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CHANGELOG.TXT
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CHANGELOG.TXT
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06 Nov 2019
- Fixes out-of-memory error when reverting large histories.
- Fixes out-of-bounds regression when deleting or merging the last cluster.
05 Nov 2019
- Display a more useful message when failing to revert history changes.
- Transient or Dependent properties are no longer saved or loaded from _res.mat.
01 Nov 2019
- New-style probe configurations are supported (alongside old-style).
- Probe plot displays multishank probes in subplots.
31 Oct 2019
- Unit subset selection supported (annotated-only and non-annotated-only units so far). Use, e.g., "View > Display annotated units only" to enable.
- Small bug fixes and performance improvements.
10 Oct 2019
- Phy-formatted SpyKING CIRCUS results can be imported with `jrc import-spyking-circus /path/to/phy/output/`.
9 Oct 2019
- Export of results struct to workspace now controlled by parameter `exportResults`.
3 Sep 2019
- Results can be exported to NWB format with jrc export-nwb /path/to/my/params.prm
30 Aug 2019
- Autodelete implemented for TemplateClustering.
29 Aug 2019
- Splitting from FigProj selects all spikes, not just plotted spikes, within polygon.
25 Jul 2019
- Revamp history mechanism.
4 Apr 2019
- Kilosort importer reads from NPY files instead of rez.mat (npy-matlab is required for this feature)
- spikesRaw and spikesFilt are written to disk as they are computed, rather than all at once, to save memory (restores v3 behavior)
- removes JRC/saveBinaries due to the above
- New parameter: extractAfterDetect allows you to specify whether you want your features computed after ALL spikes are detected or on a per-chunk, per-file basis.
29 Mar 2019 (4.0.0-beta release)
- Allow user to select exploratory clustering algorithm in main split.
- Allow user to split in FigProj.
- hClust is no longer saved to _res.mat. Now all fields are available without having a copy of JRCLUST installed.
27 Mar 2019
- Bugfix: non-integral sample rates are supported to full precision.
- Export results in phy-compatible format with jrc export-phy /path/to/your/config.prm.
- Display summaries after detect and sort, also added an option to display a summary in UI.
20 Mar 2019
- Bugfix: import-ksort didn't use the correct sites for imported spikes; this has been fixed.
Several small bug fixes.
19 Mar 2019
- New split mechanism (allows for multiple splits).
- Users can press g in the waveform view to go to a specific cluster.
- Bugfix: raw traces in chunks 2:end were being extracted nSamplesPad later than they were supposed to; this has been fixed.
12 Mar 2019
- Intan traditional recordings are now supported (but experimental; please report issues reading your Intan files).
- Users can press q in the waveform view to display quality scores for the selected cluster.
Pressing SHIFT-Q will also export them to the workspace.
Several small bug fixes.
13 Feb 2019
# mToStruct
- throws a warning if eval/parse fails
# import.v3 (formerly import.importv3)
- updates clusterCenters on import to be consistent with nClusters
- checks for hClust consistency on import
12 Feb 2019
# Parameters
- evtGroupRad introduced
- evtMergeRad (formerly maxDist_site_merge_um) (re)implemented to correct an error in parameter usage
- selection of evtDetectRad, evtGroupRad, or evtMergeRad as the parameter of choice has been corrected in some places
- exact usage of nSitesExcl clarified in docs
- nPassesMerge had reported an incorrect default value in the docs; this has been fixed
# JRC
- hCfg is now a hidden attribute but publicly settable
- `compile` command is now (re)implemented
- `auto` is now `recluster`
- steps in pipeline have been broken out into their own functions (run calls each in turn)
- saveRes and saveBinaries are separate functions
- saveRes can be called with a forceOverwrite parameter
- user is warned if spikesRaw, spikesFilt, spikeFeatures are empty on load
# Config
- automatically set to error if rawRecordings is empty
# Recording
- supply a more helpful error message if nSamples is not an integer
# DetectController
- check for error in hRec before trying to detect
- save rawShape, filtShape, featuresShape in detect()
# metaToStruct
- check given .meta file is a text file
# help
- now opens the RTD site or directs user to visit
11 Feb 2019
# Parameters
- ignoreChans (formerly viChanZero) (re)implemented to address issue #83
# Config
- canonical version of ignoreSites was computed wrong in validation; this has been fixed
# CurateController
- "File > Save" menu callback crashed with "Too many input arguments" (see #86); this has been fixed
7 Feb 2019
# Parameters
- a post-validation transform was erroneously applied to `freqLimNotch`; this has been fixed
# planLoad
- on non-Windows systems without GPUs (i.e., where no memory information is available),
JRCLUST attempts to load the entire file, potentially crashing when the file is large;
this has been fixed
# doBootstrap
- double check for binary file if binary and meta filenames don't match
# Config
- glob expansion in bin files was resulting in nested cell arrays instead of files; this has been fixed
# jrc
- try-catch around hJRC creation resulting in useless error messages; this has been corrected
6 Feb 2019
Added an importer for JRCv3 _jrc.mat files.
This can be used via `jrc importv3 /path/to/your/session_jrc.mat`
# JRC
- deprecate/warning was giving erroneous messages; this has been fixed
# Config
- make errors and warnings (if in dialogs) blocking
- make fullParams a dependent property rather than recomputing it in different places
- don't validate params if not given a filename in constructor
- removed setters for `*Samp` (dependent) properties
- check for Dependent status and membership in fullParams in setCustomProp
- added pointer to param docs when exporting prm file
# depWarn
- make deprecation warnings blocking
# jrc.json
- added link to documentation
- updated release to alpha-patch2
5 Feb 2019
# Parameters
- `realignTraces` did not have a section field, causing crashes on `Config.save`; this has been fixed
- change sections for various filtering params to "preprocessing" rather than "spike detection"
# TracesController
- spike highlights were not clearing after toggling spikes off; this has been fixed
- annoying "Beginning/End of file" message triggered before reaching BOF/EOF; this has been fixed
# PreviewController
- spike highlights were not clearing after toggling spikes off; this has been fixed
- annoying "Beginning/End of file" message triggered before reaching BOF/EOF; this has been fixed
# Config
- ignoreSites was indexed with ismember(siteMap, ignoreSites), potentially causing OOB errors; this has been fixed
# various
- replace `isfile` with `exist(., 'file') == 2` and `isdir` with `exist(., 'dir') == 7`
- `exist` called without abs path returned false positives, leading to references to nonexistent files; this has been fixed
4 Feb 2019
# Parameters
- `RDDetrendMode`: 'hidehiko' renamed to 'regress'
- `realignTraces` was overlooked; this has been fixed
- old2new parameter mapping moved into params.json
- `deprecated` field (with supported/partially supported subfields) added to params.json
# Config class
- `validateProp` method failed to check default string values because MATLAB is weird about "" strings; this has been fixed
- `save` method exported default params, not user-specified params; this has been fixed
- `oldParamSet` made a dependent property
- added `setCustomProp` method: Config no longer ignores params not found in the default set
- added `deprecatedParams` property: check for deprecated status when calling `setCustomProp`
- added `isV3Import` property: Config will export a new config file if this is true
- `save` method exports custom properties if there are any
# JRC class
- `saveFiles` saved binaries (raw/filtered traces, features) on sort without detect; this has been fixed