map, expected_exception', + [ + # not a dict, throws a TypeError + ([], TypeError), + # not all key-value pairs are string to string + ({"start_seconds": "onset_s", "stop_seconds": 0}, ValueError), + # invalid value, not in ("onset_s", "offset_s", "label") + ({"start_seconds": "onset_s", "stop_seconds": "ofset_ss"}, ValueError), + ] +) +def test_columns_map_raise( + columns_map, + expected_exception, + jourjine_et_al_2023_csv_path +): + with pytest.raises(expected_exception): + crowsetta.formats.seq.SimpleSeq.from_file( + annot_path=jourjine_et_al_2023_csv_path, + columns_map=columns_map, + ) + + +@pytest.mark.parametrize( + "default_label", + [ + None, + 'x', + '@' + ] +) +def test_default_label( + default_label, + jourjine_et_al_2023_csv_path + ): + # test fixes for https://github.com/vocalpy/crowsetta/issues/271 + if default_label is None: + simple = crowsetta.formats.seq.SimpleSeq.from_file( + annot_path=jourjine_et_al_2023_csv_path, + columns_map={"start_seconds": "onset_s", "stop_seconds": "offset_s"} + # we are using default value for `default_label` here + ) + sig = inspect.signature(crowsetta.SimpleSeq.from_file) + # replace None with the default value for default label, so assert works below + default_label = sig.parameters["default_label"].default + else: + simple = crowsetta.formats.seq.SimpleSeq.from_file( + annot_path=jourjine_et_al_2023_csv_path, + columns_map={"start_seconds": "onset_s", "stop_seconds": "offset_s"}, + default_label=default_label + ) + + assert np.array_equal( + simple.labels, + np.array([default_label] * simple.onsets_s.shape[-1]) + ) diff --git a/tests/test_sequence.py b/tests/test_sequence.py index e846139c..efad7d9c 100644 --- a/tests/test_sequence.py +++ b/tests/test_sequence.py @@ -231,3 +231,14 @@ def test_hash(): def test_seq_is_immutable(a_seq): with pytest.raises(TypeError): a_seq.labels = np.asarray(["a", "b", "c", "d", "d"]) + + +def test_len(list_of_segments): + seq = Sequence.from_segments(list_of_segments) + seq_len = len(seq) + assert seq_len == len(list_of_segments) + + +def test_len_empty_seq(): + seq = Sequence.from_keyword(onsets_s=[], offsets_s=[], labels=[]) + assert len(seq) == 0