folder reorganization

Author: ccluri

NOTES.txt

@@ -1,3 +1,55 @@
+
+2017_12_20
+1) Tagged the previous stable version as v1.0
+2) Tagged the version on elephant as v1.1
+3) Merged elephant version which is Py2/3 compatible into master
+4) Changed the folder structure a bit to accomodate for the new dev
+   -corelib has the KCSD.py file which includes all the necessary classes
+   -tests is where the unit tests will eventually go
+   -validation is where the tests from the previous edition go (poor naming choice by me, in retrospect)
+               these are being re-written in a saner 'class'y way now.
+   -tutorials is where ther ipython notebooks will eventually supposed to go.
+   
+
+NOTES FROM v1.0 which is no longer applicable. Eventually should all move to tutorials.
+=====================================================================
+Try
+---
+In file test_kCSD1D.py, test_kCSD2D.py and test_kCSD3D.py play with 
+1) csd_seed to change True CSD profile
+2) total_ele to change the number of electrodes in the plane of electrodes, n evenly spaced in 1D, n^2 in 2D and n^3 in 3D volume
+3) in main_loop change ele_lims to change the position of the electrodes 
+4) in do_kcsd function play with params for regularization 
+
+Legend
+------
+CSD.py - base class of CSD
+KCSD.py - base class for kernel CSD methods.
+KCSD1D.py - relevant KCD1D reconstruction file (Inherits from KCSD.py)
+KCSD2D.py - relevant KCD2D reconstruction file (Inherits from KCSD.py)
+KCSD3D.py - relevant KCD3D reconstruction file (inherits from KCSD.py)
+MoIKCSD.py - relevant KCSD2D which includes the method of images - models saline conductivity
+
+basis_functions.py - necessary functions that are used as basis sources
+utility_functions.py - necessary generic functions 
+
+tests/test_kCSD1D.py - file generates TrueCSD, potentials in a plane, and its kCSD reconstruction
+	     - use with relevant seed - for small sources and large sources.
+	     - illustrates the basic API of KCSD2D.py
+
+tests/test_kCSD2D.py - file generates TrueCSD, potentials in a plane, and its kCSD reconstruction
+	     - use with relevant seed - for small sources and large sources.
+	     - illustrates the basic API of KCSD2D.py
+
+tests/test_kCSD3D.py - file generates TrueCSD, potentials in a volume, and its kCSD reconstruction
+	     - use with relevant seed - for small sources, large sources, monopoles, dipole sources
+	     - illustrates the basic API of KCSD3D.py
+
+tests/csd_profile.py - used by test_kCSD1D.py, test_kCSD2D.py, test_kCSD3D.py for CSD profiles.
+
+========================================================================
+
+
 2016_04_18
 Preparing for release
 Moved functions from KCSD1D_Helpers etc into something more sane.

README.txt

@@ -1,11 +1,19 @@
-This is 1.0 version of kCSD inverse method proposed in
+This is 1.1+ version of kCSD inverse method proposed in
 
 J. Potworowski, W. Jakuczun, S. Łęski, D. K. Wójcik
 "Kernel Current Source Density Method"
 Neural Computation 24 (2012), 541–575
 
 For citation policy see the end of this file.
 
+
+Earlier Stable versions
+----------------
+Please see git tags for earlier versions
+v1.0 corresponds to the version with the test cases written inside tests folder
+v1.1 corresponds to the elephant python library version - no tests here 
+
+
 License
 -------
 Modified BSD License
@@ -17,57 +25,28 @@ d.wojcik[at]nencki[dot]gov[dot]pl
 
 Status
 ------
-KCSD1D + tests(rc)
-KCSD2D + tests(rc)
-KCSD3D + tests(rc)
-MoIKCSD (for MEA's with Saline)
+KCSD1D
+KCSD2D
+KCSD3D
+MoIKCSD
+
+Use via
+from KCSD import KCSD1D
+etc.
 
 Requirements
 ------------
-python 2.7
+python 2.7/3
 numpy 1.10
 scipy 0.17
 matplotlib 1.5 (Only For tests and visualization)
 
+
 Additional Packages - Only of 3D for newer basis functions only.
 -------------------
 scikit-monaco 0.2
 joblib
 
-Try
----
-In file test_kCSD1D.py, test_kCSD2D.py and test_kCSD3D.py play with 
-1) csd_seed to change True CSD profile
-2) total_ele to change the number of electrodes in the plane of electrodes, n evenly spaced in 1D, n^2 in 2D and n^3 in 3D volume
-3) in main_loop change ele_lims to change the position of the electrodes 
-4) in do_kcsd function play with params for regularization 
-
-Legend
-------
-CSD.py - base class of CSD
-KCSD.py - base class for kernel CSD methods.
-KCSD1D.py - relevant KCD1D reconstruction file (Inherits from KCSD.py)
-KCSD2D.py - relevant KCD2D reconstruction file (Inherits from KCSD.py)
-KCSD3D.py - relevant KCD3D reconstruction file (inherits from KCSD.py)
-MoIKCSD.py - relevant KCSD2D which includes the method of images - models saline conductivity
-
-basis_functions.py - necessary functions that are used as basis sources
-utility_functions.py - necessary generic functions 
-
-tests/test_kCSD1D.py - file generates TrueCSD, potentials in a plane, and its kCSD reconstruction
-	     - use with relevant seed - for small sources and large sources.
-	     - illustrates the basic API of KCSD2D.py
-
-tests/test_kCSD2D.py - file generates TrueCSD, potentials in a plane, and its kCSD reconstruction
-	     - use with relevant seed - for small sources and large sources.
-	     - illustrates the basic API of KCSD2D.py
-
-tests/test_kCSD3D.py - file generates TrueCSD, potentials in a volume, and its kCSD reconstruction
-	     - use with relevant seed - for small sources, large sources, monopoles, dipole sources
-	     - illustrates the basic API of KCSD3D.py
-
-tests/csd_profile.py - used by test_kCSD1D.py, test_kCSD2D.py, test_kCSD3D.py for CSD profiles.
-
 
 Citation policy
 ---------------