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144 Commits

Author SHA1 Message Date
Pedro Martinez Mediano 641d17ec24 Fix bug with normalisation in KSG mixed and change unittest accordingly. 2017-08-16 19:18:51 +01:00
Pedro Martinez Mediano faa98a8d79 Added more references and tests for KSG mixed calc. 2017-08-16 18:21:24 +01:00
Pedro Martinez Mediano 1065662739 Added more tests to KSG mixed locals. 2017-08-16 14:51:33 +01:00
Pedro Martinez Mediano 8d1d1ab0eb Moarr tests for KSG mixed. 2017-08-16 10:24:00 +01:00
Pedro Martinez Mediano 9b42911c60 Add KSG mixed unit test comparing against analytical value. 2017-08-16 01:01:31 +01:00
Pedro Martinez Mediano dcd6314082 Add a few unit tests for KSG mixed calculator. 2017-08-16 00:26:53 +01:00
jlizier ea40f48bbc Adding new methods computePValueForGivenEstimate() and computeEstimateForGivenPValue to AnalyticMeasurementDistribution and implementing in ChiSquareMeasurementDistribution. Involves importing (and refactoring) a significantly larger chunk of commons.maths3 classes (and updating existing ones to latest 3.6.1 version for consistency). Also addresses issue #23 in changing the actual value of the ChiSquareMeasurementDistribution to be that of the information theoretic measurement rather than 2*N times it (which was the value that is actually chi squared distributed), which also necessitates changes to the Discrete and Gaussian calculators computeSignificance() methods. 2017-06-14 11:09:01 +10:00
Pedro Martinez Mediano c0a4a283fa Added junit test for GPU MI calculation with non-zero exclusion window. 2017-05-31 04:20:38 +10:00
Pedro Martinez Mediano 94bcfc1477 Added conditional to Java GPU tests to ignore test if GPU disabled. 2017-05-25 02:57:13 +10:00
Pedro Martinez Mediano 6af0e22030 Merge branch 'master' into gpu 2017-05-25 02:44:59 +10:00
Pedro Martinez Mediano b2c42563d0 GPU junit tests now run without debug mode to reduce printed statements. 
The debug statements are left commented for future reference.
 2017-05-24 22:14:46 +10:00
Pedro Martinez Mediano 991ef30a1e Removed spurious array print. 2017-05-24 22:13:19 +10:00
Pedro Martinez Mediano 09548028e0 Merge remote-tracking branch 'ghub/master'. This merges Joe's v1.3.1 master into Pedro's master. 2017-05-24 20:24:32 +10:00
Pedro Martinez Mediano 63f26a60fa Added Java+C tests for reorderings and random permutations. 2017-05-24 17:06:04 +10:00
Pedro Martinez Mediano c33436e69a Added Junit tests for surrogate reorderings. 2017-05-23 16:19:52 +10:00
Pedro Martinez Mediano f2d6674a4f Added a few debug mode prints. 2017-05-23 05:13:57 +10:00
Pedro Martinez Mediano 9b455f7ef4 Added first few GPU performance tests to measure speed-up wrt CPU. 2017-05-22 15:05:43 +10:00
Pedro Martinez Mediano 118e32d9ad Separated GPU MI unit tests to separate file. 2017-05-22 14:49:21 +10:00
Pedro Martinez Mediano 71589d1150 Added Java+C tests to check consistency of local MI calculations. 2017-05-19 18:20:03 +10:00
Pedro Martinez Mediano 5a07352969 Add unit tests inside Java for GPU code. 2017-05-19 06:39:57 +10:00
jlizier c311067fe6 Extending unit test for multivariate TE calculator to compare ensemble and setObservations methods 2017-03-24 23:27:53 +11:00
jlizier bf3f26cf18 Patching TE Calculator Multivariate via conditional mutual info, which was not running (at all) for proper multivariates. Now splits the handling of solely univariate data from multivariates. 2017-03-23 14:31:03 +11:00
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 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 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
Pedro Martinez Mediano a721f26734 Discrete conditional TE now supports different bases for each variable. 
Also added some generic unit tests.
 2016-06-01 18:54:57 +01:00
Pedro Martinez Mediano 6f87aed980 Added preliminary version of Ragwitz optimization in multivariate AIS calculator. 2016-04-19 18:22:02 +01:00
Pedro Martinez Mediano 3da629a817 Preliminary commit of multivariate AIS calculators and unit tests. Fully functional, but not tested enough. 2016-03-15 22:36:12 +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 a028fe4a4e Adding getProperty method to debug class so it compiles 2015-06-05 14:42:06 +00:00
joseph.lizier b45ada1d94 Added unit tests for Kraskov TE auto embedding via Ragwitz criteria -- verifies Issue 38. Also adds further tests for AIS auto embedding. 2015-06-05 06:51:23 +00:00
joseph.lizier 8393429e26 Adding unit tests for AIS Kraskov for auto-embedding as part of partial fix for Issue 38 2015-06-04 13:59:31 +00:00
joseph.lizier a6f0e2d2ed Added new unit test for KdTree to check validity of counting neighbours when one variable has been pre-checked, and different radii are used for each variable. Verifies issue 39. 2015-01-21 12:28:19 +00:00
joseph.lizier 33ea4f6136 Unit tests for Dynamic correlation exclusion, or Theiler window, in all Kraskov estimators, plus direct validation against values from using Theiler window in TRENTOOL. Validates issue 35 2014-11-25 12:34:49 +00:00
joseph.lizier ab1d0e0c94 Minor debug print change to unit test 2014-11-14 10:30:46 +00:00
joseph.lizier 7ee34fd8a1 Minor new debug prints in unit tests 2014-11-04 00:57:55 +00:00
joseph.lizier 12faf78200 New unit tests for new methods in nearest neighbour search classes to return collections of points within ranges via arrays, and to use additional criteria in searching or take arguments for one variable that has already been tested. 2014-11-03 04:58:14 +00:00
joseph.lizier 758d9dc0c9 Unit test for inlining norms in Nearest Neighbour search classes, and adding methods to return Collections of points within ranges 2014-10-31 12:04:12 +00:00
joseph.lizier 390e1cc6be Adding more debug prints to TE unit test 2014-10-30 04:40:13 +00:00
joseph.lizier 769bf1a15d Unit tests for Kraskov predictive information calculator. Also defines an abstract PI tester. 2014-10-30 04:27:46 +00:00
joseph.lizier 9aa0e9ca0e Unit tests for Kraskov multi-info calculators using fast neighbour search and common multi-info class. Additional mutual info unit test added also on larger data set, and unit tests for the UnivariateNearestNeighbourSearcher. 2014-10-30 04:24:42 +00:00
joseph.lizier 0849db5312 Additional unit test to verify issue 32 -- for neighbour search within different radii for each variable to the k-d tree class. 2014-10-15 10:42:32 +00:00
joseph.lizier 9ef43ae753 Verifies issue 32 -- adds unit test for neighbour search within different radii for each variable to the k-d tree class. This is used for fast neighbour search to Kraskov conditional MI calculators (and by implication to TE calculators). Existing unit tests for these calculators complete the verification. 2014-10-15 10:39:11 +00:00
joseph.lizier 58c812db4e Validation of bug fix re issue 31 -- unit test to ensure that surrogate TE calculations are different to the real calculation 2014-10-15 05:07:14 +00:00
joseph.lizier f09cc221a4 Verifies issue 31 -- adding unit tests for KdTree structure (in conjunction with existing unit tests for the results of MI calculations) 2014-10-15 04:49:40 +00:00
joseph.lizier 78852bcf2a Validates issue 29 with unit tests for multi-threading of Kraskov conditional MI calculators. Also adds more substantial unit tests for Kraskov transfer entropy compared to TRENTOOL results. 2014-09-16 01:41:36 +00:00
joseph.lizier 0505641479 Unit tests which Validates issue 28 with unit tests for multithreading on Kraskov MI calculators. 2014-09-12 12:16:43 +00:00
joseph.lizier 14645d0621 Appending suffix "Discrete" to all discrete calculators. Step 4 -- refactoring within unit tests 2014-08-14 03:31:58 +00:00
joseph.lizier 0ca9990833 Adding GPLv3 license statement to all code headers in the unit tests 2014-08-06 06:59:04 +00:00
joseph.lizier 8df5d8c277 Refactoring unit tests for discrete TE calculator to take source as first argument before destination (to match continuous calculators) 2014-08-05 12:46:14 +00:00
joseph.lizier 96a9cefccf Renaming unit test for (Apparent) TE discrete calculator to remove "Apparent" -- step 2 of 2 to rename inside the class. 2014-08-05 05:03:35 +00:00
joseph.lizier b204651227 Renaming unit test for (Apparent) TE discrete calculator to remove "Apparent" 2014-08-05 05:02:51 +00:00
joseph.lizier 4e141d1398 Adding unit test for (Apparent) TE discrete calculator. Will rename it to remove Apparent shortly ... 2014-08-05 05:02:02 +00:00
joseph.lizier 71b5983e5b Added unit test for linear-Gaussian TE estimator against values produced from the Granger causality estimator of the ChaLearn Connectomics Challenge Sample Code. 2014-07-29 07:03:26 +00:00
joseph.lizier b721dd79c0 Fixing compilation of moved unit test for mixed calculators package 2014-04-17 11:22:19 +00:00
joseph.lizier cce93f2d18 Moving (only) unit test for the mixed calculators package to reflect the package move 2014-04-17 11:21:12 +00:00
joseph.lizier 926f22992e Added unit tests for conditional TE continuous calculators. 
Added some more tests for TE Kraskov also.
 2014-04-17 06:00:54 +00:00
joseph.lizier 7d95954c55 Patched bug in interface for old Kernel AIs calculator (now in unit tests) 2014-04-08 11:27:10 +00:00
joseph.lizier 9cad2737af Added unit tests for TransferEntropyCalculatorMultiVariateViaCondMutualInfo and derived classes for Kraskov and Gaussian estimators. 2014-04-08 11:21:40 +00:00
joseph.lizier b81ccccee1 Added unit tests for TransferEntropyCalculatorViaCondMutualInfo implementations: Gaussian simply tests the computeStartAndEndTimePairs; Kraskov tests against TRENTOOL. 2014-04-07 05:33:30 +00:00
joseph.lizier 1827ec23c2 Fixed lack of initialisation of MI calculators in Kraskov MI unit tests 2014-03-26 05:09:20 +00:00
joseph.lizier 3e017d1be4 Added unit tests for Rearchitecting Active Info Storage calculators to use a common parent class for data collection. Mainly includes testing kernel AIS calculator against the older direct implementation of this (which is now moved into the unit test area only) 2014-03-26 04:07:13 +00:00
joseph.lizier 5d0934bd85 Updating unit tests to reflect changes to discrete MI calculator and method of generating random permutations. 2013-10-22 04:06:58 +00:00
joseph.lizier 6fe22e39cb Added unit tests for new method generateRandomPerturbations(int, int) in RandomGenerator, and for sortIndices(double[]) method to MatrixUtils 2013-10-18 00:45:46 +00:00
joseph.lizier 1d5ae4a176 Added unit test for bug fix to computeSignificance() of ConditionalMutualInformationCalculator, simply to make sure it doesn't throw an exception 2013-10-17 13:20:42 +00:00
joseph.lizier 9c03691c09 Predictive information calculator unit tests added 2013-08-13 04:33:45 +00:00
joseph.lizier 1c0e9098cc Extra unit test for Issue 16 2013-07-06 18:36:03 +00:00
joseph.lizier bc218e291c Added new unit test for Kraskov MI calculator against MILCA for large 10000 data points of dimension 5 in each x and y; added unit tests for digamma 2013-03-07 12:50:03 +00:00
joseph.lizier cb2e0a2588 New unit tests for covariance calculation (inside conditional MI linear Gaussian), making analytic linear Gaussian signficance tests take the number of observations into account 2013-03-04 06:11:43 +00:00
joseph.lizier 4671b15d61 Added more unit tests for Kraskov conditional MI against TRENTOOL (here for multivariate data, run with TRENTOOL as univariate TE but with history lengths k=2, l=2) 2013-01-22 03:37:42 +00:00
joseph.lizier 111055fc81 Added unit tests for Kraskov Conditional MI against TEs computed by Wibral et al.'s TRENTOOL 2013-01-16 11:54:13 +00:00
joseph.lizier 40e7d4b211 Added common unit tests for conditional MI calculators, and added implementations of the tests for Kraskov and Gaussian conditional MI calculators 2013-01-14 12:57:01 +00:00
joseph.lizier 74ba272f41 Added unit test for covariance 2013-01-08 05:38:22 +00:00
joseph.lizier 8fe32003ab Adding more unit testing on Kraskov MI, including for dependent data sets 2012-12-20 13:23:52 +00:00
joseph.lizier b0bc89dcb1 Made the unit tests for Kraskov MI more streamlined; added unit test for multivariate MI 2012-12-20 10:40:42 +00:00
joseph.lizier 90c0f5a105 Renaming abstract unit test classes inside java files (missed these in previous commit) 2012-12-18 10:57:44 +00:00
joseph.lizier 74ebf27fa0 Renaming abstract unit test classes inside java files 2012-12-18 10:53:03 +00:00
joseph.lizier 653b511c24 Renaming abstract unit test classes as first step to avoid ant file running them (next commit will update names inside java files) 2012-12-18 10:51:30 +00:00
joseph.lizier 23f7f84eaa Added common functionality for unit testing multivariate MI calculators into an abstract class. 
Added basic tester for Kraskov multivariate MI, including verifying against Kraskov MILCA tool
 2012-12-18 10:34:41 +00:00
joseph.lizier a6e09c7fc4 Pulled some common functionality for testing multivariate TE calculators into an abstract class. 
Added basic tester for Kraskov multivariate TE
 2012-12-13 14:50:33 +00:00
joseph.lizier b64b0c091d Adding unit tester for TECalculatorMultiVariateKernel 2012-12-13 12:27:42 +00:00
joseph.lizier aa991901f6 Adding 3x XOR test case for MI discrete 2012-09-05 06:37:13 +00:00
joseph.lizier 65c7ac49a6 Adding folder for testing discrete calculators; 
First version of unit tests for MI discrete
 2012-09-05 06:24:47 +00:00
joseph.lizier 4a19b41a76 Adding tests for determinant via Cholesky decomposition, and more tests for MI by Gaussian method 2012-08-17 07:30:08 +00:00
joseph.lizier e79dc34efb Added unit tests for MICalculatorMultiVariateWithDiscreteGaussian 2012-08-16 06:10:19 +00:00
joseph.lizier af37fdf621 Added MatrixUtilsText (pulled some tests out of MathsUtilsTest which should have been here) 
Added more tests for MI MultiVariate Gaussain
 2012-08-16 05:42:49 +00:00
joseph.lizier 7159ecd4cc Adding unit tests for MI Kernel and Gaussian calculators, to check that their average calculations do not change across calls to compute the statistical significance (where we clone the calculator to handle the surrogates). 2012-08-07 07:34:24 +00:00
joseph.lizier 4b3c84cd22 Added test for Cholesky decomposition, inversion of symmetric positive-definite matrices, and normal PDF/CDF 2012-08-06 07:45:50 +00:00
joseph.lizier 364ebfeff7 Changing name of unit test for Gaussian Entropy calculator internally to file (step 2/2) 2012-08-01 12:18:31 +00:00
joseph.lizier 7bdac9542d Changing name of unit test for Gaussian Entropy calculator 2012-08-01 12:15:16 +00:00
joseph.lizier eee753bc0b Adding unit tests for Chi Square distribution in MathsUtils and for Entropy Calculator Gaussian 2012-08-01 12:14:24 +00:00