| 524a123 | Gregory Jefferis | 12 January 2014, 22:40:00 UTC | Deprecate plot3dsurface, add as.hxsurf * and add a plot3dsurface to AnalysisSuite tests | 12 January 2014, 22:40:00 UTC |
| 96b6c1e | Gregory Jefferis | 12 January 2014, 22:39:26 UTC | Deprecate ParseAMSurfToContourList in favour of nat::read.hxsurf | 12 January 2014, 22:39:26 UTC |
| c08f374 | Gregory Jefferis | 11 January 2014, 16:39:34 UTC | change surface class to hxsurf (all lower case) | 11 January 2014, 16:39:34 UTC |
| 40f028c | Gregory Jefferis | 11 January 2014, 16:37:38 UTC | Merge branch 'feature/surfcolours' of github.com:ajdm/AnalysisSuite into ajdm-feature/surfcolours * 'feature/surfcolours' of github.com:ajdm/AnalysisSuite: Fix regex to deal with blue value in color spec being 1 Fix regex and add class assignment Remove outdated commented-out lines containing previous methods Improve regex for colour extraction to deal with trailing comma Change Amira surface loading to put different regions in surf$Regions Add functionality to load colours of regions for Amira surfaces | 11 January 2014, 16:37:38 UTC |
| 2848df1 | Gregory Jefferis | 11 January 2014, 11:18:58 UTC | deprecate plotneuron3d.simple (and remove plot3d.neuron method defined here) | 11 January 2014, 11:18:58 UTC |
| 258757c | Ashley Manton | 10 January 2014, 19:38:29 UTC | Fix regex to deal with blue value in color spec being 1 | 10 January 2014, 19:39:47 UTC |
| 47db2f6 | Ashley Manton | 10 January 2014, 18:58:28 UTC | Fix regex and add class assignment | 10 January 2014, 18:58:28 UTC |
| c8ec46e | Ashley Manton | 10 January 2014, 18:52:45 UTC | Remove outdated commented-out lines containing previous methods | 10 January 2014, 18:52:45 UTC |
| b762add | Ashley Manton | 10 January 2014, 18:50:26 UTC | Improve regex for colour extraction to deal with trailing comma | 10 January 2014, 18:50:26 UTC |
| d4978b1 | Ashley Manton | 10 January 2014, 18:14:52 UTC | Change Amira surface loading to put different regions in surf$Regions | 10 January 2014, 18:14:52 UTC |
| 1cc7289 | Gregory Jefferis | 09 January 2014, 18:08:20 UTC | remove neuronlist arithmetic to nat | 09 January 2014, 18:10:06 UTC |
| 699f02d | Gregory Jefferis | 09 January 2014, 18:08:03 UTC | rename neuron-arithmetic arguments before transferring to nat | 09 January 2014, 18:08:03 UTC |
| 93eb914 | Gregory Jefferis | 08 January 2014, 22:35:50 UTC | move to nat: neuronlist, is.neuronlist, as.neuronlist, [.neuronlist, nlapply, plot3d.neuronlist | 08 January 2014, 22:35:50 UTC |
| e0f11a1 | Gregory Jefferis | 08 January 2014, 21:30:21 UTC | deprecate DotProperties | 08 January 2014, 21:30:21 UTC |
| c831df5 | Gregory Jefferis | 08 January 2014, 20:58:47 UTC | remove core dotprops methods | 08 January 2014, 20:58:47 UTC |
| 6e90c6f | Gregory Jefferis | 08 January 2014, 20:54:22 UTC | remove core neuron methods and deprecate transform.neuron, transform.points3d and transform.dotprops | 08 January 2014, 20:57:29 UTC |
| fce8684 | Ashley Manton | 08 January 2014, 17:30:36 UTC | Add functionality to load colours of regions for Amira surfaces | 08 January 2014, 17:30:36 UTC |
| afdb7d4 | Gregory Jefferis | 08 January 2014, 15:21:27 UTC | Merge branch 'master' of github.com:jefferis/AnalysisSuite * 'master' of github.com:jefferis/AnalysisSuite: Fix issue when loading surface that has regions containing 0 triangles Fix typos | 08 January 2014, 15:21:27 UTC |
| 3413332 | jefferis | 08 January 2014, 15:17:35 UTC | Merge pull request #2 from ajdm/patch-1 Fix issue when loading surface that has regions containing 0 triangles | 08 January 2014, 15:17:35 UTC |
| 11e7b0a | ajdm | 08 January 2014, 15:08:31 UTC | Fix issue when loading surface that has regions containing 0 triangles | 08 January 2014, 15:08:31 UTC |
| 68d829d | Gregory Jefferis | 07 January 2014, 21:50:52 UTC | Fix bug introduced in CMTKParamsToCMTKRegistration when deprecating | 07 January 2014, 21:50:52 UTC |
| 9854b0c | jefferis | 06 January 2014, 20:55:16 UTC | Merge pull request #1 from ajdm/patch-1 Fix typos | 06 January 2014, 20:55:16 UTC |
| f789605 | ajdm | 06 January 2014, 20:51:12 UTC | Fix typos | 06 January 2014, 20:51:12 UTC |
| 4d330f9 | Gregory Jefferis | 06 January 2014, 16:48:38 UTC | Deprecate/remove Read/WriteIGSLandmarks and IGSLandmarkList to nat package | 06 January 2014, 16:48:38 UTC |
| 0ed76da | Gregory Jefferis | 06 January 2014, 05:29:00 UTC | add irtk.present() and use it to guard irtk unit tests (since irtk is usually not installed) | 06 January 2014, 05:29:00 UTC |
| b170a75 | Gregory Jefferis | 06 January 2014, 05:03:20 UTC | move internal CMTK affine geometry routines to nat (and deprecate existing nat.as functions) | 06 January 2014, 05:03:20 UTC |
| e61916c | Gregory Jefferis | 06 January 2014, 03:13:32 UTC | move trim next to ReadAmiramesh.Header * since that is the only place it is still used in AnalysisSuite | 06 January 2014, 03:13:32 UTC |
| 902402e | Gregory Jefferis | 05 January 2014, 23:25:15 UTC | nat: remove mat2dof/dof2mat tests | 05 January 2014, 23:25:15 UTC |
| 7a44f1f | Gregory Jefferis | 05 January 2014, 23:24:46 UTC | remove code to nat (and deprecate left over functions) * relevant tests still pass | 05 January 2014, 23:24:46 UTC |
| cdd3db5 | Gregory Jefferis | 05 January 2014, 21:17:48 UTC | cmtk.mat2dof and cmtk.dof2mat have been moved to nat | 05 January 2014, 21:17:48 UTC |
| 2d03b92 | Gregory Jefferis | 05 January 2014, 21:12:52 UTC | All AnalysisSuite users now require nat package * which brings nat.utils with it | 05 January 2014, 21:12:52 UTC |
| 70b5d45 | Gregory Jefferis | 05 January 2014, 21:11:25 UTC | Development of AnalysisSuite (including tests) will now assume the presence of nat.as package | 05 January 2014, 21:11:25 UTC |
| 270b8c7 | Gregory Jefferis | 03 January 2014, 21:21:52 UTC | Switch to sys.source in startup - loads into .GlobalEnv or nat.as namespace * this change should have no effect on the traditional style of AnalysisSuite startup ie source("~/projects/AnalysisSuite/R/Code/Startup.R") * but should also allow the objects to be loaded into the nat.as namespace when AnalysisSuite is loaded through that wrapper package. | 03 January 2014, 21:21:52 UTC |
| 9c32008 | Gregory Jefferis | 18 December 2013, 23:17:19 UTC | Give NrrdProject cropmin and cropmax options * and add docs and a test | 30 December 2013, 09:43:35 UTC |
| 2e509b8 | Gregory Jefferis | 12 December 2013, 06:33:44 UTC | Add segmentgraph() to generate a simplified segment graph | 12 December 2013, 06:33:44 UTC |
| 6f62972 | Gregory Jefferis | 09 December 2013, 11:00:44 UTC | use first endpoint rather than first point when no origin specified * usually the first point is an endpoint but sometimes not and using an endpoint as the origin always makes more sense. * NB first means first in raw vertex id sequence | 09 December 2013, 11:00:44 UTC |
| 9c37090 | Gregory Jefferis | 09 December 2013, 10:17:58 UTC | Merge branch 'feature/igraph-subtrees' * feature/igraph-subtrees: Teach graph2seglist to cope with undirected graphs comprehensive tests for CoreNeuronFromGraph sort remaining subgraphs by descending length when origin specified Fix CoreNeuronFromGraph for subgraphs when origin specified Fix CoreNeuronFromGraph interpretation of origin Add additional comprehensive tests for graph2seglist Add test for trifurcation Fully implement CoreNeuronFromGraph for multiple subgraphs factor out graph.nodes and make endpoints functions FIX graph2seglist when no explicit origin specified and multiple subgraphs graph2seglist now returns a list with a single point for floating points Reimplement CoreNeuronFromGraph using graph2seglist Well-behaved graph2seglist() for fully-connected graphs Add neurongraph() functions designed to construct well-behaved graph change test neuron data to avoid overlapping points FIXMEs | 09 December 2013, 10:17:58 UTC |
| 27fd51b | Gregory Jefferis | 06 December 2013, 23:38:10 UTC | Teach graph2seglist to cope with undirected graphs * at the expense of not being able to check for cycles in those undirected graphs | 09 December 2013, 10:17:41 UTC |
| 06e9e2a | Gregory Jefferis | 06 December 2013, 19:54:19 UTC | comprehensive tests for CoreNeuronFromGraph | 09 December 2013, 10:17:41 UTC |
| 032fea4 | Gregory Jefferis | 06 December 2013, 19:54:01 UTC | sort remaining subgraphs by descending length when origin specified * so that we get an identical result to situation when no origin was specified | 09 December 2013, 10:17:41 UTC |
| f9daa52 | Gregory Jefferis | 06 December 2013, 19:45:48 UTC | Fix CoreNeuronFromGraph for subgraphs when origin specified | 09 December 2013, 10:17:41 UTC |
| 2a05c29 | Gregory Jefferis | 06 December 2013, 19:33:26 UTC | Fix CoreNeuronFromGraph interpretation of origin | 09 December 2013, 10:17:41 UTC |
| 8cc9054 | Gregory Jefferis | 06 December 2013, 19:04:21 UTC | Add additional comprehensive tests for graph2seglist | 09 December 2013, 10:17:41 UTC |
| c3b0202 | Gregory Jefferis | 06 December 2013, 18:27:36 UTC | Add test for trifurcation | 09 December 2013, 10:17:41 UTC |
| 35fc900 | Gregory Jefferis | 06 December 2013, 14:45:16 UTC | Fully implement CoreNeuronFromGraph for multiple subgraphs | 09 December 2013, 10:17:41 UTC |
| 50bfb78 | Gregory Jefferis | 06 December 2013, 14:04:03 UTC | factor out graph.nodes and make endpoints functions * add some more tests | 09 December 2013, 10:17:41 UTC |
| 4276be9 | Gregory Jefferis | 06 December 2013, 14:01:51 UTC | FIX graph2seglist when no explicit origin specified and multiple subgraphs * internally we need the raw vertex id but rootpoints returns the original vertex id by default. | 09 December 2013, 10:17:41 UTC |
| ec1e007 | Gregory Jefferis | 06 December 2013, 13:42:39 UTC | graph2seglist now returns a list with a single point for floating points * also test for this behaviour | 09 December 2013, 10:17:40 UTC |
| 484c158 | Gregory Jefferis | 06 December 2013, 11:42:37 UTC | Reimplement CoreNeuronFromGraph using graph2seglist * still doesn't work for graphs with multiple subgraphs * also removed dfs parameter meaning that .... * RerootNeuron also had to be changed slightly | 09 December 2013, 10:17:40 UTC |
| d4dbfe3 | Gregory Jefferis | 06 December 2013, 09:20:41 UTC | Well-behaved graph2seglist() for fully-connected graphs * and appropriate tests | 09 December 2013, 10:17:40 UTC |
| fcea916 | Gregory Jefferis | 05 December 2013, 18:38:40 UTC | Add neurongraph() functions designed to construct well-behaved graph * also neurongraph.swc() | 09 December 2013, 10:17:40 UTC |
| 2147564 | Gregory Jefferis | 05 December 2013, 18:07:00 UTC | change test neuron data to avoid overlapping points | 09 December 2013, 10:17:40 UTC |
| e7b34bf | Gregory Jefferis | 20 November 2013, 09:47:08 UTC | FIXMEs | 09 December 2013, 10:17:40 UTC |
| 1640de0 | Gregory Jefferis | 06 December 2013, 14:07:33 UTC | Add missing legacy test registration for dof2mat | 09 December 2013, 10:17:04 UTC |
| 51e19f0 | Gregory Jefferis | 05 December 2013, 19:47:17 UTC | fix small code duplication in read.zlib * readBin on raw data wasn't doing anything * and add test for decompression of raw vector | 09 December 2013, 10:17:04 UTC |
| ad66193 | Gregory Jefferis | 09 December 2013, 10:15:39 UTC | Merge branch 'fix/cmtkaffinecompose' * fix/cmtkaffinecompose: (32 commits) Add test.CMTKRegFromAmira More cleanup in Affine.R Merge ComposeAffineFromIGSParams.named into ComposeAffineFromIGSParams More work to handle versions for CMTK registrations OBS: Remove incomplete FindTorstenFromAffine() fix bug in names introduced in ReadIGSRegistration Teach IGSTypedStream functions to handle versions Test for CMTK legacy decomposition Add option to Decompose legacy CMTK registrations Check CMTK version and omit some tests when <=2.4.0 Add tests including mirroring along x,y,z axes New round trip function starting (and finishing) with affine matrix Update direct tests of ComposeAffineFromIGSParams and DecomposeAffineToIGSParams minor code tidying in DecomposeAffineToIGSParams() Fix DecomposeAffineToIGSParams() - matches svn 5050 Fix ComposeAffineFromIGSParams.named - matches svn r5050 Use cmtk.dof2mat/mat2dof by default for tests Tidying up affine tests Add test for pure R Affine Decomposition Simple tests for cmtk.(mat2dof|dof2mat) ... | 09 December 2013, 10:15:39 UTC |
| db414d7 | Gregory Jefferis | 04 December 2013, 21:15:01 UTC | Add test.CMTKRegFromAmira | 09 December 2013, 10:13:03 UTC |
| ddf95fe | Gregory Jefferis | 04 December 2013, 20:58:03 UTC | More cleanup in Affine.R | 09 December 2013, 10:13:02 UTC |
| a35004d | Gregory Jefferis | 04 December 2013, 20:37:56 UTC | Merge ComposeAffineFromIGSParams.named into ComposeAffineFromIGSParams * not much point in having these two separate functions | 09 December 2013, 10:13:02 UTC |
| 1003192 | Gregory Jefferis | 04 December 2013, 20:36:22 UTC | More work to handle versions for CMTK registrations * will always write registrations as v2.4 * should keep a version attribute when reading from registration file * will assume v2.4 when converting affine to params | 09 December 2013, 10:13:02 UTC |
| 5a18c05 | Gregory Jefferis | 04 December 2013, 20:17:41 UTC | OBS: Remove incomplete FindTorstenFromAffine() | 09 December 2013, 10:13:02 UTC |
| 48818fd | Gregory Jefferis | 02 December 2013, 22:10:51 UTC | fix bug in names introduced in ReadIGSRegistration * was overwriting names with mostattributes<- call | 09 December 2013, 10:13:02 UTC |
| bd2c587 | Gregory Jefferis | 02 December 2013, 19:00:13 UTC | Teach IGSTypedStream functions to handle versions | 09 December 2013, 10:13:02 UTC |
| 003485c | Gregory Jefferis | 02 December 2013, 14:11:53 UTC | Test for CMTK legacy decomposition | 09 December 2013, 10:13:02 UTC |
| 7513e7d | Gregory Jefferis | 02 December 2013, 13:03:33 UTC | Add option to Decompose legacy CMTK registrations i.e. those marked as TYPEDSTREAM 1.1 | 09 December 2013, 10:13:02 UTC |
| f2e9e76 | Gregory Jefferis | 02 December 2013, 11:05:24 UTC | Check CMTK version and omit some tests when <=2.4.0 * No point in giving a large number of failures when CMTK is not up to date | 09 December 2013, 10:13:02 UTC |
| c8d6ac1 | Gregory Jefferis | 02 December 2013, 01:51:41 UTC | Add tests including mirroring along x,y,z axes | 09 December 2013, 10:13:01 UTC |
| a526e78 | Gregory Jefferis | 02 December 2013, 01:51:21 UTC | New round trip function starting (and finishing) with affine matrix * this makes more sense because many different 15 dof sets can map onto a single homogeneous affine matrix * both because of different rotation centres (obvious) and for more subtle reasons like the equivalence of two flips to a rotation, or the equivalence of a -180 to +180 rotation | 09 December 2013, 10:13:01 UTC |
| 00cba79 | Gregory Jefferis | 02 December 2013, 01:48:51 UTC | Update direct tests of ComposeAffineFromIGSParams and DecomposeAffineToIGSParams Needed new _correct_ baseline date for shear cases | 09 December 2013, 10:13:01 UTC |
| 98e0c6d | Gregory Jefferis | 01 December 2013, 23:46:05 UTC | minor code tidying in DecomposeAffineToIGSParams() * no change in logic | 09 December 2013, 10:13:01 UTC |
| ba19526 | Gregory Jefferis | 01 December 2013, 23:42:53 UTC | Fix DecomposeAffineToIGSParams() - matches svn 5050 * However, have noticed that this cannot cope with a flip on anything other than the X axis. | 09 December 2013, 10:13:01 UTC |
| 03a9855 | Gregory Jefferis | 01 December 2013, 17:25:33 UTC | Fix ComposeAffineFromIGSParams.named - matches svn r5050 * Also slightly harden the comparative unit test (which now passes) | 09 December 2013, 10:13:01 UTC |
| 218648f | Gregory Jefferis | 01 December 2013, 16:35:41 UTC | Use cmtk.dof2mat/mat2dof by default for tests * this now works with CMTK v2.4.0 svn >= 5050 | 09 December 2013, 10:13:01 UTC |
| 0ccd4f0 | Gregory Jefferis | 01 December 2013, 16:33:37 UTC | Tidying up affine tests | 09 December 2013, 10:13:01 UTC |
| 55620db | Gregory Jefferis | 01 December 2013, 16:33:00 UTC | Add test for pure R Affine Decomposition doesn't pass yet | 09 December 2013, 10:13:00 UTC |
| e7ca0be | Gregory Jefferis | 01 December 2013, 16:19:50 UTC | Simple tests for cmtk.(mat2dof|dof2mat) * includes registration .list checked with dof2mat command line tool from CMTK 2.4.0svn | 09 December 2013, 10:13:00 UTC |
| 8b41140 | Gregory Jefferis | 01 December 2013, 16:13:28 UTC | Retire HomogenousAffineFromCMTKParams() * subsumed within cmtk.dof2mat | 09 December 2013, 10:13:00 UTC |
| 2aabff7 | Gregory Jefferis | 01 December 2013, 16:12:42 UTC | Doc HomogenousAffineFromCMTKParams() | 09 December 2013, 10:13:00 UTC |
| 85774c1 | Gregory Jefferis | 01 December 2013, 16:11:28 UTC | Make write.cmtkreg write version 2.4 TYPEDSTREAM by default | 09 December 2013, 10:13:00 UTC |
| a1807d3 | Gregory Jefferis | 01 December 2013, 16:04:54 UTC | Teach cmtk.mat2dof to accept matrix input * also add version argument | 09 December 2013, 10:13:00 UTC |
| ed3556c | Gregory Jefferis | 01 December 2013, 15:54:14 UTC | Add optional centre parameter to cmtk.mat2dof * also version | 09 December 2013, 10:13:00 UTC |
| af930d5 | Gregory Jefferis | 29 November 2013, 22:38:46 UTC | Fix: cmtk.mat2dof() was not honouring transpose() | 09 December 2013, 10:13:00 UTC |
| b0f6a7c | Gregory Jefferis | 25 November 2013, 09:33:02 UTC | Make sure cmtk.dof2mat returns matrix visibly | 09 December 2013, 10:12:59 UTC |
| a040e85 | Gregory Jefferis | 25 November 2013, 00:03:21 UTC | New tests of CMTK/affine functions confirm problem in shear calculation * cmtk.dof2mat / cmtk.mat2dof round trips work with 9 dof affine transforms but not ones with shears. * the errors are consistent between my ComposeAffineFromIGSParams and DecomposeAffineToIGSParams functions and cmtk.dof2mat, cmtk.mat2dof * this suggests that the problem in handling shears has not gone away even in modern CMTK. | 09 December 2013, 10:12:59 UTC |
| 8bc673b | Gregory Jefferis | 24 November 2013, 23:16:15 UTC | Add new functions to use the CMTK floating image notation * early IGS registration files used model_study rather than floating_study. Since this gave the registration in the forward direction model->template this resulted in an implicit inversion by CMTK tools that normally need the reverse registration used for volume reformatting. | 09 December 2013, 10:12:59 UTC |
| 9261fda | Gregory Jefferis | 24 November 2013, 11:47:09 UTC | HomogenousAffineFromCMTK -> HomogenousAffineFromCMTKParams * ie input and output in memory (even if it uses a temporary file with dof2mat) | 09 December 2013, 10:12:59 UTC |
| 8d3f2d5 | Gregory Jefferis | 24 November 2013, 11:45:29 UTC | Add cmtk.dof2mat and cmtk.mat2dof to wrap cmtk commandline tools | 09 December 2013, 10:12:59 UTC |
| 807aac6 | Gregory Jefferis | 23 November 2013, 15:27:17 UTC | fix path to run runitAffine | 09 December 2013, 10:12:59 UTC |
| b82a87c | Gregory Jefferis | 01 December 2013, 12:39:59 UTC | Minor adjustments to runitGeneralImageProcessing.R | 09 December 2013, 10:11:35 UTC |
| 2f23c10 | Gregory Jefferis | 01 December 2013, 12:07:48 UTC | Fix handling of Entropy column for cmtk statistics v>=2.3.1 * also simplify reading of table * improve docs | 09 December 2013, 10:11:35 UTC |
| 48db1ee | Gregory Jefferis | 09 December 2013, 10:08:50 UTC | Merge branch 'fix/hxzip' * fix/hxzip: Stop tracking java Read|WriteHxZipData class Allow runAllTests to be called as script Replace DecodeHxZip and EncodeHxZip with read.zlib and write.zlib Faster test for reading hxzip data Make new implementation of hxzip decoding the default New in memory, base R zlib compression/decompression Add round trip test for Amira hxzip data | 09 December 2013, 10:08:50 UTC |
| 8c67ca8 | Gregory Jefferis | 29 November 2013, 01:42:32 UTC | Stop tracking java Read|WriteHxZipData class * obsolete now that I have a base R way of doing this | 29 November 2013, 01:42:32 UTC |
| ebe315e | Gregory Jefferis | 29 November 2013, 01:40:02 UTC | Allow runAllTests to be called as script | 29 November 2013, 01:40:02 UTC |
| 9734edd | Gregory Jefferis | 28 November 2013, 17:09:16 UTC | Replace DecodeHxZip and EncodeHxZip with read.zlib and write.zlib * these functions depend solely on base R (i.e. not java code) | 28 November 2013, 17:09:16 UTC |
| 81da154 | Gregory Jefferis | 28 November 2013, 09:56:51 UTC | Faster test for reading hxzip data * tabulate is _much_ faster than table | 28 November 2013, 09:56:51 UTC |
| 86601b9 | Gregory Jefferis | 28 November 2013, 09:56:29 UTC | Make new implementation of hxzip decoding the default | 28 November 2013, 09:56:29 UTC |
| 18c99f2 | Gregory Jefferis | 28 November 2013, 09:47:23 UTC | New in memory, base R zlib compression/decompression | 28 November 2013, 09:47:23 UTC |
| 0e83de6 | Gregory Jefferis | 28 November 2013, 09:46:10 UTC | Add round trip test for Amira hxzip data * fails for existing java based implementation | 28 November 2013, 09:46:10 UTC |
| 841b16e | Gregory Jefferis | 20 November 2013, 22:10:00 UTC | Fix (+test) for long standing bug in DirectPotentialSynapses * apply was being used with the expectation that it would return a list. This was not the case when segswithin returned the same number of segments from b for each segment in matrix a * the code assumed that matrix a had rownames It is still not exactly beautiful code, but it should now work for the corner cases that I can envisage. | 20 November 2013, 22:10:00 UTC |
| 8ac4c29 | Gregory Jefferis | 20 November 2013, 11:31:06 UTC | Fix bug in is.nrrd and add tests * when trusting suffix | 20 November 2013, 11:31:06 UTC |
