[Feature] Merging "Total spiking probability edges" into elephant (#560)

* Feat: Add basic scaffold for total_spiking_probability_edges

* Feat: Add filterpair generation

* Feat: Add normalized_cross_correlation

* Feat: Add total_spiking_probability_edges

* Refactor: Rename filter parameters

* Feat: Add function to compute connectivity_matrix

* Feat: Combine total_spiking_probability_edges and get_connectivty_matrix

* Docs: Explenation why mean values are ommited in NCC

* Refactor: Naming conventions

* Fix: Extra dimension on delay_matrix

* Test: Add test for total_spiking_probability_edges

* Fix: Incorrect repo path

* Fix Incorrect repo path part 2

* Docs: Add further documentation

* docs: Fix typos

Co-authored-by: Moritz Kern <92092328+Moritz-Alexander-Kern@users.noreply.github.com>

* fixed pep8 issue in total_spiking_probability_edges.py

* fixed pep8 issue in test_total_spiking_probability_edges.py

* convert tests to unittest.TestCase classes

* add zenodo info

---------

Co-authored-by: Moritz Kern <92092328+Moritz-Alexander-Kern@users.noreply.github.com>
Co-authored-by: Moritz-Alexander-Kern <moritz.kern@ymail.com>

Author: 3 people

.zenodo.json

@@ -9,6 +9,11 @@
             "orcid": "0000-0001-7292-1982",
             "affiliation": "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany",
             "name": "Kern, Moritz"
+        },
+        {
+            "orcid": "0009-0003-9352-9826",
+            "affiliation": "BioMEMS Lab, University of Applied Sciences Aschaffenburg, Germany",
+            "name": "Richter, Felician"
         }
     ],
 

doc/authors.rst

@@ -51,6 +51,7 @@ contribution, and may not be the current affiliation of a contributor.
 * Florian Porrmann [13]
 * Sarah Pilz [13]
 * Oliver Kloß [1]
+* Felician Richter [12]
 
 1. Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany
 2. Unité de Neurosciences, Information et Complexité, CNRS UPR 3293, Gif-sur-Yvette, France

doc/bib/elephant.bib

@@ -466,3 +466,17 @@ @article{Deger12_443
 	title = {Statistical properties of superimposed stationary spike trains},
 	volume = 32,
 	year = 2012}
+
+
+@article{de_blasi19_169,
+	title = {Total spiking probability edges: {A} cross-correlation based method for effective connectivity estimation of cortical spiking neurons},
+	volume = {312},
+	shorttitle = {Total spiking probability edges},
+	doi = {10.1016/j.jneumeth.2018.11.013},
+	language = {en},
+	journal = {Journal of Neuroscience Methods},
+	author = {{De Blasi}, Stefano and Ciba, Manuel and Bahmer, Andreas and Thielemann, Christiane},
+	month = jan,
+	year = {2019},
+	pages = {169--181},
+}

doc/modules.rst

@@ -32,11 +32,17 @@ Spike trains
     reference/_spike_train_processing
     reference/_spike_train_patterns
 
+.. toctree::
+    :maxdepth: 1
+
+    reference/functional_connectivity_estimation.rst
+
 .. toctree::
     :maxdepth: 1
 
     reference/change_point_detection
     reference/gpfa
+
 .. toctree::
     :maxdepth: 1
 

doc/reference/functional_connectivity_estimation.rst

@@ -0,0 +1,5 @@
+==================================
+Functional connectivity estimation
+==================================
+
+.. automodule:: elephant.functional_connectivity

elephant/functional_connectivity.py

@@ -0,0 +1,31 @@
+"""
+Functions for analysing and estimating firing-patterns and connectivity among neurons
+in order to better understand the underlying neural-networks and information-flow
+between neurons.
+
+
+Network connectivity estimation
+*******************************
+
+.. autosummary::
+    :toctree: _toctree/functional_connectivity/
+
+    total_spiking_probability_edges
+
+References
+----------
+
+.. bibliography::
+   :keyprefix: functional_connectivity-
+
+
+:copyright: Copyright 2014-2023 by the Elephant team, see `doc/authors.rst`.
+:license: Modified BSD, see LICENSE.txt for details.
+"""
+
+from elephant.functional_connectivity_src.total_spiking_probability_edges import (
+    total_spiking_probability_edges,
+)
+
+__all__ = ["total_spiking_probability_edges"]
+