| 87ef079 | Gregory Jefferis | 20 August 2019, 11:05:36 UTC | Update README.md | 20 August 2019, 11:05:36 UTC |
| b2a547f | Gregory Jefferis | 19 May 2018, 22:34:23 UTC | Update README.md | 19 May 2018, 22:34:23 UTC |
| e57c060 | Gregory Jefferis | 05 January 2018, 21:02:39 UTC | point to nat | 05 January 2018, 21:02:39 UTC |
| 53abf53 | Gregory Jefferis | 24 May 2017, 11:20:09 UTC | fix longstanding bug in NrrdHisto with mask * can't understand why this didn't come up before! | 24 May 2017, 11:20:09 UTC |
| 8b21612 | Gregory Jefferis | 14 December 2016, 22:39:33 UTC | Correct order of classes in MyNeurons * closes #7 | 14 December 2016, 22:39:33 UTC |
| f164fee | Gregory Jefferis | 28 October 2016, 10:17:34 UTC | ::: since nrrd.datafiles is not exported * maybe it should be * see https://github.com/jefferis/nat/issues/316 | 28 October 2016, 10:17:53 UTC |
| 07a2275 | Gregory Jefferis | 28 October 2016, 10:00:39 UTC | Use nat::nrrd.datafiles in NrrdTestDataLength * we don’t need the deprecation message | 28 October 2016, 10:00:39 UTC |
| c23bf87 | Gregory Jefferis | 28 October 2016, 09:58:55 UTC | typo in deprecated message | 28 October 2016, 09:58:55 UTC |
| 3a02978 | Gregory Jefferis | 28 October 2016, 09:56:25 UTC | Fix bug in NrrdDataFiles * fine to say it’s deprecated, but no need to leave it broken! | 28 October 2016, 09:56:25 UTC |
| 644ff7f | Gregory Jefferis | 28 October 2016, 09:55:53 UTC | Add WriteVTKMesh (legacy ascii format) | 28 October 2016, 09:55:53 UTC |
| 6104897 | Gregory Jefferis | 28 October 2016, 09:54:51 UTC | fix ssl error in installer | 28 October 2016, 09:54:51 UTC |
| f02c511 | Gregory Jefferis | 15 November 2014, 09:39:11 UTC | Simple Neurite Tracer (Longair) handled separately | 15 November 2014, 09:39:11 UTC |
| a3ae8d8 | Gregory Jefferis | 15 November 2014, 09:38:00 UTC | change baseline to reflect new behaviour re Longair Traces | 15 November 2014, 09:38:00 UTC |
| c1966e5 | Gregory Jefferis | 15 November 2014, 09:32:50 UTC | ReadNeuronsFromLongairTraces now a thin wrapper for nat | 15 November 2014, 09:37:56 UTC |
| 6304e77 | Gregory Jefferis | 01 October 2014, 22:28:48 UTC | Fix bug in SWC2Neuron revealed for Longair traces * closes #6 | 01 October 2014, 22:28:52 UTC |
| 7181b8e | Gregory Jefferis | 04 August 2014, 11:30:44 UTC | Bump version to match nat | 04 August 2014, 11:30:44 UTC |
| e9ec0fc | Gregory Jefferis | 04 August 2014, 11:05:26 UTC | write.neuron now appends a file extension automatically * this makes me wonder if that is a good idea, but I think on balance it is what one wants much more often than the ability to write a file without an extension | 04 August 2014, 11:05:53 UTC |
| 531ee91 | Gregory Jefferis | 04 August 2014, 10:52:57 UTC | deprecate CMTKStatistics * use nat::cmtk.statistics | 04 August 2014, 10:55:05 UTC |
| db3b232 | Gregory Jefferis | 03 August 2014, 09:04:12 UTC | gzip encide dataforstats.nrrd | 03 August 2014, 09:04:12 UTC |
| 2ba75bc | Gregory Jefferis | 04 July 2014, 16:33:12 UTC | Remove redundant WeightedNNBasedLinesetMatching functions * includes some helper functions * and .RemoveNNRepeats which seemed unused | 04 July 2014, 16:33:12 UTC |
| d832420 | Gregory Jefferis | 26 June 2014, 10:42:14 UTC | Bump version to 1.5.5 to sync with nat | 26 June 2014, 10:42:14 UTC |
| 2daa2b8 | Gregory Jefferis | 26 June 2014, 10:41:48 UTC | Fix deprecated messages * note package refers to the one with information about the deprecated function, not the one that contains the suggested replacement function | 26 June 2014, 10:41:48 UTC |
| 5235489 | Gregory Jefferis | 26 June 2014, 09:44:47 UTC | remove segmentgraph function (now in nat) | 26 June 2014, 09:44:51 UTC |
| e5f1f70 | Gregory Jefferis | 23 May 2014, 18:08:03 UTC | inactivate failing test – reading binary hxsurf file * don’t think this ever worked * possible that file has changed format? | 23 May 2014, 18:08:03 UTC |
| e8c55a4 | Gregory Jefferis | 22 May 2014, 17:12:27 UTC | remove prune.dotprops * superseded by nat::prune method | 22 May 2014, 17:12:57 UTC |
| 9455915 | Gregory Jefferis | 08 April 2014, 22:49:37 UTC | bump nat.as package version | 08 April 2014, 22:52:07 UTC |
| 882074b | Gregory Jefferis | 08 April 2014, 21:46:12 UTC | Change test since ind2coord params have changed * made some attempts to try and ensure backwards compatibility but ended up requiring too much messy code in nat and have therefore shelved. | 08 April 2014, 22:51:35 UTC |
| 7f55d31 | Gregory Jefferis | 07 April 2014, 16:31:57 UTC | remove ind2coord, coord2ind * leave behind an ind2coord.array method to handle gjdens objects | 07 April 2014, 16:31:57 UTC |
| 47dab06 | Gregory Jefferis | 17 March 2014, 17:10:22 UTC | bump analysis suite version to 1.4.3 to sync with nat * also make upgrade message a bit more obvious | 17 March 2014, 20:42:17 UTC |
| 236cf90 | Gregory Jefferis | 17 March 2014, 14:59:31 UTC | Remove MakeMaskFromDensity - should use nat::threshold * MakeMaskFromDensity was buggy and essentially unused | 17 March 2014, 17:09:26 UTC |
| 420245c | Gregory Jefferis | 17 March 2014, 13:49:13 UTC | Deprecate digest.dotprops | 17 March 2014, 13:49:13 UTC |
| 4834abf | Gregory Jefferis | 01 March 2014, 00:19:25 UTC | Bump AnalysisSuite version to 1.3.0 | 01 March 2014, 00:19:25 UTC |
| b6c979a | Gregory Jefferis | 01 March 2014, 00:18:04 UTC | deprecate makeScaleBar | 01 March 2014, 00:18:19 UTC |
| db36151 | Gregory Jefferis | 01 March 2014, 00:17:53 UTC | Add test for image.gjdens/makescalebar | 01 March 2014, 00:17:53 UTC |
| 622e4fd | Gregory Jefferis | 28 February 2014, 22:48:45 UTC | Deprecate expand.grid.gjdens, image.gjdens, xyzpos.gjdens, ijkpos.gjdens * nb all tests passing | 28 February 2014, 22:48:53 UTC |
| 7e219f2 | Gregory Jefferis | 28 February 2014, 22:48:11 UTC | Remove unmask, projection, clampmax, flip.array/vector/matrix | 28 February 2014, 22:48:11 UTC |
| b15d888 | Gregory Jefferis | 28 February 2014, 22:35:33 UTC | Deprecate Write3DDensityToNrrd in favour of nat::write.nrrd | 28 February 2014, 22:35:33 UTC |
| 1661f8f | Gregory Jefferis | 26 February 2014, 18:01:23 UTC | use nat::boundingbox function where appropriate | 26 February 2014, 18:01:23 UTC |
| fad5522 | Gregory Jefferis | 19 February 2014, 22:52:12 UTC | give AnalysisSuite a version number that we will match with nat * Examples: - AnalysisSuite 1.2.0.99 will insist on nat >=1.2.0 - nat 1.3.x will will give a warning when loaded by AnalysisSuite 1.2.x | 19 February 2014, 22:52:12 UTC |
| 5ebe616 | Gregory Jefferis | 19 February 2014, 22:49:50 UTC | remove read.neurons (now in nat more or less verbatim) | 19 February 2014, 22:49:50 UTC |
| c9e5eb6 | Gregory Jefferis | 19 February 2014, 12:38:14 UTC | remove use of Neuron2Graph in tests | 19 February 2014, 12:38:14 UTC |
| d640170 | Gregory Jefferis | 19 February 2014, 12:37:38 UTC | remove more unused functions | 19 February 2014, 12:37:38 UTC |
| b06379c | Gregory Jefferis | 19 February 2014, 12:36:33 UTC | remove read.im3d from AnalysisSuite | 19 February 2014, 12:36:33 UTC |
| b856759 | Gregory Jefferis | 19 February 2014, 12:19:32 UTC | remove as.directed.usingroot (now in nat) | 19 February 2014, 12:22:00 UTC |
| 862cae9 | Gregory Jefferis | 19 February 2014, 01:26:23 UTC | Insist on v1.2 (or higher) of nat | 19 February 2014, 01:26:23 UTC |
| 035afa0 | Gregory Jefferis | 18 February 2014, 14:32:37 UTC | fix voxdim.gjdens | 18 February 2014, 14:32:37 UTC |
| eb651db | Gregory Jefferis | 16 February 2014, 23:27:53 UTC | Inactivate test.igraphvsoriginal test for amira neurons * basically committed to igraph approach at this point * some neurons with loops are now unreadable but they were not being read correctly by the previous code | 16 February 2014, 23:27:53 UTC |
| 666c34b | Gregory Jefferis | 16 February 2014, 22:01:32 UTC | update test for amira neuron with isolated points * the old version was incorrect (e.g. using an isolated point as the start point makes little sense and more generally the fields in the main part of the neuron structure should all refer to the master tree - which unless specified will now always be the largest by number of points. | 16 February 2014, 22:21:57 UTC |
| 1be1c6d | Gregory Jefferis | 16 February 2014, 21:36:04 UTC | bring one read.neuron test up to date and retire another | 16 February 2014, 22:21:57 UTC |
| f9fa117 | Gregory Jefferis | 16 February 2014, 17:00:43 UTC | match.fun doesn't seem to work with a function specified as "package::FUN" | 16 February 2014, 22:21:57 UTC |
| db5a90a | Gregory Jefferis | 16 February 2014, 16:45:04 UTC | deprecate voxdims.gjdens | 16 February 2014, 22:21:57 UTC |
| b9087cf | Gregory Jefferis | 15 February 2014, 11:53:16 UTC | Deprecate Read3DDensityFromNrrd and NrrdDataFiles | 16 February 2014, 22:21:57 UTC |
| e02b484 | Gregory Jefferis | 15 February 2014, 10:30:33 UTC | Deprecate NrrdVoxDims, ReadNrrdHeader and remove is.nrrd * also make .standardNrrdType a wrapper | 16 February 2014, 22:21:57 UTC |
| d3ab50d | Gregory Jefferis | 14 February 2014, 17:34:24 UTC | Don't test SingleFromDoubleEdgeList and ParseEdgeList since part of graph-based parsing | 16 February 2014, 22:21:10 UTC |
| 759ffc3 | Gregory Jefferis | 14 February 2014, 17:33:37 UTC | remove direct references to ReadNeuronFromAM3D | 14 February 2014, 17:33:37 UTC |
| 06d3cde | Gregory Jefferis | 14 February 2014, 17:24:32 UTC | remove all old code for reading neurons in Amira formats * has been superseded by nat::read.neuron and the functions it wraps | 14 February 2014, 17:24:32 UTC |
| dfa3631 | Gregory Jefferis | 14 February 2014, 14:26:16 UTC | fix a couple of overzealous tests | 14 February 2014, 14:26:16 UTC |
| 4d53ce0 | Gregory Jefferis | 09 February 2014, 18:56:15 UTC | Signal that write.neuronlist is deprecated - but don't convert to wrapper yet | 09 February 2014, 18:56:15 UTC |
| f91a5af | Gregory Jefferis | 09 February 2014, 17:48:45 UTC | write.neuron -> write.neuron.extra (asc and Borst ftypes only) * nat::write.neuron does all the types we care about these days | 09 February 2014, 17:48:45 UTC |
| 19ed570 | Gregory Jefferis | 09 February 2014, 17:47:39 UTC | read.neuron -> read.neuron.extra and register it as a fall-through reader * this way it will be called by nat::read.neuron if all else fails | 09 February 2014, 17:47:39 UTC |
| 8f58b73 | Gregory Jefferis | 09 February 2014, 16:40:24 UTC | Fix ignored Force argument in WriteNeuronToAM3D | 09 February 2014, 16:40:24 UTC |
| a7c5f7c | Gregory Jefferis | 09 February 2014, 16:39:58 UTC | Deprecate WriteNeuronToAM (-> nat) | 09 February 2014, 16:39:58 UTC |
| 88da519 | Gregory Jefferis | 09 February 2014, 16:09:38 UTC | deprecate WriteNeuronToAM3D | 09 February 2014, 16:09:38 UTC |
| b1a9ef3 | Gregory Jefferis | 09 February 2014, 15:47:52 UTC | Teach DotPropertiesFromFile to get points from any neuron & cut ReadSWCFile | 09 February 2014, 15:47:52 UTC |
| e0797b1 | Gregory Jefferis | 09 February 2014, 15:45:09 UTC | Rm testParseSWCTreeEquivalent - methods are equivalent both will be replaced | 09 February 2014, 15:45:09 UTC |
| d2b951c | Gregory Jefferis | 09 February 2014, 15:44:03 UTC | Deprecate ReadNeuronFromSWC, WriteSWCFile, ParseSWC, WriteSWCFile | 09 February 2014, 15:44:03 UTC |
| 0baf3c7 | Gregory Jefferis | 08 February 2014, 21:28:36 UTC | don't check for NeuronName | 08 February 2014, 21:28:36 UTC |
| 5d8b816 | Gregory Jefferis | 08 February 2014, 21:28:16 UTC | Deprecate ReadNeuronFromAM | 08 February 2014, 21:28:16 UTC |
| 1fbadb6 | Gregory Jefferis | 30 January 2014, 21:35:04 UTC | Deprecate Read/WriteAmiraLandmarks in favour of nat | 30 January 2014, 21:35:04 UTC |
| fccf6f6 | Gregory Jefferis | 30 January 2014, 21:16:27 UTC | move read.zlib/write.zlib and DecodeRLEBytes to nat | 30 January 2014, 21:34:43 UTC |
| 68f5e1d | Gregory Jefferis | 30 January 2014, 21:15:06 UTC | move is.amiramesh/amiratype to nat | 30 January 2014, 21:15:12 UTC |
| 22a9dd2 | Gregory Jefferis | 27 January 2014, 07:21:04 UTC | Merge branch 'feature/amira-igraph' * feature/amira-igraph: new as.directed.usingroot() FIXME improve name Some tidying of tests of all SkeletonGraph neurons Fix SWC Parents CoreNeuronFromAmiraSkel() Improve RecalculateSWCData (which was unused to date) be quiet when reading header in amiratype() Test as many amiramesh SkeltonGraph files as we can find on my machine! small fixes (inc docs/tests) for is.amiramesh and amiratype test functions to verify that amira neurons are still read correctly new functions to test files for amiramesh / content Teach ParseAM3DToNeuron to use either method to parse am3d neuron ADD: CoreNeuronFromAmiraSkel() using igraph | 27 January 2014, 07:21:04 UTC |
| 091ed53 | Gregory Jefferis | 27 January 2014, 07:20:37 UTC | test data for test.ReadAmiramesh | 27 January 2014, 07:20:52 UTC |
| 438e6fe | Gregory Jefferis | 27 January 2014, 07:19:32 UTC | Deprecate core ReadAmiramesh functions | 27 January 2014, 07:19:32 UTC |
| 7375a2c | Gregory Jefferis | 26 January 2014, 22:19:50 UTC | add tests for generic amiramesh reader/writer * mostly so that we can check all is still well when we move them to nat | 26 January 2014, 22:19:50 UTC |
| 5836393 | Gregory Jefferis | 26 January 2014, 16:16:18 UTC | remove unused ReadAmiramesh.ASCIIData | 26 January 2014, 16:16:18 UTC |
| a7b2dfd | Gregory Jefferis | 25 January 2014, 15:09:43 UTC | more test fixes for seglist class | 25 January 2014, 15:09:43 UTC |
| 3352820 | Gregory Jefferis | 25 January 2014, 15:09:21 UTC | Deprecate CoreNeuronFromSWC | 25 January 2014, 15:09:21 UTC |
| a0db4e3 | Gregory Jefferis | 25 January 2014, 14:54:36 UTC | fix seglist tests (due to seglist now having a class) * and remove graph2seglist tests since these now take place directly in nat | 25 January 2014, 14:55:12 UTC |
| 315c88c | Gregory Jefferis | 25 January 2014, 14:54:16 UTC | Deprecate CoreNeuronFromGraph and remove graph2seglist | 25 January 2014, 14:54:16 UTC |
| fabb839 | Gregory Jefferis | 25 January 2014, 12:52:28 UTC | Fix test.PotentialSynapes.neuron * change in first argument name in as.neuron | 25 January 2014, 12:52:28 UTC |
| 090c5a7 | Gregory Jefferis | 25 January 2014, 12:42:37 UTC | Remove branchpoints etc methods * these are now in nat | 25 January 2014, 12:42:37 UTC |
| 5a17d7f | Gregory Jefferis | 19 January 2014, 01:04:02 UTC | Make sure that all uses of CMTK tools use cmtk.bindir() * also remove IGSRegToolsDir from startup | 19 January 2014, 01:04:02 UTC |
| c5e0d6c | Gregory Jefferis | 18 January 2014, 21:49:36 UTC | insist on nat >=0.5.2 * now that we have removed subset.neuronlist | 18 January 2014, 21:49:36 UTC |
| e931a06 | Gregory Jefferis | 18 January 2014, 21:35:05 UTC | move subset.neuronlist to nat | 18 January 2014, 21:35:05 UTC |
| f778457 | Gregory Jefferis | 18 January 2014, 12:49:21 UTC | docs for set3d | 18 January 2014, 12:49:21 UTC |
| 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 |
