py-neuromodulation 0.0.2__tar.gz → 0.0.4__tar.gz

py_neuromodulation-0.0.4/.gitignore

@@ -0,0 +1,175 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.pypirc/
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+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/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
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+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.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/
+
+# Visual Studio Code
+.vscode
+
+# PyCharm
+.idea
+
+# Spyder project settings
+.spyderproject
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+.ropeproject
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+# mkdocs documentation
+/site
+
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+.mypy_cache/
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+.pyre/
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+# Ignore pickles
+*.pkl
+**/*.pkl
+*.p
+
+.pdf
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+
+docs/build/*
+docs/source/_build/*
+docs/previous/*
+docs/source/auto_examples/*
+docs/source/data/*
+
+examples/data/derivatives/*
+examples/other_examples/*
+
+examples/sub/*
+examples/utils/*
+
+sub/
+
+py_neuromodulation/data/derivatives/*
+
+requirements.lock
+requirements-dev.lock
+
+.python-version
+
+py_neuromodulation/ConnectivityDecoding/connectome_folder/*
+
+plot_0_first_demo.py
+
+requirements.lock
+requirements-dev.lock
+
+plot_1_example_BIDS.py

py_neuromodulation-0.0.4/.readthedocs.yaml

@@ -0,0 +1,25 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/source/conf.py
+   builder: html
+   fail_on_warning: false
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+   - method: pip
+     path: .
+   - requirements: requirements_rtd.txt

{py_neuromodulation-0.0.2 → py_neuromodulation-0.0.4}/PKG-INFO

@@ -1,44 +1,73 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: py_neuromodulation
-Version: 0.0.2
+Version: 0.0.4
 Summary: Real-time analysis of intracranial neurophysiology recordings.
-Keywords: real-time,eeg,ieeg,dbs,ecog,electrocorticography,deep-brain-stimulation,machine-learning
+Project-URL: bugtracker, https://github.com/neuromodulation/py_neuromodulation/issues
+Project-URL: repository, https://github.com/neuromodulation/py_neuromodulation
 Author-email: Timon Merk <timon.merk@charite.de>
 Maintainer: Timon Merk
-Requires-Python: >=3.10
-Description-Content-Type: text/x-rst
+License: MIT License
+        
+        Copyright (c) 2021 Interventional Cognitive Neuromodulation - Neumann Lab Berlin
+        
+        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
+Keywords: dbs,deep-brain-stimulation,ecog,eeg,electrocorticography,ieeg,machine-learning,real-time
 Classifier: Development Status :: 2 - Pre-Alpha
-Classifier: License :: OSI Approved :: MIT License 
+Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
-Requires-Dist: mne
-Requires-Dist: filterpy >= 1.4.5
+Requires-Python: >=3.10
+Requires-Dist: black>=24.2.0
+Requires-Dist: filterpy>=1.4.5
 Requires-Dist: fooof
+Requires-Dist: hatch>=1.9.4
 Requires-Dist: imbalanced-learn
-Requires-Dist: matplotlib >= 3.3.4
-Requires-Dist: mne-bids >= 0.8
+Requires-Dist: ipython
+Requires-Dist: joblib>=1.3.2
+Requires-Dist: matplotlib>=3.3.4
+Requires-Dist: mne
+Requires-Dist: mne-bids>=0.8
 Requires-Dist: mne-connectivity
 Requires-Dist: mrmr-selection
 Requires-Dist: nolds
-Requires-Dist: numpy >= 1.21.2
-Requires-Dist: pandas >= 1.2.2
+Requires-Dist: notebook
+Requires-Dist: numpy>=1.21.2
+Requires-Dist: pandas>=1.2.2
 Requires-Dist: pip
-Requires-Dist: pynput
+Requires-Dist: pyarrow>=14.0.2
 Requires-Dist: pybids
+Requires-Dist: pybispectra>=1.0.0
+Requires-Dist: pynput
+Requires-Dist: pyparrm
+Requires-Dist: pytest>=8.0.2
 Requires-Dist: scikit-image
-Requires-Dist: scikit-learn >= 0.24.2
+Requires-Dist: scikit-learn>=0.24.2
 Requires-Dist: scikit-optimize
-Requires-Dist: scipy >= 1.7.1
-Requires-Dist: seaborn >= 0.11
-Requires-Dist: notebook
-Requires-Dist: ipython
-Requires-Dist: pybispectra
-Requires-Dist: black ; extra == "dev"
-Requires-Dist: pytest ; extra == "dev"
-Requires-Dist: pytest-cov ; extra == "dev"
-Project-URL: bugtracker, https://github.com/neuromodulation/py_neuromodulation/issues
-Project-URL: repository, https://github.com/neuromodulation/py_neuromodulation
+Requires-Dist: scipy>=1.7.1
+Requires-Dist: seaborn>=0.11
+Requires-Dist: wget
 Provides-Extra: dev
+Requires-Dist: black; extra == 'dev'
+Requires-Dist: pytest; extra == 'dev'
+Requires-Dist: pytest-cov; extra == 'dev'
+Description-Content-Type: text/x-rst
 
 py_neuromodulation
 ==================
@@ -82,12 +111,24 @@ py_neuromodulation requires at least python 3.10. For installation you can use p
 
     pip install py-neuromodulation
 
-We recommend however installing the package in a new new conda environment:
+
+We recommend however installing the package using `rye <https://rye-up.com/guide/installation/>`_:
 
 .. code-block::
 
     git clone https://github.com/neuromodulation/py_neuromodulation.git
-    conda create -n pynm-test python=3.10
+    rye pin 3.11
+    rye sync
+
+And then activating the virtual environment e.g. in Windows using:
+
+.. code-block::
+
+    .\.venv\Scripts\activate
+
+Alternatively you can also install the package in a conda environment:
+
+    conda create -n pynm-test python=3.11
     conda activate pynm-test
 
 Then install the packages listed in the `pyproject.toml`:
@@ -107,27 +148,27 @@ Then *py_neuromodulation* can be imported via:
 
 .. code-block::
 
-    import py_neuromodulation as py_nm
+    import py_neuromodulation as nm
 
 Basic Usage
 ===========
 
 .. code-block:: python
     
-    import py_neuromodulation as pn
+    import py_neuromodulation as nm
     import numpy as np
     
     NUM_CHANNELS = 5
     NUM_DATA = 10000
     sfreq = 1000  # Hz
-    feature_freq = 3  # Hz
+    sampling_rate_features_hz = 3  # Hz
 
     data = np.random.random([NUM_CHANNELS, NUM_DATA])
 
-    stream = pn.Stream(sfreq=sfreq, data=data, sampling_rate_features_hz=sampling_rate_features_hz)
+    stream = nm.Stream(sfreq=sfreq, data=data, sampling_rate_features_hz=sampling_rate_features_hz)
     features = stream.run()
 
-Check the `Usage <https://py-neuromodulation.readthedocs.io/en/latest/usage.html>`_ and `First examples <https://py-neuromodulation.readthedocs.io/en/latest/auto_examples/plot_first_demo.html>`_ for further introduction.
+Check the `Usage <https://py-neuromodulation.readthedocs.io/en/latest/usage.html>`_ and `First examples <https://py-neuromodulation.readthedocs.io/en/latest/auto_examples/plot_0_first_demo.html>`_ for further introduction.
 
 Contact information
 -------------------
@@ -139,4 +180,3 @@ References
 
 .. [1] Merk, T. et al. *Invasive neurophysiology and whole brain connectomics for neural decoding in patients with brain implants*, `https://doi.org/10.21203/rs.3.rs-3212709/v1` (2023).
 .. [2] Merk, T. et al. *Electrocorticography is superior to subthalamic local field potentials for movement decoding in Parkinson’s disease*. Elife 11, e75126, `https://doi.org/10.7554/eLife.75126` (2022).
-

{py_neuromodulation-0.0.2 → py_neuromodulation-0.0.4}/README.rst

@@ -40,12 +40,24 @@ py_neuromodulation requires at least python 3.10. For installation you can use p
 
     pip install py-neuromodulation
 
-We recommend however installing the package in a new new conda environment:
+
+We recommend however installing the package using `rye <https://rye-up.com/guide/installation/>`_:
 
 .. code-block::
 
     git clone https://github.com/neuromodulation/py_neuromodulation.git
-    conda create -n pynm-test python=3.10
+    rye pin 3.11
+    rye sync
+
+And then activating the virtual environment e.g. in Windows using:
+
+.. code-block::
+
+    .\.venv\Scripts\activate
+
+Alternatively you can also install the package in a conda environment:
+
+    conda create -n pynm-test python=3.11
     conda activate pynm-test
 
 Then install the packages listed in the `pyproject.toml`:
@@ -65,27 +77,27 @@ Then *py_neuromodulation* can be imported via:
 
 .. code-block::
 
-    import py_neuromodulation as py_nm
+    import py_neuromodulation as nm
 
 Basic Usage
 ===========
 
 .. code-block:: python
     
-    import py_neuromodulation as pn
+    import py_neuromodulation as nm
     import numpy as np
     
     NUM_CHANNELS = 5
     NUM_DATA = 10000
     sfreq = 1000  # Hz
-    feature_freq = 3  # Hz
+    sampling_rate_features_hz = 3  # Hz
 
     data = np.random.random([NUM_CHANNELS, NUM_DATA])
 
-    stream = pn.Stream(sfreq=sfreq, data=data, sampling_rate_features_hz=sampling_rate_features_hz)
+    stream = nm.Stream(sfreq=sfreq, data=data, sampling_rate_features_hz=sampling_rate_features_hz)
     features = stream.run()
 
-Check the `Usage <https://py-neuromodulation.readthedocs.io/en/latest/usage.html>`_ and `First examples <https://py-neuromodulation.readthedocs.io/en/latest/auto_examples/plot_first_demo.html>`_ for further introduction.
+Check the `Usage <https://py-neuromodulation.readthedocs.io/en/latest/usage.html>`_ and `First examples <https://py-neuromodulation.readthedocs.io/en/latest/auto_examples/plot_0_first_demo.html>`_ for further introduction.
 
 Contact information
 -------------------

py_neuromodulation-0.0.4/examples/README.rst

@@ -0,0 +1,5 @@
+.. _examples-index:
+
+Examples
+========
+

py_neuromodulation-0.0.4/examples/plot_2_example_add_feature.py

@@ -0,0 +1,76 @@
+"""
+===================
+Adding New Features 
+===================
+
+"""
+
+import py_neuromodulation as nm
+from py_neuromodulation import nm_features_abc
+import numpy as np
+from typing import Iterable
+
+# %%
+# In this example we will demonstrate how a new feature can be added to the existing feature pipeline.
+# This can be done simply by adding an object of the inherited :class:`~nm_features_abc.Feature`
+# class to the stream `stream.run_analysis.features.features` list.
+
+data = np.random.random([1, 1000])
+
+stream = nm.Stream(
+    sfreq=1000,
+    data=data,
+    sampling_rate_features_hz=10,
+    verbose=False,
+)
+
+
+class NewFeature(nm_features_abc.Feature):
+    def __init__(
+        self, settings: dict, ch_names: Iterable[str], sfreq: float
+    ) -> None:
+        self.s = settings
+        self.ch_names = ch_names
+
+    def calc_feature(self, data: np.array, features_compute: dict) -> dict:
+        for ch_idx, ch in enumerate(self.ch_names):
+            features_compute[f"new_feature_{ch}"] = np.mean(data[ch_idx, :])
+
+        return features_compute
+
+    def test_settings():
+        pass
+
+
+newFeature = NewFeature(
+    stream.settings, list(stream.nm_channels["name"]), stream.sfreq
+)
+stream.run_analysis.features.features.append(newFeature)
+
+features = stream.run_analysis.process(data)
+feature_name = f"new_feature_{stream.nm_channels['name'][0]}"
+
+print(f"{feature_name}: {features[feature_name]}")
+
+# %%
+# This example shows a simple newly instantiated feature class called `NewFeature`.
+# The instantiated `newFeature` object could then be added to the existing feature list by calling
+# `stream.run_analysis.features.features.append(newFeature)`.
+#
+# To permanently add a novel feature, the new feature class needs to be added to
+# the :class:`~nm_features` class. This can be done by inserting the feature_name in
+# in the :class:`~nm_features.Feature` init function:
+#
+# .. code-block:: python
+#
+#    for feature in s["features"]:
+#        if s["features"][feature] is False:
+#            continue
+#        match feature:
+#            case "new_feature":
+#                FeatureClass = nm_new_feature.NewFeature
+#            ...
+#
+# The new feature class can then be used by setting the `settings["feature"]["new_feature"]` value in the
+# settings to true.
+#