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219 Commits

Author SHA1 Message Date
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 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
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 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
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 72024c7299 Updating demo PDFs and version number ahead of new v1.6 distribution 2022-09-05 17:43:14 +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 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 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
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
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 41361417ae Updates to flocking demo including plotting local TEs per individual per time frame 2022-03-31 12:14:16 +11:00
Joseph Lizier 898a04904c Added Matlab script to launch the AutoAnalyser - will be useful for Matlab users who don't have a separate JRE installed 2021-09-09 11:12:46 +10:00
Joseph Lizier 2caab8593e Adding option for generated CA cells to be stochastically altered in CA utility code 2021-09-06 12:51:14 +10:00
Joseph Lizier 5da70db3ae Updating readme pdfs for various demos from the JIDT wiki 2021-09-06 12:49:50 +10:00
Joseph Lizier 70a7f5c33a Clarifying how to access an attribute (pValue) in the R demos 2021-04-19 11:32:23 +10:00
Joseph Lizier 8ecb512ce0 Updating flocking analysis to save AIS/TE from all parameters tested in an autoembedding process 2020-09-03 22:20:03 +10:00
Joseph Lizier 4c95b4ee86 Updating Flocking analysis demo to have more aggressive dynamic correlation exclusion. Also adding utility to plot the raw positions of the floc 2020-09-01 11:22:31 +10:00
Joseph Lizier 820f700cb8 Fixed python write file utilities to work with unidimensional arrays 2020-05-21 00:19:16 +10:00
Joseph Lizier 471ea59bb2 Adding utilities for writing text files in python (can be done with numpy, but just making something quick my way) 2020-05-20 23:46:55 +10:00
Joseph Lizier edb8f997cb Added new loader file for 2D xls format to flocking analysis demo 2019-12-17 17:08:27 +11:00
Joseph Lizier 2c2d012e20 Sooraj Sekhar's addition to flocking analysis of allowing speed to be included in the information-theoretic calculations. Includes updated NetLogo demo where speed coherence is also added 2019-12-13 11:40:58 +11:00
Joseph Lizier 4966fdabc2 Adding a code suite to run active information storage and transfer entropy analysis of positional / heading data from swarms/flocks/schools, including a demonstration of how to use the suite with a NetLogo example. Documentation on a wiki page to follow later ... 2019-08-29 23:08:16 +10:00
Joseph Lizier 17bf0e0be7 Updating octave-java interface to use non-overloaded method signatures for int and boolean arrays (this seemed to have caused an issue on some versions with ints being converted to boolean first, thus losing all values except 0-1) 2019-07-23 11:33:04 +10:00
Joseph Lizier 1d2c7c42b9 Updating javaMatrixToOctave to handle new conversion routine in octave (and be backwards compatible to old) 2019-03-21 09:35:41 +11:00
Pedro Martinez Mediano 4908276333 GPU tests and example now compute multiple surrogates. 2018-11-25 19:45:48 +02:00
jlizier a3ec963618 Updating demos PDFs again 2018-11-25 23:38:49 +11:00
jlizier 603445651c Moving GPU readme from wiki into CUDA folder 2018-11-25 23:27:27 +11:00
jlizier 7bd6496a40 Removed old .sh and .bat files for running AutoAnalyser for individual measures (now replaced by launchAutoAnalyser) 2018-11-25 22:38:08 +11:00
jlizier cd1d4c2684 Adding executable permission to Java demo 10 for GPU 2018-11-25 21:57:25 +11:00
jlizier 3c24debea5 Updating PDFs of wiki pages of all demos to make sure they are up to date; includes adding the new wiki page for GPU 2018-11-25 21:47:41 +11:00
jlizier 1c2082e74a Adding a new data set with 2 step Gaussian self dependence plus noise 2018-08-27 14:09:16 +10:00
jlizier d69d503492 Allowing figure number to be specified in plotOptions for Matlab/Octave plotLocalInfoMeasureFoooorCA 2018-08-21 20:54:41 +10:00
jlizier a4b9f20801 Java matrix to matlab conversion was accidentally falling through to element by element; was correct but slow. Fixed this, should be more efficient now 2018-08-20 10:30:28 +10:00
jlizier 97e46c66a3 Added extract of SFI heart rate - breath rate file, for simpler analysis of only a clean part of the data. 2018-08-10 15:52:15 +10:00