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https://github.com/OHBA-analysis/HMM-MAR
29 August 2022, 04:57:29 UTC
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Revision Author Date Message Commit Date
d99f8f9 GilesColclough 11 February 2016, 16:35:11 UTC Merge branch 'develop-MEX' of github.com:OHBA-analysis/HMM-MAR into develop-MEX 11 February 2016, 16:35:11 UTC
fbb3253 GilesColclough 11 February 2016, 16:34:31 UTC Updated linux install instructions after testing on hbaws23. 11 February 2016, 16:34:31 UTC
6959078 Giles Colclough 11 February 2016, 12:39:20 UTC Updated readme Signed-off-by: Giles Colclough <giles.colclough@gmail.com> 11 February 2016, 12:39:20 UTC
7739885 Giles Colclough 11 February 2016, 12:34:34 UTC Adjusted hsinference to use mex Mex file now works for all orders. Adjusted main code to take account of this. Signed-off-by: Giles Colclough <giles.colclough@gmail.com> 11 February 2016, 12:34:34 UTC
1d61002 Giles Colclough 11 February 2016, 12:33:40 UTC Added readme to project Signed-off-by: Giles Colclough <giles.colclough@gmail.com> 11 February 2016, 12:33:40 UTC
7bef8ad GilesColclough 11 February 2016, 12:28:59 UTC Updated linux mex file to version which can deal with all orders. 11 February 2016, 12:28:59 UTC
8ab78fa Giles Colclough 11 February 2016, 12:22:45 UTC Merge branch 'develop-MEX' of ssh://github.com/OHBA-analysis/HMM-MAR into develop-MEX 11 February 2016, 12:22:45 UTC
4073b72 Giles Colclough 11 February 2016, 12:22:00 UTC Fix issues with order != 0 The code should now run cleanly, replicating results from matlab, for all values of order parameter Signed-off-by: Giles Colclough <giles.colclough@gmail.com> 11 February 2016, 12:22:00 UTC
80f3793 GilesColclough 11 February 2016, 10:19:25 UTC Removed documentation User can add the documentation themselves, by running make docs. 11 February 2016, 10:19:25 UTC
ec664a2 GilesColclough 11 February 2016, 10:13:57 UTC Revert "Remove docs" Accidentaly removed the linux folder. This commit reverts that process. Desired change will be implemented next. This reverts commit 66b91f72f40e7c06fcdb9d5f3ed40a2c63abd9a7. 11 February 2016, 10:13:57 UTC
66b91f7 Giles Colclough 10 February 2016, 18:06:46 UTC Remove docs User can build themselves. Signed-off-by: Giles Colclough <giles.colclough@gmail.com> 10 February 2016, 18:06:46 UTC
6397461 Giles Colclough 10 February 2016, 18:02:05 UTC Now working mex compilation on linux and mac Signed-off-by: Giles Colclough <giles.colclough@gmail.com> 10 February 2016, 18:02:05 UTC
1a7daaf Giles Colclough 10 February 2016, 17:39:38 UTC interface fix Mex file only works for order=0 atm. Prevented user accidentally encountering errors Signed-off-by: Giles Colclough <giles.colclough@gmail.com> 10 February 2016, 17:39:38 UTC
16c2aa1 GilesColclough 10 February 2016, 17:29:44 UTC File now can use compiled mex version 10 February 2016, 17:29:44 UTC
bf72503 GilesColclough 10 February 2016, 17:29:19 UTC Finished moving files and setting up compilation on linux 10 February 2016, 17:29:19 UTC
f96f5d7 Giles Colclough 10 February 2016, 14:41:52 UTC Doc change Missed a bit Signed-off-by: Giles Colclough <giles.colclough@gmail.com> 10 February 2016, 14:41:52 UTC
36bee98 Giles Colclough 10 February 2016, 14:41:41 UTC Updated documentation To take account of new test subfolder Signed-off-by: Giles Colclough <giles.colclough@gmail.com> 10 February 2016, 14:41:41 UTC
b379efe Giles Colclough 10 February 2016, 14:28:05 UTC continuing glnx development Signed-off-by: Giles Colclough <giles.colclough@gmail.com> 10 February 2016, 14:28:05 UTC
ac7f482 Giles Colclough 10 February 2016, 14:27:12 UTC Attempt to compile on linux Will it work without c++11, and compiled against blas, lapack, arpack? Signed-off-by: Giles Colclough <giles.colclough@gmail.com> 10 February 2016, 14:27:12 UTC
a35c363 GilesColclough 10 February 2016, 12:40:03 UTC making it work on linux 10 February 2016, 12:40:03 UTC
e76c552 Giles Colclough 10 February 2016, 11:49:16 UTC Moving to c++98 Because c++11 is not supported on SLES11 Signed-off-by: Giles Colclough <giles.colclough@gmail.com> 10 February 2016, 11:49:16 UTC
53b2033 GilesColclough 09 February 2016, 13:58:00 UTC more test file reorg 09 February 2016, 13:58:00 UTC
15ce61c GilesColclough 09 February 2016, 13:57:09 UTC Added test files and reorganised 09 February 2016, 13:57:09 UTC
fc9bf95 Giles Colclough 05 February 2016, 13:30:14 UTC Added check for mac OS The mexfile only works on MAC atm. Signed-off-by: Giles Colclough <giles.colclough@gmail.com> 05 February 2016, 13:30:14 UTC
a7a4293 Giles Colclough 05 February 2016, 13:26:59 UTC Hidden state inference mex project Added C++ files, make files and mex files, with documentation in html and tex, to speed up the hidden state inference process. Signed-off-by: Giles Colclough <giles.colclough@gmail.com> 05 February 2016, 13:26:59 UTC
a9ef366 Giles Colclough 05 February 2016, 13:17:31 UTC Added option to use mex function It looks like this function gives a roughly x8 speedup for small datasets Signed-off-by: Giles Colclough <giles.colclough@gmail.com> 05 February 2016, 13:17:31 UTC
de009bc Giles Colclough 05 February 2016, 13:04:42 UTC Fixed typo On number of arguments: generalised to account for changes in output argument. Signed-off-by: Giles Colclough <giles.colclough@gmail.com> 05 February 2016, 13:04:42 UTC
003ed2b dvidaurre@gmail.com 05 February 2016, 10:23:34 UTC Completion of the last commit 05 February 2016, 10:23:34 UTC
4cafdc1 dvidaurre@gmail.com 05 February 2016, 10:12:30 UTC Bug in the errors of the MAR spectra 05 February 2016, 10:12:30 UTC
476f291 dvidaurre@gmail.com 04 February 2016, 18:15:42 UTC Accelerated multitaper errors' computation applies when options.p>0 04 February 2016, 18:15:42 UTC
af9cf9e dvidaurre@gmail.com 04 February 2016, 17:47:11 UTC Update on the BigHMM algorithm 04 February 2016, 17:47:11 UTC
132c80b dvidaurre@gmail.com 04 February 2016, 16:45:17 UTC Fixed bug when mean is not modelled and there is only one channel 04 February 2016, 16:45:17 UTC
d309fa8 Giles Colclough 04 February 2016, 11:33:57 UTC hsinference.m Ouput log probabilities Signed-off-by: Giles Colclough <giles.colclough@gmail.com> 04 February 2016, 11:33:57 UTC
7ad0e55 Diego Vidaurre 03 February 2016, 22:24:59 UTC Delete HMM-MAR Manual.pdf 03 February 2016, 22:24:59 UTC
1711f77 dvidaurre@gmail.com 03 February 2016, 22:14:09 UTC Sign disambiguation of M/EEG source-reconstructed data Added an utility (unflipchannels.m) to flip the sign of some channels/subjects, in order to solve the sign ambiguity problem produced by M/EEG source reconstruction. 03 February 2016, 22:14:09 UTC
53c9cad Giles Colclough 03 February 2016, 14:56:14 UTC Merge branch 'master' of ssh://github.com/OHBA-analysis/HMM-MAR 03 February 2016, 14:56:14 UTC
8640ae7 Giles Colclough 03 February 2016, 14:53:28 UTC DTF Added computation of DTF non-parametrically Signed-off-by: Giles Colclough <giles.colclough@gmail.com> 03 February 2016, 14:53:28 UTC
852de02 Giles Colclough 03 February 2016, 14:53:08 UTC Added manual Signed-off-by: Giles Colclough <giles.colclough@gmail.com> 03 February 2016, 14:53:08 UTC
7c70b8d dvidaurre@gmail.com 01 February 2016, 14:04:45 UTC little mistake in the PDC error bar calculations of the parametric estiamtion 01 February 2016, 14:04:45 UTC
173138e dvidaurre@gmail.com 01 February 2016, 11:47:31 UTC removing debugging output 01 February 2016, 11:47:31 UTC
b509506 dvidaurre@gmail.com 01 February 2016, 11:40:25 UTC Fixed a bug in the BigHMM, in the computation of the covariance matrix of the coefficients (and other stuff about style) 01 February 2016, 11:40:25 UTC
b284f51 dvidaurre@gmail.com 30 January 2016, 18:06:56 UTC Changed MAR spectra so that the diagonals of the PSD are presented in its absolute value, and change of default value for completelags to 1 30 January 2016, 18:06:56 UTC
6402933 dvidaurre@gmail.com 25 January 2016, 18:40:30 UTC Added some regularisation in the the initialisation to prevent overflow in the first iteration when data is too extreme 25 January 2016, 18:40:30 UTC
9ccc216 dvidaurre@gmail.com 19 January 2016, 18:14:56 UTC Introduced a stochastic variational optimization strategy to make possible the computation of the Gaussian (order=0) HMM for massive data sets, with very high number of subjects 19 January 2016, 18:14:56 UTC
7c31eb7 dvidaurre@gmail.com 19 January 2016, 18:13:24 UTC The normalisation in the entropy calculation of P(X_t |X_t-1) had a little error - fixed 19 January 2016, 18:13:24 UTC
6fbe7a9 dvidaurre@gmail.com 18 January 2016, 17:58:43 UTC remove annoying output introduced in the last commit 18 January 2016, 17:58:43 UTC
2093572 dvidaurre@gmail.com 18 January 2016, 17:54:59 UTC Fixed little mistake in the computation of the state time course entropy (makes little difference) 18 January 2016, 17:54:59 UTC
703aa87 dvidaurre@gmail.com 17 January 2016, 12:29:08 UTC Added the possibility to complete to the full set of lags when computing the parametric spectra 17 January 2016, 12:29:08 UTC
a311243 dvidaurre@gmail.com 30 December 2015, 18:34:03 UTC Fixed a couple of things when the covariance matrix is not subject-specific 30 December 2015, 18:34:08 UTC
3bff6b8 woolrich 18 December 2015, 19:31:15 UTC statepath is returned as empty if Gamma is passed in 18 December 2015, 19:31:15 UTC
f868c2d woolrich 18 December 2015, 17:56:38 UTC Added option sim_state_tcs_only to avoid computing X if not needed, and also now returns the statepath 18 December 2015, 17:56:43 UTC
1d8b955 dvidaurre@gmail.com 10 December 2015, 11:28:45 UTC Included tool to compute the transition probability matrix for separated segments of the data 10 December 2015, 11:28:45 UTC
e413a78 dvidaurre@gmail.com 01 December 2015, 13:59:15 UTC GMM initialisation has been modified so that it doesn't break when the data is poorly conditioned 01 December 2015, 13:59:15 UTC
d0a3137 dvidaurre@gmail.com 23 November 2015, 16:31:43 UTC Introduced the possibility of using the multitaper/MAR frequency analysis for stationary signals, where no segmentation has been performed 23 November 2015, 16:31:43 UTC
d6b8472 dvidaurre@gmail.com 18 November 2015, 13:58:17 UTC Corrected dumb typo introduced in last commit 18 November 2015, 13:58:17 UTC
dd93c64 dvidaurre@gmail.com 18 November 2015, 11:08:46 UTC Small bug corrected in the computation of the state time courses entropy (free energy) 18 November 2015, 11:08:46 UTC
cafe533 dvidaurre@gmail.com 18 November 2015, 11:08:08 UTC Small bug corrected in the kullback leibler divergence between gamma distributions 18 November 2015, 11:08:08 UTC
f2938ed dvidaurre@gmail.com 18 November 2015, 10:49:16 UTC tweak to make computations faster when the number of channels is high 18 November 2015, 10:49:16 UTC
948f5f1 dvidaurre@gmail.com 18 November 2015, 10:47:31 UTC Netlab modified to suppress annoying screen output 18 November 2015, 10:47:31 UTC
763b519 dvidaurre@gmail.com 17 November 2015, 13:19:36 UTC Delete temporal files 17 November 2015, 13:19:36 UTC
c013f20 dvidaurre@gmail.com 14 November 2015, 09:52:33 UTC Fixed small bug in the computation of the entropy of the state time courses (evaluation of the free energy) 14 November 2015, 09:52:33 UTC
0016d95 dvidaurre@gmail.com 06 November 2015, 19:55:50 UTC Corrected bug when the number of channels is 1 06 November 2015, 19:55:50 UTC
b38a86e dvidaurre@gmail.com 06 November 2015, 18:47:06 UTC Removed a pedantic control of the type of covariance matrix when the number of channels is 1 (when it is specified to be full or uniquefull it does not give an error, and just corrects it to be diagonal) 06 November 2015, 18:47:06 UTC
de80c34 dvidaurre@gmail.com 05 November 2015, 15:14:43 UTC Solved bug in hmmspectramar 05 November 2015, 15:14:43 UTC
5db1079 dvidaurre@gmail.com 05 November 2015, 12:20:10 UTC Added the possibililty of using a Bayesian estimation of the MARs in hmmspectramar 05 November 2015, 12:20:10 UTC
70951b1 dvidaurre@gmail.com 05 November 2015, 11:17:36 UTC Small change in mlhmmmar to ease compatibility with older versions of the software 05 November 2015, 11:17:36 UTC
27c7527 dvidaurre@gmail.com 04 November 2015, 17:29:38 UTC Added a missing scaling factor in the parametric spectra estimation - function hmmspectramar 04 November 2015, 17:29:38 UTC
2bb3ad5 dvidaurre@gmail.com 03 November 2015, 09:37:44 UTC Add .gitignore, to ignore *.m~ files 03 November 2015, 09:37:44 UTC
dc32f59 dvidaurre@gmail.com 02 November 2015, 18:49:25 UTC Fixed typo in hmmspectramar 02 November 2015, 18:49:25 UTC
f920970 vidaurre 02 November 2015, 16:36:35 UTC remove clear all in example script 02 November 2015, 16:36:35 UTC
784f2b3 dvidaurre@gmail.com 02 November 2015, 16:35:24 UTC clear all in example script 02 November 2015, 16:35:24 UTC
0d54fd3 dvidaurre@gmail.com 02 November 2015, 16:30:45 UTC Add all existing files 02 November 2015, 16:30:45 UTC
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