fixing the 3D cases for the tutorial and adding sphinx documentation

Author: ccluri

docs/AUTHORS.rst

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+Authors
+-------
+
+- Chaitanya Chintaluri[1, 2]
+- Marta Kowalska[1]
+- Michał Czerwinski[1]
+- Joanna Jędrzejewska–Szmek[1] 
+- Jakub Dzik[1]
+- Władysław Średniawa[1] 
+- Jan Mąka [1, 4]
+- Grzegorz Parka[3]
+
+- Daniel K. Wójcik[1]
+
+1. Nencki Institute of Experimental Biology, Warsaw, Poland
+2. University of Oxford, United Kingdom
+3. Google Summer of Code 2014, INCF/pykCSD
+4. University of Warsaw, Poland 
+
+Contributions
+-------------
+
+- C.C : Design, implentation kcsd core classes, validation, tests, binder, tutorials
+- M.K : Reliability maps, Spectral decomposition, validation class, tutorials
+- M.C : KCSD1D class
+- J.J-S : skCSD class, tests
+- J.D : Error propagation maps
+- J.M : initial work on sKCSD class
+- W.S : L-curve implementation
+- G.P : first pass python library for kCSD as part of GSoC.
+
+- D.W : supervision, code quality
+
+
+Contact
+-------
+Prof. Daniel K. Wójcik : d.wojcik[at]nencki[dot]gov[dot]pl
+
+
+Contribute
+----------
+If you wish to contribute to this code, please get it touch with Prof. Wójcik

docs/source/AUTHORS.rst

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+Citation policy
+---------------
+If you use this software in published research please cite the following work
+
+- KCSD1D - [1, 2]
+- KCSD2D - [1, 3]
+- KCSD3D - [1, 4]
+- MoIkCSD - [1, 3, 5]
+- sKCSD - [6]
+  
+1) Potworowski, J., Jakuczun, W., Łęski, S. & Wójcik, D. (2012) 'Kernel current source density method.' Neural Comput 24(2), 541-575.
+
+2) Pettersen, K. H., Devor, A., Ulbert, I., Dale, A. M. & Einevoll, G. T. (2006) 'Current-source density estimation based on inversion of electrostatic forward solution: effects of finite extent of neuronal activity and conductivity discontinuities.' J Neurosci Methods 154(1-2), 116-133.
+
+3) Łęski, S., Pettersen, K. H., Tunstall, B., Einevoll, G. T., Gigg, J. & Wójcik, D. K. (2011) 'Inverse Current Source Density method in two dimensions: Inferring neural activation from multielectrode recordings.' Neuroinformatics 9(4), 401-425.
+
+4) Łęski, S., Wójcik, D. K., Tereszczuk, J., Świejkowski, D. A., Kublik, E. & Wróbel, A. (2007) 'Inverse current-source density method in 3D: reconstruction fidelity, boundary effects, and influence of distant sources.' Neuroinformatics 5(4), 207-222.
+
+5) Ness, T. V., Chintaluri, C., Potworowski, J., Łeski, S., Głabska, H., Wójcik, D. K. & Einevoll, G. T. (2015) 'Modelling and Analysis of Electrical Potentials Recorded in Microelectrode Arrays (MEAs).' Neuroinformatics 13(4), 403-426.
+
+6) Cserpan, D., Meszena, D., Wittner, L., Toth, K., Ulbert, I., Somogyvari, Z., Wójcik, D. K. (2017) 'Revealing The Distribution Of Transmembrane Currents Along The Dendritic Tree Of A Neuron From Extracellular Recordings.' eLife (2017) 6:e29384

docs/source/CITE.rst

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+Documentation
+------------
+.. toctree::
+   :maxdepth: 1
+   :caption: Contents:
+
+KCSD Methods
+~~~~~~~~~~~~
+
+.. automodule:: kcsd.KCSD
+   :members:
+
+.. autoclass:: kcsd.sKCSD
+   :members:
+      
+      
+Spectral Structure
+~~~~~~~~~~~~~~~~~~
+
+.. autoclass:: kcsd.validation.ValidateKCSD.SpectralStructure
+   :members:
+      
+Validation
+~~~~~~~~~~
+
+.. autoclass:: kcsd.validation.ValidateKCSD.ValidateKCSD
+   :members:
+   
+.. autoclass:: kcsd.validation.ValidateKCSD.ValidateKCSD1D
+   :members:
+		
+.. autoclass:: kcsd.validation.ValidateKCSD.ValidateKCSD2D
+   :members:
+		
+.. autoclass:: kcsd.validation.ValidateKCSD.ValidateKCSD3D
+   :members:
+
+Reliability Maps
+~~~~~~~~~~~~~~~~
+
+.. automodule:: kcsd.validation.VisibilityMap
+   :members:
+
+Basis functions
+~~~~~~~~~~~~~~~
+
+1-Dimensional
++++++++++++++
+
+.. autofunction:: kcsd.basis_functions.gauss_1D
+
+.. autofunction:: kcsd.basis_functions.gauss_lim_1D
+
+.. autofunction:: kcsd.basis_functions.step_1D		  
+
+2-Dimensional
++++++++++++++
+
+.. autofunction:: kcsd.basis_functions.gauss_2D
+
+.. autofunction:: kcsd.basis_functions.gauss_lim_2D
+		  
+.. autofunction:: kcsd.basis_functions.step_2D
+
+3-Dimensional
++++++++++++++
+		  
+.. autofunction:: kcsd.basis_functions.gauss_3D
+
+.. autofunction:: kcsd.basis_functions.gauss_lim_3D
+
+.. autofunction:: kcsd.basis_functions.step_3D		  
+
+
+CSD Test Sources
+~~~~~~~~~~~~~~~~
+
+Variable (Seedable)
++++++++++++++++++++
+
+.. autofunction:: kcsd.validation.csd_profile.gauss_1d_dipole
+
+.. autofunction:: kcsd.validation.csd_profile.gauss_1d_mono
+
+.. autofunction:: kcsd.validation.csd_profile.gauss_2d_small
+
+.. autofunction:: kcsd.validation.csd_profile.gauss_2d_large
+
+.. autofunction:: kcsd.validation.csd_profile.gauss_3d_small
+
+.. autofunction:: kcsd.validation.csd_profile.gauss_3d_large
+
+Fixed (Non seedable)
+++++++++++++++++++++
+		  
+.. autofunction:: kcsd.validation.csd_profile.gauss_1d_dipole_f
+
+.. autofunction:: kcsd.validation.csd_profile.gauss_2d_large_f
+
+.. autofunction:: kcsd.validation.csd_profile.gauss_2d_small_f
+
+.. autofunction:: kcsd.validation.csd_profile.gauss_3d_mono1_f
+
+.. autofunction:: kcsd.validation.csd_profile.gauss_3d_mono2_f
+
+.. autofunction:: kcsd.validation.csd_profile.gauss_3d_mono3_f		  

docs/source/DOCUMENTATION.rst

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+Installation
+------------
+
+Clone repository
+~~~~~~~~~~~~~~~~
+
+.. code-block:: bash
+
+   user:~$ git clone https://github.com/Neuroinflab/kCSD-python.git
+   user:~$ cd kCSD-python
+   user:~/kCSD-python$
+   
+
+Bash or Anaconda env
+~~~~~~~~~~~~~~~~~~~~
+
+.. code-block:: bash
+
+   user:~/kCSD-python$ pip install .
+
+
+or
+
+.. code-block:: bash
+
+   user:~/kCSD-python$ python setup.py install
+
+
+
+Development and testing
+~~~~~~~~~~~~~~~~~~~~~~~
+
+.. code-block:: bash
+
+   user:~/kCSD-python$ pip install -e .
+
+or
+
+.. code-block:: bash
+
+   user:~/kCSD-python$ python setup.py develop

docs/source/INSTALL.rst

@@ -1,6 +1,10 @@
+License
+-------
+
 BSD 3-Clause License
+~~~~~~~~~~~~~~~~~~~~
 
-Copyright (c) 2018, Laboratory of Neuroinformatics, Nencki Institute
+Copyright (c) 2019, Laboratory of Neuroinformatics, Nencki Institute
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

docs/LICENSE docs/source/LICENSE.rstdocs/LICENSE renamed to docs/source/LICENSE.rst

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+Tutorials
+---------
+
+kcsd-python library comes with two extensive tutorials (at this
+moment, more soon). These can be tested using Jupyter notebook on your
+desktop after installing the kCSD-python package. Alternatively, they
+can be played around with without any installation on Binder in a
+web-browser. Note that in this case, the results from a browser are
+not saved, and cannot be retreived.
+
+Basic Features
+~~~~~~~~~~~~~~
+
+This tutorial showcases, the use of the kCSD-python package in the
+case of the simplest 2D square grid of electrodes. It defines a region
+where can place true current sources, probe it with a grid or
+electrodes, based on these measurements and using the proposed method,
+estimate the CSD. Since we also know the true sources, we can now
+estimate the error in the estimation method as well. To this
+preliminary setup, we add noise to the measurements at the electrodes,
+and repeat the procedure. We also explore the situation when certain
+number of the electrode are broken, and how that would effect the
+reconstructions.
+
+The tutorial is provided with Binder access, click the button below to
+interact with it in a browser, no installation necessary.
+
+.. image:: https://mybinder.org/badge.svg
+   :target: https://mybinder.org/v2/gh/Neuroinflab/kCSD-python/master?filepath=tutorials%2Ftutorial_basic.ipynb
+
+	    
+For a non-interactive version of this tutorial, see
+`Tutorail1<https://github.com/Neuroinflab/kCSD-python/blob/master/tutorials/tutorial_basic.ipynb>`_.
+
+	    
+	    
+Advanced Features
+~~~~~~~~~~~~~~~~~
+
+This tutorial showcases many more features of the kcsd-python package,
+especially the cases when the electrodes are distributed in 1D
+(laminar probe like), 2D (Neuropixel like), 3D (Utah array like) or on
+a microelectrode arrays (MEA, slice with saline). It is provided with
+buttons and easy clickable interface to enable the user to navigate
+the otherwise dense details. In some ways, it extends on the Basic
+Features tutorial and expands it to the other dimensions. NOTE, the
+user might have to 'Reset this tutorial' before using to enable the
+buttons (Kernel>Restart & Run All).
+
+The tutorial is provided with Binder access, click the button below to
+interact with it in a browser, no installation necessary.
+
+.. image:: https://mybinder.org/badge.svg
+   :target: https://mybinder.org/v2/gh/Neuroinflab/kCSD-python/master?filepath=tutorials%2Ftutorial_advanced.ipynb
+
+
+For a non-inteactive version of this tutorial, see
+`Tutorail2<https://github.com/Neuroinflab/kCSD-python/blob/master/tutorials/tutorial_advanced.ipynb>`_.
+
+
+More Tutorials
+~~~~~~~~~~~~~~
+
+There are many more ways to test this method some of these can be made
+into tutorials for easier understanding. While we are working on this,
+they will appear here once they reach production level. Please
+watch-out this space in the near future. We also take requests for
+tutorials.
+
+Do you wish there was a tutorial for your setup? Can you provide us
+with the electrode positions and some sample recordings under open
+license? If so, we might be able to tailor-make a tutorial for you!
+Please get in touch. See Contacts.