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338 Commits

Author SHA1 Message Date
jlizier 1f625b59f0 AutoAnalyser: fixing bug where column numbers for data are all set to zero if the user unclicks the "compute result?" button 2018-05-07 22:57:10 +10:00
jlizier d1bba0e4c1 Adding computeLocalOfPreviousObservations() to continuous Entropy estimator interface and all underlying implementations. Added unit tests that locals should average back ok. Also fixing multivariate Entropy estimator interface to implement the univariate interface also (and fixing underlying implementations to comply) 2018-04-27 11:20:25 +10:00
jlizier bf0062b902 Switching new debug method in KSG conditional MI calculator 1 to be publicly accessible 2018-04-26 11:43:04 +10:00
jlizier 7d76f82bb2 Adding partialNeighbourCountFromObservations() method to KSG conditional MI calculator 1 for debugging investigations into the neighbour counts 2018-04-26 11:24:56 +10:00
Pedro Martinez Mediano df8eec27cd Added MAX_CORR_AIS_AND_TE embedding to univariate KSG TE calculator. 2018-04-22 22:25:05 +01:00
Pedro Martinez Mediano f8bca3275d Fixed docs for new MAX_CORR_AIS_AND_TE embedding method. 2018-04-22 20:45:06 +01:00
Pedro Martinez Mediano 02dad26a94 Added brief mention of AUTO_EMBED_METHOD_MAX_CORR_AIS_AND_TE to javadocs. 2018-02-27 20:29:39 +00:00
Pedro Martinez Mediano 5f6671aa2b Added AUTO_EMBED_METHOD_MAX_CORR_AIS_AND_TE to multivariate KSG TE. 2018-02-27 20:18:04 +00:00
Pedro Martinez Mediano 550ff793eb Fixed bug in KSG TE multivariate embeddings and setObservations. 2018-02-27 20:14:08 +00:00
Pedro Martinez Mediano 8be6a037af Added auto-embedding methods to multivariate KSG TE calculator. 2018-02-25 19:23:09 +00:00
Pedro Martinez Mediano ce4b1599c6 Added MAX_CORR_AIS embedding method to multivariate KSG AIS. 2018-02-25 18:57:15 +00:00
Pedro Martinez Mediano 75bb2c814a Added addObservations-related methods to multivariate TE calculators. 
This is needed to implement auto-embedding methods later.
 2018-02-25 18:54:36 +00:00
Pedro Martinez Mediano b0fc309d6a Add overloadings for 1d continuous variables in KSG mixed calc. 2018-01-12 22:22:46 +00:00
jlizier 0278f95ae9 Enabled use of USE_GPU property for KSG calculators in the AutoAnalysers for CMI, TE, CTE and AIS 2017-12-30 12:03:17 +11:00
Pedro Martinez Mediano 64f1142b40 Added argument to choose which variable to reorder in GPU CMI code. 2017-12-19 20:42:58 +00:00
Pedro Martinez Mediano 65ac0e9ff8 Removed unnecesary overloaded method in KSG CMI calc. 2017-12-19 20:41:11 +00:00
Pedro Martinez Mediano 2f1cd192b8 Fixed small typo in Java KSG CMI calculator. 2017-12-18 17:50:37 +00:00
Pedro Martinez Mediano d0304ae0c4 Added Java-side JNI functions and ensureKdTreesConstructed to KSG CMI. 2017-12-12 11:19:40 +00:00
Pedro Martinez Mediano f4ca442de4 Now KSG MI calc does not build KdTrees if GPU is going to be used. 2017-12-12 11:10:50 +00:00
Pedro Martinez Mediano d010f32635 Updated getProperty and removed spurious dependency in KSG MI calc. 2017-12-12 11:04:32 +00:00
Pedro Martinez Mediano eabd7f3701 Fixed typo in Kozachenko entropy calculator. 2017-11-28 16:58:13 +00:00
Pedro Martinez Mediano 444fb70801 Added addObservations-type functions to Kozachenko entropy calculator. 2017-11-28 16:56:51 +00:00
Pedro Martinez Mediano e290040d8d Added docs to Kozachenko entropy calculator. 2017-11-28 16:26:46 +00:00
Pedro Martinez Mediano 35df6ca3da Kozachenko entropy estimator now adds noise to data by default. 2017-11-28 16:04:09 +00:00
jlizier 9c96ceb850 Fixed logic for when parameter values (in particular auto-embedded properties) are written back into the properties table after the calculation. This was happening only when we had the "all pairs" option selection, when it should only happen when this is not selected. 2017-11-28 12:36:06 +11:00
jlizier 589d51674e Altering the escaped data filename in AutoAnalyser to be properly escaped using non-regex replace, and also rolling back the use of escaping to only Java (Matlab and Python on windows seem fine with the non-escaped filenames, for e.g. the paths earlier in the generated code) 2017-11-27 10:19:36 +11:00
jlizier 3bfbaa7ad3 In AutoAnalyser escaping data filenames when they are written to the generated code. This is important for windows filenames. Am not sure why it didn't come up before as an issue though. 2017-11-27 09:57:07 +11:00
jlizier 61f4bf3276 Adding getProperty lines to handle USE_GPU property for KSG MI calculator 2017-11-27 09:26:19 +11:00
jlizier db0503d763 Having AutoAnalyser continue with the calculation where the generated code cannot be written 2017-11-26 18:04:29 +11:00
jlizier df8724b872 Altered AutoAnalyserLauncher to either auto-detect jar location or assume demos/AutoAnalyser folder is current location (if a command line argument is given). Similarly, altered AutoAnalyser to either take location of demos/AutoAnalyser folder, or assume it is the current folder. 2017-11-26 01:10:30 +11:00
jlizier fd804d0d0c Added properties for running GPU calculation to MI AutoAnalyser 2017-11-26 01:07:19 +11:00
jlizier 69af7252cd Added debug print on working directory to AutoAnalyser startup 2017-11-25 00:15:37 +11:00
jlizier ddf3b4de0a Moving AutoAnalyser java files into the main source location rather than in the demos location. This commit includes the moving of the files themselves. Further commits will alter the ant script and run scripts to have correct classpath, etc. 2017-11-24 21:07:33 +11:00
jlizier 142fbb4541 Merge branch 'master' of github.com:jlizier/jidt 
Merging in Pedro's mixed Kraskov changes, plus further work on GPU for Kraskov MI
 2017-11-24 15:30:20 +11:00
jlizier 9e77ebdadf Tweak to method to print out an array of ints 2017-11-22 20:49:05 +11:00
jlizier 1bb67f0840 Adding neighbour search utilities in preparation for attempting fast surrogate generation (performing multiple neighbour searches at once where we can); in particular adding a countPointsWithinR with a remapping of the point's indices. Unit test added as well for this. 2017-11-22 20:48:30 +11:00
Pedro Martinez Mediano 446ac4ae59 Merge branch 'master' into gpu 2017-11-21 14:58:15 +00:00
Joseph Lizier c5c38335ef
Merge pull request #58 from pmediano/master 
Major improvements to KSG mixed (continuous-discrete) MI calculator.
 2017-11-22 00:23:10 +11:00
Pedro Martinez Mediano ecda70f8e9 Hard-setting dynCorrExclTime to 0 in KSG mixed calc. 
Previous implementation was incomplete due to a mismatch between the
sample indices in the full and marginal KdTrees. Some code has been left
to guide future development.
 2017-11-20 14:47:00 +00:00
Pedro Martinez Mediano 25df49fa5a KSG mixed calc now allocates memory for locals only if requested. 2017-11-20 14:26:25 +00:00
Pedro Martinez Mediano 8f169171e1 Fixed small bug in KSG mixed calc surrogates. 
Surrogate calculator was applying timeDiff twice, so surrogate
dataset had abs(timeDiff) less observations than it should.
 2017-11-20 14:14:49 +00:00
Pedro Martinez Mediano d40024e1cd Allow negative timeDiff in KSG mixed calc. 2017-11-20 14:02:00 +00:00
jlizier 0e27dbcbc2 Fixed default value of dynamic exclusion window in Kernel MI calculator to be 0. Technically it is zero (because dynCorrExcl boolean is set to false, but gets reported as 100 because the integer value of dynCorrExclTime was not set to 0 itself) 2017-09-02 20:18:36 +10:00
Pedro Martinez Mediano ed71502bc2 Remove old cudaLibraryLoad code and unnecessary dependencies. 2017-08-31 16:22:12 +01:00
Pedro Martinez Mediano 83e77e8b3a Merge Joe's master into Pedro's master with KSG mixed changes. 2017-08-30 17:36:32 +01:00
Pedro Martinez Mediano f56ac6e69e Fix bug with Theiler window in KSG mixed calc. 2017-08-30 13:30:30 +01:00
Pedro Martinez Mediano 5961fb6246 Add Theiler window and jitter to KSG mixed calc. 2017-08-30 12:17:02 +01:00
jlizier d36c803e41 Added utilities to convert between estimate values and p-values for an analytic null distribution in bulk (array calls) 2017-08-30 16:24:17 +10:00
Pedro Martinez Mediano 626293b84d More docs for KSG mixed calc. 2017-08-30 01:19:54 +01:00
Pedro Martinez Mediano e11218631e Added myself as author of KSG mixed calculator. 2017-08-29 23:56:28 +01:00