py-neuromodulation 0.0.3__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:
+instance/
+.webassets-cache
+
+# 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
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# Ignore pickles
+*.pkl
+**/*.pkl
+*.p
+
+.pdf
+
+sphinx/sub/*
+
+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-0.0.3 → py_neuromodulation-0.0.4}/PKG-INFO

@@ -1,182 +1,182 @@
-Metadata-Version: 2.1
-Name: py_neuromodulation
-Version: 0.0.3
-Summary: Real-time analysis of intracranial neurophysiology recordings.
-Author-email: Timon Merk <timon.merk@charite.de>
-Maintainer: Timon Merk
-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.
-        
-Project-URL: bugtracker, https://github.com/neuromodulation/py_neuromodulation/issues
-Project-URL: repository, https://github.com/neuromodulation/py_neuromodulation
-Keywords: real-time,eeg,ieeg,dbs,ecog,electrocorticography,deep-brain-stimulation,machine-learning
-Classifier: Development Status :: 2 - Pre-Alpha
-Classifier: License :: OSI Approved :: MIT License 
-Classifier: Programming Language :: Python
-Classifier: Topic :: Software Development :: Libraries :: Python Modules
-Requires-Python: >=3.10
-Description-Content-Type: text/x-rst
-License-File: LICENSE
-Requires-Dist: mne
-Requires-Dist: filterpy>=1.4.5
-Requires-Dist: fooof
-Requires-Dist: imbalanced-learn
-Requires-Dist: matplotlib>=3.3.4
-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: pip
-Requires-Dist: pynput
-Requires-Dist: pybids
-Requires-Dist: scikit-image
-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>=1.0.0
-Requires-Dist: pyparrm
-Requires-Dist: pyarrow>=14.0.2
-Requires-Dist: joblib>=1.3.2
-Requires-Dist: black>=24.2.0
-Requires-Dist: pytest>=8.0.2
-Requires-Dist: wget
-Provides-Extra: dev
-Requires-Dist: black; extra == "dev"
-Requires-Dist: pytest; extra == "dev"
-Requires-Dist: pytest-cov; extra == "dev"
-
-py_neuromodulation
-==================
-
-Analyzing neural data can be a troublesome, trial and error prone,
-and beginner unfriendly process. *py_neuromodulation* allows using a simple
-interface for extraction of established neurophysiological features and includes commonly applied pre -and postprocessing methods.
-
-Only **time series data** with a corresponding **sampling frequency** are required for feature extraction.
-
-The output will be a `pandas.DataFrame <https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.html>`_ including different time-resolved computed features. Internally a **stream** get's initialized,
-which resembles an *online* data-stream that can in theory also be be used with a hardware acquisition system. 
-
-The following features are currently included:
-
-* oscillatory: fft, stft or bandpass filtered band power
-* `temporal waveform shape <https://www.sciencedirect.com/science/article/pii/S1364661316302182>`_
-* `fooof <https://fooof-tools.github.io/fooof/>`_
-* `mne_connectivity estimates <https://mne.tools/mne-connectivity/stable/index.html>`_ 
-* `Hjorth parameter <https://en.wikipedia.org/wiki/Hjorth_parameters>`_
-* `non-linear dynamical estimates <https://nolds.readthedocs.io/en/latest/>`_
-* various burst features
-* line length 
-* and more...
-
-
-Find here the preprint of **py_neuromodulation** called *"Invasive neurophysiology and whole brain connectomics for neural decoding in patients with brain implants"* [1]_.
-
-The original intention for writing this toolbox was movement decoding from invasive brain signals [2]_.
-The application however could be any neural decoding problem.
-*py_neuromodulation* offers wrappers around common practice machine learning methods for efficient analysis.
-
-Find the documentation here http://py-neuromodulation.readthedocs.io for example usage and parametrization.
-
-Installation
-============
-
-py_neuromodulation requires at least python 3.10. For installation you can use pip:
-
-.. code-block::
-
-    pip install py-neuromodulation
-
-
-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
-    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`:
-
-.. code-block::
-
-    pip install .
-
-
-Optionally the ipython kernel can be specified for the installed pynm-test conda environment:
-
-.. code-block::
-
-    ipython kernel install --user --name=pynm-test
-
-Then *py_neuromodulation* can be imported via:
-
-.. code-block::
-
-    import py_neuromodulation as nm
-
-Basic Usage
-===========
-
-.. code-block:: python
-    
-    import py_neuromodulation as nm
-    import numpy as np
-    
-    NUM_CHANNELS = 5
-    NUM_DATA = 10000
-    sfreq = 1000  # Hz
-    sampling_rate_features_hz = 3  # Hz
-
-    data = np.random.random([NUM_CHANNELS, NUM_DATA])
-
-    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_0_first_demo.html>`_ for further introduction.
-
-Contact information
--------------------
-For any question or suggestion please find my contact
-information at `my GitHub profile <https://github.com/timonmerk>`_.
-
-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).
+Metadata-Version: 2.3
+Name: py_neuromodulation
+Version: 0.0.4
+Summary: Real-time analysis of intracranial neurophysiology recordings.
+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
+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: Programming Language :: Python
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+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: 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: notebook
+Requires-Dist: numpy>=1.21.2
+Requires-Dist: pandas>=1.2.2
+Requires-Dist: pip
+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-optimize
+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
+==================
+
+Analyzing neural data can be a troublesome, trial and error prone,
+and beginner unfriendly process. *py_neuromodulation* allows using a simple
+interface for extraction of established neurophysiological features and includes commonly applied pre -and postprocessing methods.
+
+Only **time series data** with a corresponding **sampling frequency** are required for feature extraction.
+
+The output will be a `pandas.DataFrame <https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.html>`_ including different time-resolved computed features. Internally a **stream** get's initialized,
+which resembles an *online* data-stream that can in theory also be be used with a hardware acquisition system. 
+
+The following features are currently included:
+
+* oscillatory: fft, stft or bandpass filtered band power
+* `temporal waveform shape <https://www.sciencedirect.com/science/article/pii/S1364661316302182>`_
+* `fooof <https://fooof-tools.github.io/fooof/>`_
+* `mne_connectivity estimates <https://mne.tools/mne-connectivity/stable/index.html>`_ 
+* `Hjorth parameter <https://en.wikipedia.org/wiki/Hjorth_parameters>`_
+* `non-linear dynamical estimates <https://nolds.readthedocs.io/en/latest/>`_
+* various burst features
+* line length 
+* and more...
+
+
+Find here the preprint of **py_neuromodulation** called *"Invasive neurophysiology and whole brain connectomics for neural decoding in patients with brain implants"* [1]_.
+
+The original intention for writing this toolbox was movement decoding from invasive brain signals [2]_.
+The application however could be any neural decoding problem.
+*py_neuromodulation* offers wrappers around common practice machine learning methods for efficient analysis.
+
+Find the documentation here http://py-neuromodulation.readthedocs.io for example usage and parametrization.
+
+Installation
+============
+
+py_neuromodulation requires at least python 3.10. For installation you can use pip:
+
+.. code-block::
+
+    pip install py-neuromodulation
+
+
+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
+    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`:
+
+.. code-block::
+
+    pip install .
+
+
+Optionally the ipython kernel can be specified for the installed pynm-test conda environment:
+
+.. code-block::
+
+    ipython kernel install --user --name=pynm-test
+
+Then *py_neuromodulation* can be imported via:
+
+.. code-block::
+
+    import py_neuromodulation as nm
+
+Basic Usage
+===========
+
+.. code-block:: python
+    
+    import py_neuromodulation as nm
+    import numpy as np
+    
+    NUM_CHANNELS = 5
+    NUM_DATA = 10000
+    sfreq = 1000  # Hz
+    sampling_rate_features_hz = 3  # Hz
+
+    data = np.random.random([NUM_CHANNELS, NUM_DATA])
+
+    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_0_first_demo.html>`_ for further introduction.
+
+Contact information
+-------------------
+For any question or suggestion please find my contact
+information at `my GitHub profile <https://github.com/timonmerk>`_.
+
+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-0.0.4/examples/README.rst

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

py_neuromodulation-0.0.4/py_neuromodulation/ConnectivityDecoding/_get_grid_hull.m

@@ -0,0 +1,34 @@
+addpath('C:\code\wjn_toolbox');
+addpath(genpath('C:\code\leaddbs'));
+addpath(genpath('C:\code\spm12'));
+
+
+%%
+ctx = wjn_mni_cortex();
+downsample_ctx=ctx.vertices(1:20:end,:); %downsample by 10
+
+save("downsampled_cortex.mat", "downsample_ctx")
+
+figure;
+scatter3(downsample_ctx(:,1), downsample_ctx(:,2), downsample_ctx(:,3), 'filled');
+title('3D Scatter Plot Example');
+xlabel('X-axis');
+ylabel('Y-axis');
+zlabel('Z-axis');
+grid on;
+
+
+
+PATH_OUT = "D:\Connectome_RMAP_OUT\ROIs";
+
+for a =1:size(downsample_ctx,1)
+    disp(a)
+    roiname  = fullfile(PATH_OUT, strcat('ROI-', string(a), '.nii'));
+    mni = [downsample_ctx(a, 1) downsample_ctx(a, 2) downsample_ctx(a, 3)];
+    wjn_spherical_roi(roiname,mni,4);
+end
+
+
+
+
+