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934 Commits

Author SHA1 Message Date
Joseph Lizier fea2cb4bfa Targeting Java version 8 in our builds now, in part to be compatible with latest Jpype in python 2025-10-16 09:17:00 +11:00
Joseph Lizier cb12914e7a Changing spiking TE code to return all embeddings with the local TE contributions at each spike 2025-05-02 16:06:52 +10:00
Joseph Lizier d773508cf9 Fixing handling of data normalisation in the KNN computation methods 2025-04-01 23:09:09 +11:00
Joseph Lizier 333a00fc07 Adding method to compute kNN distances for KSG AIS estimator 2025-04-01 22:55:28 +11:00
Joseph Lizier 2ab3ec347c Adding method for KSG TE estimator to return KNN distances 2025-04-01 22:49:45 +11:00
Joseph Lizier 5dc9d00aff Adding univariate calls for KNN distances in KSG MI estimators 2025-04-01 22:33:45 +11:00
Joseph Lizier c08aeb1783 Adding univariate calls for cross CMI 2025-04-01 22:33:02 +11:00
Joseph Lizier fa21f7343a Adding debug methods to KSG estimators to retrieve knn distances 2025-04-01 18:08:38 +11:00
Joseph Lizier 13251a0104 Cleaning up code of the spiking TE estimator 2025-04-01 15:29:20 +11:00
Joseph Lizier 283dcb3b94 Adding a field to the object returned from local TE for spike trains which holds the ISI to previous (selected) source spike 2025-03-28 18:09:28 +11:00
Joseph Lizier cab3de8b07 Bug fix to local TE for spike trains code; forgot to increment the index when computing local values, fixed. 2025-03-28 15:15:30 +11:00
Joseph Lizier efd3943697 Implementing local TE contributions for the spiking estimator 2025-03-21 16:08:39 +11:00
Joseph Lizier 912bdf94e1 Flocking demo: comments added to properties file on how to handle individuals not being present at any given time step. 2024-11-04 12:21:22 +11:00
Joseph Lizier 5d4419d734 Batch file to setup a python virtual environment 2024-07-19 13:54:24 +10:00
Joseph Lizier a9b6b3e77c Adding property to set random seed for noise addition to EntropyMultiVariate estimators (mimicing that for MI/CMI estimators), extending the fix for issue #99 to Entropy estimators 2024-04-20 18:52:10 +10:00
Joseph Lizier 3d1f3fec86 Gathering common functionality of EntropyMultiVariate estimators into a Common class. Adds some new functionality (e.g. addObservations() for Gaussian and Kernel) 2024-04-20 17:57:38 +10:00
Joseph Lizier 2a18cd0e74 Adding property to allow used to set random seed for noise addition to data in MI, CMI and wrapped estimators. Closes issue #99 2024-04-16 14:08:04 +10:00
Joseph Lizier 2130985c34 Adding/implementing interfaces for continuous CMI estimators to allow all combinations of univariate/multivariate arrays to be passed for var1/var2/conditional 2023-10-27 10:04:25 +11:00
Joseph Lizier 7d8b501127 Adding new unit test for dynamic correlation exclusion, testing both an analytic result, and also the effect of using seperate observation sets 2023-10-10 22:38:21 +11:00
Joseph Lizier 4b85a7fd46 AIS and TE estimators (for KSG in particular) utilising the underlying NN Searchers holding the different data sets separately. 2023-10-09 13:16:27 +11:00
Joseph Lizier ec8e7f848f CMI common estimators utilising underlying nearest neighbour searchers holding different data sets separately (for dynamic correlation exclusion) 2023-10-09 13:15:56 +11:00
Joseph Lizier 5f87e2018b MI common estimators utilising underlying nearest neighbour searchers holding different data sets separately (for dynamic correlation exclusion) 2023-10-09 13:14:29 +11:00
Joseph Lizier 938dd7c4fb Implementing multiple data sets in the nearest neighbour searches, to facilitate dynamic correlation exclusion only for points within the same data set 2023-10-09 13:12:07 +11:00
Joseph Lizier a554361de9 Adding unit test for no conditional on CMI Gaussian 2023-10-06 12:29:37 +11:00
Joseph Lizier 4f5d8f894b Updating documentation to v1.6.1 minor release 2023-08-22 13:02:19 +10:00
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