initial push to repo

Author: FrancisTong

Python.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$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/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/

scatnet/__init__.py

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+# coding=utf-8
+"""Deep scattering transform clustering on segmented time series."""
+
+__all__ = [
+    "display",
+    "parse",
+    "Network",
+    "inventory",
+    "signal",
+    "wavelet",
+    "hierarchy",
+]
+
+from . import display
+from . import wavelet
+from . import inventory
+from . import signal
+from . import hierarchy
+from .io import parse
+from .network import Network

scatnet/cli/__init__.py

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+# coding=utf-8
+"""Command-line interface tools."""
+
+__all__ = ["cli"]
+
+from . import cli

scatnet/cli/cli.py

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+# coding: utf-8
+"""Command-line interface module.
+
+The subcommands are defined in dedicated modules. Note that all subcommands
+share a subset of options defined in the "common.py" module. The "main"
+function defined here is a group for attaching all the subcommands, and it
+establishes the program's entry point.
+
+Author: Leonard Seydoux Date: June, 2021 Email:
+leonard.seydoux@univ-grenoble-alpes.fr
+"""
+
+import click
+
+from .inventory import inventory
+from .linkage import linkage
+from .features import features
+from .transform import transform
+from .waveforms import waveforms
+
+
+@click.group()
+def main():
+    """Deep scattering transform on segmented time series.
+
+    This program contains a series of command-line tools for clustering
+    continuous time series with a deep scattering network. The following
+    sub-commands must be run in a specific order from the continuous data to
+    the cluster results.
+
+    1. The inventorize command lists and selects the data based on usual meta
+    parameters (sampling rate, duration, channels) and stores the relevant
+    datapaths into an inventory file. This first command helps explore the data
+    coverage in time, selecting appropriate time segments, and running the
+    remaining steps on the actual data.
+
+    2. The transform command runs the deep scattering transform on the
+    segmented time series and stores the scattering coefficients for later
+    feature extraction. 
+
+    3. With the features command, the large-dimensional scattering coefficients
+    are reduced to a low-dimensional space which dimensions are considered
+    features here. These features are used in the clustering step next.
+
+    4. The command calculates the linkage matrix that helps cluster the data
+    based on some criteria of similarity (a metric and a method). Once this
+    matrix is calculated, the clusters are extracted for further analyses.
+
+    Created in May, 2021 by Leonard Seydoux
+    (leonard.seydoux@univ-grenoble-alpes.fr) and Randall Balestriero.
+
+    """
+    pass
+
+
+# Add subcommands
+main.add_command(inventory)
+main.add_command(transform)
+main.add_command(features)
+main.add_command(linkage)
+main.add_command(waveforms)

scatnet/cli/common.py

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+# coding: utf-8
+"""Common subcomands options for command-line interface.
+
+Authors: Leonard Seydoux and Randall Balestriero
+Email: leonard.seydoux@univ-grenoble-alpes.fr
+Date: May, 2021
+"""
+
+
+import click
+import os
+import functools
+
+COMMON_OPTIONS = [
+    click.option(
+        "--savepath",
+        default=os.environ.get("SAVEPATH", "."),
+        show_default=".",
+        help="output directory",
+        type=click.Path(resolve_path=True, writable=True),
+    ),
+    click.option(
+        "--datapath",
+        default=os.environ.get("DATAPATH", "."),
+        show_default=".",
+        help="input data path to scan",
+    ),
+    click.option(
+        "--figpath",
+        default=os.environ.get("FIGPATH", "."),
+        show_default=".",
+        help="path to save figures",
+        type=click.Path(resolve_path=True, writable=True),
+    ),
+    click.option(
+        "--start",
+        type=click.DateTime(),
+        default="0001-01-01 00:00:00",
+        help="Select data after start time.",
+    ),
+    click.option(
+        "--end",
+        type=click.DateTime(),
+        default="9999-01-01 00:00:00",
+        help="Select data after start time.",
+    ),
+    click.option(
+        "--channels",
+        type=str,
+        default="*",
+        show_default=True,
+        help="Channels to search for.",
+    ),
+    click.option(
+        "--filename_inventory",
+        type=str,
+        default="inventory",
+        show_default=True,
+        help="Basename for inventory file.",
+    ),
+    click.option(
+        "--filename_network",
+        type=str,
+        default="network",
+        show_default=True,
+        help="Basename for network file.",
+    ),
+    click.option(
+        "--filename_reduction",
+        type=str,
+        default="reduction_{}",
+        show_default=True,
+        help="Basename for network file.",
+    ),
+    click.option(
+        "--path_scatterings",
+        type=str,
+        default="scatterings",
+        show_default=True,
+        help="Name of scattering files directory.",
+    ),
+    click.option(
+        "--path_features",
+        type=str,
+        default="features",
+        show_default=True,
+        help="Name of feature files directory.",
+    ),
+    click.option(
+        "--path_clusters",
+        type=str,
+        default="clusters",
+        show_default=True,
+        help="Name of cluster files directory.",
+    ),
+    click.option(
+        "--show",
+        is_flag=True,
+        default=False,
+        show_default=True,
+        help="Excluding flag to show or calculate.",
+    ),
+]
+
+
+def common_options(f):
+    return functools.reduce(lambda x, opt: opt(x), COMMON_OPTIONS, f)
+