Merge pull request GazzolaLab#29 from GazzolaLab/update-0.0.3

Merging 0.0.3 into main. Update mostly includes bugfix, test cases, and documentation. - Spike cutout visualization - PCA+GMM clustering - Wavelet decomposition - Spike sorting documentation - Data and DataManger module - Signal to noise utility - FFT plotting
Gauravu2 · May 19, 2022 · fd75a1f · fd75a1f
2 parents 7962a86 + 584eb4f
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diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -4,7 +4,7 @@ Thanks for your interest in contributing MiV-OS project.
 
 The following is a set of guidelines how to contributes. These are mostly guidelines, not rules. Use your best judgment, and feel free to propose changes to this document in a pull request.
 
-#### Table Of Contents
+**Table Of Contents**
 
 [TLTR! I need three-line summary!!](#three-line-summary)
 
@@ -36,10 +36,15 @@ The following is a set of guidelines how to contributes. These are mostly guidel
 ### Installation and packages
 
 First **create the fork repository and clone** to your local machine.
-We provide [requirements.txt](requirements.txt) to include all the dependencies.
+We provide [requirements.txt](https://github.com/GazzolaLab/MiV-OS/blob/main/requirements.txt) to include all the dependencies that is required to develop. You can either install using `pip install -r requirements.txt` or
 ```bash
-$ pip install -r requirements.txt
+$ pip install miv-os[dev]
 ```
+If you are more interested in working for documentation, use
+```bash
+$ pip install miv-os[docs]
+```
+More details are included [here](https://github.com/GazzolaLab/MiV-OS/blob/main/docs/README.md).
 
 ### Pre-Commit
 

diff --git a/Makefile b/Makefile
@@ -7,5 +7,5 @@ mypy:
 coverage:
 	@pytest --cov=miv tests/
 
-all:test mypy
+all:test mypy coverage
 ci: test mypy
diff --git a/README.md b/README.md
@@ -9,7 +9,7 @@
 [![codecov][badge-codecov]][link-codecov]
 
 [//]: # (Remove this line for the first release)
-_The package is under pre-alpha development. First Alpha release target mid-April 2022._
+_The package is under pre-alpha development. First Alpha release target mid-May 2022._
 
 </div>
 

diff --git a/docs/_static/assets/spike_cutout_example.png b/docs/_static/assets/spike_cutout_example.png
diff --git a/docs/api/_toctree/FilterAPI/miv.signal.filter.FilterCollection.rst b/docs/api/_toctree/FilterAPI/miv.signal.filter.FilterCollection.rst
diff --git a/docs/api/_toctree/SpikeSortingAPI/miv.signal.spike.PCADecomposition.rst b/docs/api/_toctree/SpikeSortingAPI/miv.signal.spike.PCADecomposition.rst
@@ -0,0 +1,13 @@
+miv.signal.spike.PCADecomposition
+=================================
+
+.. currentmodule:: miv.signal.spike
+
+.. autoclass:: PCADecomposition
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~PCADecomposition.__init__
+      ~PCADecomposition.project
diff --git a/...pi/_toctree/SpikeSortingAPI/miv.signal.spike.SpikeFeatureExtractionProtocol.rst b/...pi/_toctree/SpikeSortingAPI/miv.signal.spike.SpikeFeatureExtractionProtocol.rst
@@ -0,0 +1,13 @@
+miv.signal.spike.SpikeFeatureExtractionProtocol
+===============================================
+
+.. currentmodule:: miv.signal.spike
+
+.. autoclass:: SpikeFeatureExtractionProtocol
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~SpikeFeatureExtractionProtocol.__init__
diff --git a/docs/api/_toctree/SpikeSortingAPI/miv.signal.spike.SuperParamagneticClustering.rst b/docs/api/_toctree/SpikeSortingAPI/miv.signal.spike.SuperParamagneticClustering.rst
@@ -0,0 +1,13 @@
+miv.signal.spike.SuperParamagneticClustering
+============================================
+
+.. currentmodule:: miv.signal.spike
+
+.. autoclass:: SuperParamagneticClustering
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~SuperParamagneticClustering.__init__
diff --git a/...tree/SpikeSortingAPI/miv.signal.spike.UnsupervisedFeatureClusteringProtocol.rst b/...tree/SpikeSortingAPI/miv.signal.spike.UnsupervisedFeatureClusteringProtocol.rst
@@ -0,0 +1,14 @@
+miv.signal.spike.UnsupervisedFeatureClusteringProtocol
+======================================================
+
+.. currentmodule:: miv.signal.spike
+
+.. autoclass:: UnsupervisedFeatureClusteringProtocol
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~UnsupervisedFeatureClusteringProtocol.__init__
+      ~UnsupervisedFeatureClusteringProtocol.fit
+      ~UnsupervisedFeatureClusteringProtocol.predict
diff --git a/docs/api/_toctree/SpikeSortingAPI/miv.signal.spike.WaveletDecomposition.rst b/docs/api/_toctree/SpikeSortingAPI/miv.signal.spike.WaveletDecomposition.rst
@@ -0,0 +1,13 @@
+miv.signal.spike.WaveletDecomposition
+=====================================
+
+.. currentmodule:: miv.signal.spike
+
+.. autoclass:: WaveletDecomposition
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~WaveletDecomposition.__init__
+      ~WaveletDecomposition.project
diff --git a/docs/api/_toctree/StatisticsAPI/miv.statistics.spikestamps_statistics.rst b/docs/api/_toctree/StatisticsAPI/miv.statistics.spikestamps_statistics.rst
@@ -0,0 +1,6 @@
+miv.statistics.spikestamps\_statistics
+======================================
+
+.. currentmodule:: miv.statistics
+
+.. autofunction:: spikestamps_statistics
diff --git a/docs/api/_toctree/StatisticsAPI/miv.statistics.summarizer.StatisticsSummary.rst b/docs/api/_toctree/StatisticsAPI/miv.statistics.summarizer.StatisticsSummary.rst
diff --git a/...toctree/VisualizationAPI/miv.visualization.fft_domain.plot_frequency_domain.rst b/...toctree/VisualizationAPI/miv.visualization.fft_domain.plot_frequency_domain.rst
@@ -0,0 +1,6 @@
+miv.visualization.fft\_domain.plot\_frequency\_domain
+=====================================================
+
+.. currentmodule:: miv.visualization.fft_domain
+
+.. autofunction:: plot_frequency_domain
diff --git a/.../api/_toctree/VisualizationAPI/miv.visualization.waveform.extract_waveforms.rst b/.../api/_toctree/VisualizationAPI/miv.visualization.waveform.extract_waveforms.rst
@@ -0,0 +1,6 @@
+miv.visualization.waveform.extract\_waveforms
+=============================================
+
+.. currentmodule:: miv.visualization.waveform
+
+.. autofunction:: extract_waveforms
diff --git a/docs/api/_toctree/VisualizationAPI/miv.visualization.waveform.plot_waveforms.rst b/docs/api/_toctree/VisualizationAPI/miv.visualization.waveform.plot_waveforms.rst
@@ -0,0 +1,6 @@
+miv.visualization.waveform.plot\_waveforms
+==========================================
+
+.. currentmodule:: miv.visualization.waveform
+
+.. autofunction:: plot_waveforms
diff --git a/docs/api/io.rst b/docs/api/io.rst
@@ -1,6 +1,8 @@
-*********************
-Input / Output Module
-*********************
+********************
+Data Managing Module
+********************
+
+.. automodule:: miv.io.data
 
 .. automodule:: miv.io.binary
    :members:
diff --git a/docs/api/signal.rst b/docs/api/signal.rst
@@ -1,34 +1,7 @@
-*************************
-Signal Processing Modules
-*************************
+*********************
+Signal Pre-Processing
+*********************
 
+.. automodule:: miv.signal.filter.filter_collection
 
-Filter
-######
-
-.. currentmodule:: miv.signal.filter
-
-.. automodule:: miv.signal.filter
-
-   .. autosummary::
-       :nosignatures:
-       :toctree: _toctree/FilterAPI
-
-       FilterProtocol
-       ButterBandpass
-       FilterCollection
-
-Spike Detection
-###############
-
-.. automodule:: miv.signal.spike
-
-   .. autosummary::
-       :nosignatures:
-       :toctree: _toctree/DetectionAPI
-
-       SpikeDetectionProtocol
-       ThresholdCutoff
-
-Spike Sorting
-#############
+.. automodule:: miv.signal.spike.detection
diff --git a/docs/api/sorting.rst b/docs/api/sorting.rst
@@ -0,0 +1,5 @@
+********************
+Spike Sorting Module
+********************
+
+.. automodule:: miv.signal.spike.sorting
diff --git a/docs/api/statistics.rst b/docs/api/statistics.rst
@@ -2,40 +2,4 @@
 Statistics Modules
 ******************
 
-Statistics Tools
-================
-
-Spikestamps
------------
-
-.. currentmodule:: miv.statistics
-
 .. automodule:: miv.statistics.summarizer
-
-   .. autosummary::
-      :nosignatures:
-      :toctree: _toctree/StatisticsAPI
-
-      StatisticsSummary
-
-Useful External Packages
-########################
-
-scipy statistics
-================
-
-`scipy <https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.describe.html>`_
-
-.. autosummary::
-
-   scipy.stats.describe
-
-elephant.statistics
-===================
-
-`elephant documentation: <https://elephant.readthedocs.io/en/latest/reference/statistics.html>`_
-
-.. autosummary::
-
-   elephant.statistics.mean_firing_rate
-   elephant.statistics.instantaneous_rate
diff --git a/docs/api/visualization.rst b/docs/api/visualization.rst
@@ -0,0 +1,48 @@
+*******************
+Visualization Tools
+*******************
+
+Plotting Tools
+==============
+
+DFT Plot
+--------
+
+.. currentmodule:: miv.visualization
+
+.. automodule:: miv.visualization.fft_domain
+
+   .. autosummary::
+      :nosignatures:
+      :toctree: _toctree/VisualizationAPI
+
+      plot_frequency_domain
+
+Spike Waveform Overlap
+----------------------
+
+.. currentmodule:: miv.visualization
+
+.. automodule:: miv.visualization.waveform
+
+   .. autosummary::
+      :nosignatures:
+      :toctree: _toctree/VisualizationAPI
+
+      extract_waveforms
+      plot_waveforms
+
+Useful External Packages
+========================
+
+Here are few external `python` packages that can also be used for visualization.
+
+Viziphant
+---------
+
+`viziphant (elephant) documentation: <https://viziphant.readthedocs.io/en/latest/modules.html>`_
+
+.. autosummary::
+
+   viziphant.rasterplot.rasterplot
+   viziphant.rasterplot.rasterplot_rates
diff --git a/docs/conf.py b/docs/conf.py
@@ -108,7 +108,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ["_static"]
+html_static_path = ["_static", "_static/assets"]
 html_css_files = ["css/*", "css/logo.css"]
 
 # -- Options for numpydoc ---------------------------------------------------