lingualabpy 0.0.6__tar.gz → 0.1.1__tar.gz

lingualabpy-0.1.1/.gitignore

@@ -0,0 +1,80 @@
+# lingualabpy
+idea/
+docs/
+
+# hatch.build.hooks.vcs
+_version.py
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#   Usually these files are written by a python script from a template
+#   before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py.cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Environments
+.env
+.envrc
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Ruff stuff:
+.ruff_cache/

{lingualabpy-0.0.6 → lingualabpy-0.1.1}/LICENSE

@@ -1,21 +1,21 @@
-MIT License
-
-Copyright (c) 2024 Lingua Laboratory
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+MIT License
+
+Copyright (c) 2024 Lingua Laboratory
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

lingualabpy-0.1.1/PKG-INFO

@@ -0,0 +1,66 @@
+Metadata-Version: 2.4
+Name: lingualabpy
+Version: 0.1.1
+Summary: Tools and utilities from the LINGUA laboratory
+Project-URL: Documentation, https://github.com/lingualab/lingualabpy
+Project-URL: Source, https://github.com/lingualab/lingualabpy
+Project-URL: Tracker, https://github.com/lingualab/lingualabpy/issues
+Author-email: Christophe Bedetti <christophe.bedetti@umontreal.ca>
+License: MIT License
+        
+        Copyright (c) 2024 Lingua Laboratory
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.8.1
+Requires-Dist: click
+Requires-Dist: matplotlib
+Requires-Dist: nilearn==0.12.1
+Requires-Dist: opencv-python
+Requires-Dist: pandas
+Requires-Dist: praat-parselmouth
+Requires-Dist: praat-textgrids
+Requires-Dist: pydub
+Requires-Dist: python-docx
+Provides-Extra: style
+Requires-Dist: black; extra == 'style'
+Requires-Dist: ruff; extra == 'style'
+Provides-Extra: test
+Requires-Dist: pytest; extra == 'test'
+Requires-Dist: pytest-cov; extra == 'test'
+Description-Content-Type: text/markdown
+
+# lingualabpy
+
+Tools and utilities from the LINGUA laboratory
+
+These tools are used in the pipeline [speechmetryflow](https://github.com/lingualab/speechmetryflow)

{lingualabpy-0.0.6 → lingualabpy-0.1.1}/README.md

@@ -1,5 +1,5 @@
-# lingualabpy
-
-Tools and utilities from the LINGUA laboratory
-
+# lingualabpy
+
+Tools and utilities from the LINGUA laboratory
+
 These tools are used in the pipeline [speechmetryflow](https://github.com/lingualab/speechmetryflow)

{lingualabpy-0.0.6/src → lingualabpy-0.1.1}/lingualabpy/__init__.py

@@ -1,20 +1,25 @@
-#   -------------------------------------------------------------
-#   Licensed under the MIT License. See LICENSE in project root for information.
-#   -------------------------------------------------------------
-"""lingualabpy"""
-from __future__ import annotations
-
-__version__ = "0.0.6"
-
-default_config = {
-    "participant_col": "participant_id",
-    "participant_label": "IE",
-    "clinician_label": "IV",
-    "f0_bounds": {
-        "female": [100.0, 600.0],
-        "male": [75.0, 300.0],
-    },
-    "unit_frequency": "Hertz",
-}
-
-from lingualabpy.io import read_audio, read_docx, read_json, write_json, read_textgrid
+#   -------------------------------------------------------------
+#   Licensed under the MIT License. See LICENSE in project root for information.
+#   -------------------------------------------------------------
+"""lingualabpy"""
+
+from __future__ import annotations
+
+try:
+    from lingualabpy._version import __version__
+except ImportError:
+    pass
+
+
+default_config = {
+    "participant_col": "participant_id",
+    "participant_label": "IE",
+    "clinician_label": "IV",
+    "f0_bounds": {
+        "female": [100.0, 600.0],
+        "male": [75.0, 300.0],
+    },
+    "unit_frequency": "Hertz",
+}
+
+from lingualabpy.io import read_audio, read_docx, read_json, write_json, read_textgrid

lingualabpy-0.1.1/lingualabpy/_version.py

@@ -0,0 +1,34 @@
+# file generated by setuptools-scm
+# don't change, don't track in version control
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple
+    from typing import Union
+
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+    COMMIT_ID = Union[str, None]
+else:
+    VERSION_TUPLE = object
+    COMMIT_ID = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+commit_id: COMMIT_ID
+__commit_id__: COMMIT_ID
+
+__version__ = version = '0.1.1'
+__version_tuple__ = version_tuple = (0, 1, 1)
+
+__commit_id__ = commit_id = None

{lingualabpy-0.0.6/src → lingualabpy-0.1.1}/lingualabpy/audio/metrics.py

@@ -1,85 +1,85 @@
-from collections import defaultdict
-import numpy as np
-from parselmouth import Sound
-from parselmouth.praat import call
-
-from lingualabpy.tools.data import UnchangeableDict
-
-
-def measure_pitch(sound: Sound, f0min: str, f0max: str, unit: str) -> UnchangeableDict:
-    """
-    This function measures duration, pitch, HNR, jitter, and shimmer
-    This is the function to measure source acoustics using default male parameters.
-    """
-    # compute usefull praat object
-    pitch = call(sound, "To Pitch", 0.0, f0min, f0max)
-    harmonicity = call(sound, "To Harmonicity (cc)", 0.01, f0min, 0.1, 1.0)
-    point_process = call(sound, "To PointProcess (periodic, cc)", f0min, f0max)
-
-    # metrics container
-    metrics = UnchangeableDict()
-
-    # Metrics computation
-    metrics["duration"] = call(sound, "Get total duration")
-    metrics["f0_mean"] = call(pitch, "Get mean", 0, 0, unit)
-    metrics["F0_std"] = call(pitch, "Get standard deviation", 0, 0, unit)
-    metrics["hnr"] = call(harmonicity, "Get mean", 0, 0)
-
-    # jitter
-    jitter_types = ["local", ["local", "absolute"], "rap", "ppq5", "ddp"]
-    for jitter_type in jitter_types:
-        if isinstance(jitter_type, list):
-            metric_name = f"jitter_{'_'.join(jitter_type)}"
-            praat_function = f"Get jitter ({', '.join(jitter_type)})"
-        else:
-            metric_name = f"jitter_{jitter_type}"
-            praat_function = f"Get jitter ({jitter_type})"
-        metrics[metric_name] = call(
-            point_process, praat_function, 0, 0, 0.0001, 0.02, 1.3
-        )
-
-    # shimmer
-    shimmer_types = ["local", "local_dB", "apq3", "apq5", "apq11", "dda"]
-    for shimmer_type in shimmer_types:
-        metric_name = f"shimmer_{shimmer_type}"
-        praat_function = f"Get shimmer ({shimmer_type})"
-        metrics[metric_name] = call(
-            [sound, point_process], praat_function, 0, 0, 0.0001, 0.02, 1.3, 1.6
-        )
-
-    return metrics
-
-
-def measure_formants(
-    sound: Sound, f0min: str, f0max: str, unit: str
-) -> UnchangeableDict:
-    """
-    This function measures formants at each glottal pulse
-
-    Puts, D. A., Apicella, C. L., & Cárdenas, R. A. (2012). Masculine voices signal men's threat potential in forager and industrial societies. Proceedings of the Royal Society of London B: Biological Sciences, 279(1728), 601-609.
-
-    Adapted from: DOI 10.17605/OSF.IO/K2BHS
-    """
-    # compute usefull praat object
-    point_process = call(sound, "To PointProcess (periodic, cc)", f0min, f0max)
-    formants = call(sound, "To Formant (burg)", 0.0025, 5, 5000, 0.025, 50)
-    number_of_points = call(point_process, "Get number of points")
-
-    # metrics container
-    metrics = UnchangeableDict()
-
-    # Measure formants only at glottal pulses
-    formants_list = defaultdict(list)
-    for index in range(1, number_of_points + 1):
-        time = call(point_process, "Get time from index", index)
-        for pulse in [1, 2, 3, 4]:
-            value = call(formants, "Get value at time", pulse, time, unit, "Linear")
-            if str(value) != "nan":
-                formants_list[pulse].append(value)
-
-    # calculate mean and median formants across pulses, median is what is used in all subsequent calculations
-    for pulse in [1, 2, 3, 4]:
-        metrics[f"formants_{pulse}_mean"] = np.mean(formants_list[pulse])
-        metrics[f"formants_{pulse}_median"] = np.median(formants_list[pulse])
-
-    return metrics
+from collections import defaultdict
+import numpy as np
+from parselmouth import Sound
+from parselmouth.praat import call
+
+from lingualabpy.tools.data import UnchangeableDict
+
+
+def measure_pitch(sound: Sound, f0min: str, f0max: str, unit: str) -> UnchangeableDict:
+    """
+    This function measures duration, pitch, HNR, jitter, and shimmer
+    This is the function to measure source acoustics using default male parameters.
+    """
+    # compute usefull praat object
+    pitch = call(sound, "To Pitch", 0.0, f0min, f0max)
+    harmonicity = call(sound, "To Harmonicity (cc)", 0.01, f0min, 0.1, 1.0)
+    point_process = call(sound, "To PointProcess (periodic, cc)", f0min, f0max)
+
+    # metrics container
+    metrics = UnchangeableDict()
+
+    # Metrics computation
+    metrics["duration"] = call(sound, "Get total duration")
+    metrics["f0_mean"] = call(pitch, "Get mean", 0, 0, unit)
+    metrics["F0_std"] = call(pitch, "Get standard deviation", 0, 0, unit)
+    metrics["hnr"] = call(harmonicity, "Get mean", 0, 0)
+
+    # jitter
+    jitter_types = ["local", ["local", "absolute"], "rap", "ppq5", "ddp"]
+    for jitter_type in jitter_types:
+        if isinstance(jitter_type, list):
+            metric_name = f"jitter_{'_'.join(jitter_type)}"
+            praat_function = f"Get jitter ({', '.join(jitter_type)})"
+        else:
+            metric_name = f"jitter_{jitter_type}"
+            praat_function = f"Get jitter ({jitter_type})"
+        metrics[metric_name] = call(
+            point_process, praat_function, 0, 0, 0.0001, 0.02, 1.3
+        )
+
+    # shimmer
+    shimmer_types = ["local", "local_dB", "apq3", "apq5", "apq11", "dda"]
+    for shimmer_type in shimmer_types:
+        metric_name = f"shimmer_{shimmer_type}"
+        praat_function = f"Get shimmer ({shimmer_type})"
+        metrics[metric_name] = call(
+            [sound, point_process], praat_function, 0, 0, 0.0001, 0.02, 1.3, 1.6
+        )
+
+    return metrics
+
+
+def measure_formants(
+    sound: Sound, f0min: str, f0max: str, unit: str
+) -> UnchangeableDict:
+    """
+    This function measures formants at each glottal pulse
+
+    Puts, D. A., Apicella, C. L., & Cárdenas, R. A. (2012). Masculine voices signal men's threat potential in forager and industrial societies. Proceedings of the Royal Society of London B: Biological Sciences, 279(1728), 601-609.
+
+    Adapted from: DOI 10.17605/OSF.IO/K2BHS
+    """
+    # compute usefull praat object
+    point_process = call(sound, "To PointProcess (periodic, cc)", f0min, f0max)
+    formants = call(sound, "To Formant (burg)", 0.0025, 5, 5000, 0.025, 50)
+    number_of_points = call(point_process, "Get number of points")
+
+    # metrics container
+    metrics = UnchangeableDict()
+
+    # Measure formants only at glottal pulses
+    formants_list = defaultdict(list)
+    for index in range(1, number_of_points + 1):
+        time = call(point_process, "Get time from index", index)
+        for pulse in [1, 2, 3, 4]:
+            value = call(formants, "Get value at time", pulse, time, unit, "Linear")
+            if str(value) != "nan":
+                formants_list[pulse].append(value)
+
+    # calculate mean and median formants across pulses, median is what is used in all subsequent calculations
+    for pulse in [1, 2, 3, 4]:
+        metrics[f"formants_{pulse}_mean"] = np.mean(formants_list[pulse])
+        metrics[f"formants_{pulse}_median"] = np.median(formants_list[pulse])
+
+    return metrics

{lingualabpy-0.0.6/src → lingualabpy-0.1.1}/lingualabpy/audio/triming.py

@@ -1,11 +1,11 @@
-from pydub import AudioSegment
-
-
-def extract_audio(audio: AudioSegment, intervals: list[list[float]]) -> AudioSegment:
-    """"""
-    new_audio = AudioSegment.empty()
-
-    for start, end in intervals:
-        new_audio += audio[start * 1000 : end * 1000]
-
-    return new_audio
+from pydub import AudioSegment
+
+
+def extract_audio(audio: AudioSegment, intervals: list[list[float]]) -> AudioSegment:
+    """"""
+    new_audio = AudioSegment.empty()
+
+    for start, end in intervals:
+        new_audio += audio[start * 1000 : end * 1000]
+
+    return new_audio

{lingualabpy-0.0.6/src → lingualabpy-0.1.1}/lingualabpy/cli/audio_metrics.py

@@ -1,59 +1,59 @@
-import click
-from parselmouth import Sound
-from pathlib import Path
-
-from lingualabpy import default_config, write_json
-from lingualabpy.audio.metrics import measure_pitch, measure_formants
-
-
-@click.command()
-@click.option(
-    "--sex",
-    type=click.Choice(["female", "male"]),
-    help=f"Set f0min and f0max for praat analysis. {default_config['f0_bounds']}",
-)
-@click.option(
-    "--f0min",
-    type=float,
-    help="Define f0min for praat analysis. Not required if sex is specify",
-)
-@click.option(
-    "--f0max",
-    type=float,
-    help="Define f0max for praat analysis. Not required if sex is specify",
-)
-@click.option(
-    "--unit_frequency",
-    default=default_config["unit_frequency"],
-    show_default=True,
-)
-@click.option("--participant_id", "-p", default=None, help="")
-@click.option("--output_json", default=None, help="")
-@click.argument("audiofile", nargs=1, type=click.Path(exists=True))
-def main(sex, f0min, f0max, unit_frequency, participant_id, output_json, audiofile):
-    """Doc"""
-    if sex:
-        f0min, f0max = default_config["f0_bounds"][sex]
-    else:
-        if not f0min or not f0max:
-            raise click.UsageError(
-                "'--f0min' and '--f0max' are required if '--sex' is not specified"
-            )
-
-    sound = Sound(audiofile)
-    metrics = measure_pitch(sound, f0min, f0max, unit_frequency)
-    metrics.update(measure_formants(sound, f0min, f0max, unit_frequency))
-
-    audiofile_stem = Path(audiofile).stem
-
-    if participant_id:
-        metrics["participant_id"] = participant_id
-
-    audiofile = Path(audiofile)
-
-    metrics["filename"] = audiofile.name
-
-    if not output_json:
-        output_json = audiofile.stem + "_metric-audio.json"
-
-    write_json(dict(metrics), output_json)
+import click
+from parselmouth import Sound
+from pathlib import Path
+
+from lingualabpy import default_config, write_json
+from lingualabpy.audio.metrics import measure_pitch, measure_formants
+
+
+@click.command()
+@click.option(
+    "--sex",
+    type=click.Choice(["female", "male"]),
+    help=f"Set f0min and f0max for praat analysis. {default_config['f0_bounds']}",
+)
+@click.option(
+    "--f0min",
+    type=float,
+    help="Define f0min for praat analysis. Not required if sex is specify",
+)
+@click.option(
+    "--f0max",
+    type=float,
+    help="Define f0max for praat analysis. Not required if sex is specify",
+)
+@click.option(
+    "--unit_frequency",
+    default=default_config["unit_frequency"],
+    show_default=True,
+)
+@click.option("--participant_id", "-p", default=None, help="")
+@click.option("--output_json", default=None, help="")
+@click.argument("audiofile", nargs=1, type=click.Path(exists=True))
+def main(sex, f0min, f0max, unit_frequency, participant_id, output_json, audiofile):
+    """Doc"""
+    if sex:
+        f0min, f0max = default_config["f0_bounds"][sex]
+    else:
+        if not f0min or not f0max:
+            raise click.UsageError(
+                "'--f0min' and '--f0max' are required if '--sex' is not specified"
+            )
+
+    sound = Sound(audiofile)
+    metrics = measure_pitch(sound, f0min, f0max, unit_frequency)
+    metrics.update(measure_formants(sound, f0min, f0max, unit_frequency))
+
+    audiofile_stem = Path(audiofile).stem
+
+    if participant_id:
+        metrics["participant_id"] = participant_id
+
+    audiofile = Path(audiofile)
+
+    metrics["filename"] = audiofile.name
+
+    if not output_json:
+        output_json = audiofile.stem + "_metric-audio.json"
+
+    write_json(dict(metrics), output_json)