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909 Commits

Author SHA1 Message Date
Joseph Lizier 90baf68ee7 Making AutoAnalyser Python code only start JVM if not already started 2023-08-21 17:55:16 +10:00
Joseph Lizier 817abd1de0 For Autoanalyser Python code adding \ at the end of line for print statement 2023-08-15 16:28:04 +10:00
Joseph Lizier f643632df4 Adding AutoAnalyser launcher in python 2023-08-11 18:03:28 +10:00
Joseph Lizier f55737c650 Further refinements to python environment start code 2023-07-26 15:02:58 +10:00
Joseph Lizier 107fabad32 Small fixed to spiking TE demo (sent from David) 2023-07-26 14:52:03 +10:00
Joseph Lizier d920b1e9a9 Minor tweaks to Flocking analysis demo 2023-07-26 14:48:55 +10:00
Joseph Lizier 23bfeded27 Updating python environment scripts, and adding one to start jupyter in the environment 2023-07-26 14:46:51 +10:00
Joseph Lizier 40d51ed542
Merge pull request #95 from dpshorten/master 
sensible parameter choices for SpikeTrainTETesting.py
 2023-02-20 11:36:26 +01:00
David Shorten 0cef502948 sensible parameter choices for SpikeTrainTETesting.py 2023-02-20 12:54:16 +10:30
jlizier 28954585f4 Updated a file loader for Flocking demo 2022-09-08 16:14:53 +10:00
jlizier 26e3cd8afb Supporting AIS only calculation in flocking demo 2022-09-08 11:27:27 +10:00
jlizier 6dc6b8fa11 Merge branch 'master' of github.com:jlizier/jidt 2022-09-08 10:26:59 +10:00
jlizier 865d82630a Altering AutoAnalyser generated python code to set flag convertStrings=True in JVM start, as per PR #94 2022-09-08 10:20:20 +10:00
jlizier ee3ce5dd51 Corrected function signature in loadxls2d for fish data loading 2022-09-07 09:17:51 +10:00
jlizier 8bc6d87d9b Adding scripts to create and start a python virtual environment with jpype1 etc installed 2022-09-06 10:27:38 +10:00
jlizier 348587ee59 Python demo 1 - removing deprecated type call in script 2022-09-06 10:27:08 +10:00
Joseph Lizier 8c001e6ddd
Updated links for v1.6 release 2022-09-06 00:02:37 +10:00
jlizier 65aa685d11 Fixing python demo 6, where the multivariate array conversion wasn't working for Python3 with Jpype. Fixed to use recommended array conversion as per UseInPython wiki. Addresses issue raised in PR #87 also. 2022-09-05 23:13:52 +10:00
jlizier 2b0a5cb943 Updated mixed-continiuous CMI KSG estimator, for the bias correction based on number of continuous variables. This was identified from testing, and aligns with testing so far. 2022-09-05 17:51:49 +10:00
jlizier 72024c7299 Updating demo PDFs and version number ahead of new v1.6 distribution 2022-09-05 17:43:14 +10:00
Joseph Lizier d750a737be
Removing what appears to be an old test file from the integrated Spiking TE code from David 2022-09-05 17:08:10 +10:00
jlizier 003a187a7a moving the demos using spiking TE estimator into different folder locations 2022-09-05 15:00:05 +10:00
Joseph Lizier fcfcca962b
Adding David Shorten to the authors list 2022-09-05 14:54:30 +10:00
Joseph Lizier 27f9cccf65
Don't need code for old way of doing spiking TE estimation 2022-09-05 14:45:50 +10:00
Joseph Lizier 47be5df74b
editing comment on how to implement dynamic correlation exclusions in spiking TE estimator 2022-09-05 14:43:18 +10:00
Joseph Lizier e747e8aa93
Merge pull request #93 from dpshorten/master 
Spike train TE estimation
 2022-09-05 14:38:21 +10:00
Joseph Lizier 8db0c12c37
Brief update to header comments on spiking TE example 2022-09-05 14:32:14 +10:00
jlizier 05248ef105 Extra fixing windows paths generated from AutoAnalyser to be properly escaped in data filename for Python/Matlab 2022-09-01 15:50:27 +10:00
jlizier c233485c90 Fixing windows paths generated from AutoAnalyser to be properly escaped 2022-09-01 15:28:28 +10:00
jlizier 9c2a25492f Clarifying where Econometrics Toolbox is required for Flocking demo 2022-08-30 12:38:10 +10:00
jlizier 5398785a67 Adding comment to Flocking demo that Econometrics Toolbox may be required 2022-08-30 12:37:03 +10:00
jlizier d250c6b24c Updating error comment in Flocking demo 2022-08-30 12:33:55 +10:00
dpshorten dc3874c72b
Update net_inf.py 
Comments to the net_inf.py file.
 2022-08-25 16:12:35 +09:30
Joseph Lizier a040cde6da
Adding header comment to spk_to_pk.py and changing filename 2022-08-25 15:24:51 +10:00
jlizier 0935806338 Moving ant targets up to Java 7 instead of Java 6 (newer java versions are complaining now that 6 is too old to target) 2022-08-16 15:50:17 +10:00
David Shorten bcefd900c4 moved the location of the Python testing script 2022-08-04 16:06:25 +09:30
David Shorten a398c925a8 added python for spiking network inference 2022-08-04 16:03:12 +09:30
jlizier 9dfafda555 Merge branch 'master' of github.com:jlizier/jidt 2022-06-16 21:33:41 +10:00
jlizier 2714650cfa Amending Kraskov (KSG) MI estimators to have an experimental method to provide conditional entropy of the first variable given the second. Works by removing the Kozachenko Leonenko entropy of variable 1 from the MI, using the same kNN radii as the MI estimator. Includes Unit tests to provide some initial validation. 2022-06-16 21:29:29 +10:00
Joseph Lizier 2c72eb05f9
Specified AntScripts for quick build 2022-06-14 09:54:49 +10:00
jlizier 25159009ca updating max entropy discretisation to gracefully handle NaNs in the input (which shouldn't be there anyway) 2022-06-09 12:39:59 +10:00
Joseph Lizier e9fc39c4c2 Added simple Matlab script implementing the muiltivariate/iterative/greedy algorithm for effective network inference. Is a simplified version of the full algorithm in IDTxl, for demonstration purposes. Also includes calls to Oliver Cliff's toolkit for granger causality, which won't be functional for users who have not downloaded that; will be removed when the autocorrelation correction is added to JIDT for linear. 2022-04-08 10:49:57 +10:00
Joseph Lizier 899a5607f8 Merge branch 'master' of github.com:jlizier/JIDT 2022-03-31 12:16:21 +11:00
Joseph Lizier 41361417ae Updates to flocking demo including plotting local TEs per individual per time frame 2022-03-31 12:14:16 +11:00
David Shorten c068c8308d improving jittered surrogates 2022-02-25 18:49:12 +11:00
David Shorten 285c95947a integrating artemis changes 2022-02-22 14:39:15 +11:00
David Shorten b4e32727c9 merge 2022-02-22 11:55:09 +11:00
Joseph Lizier 0e33393cdc
Merge pull request #86 from pmediano/master 
Thanks Pedro, and sorry to take so long to attend to this
 2021-11-15 12:08:57 +11:00
Joseph Lizier b02760ddd3 Adding overloads on setObservations and addObservations for MI and TE calculators to handle one variable univariate and one variable multivariate 2021-11-15 10:58:59 +11:00
Joseph Lizier 8e55cf05d9 Merge branch 'master' of github.com:jlizier/JIDT 2021-11-02 23:13:59 +11:00