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jidt
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381 Commits

Author SHA1 Message Date
jlizier b0d48bc96c Unit tests for conditional MI on new observations, and for no conditionals 2016-10-20 09:29:56 +11:00
jlizier 9a7ff306c8 Adding utilities for fast nearest neighbour searchers to handle calculations on new samples and prepare for conditional MI fast surrogates computation 2016-10-20 09:26:12 +11:00
jlizier 2d4e30aeb4 Minor bug patch for readFloatsFile for python demos 2016-10-18 15:09:59 +11:00
jlizier d74749f17d Showing how to use numpy arrays of ints with JIDT in python 3 with jpype1 in python demo 1 2016-10-18 15:08:15 +11:00
jlizier 0386991f00 Altering use of class methods for python demo 6 (I think this was required for python 3 compliance?) 2016-10-18 15:07:15 +11:00
jlizier 05beb63e58 Added unit test for AND function 2016-10-18 15:05:28 +11:00
jlizier 4cac043aff Added unit test for TE continuous getSeparateNumObservations (in Kraskov class) 2016-10-18 15:05:15 +11:00
jlizier e2182c40c2 Update to AIS kernel direct class in unit tests to align with update to AIS interface definition 2016-10-18 15:04:42 +11:00
jlizier 3118e57384 Making conditional MI calculators (continuous) handle empty conditionals, and properly normalise new data according to the old (except for linear Gaussian calculator, which explicitly bars normalisation now). 2016-10-18 13:21:29 +11:00
jlizier b01c01ca3b Ant script now builds class files for the auto-analyser and includes these in the distribution. Also a patch to stop errors when the JIDT-logo file is not found (in zip dists) 2016-10-18 12:53:26 +11:00
jlizier e0fb7de856 Added auto-embedding method for AIS and TE Kraskov (KSG) calculators which maximises the bias-corrected AIS. This commit includes the AIS and TE calculators themselves, an update to the TE auto analyser (with comments on the auto embed method property) 2016-10-18 12:52:31 +11:00
jlizier 0ed74612a7 Altering kernel estimator classes so that the return values for getProbability are proper probability densities rather than probabilities (by now dividing by the kernel diameter/volume). This patches the EntropyCalculatorKernel and the EntropyCalculatorMultiVariateKernel to properly return differential entropy, as advertised. Makes no difference to the MI and TE kernel calculators, as they use counts anyway rather than probability densities. 2016-10-18 11:56:38 +11:00
jlizier 7d28e93913 Bug fix in mixed Kraskov implementation for computeUsingPreviousObservations (picked up by Rose Wang). Also acknowledged that this implementation is (mostly) as per Ross 2014. 2016-10-18 00:18:37 +11:00
jlizier 9785e2a71f Enabled Active Info Storage calculators (continuous) to have addObservations() methods with validity supplied 2016-10-18 00:11:33 +11:00
jlizier 16239d3c3e Added method getSeparateNumObservations() to return a list of how many samples were pulled from each addObservations call, to make reconstructing/separating local values easier subsequently 2016-10-18 00:00:31 +11:00
jlizier 08d380398b For MultiInfoCalculatorDiscrete added simple interface for adding joint observations 2016-10-17 16:32:18 +11:00
jlizier 77cf8e5f8e Major update to TransferEntropyCalculatorDiscrete so as to implement arbirtray source and dest embeddings and source-dest delay. Also included are associated unit tests, and modifications to MatrixUtils to support these. 2016-10-17 16:22:59 +11:00
Joseph Lizier 13952302c1 Fixed links in README.md 2015-08-20 23:59:01 +10:00
Joseph Lizier 47eb1fc3ad Fixing links on README.md 2015-08-20 23:55:10 +10:00
Joseph Lizier 4ba8a48439 added under construction banner 
... while I'm getting the wiki up properly ...
 2015-08-19 23:51:40 +10:00
Joseph Lizier 779f5a1fe2 Created README.md 
created from the converted google code wiki front page
 2015-08-19 23:47:26 +10:00
joseph.lizier cb147feb75 Correcting readme for Schreiber TE demos 2015-07-19 17:29:43 +00:00
joseph.lizier 6ffe643439 Adding release notes to the readme file ready for release v1.3 2015-07-19 17:26:07 +00:00
joseph.lizier dbd1dcdd54 Fixing the bias correction on our experimental discrete-continuous KSG calculators 2015-07-19 17:19:59 +00:00
joseph.lizier adafad05a2 Updating tutorial slides as for ECAL, plus some minor updates to some figures and PDFs found while developing tutorial 2015-07-19 17:17:26 +00:00
joseph.lizier f23b0c6abb Adding MI Auto Analyser GUI, plus minor bug corrections to TE Auto Analyser GUI 2015-07-12 19:54:14 +00:00
joseph.lizier ed34c39660 Had to correct the auto analyser scripts for TE to call TE specifically again 2015-07-09 14:46:30 +00:00
joseph.lizier 6f8050d466 Making AutoAnalyser an abstract class with AutoAnalyserTE a child; this builds platform to allow an AutoAnalyserMI later 2015-07-09 14:43:47 +00:00
joseph.lizier f6c8d26bf8 Minor fixes to default values of TE calculator properties, and adding error messages for array file reading 2015-07-09 14:38:23 +00:00
joseph.lizier 1aa9def942 Renaming scripts to run auto generated code (in preparation for extending auto generation to MI as well as TE) 2015-07-09 14:13:58 +00:00
joseph.lizier bbbc835c1f Correcting method of deleting auto-generated AutoAnalysis files in ant clean target 2015-07-07 15:03:15 +00:00
joseph.lizier 4f88161873 Deleting auto generated AutoAnalysis files in the ant clean target 2015-07-07 14:58:01 +00:00
joseph.lizier 3f3c737ddd Updating PDFs of Demos for next release. Also updated Schreiber TE demo to add section about auto-embedding. And updated release notes and svn number in build file. 2015-07-07 14:51:04 +00:00
joseph.lizier 2974916948 Extended AutoAnalyser GUI demo to work with discrete TE calculator as well. Also added a sample discrete data set 2015-07-03 13:01:38 +00:00
joseph.lizier d4af4f127e Updating demos readme PDF, adding readme for AutoAnalyser (this now is the final step such that it fixes Issue 41), and updating the readme about the new demo 2015-07-02 13:57:30 +00:00
joseph.lizier 4c587e51d9 Updating image of AutoAnalyser GUI app before calculation for wiki page (to include some tooltiptext) 2015-07-02 13:46:45 +00:00
joseph.lizier a1eb606f12 Adding image of AutoAnalyser GUI app after calculation for wiki page 2015-07-02 13:29:02 +00:00
joseph.lizier 4e00f96647 Adding image of AutoAnalyser GUI app for wiki page 2015-07-02 13:16:40 +00:00
joseph.lizier 745aa5f20f Finalising move of AutoAnalyser up to the top of demos level, including changing paths in the java file for the demo 2015-07-01 14:28:12 +00:00
joseph.lizier f4c5591cd2 Moving files to the new AutoAnalyser demo location 2015-07-01 14:06:16 +00:00
joseph.lizier 75fca70768 Gold plating the AutoAnalyser demo to have comments in generated code, JIDT image, tool tip text for properties, etc. 2015-07-01 13:46:31 +00:00
joseph.lizier 3d4765ea6b Matlab and Python code generation added to the AutoAnalyser GUI 2015-06-29 06:49:43 +00:00
joseph.lizier 53a3cf129d First full working version of the TE Auto Analyser, including scripts to run auto generated Java code 2015-06-29 04:57:38 +00:00
joseph.lizier 6951f52f68 First version of TE Auto Analyser Java Swing GUI 2015-06-23 00:58:57 +00:00
joseph.lizier e727233bc0 Updating unit tests for small noise being default now in KSG calculators. (The update sets noise level to 0 wherever we are checking repeated calculations, or comparing to results from other toolkits). Verifies Issue 42 fix 2015-06-16 12:30:19 +00:00
joseph.lizier bb587fa345 Also allowing the KSG calculators noise property to be set to "false" to indicate 0 noise. 2015-06-16 12:27:56 +00:00
joseph.lizier c4fc334c3a Adds a small (1e-8) amount of noise to all data for the Kraskov calculations by default. Fixes Issue 42. 2015-06-16 12:01:41 +00:00
joseph.lizier 192ad12bb2 Updating python code to be compatible with both python 2 and 3. (Includes changing xrange -> range, and removing ";", as found by Michael Wibral) 2015-06-10 11:37:15 +00:00
joseph.lizier 2928dafa12 Adding new Java demo 9 for auto-embedding of Kraskov TE 2015-06-05 14:48:03 +00:00
joseph.lizier a028fe4a4e Adding getProperty method to debug class so it compiles 2015-06-05 14:42:06 +00:00