Updates on plotting colors and ss fade thres #198
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…s related to file storing
…tion artefacts detection and correction
…e and plotting). Adds hyperlinks to each section in the tutorial
…tion text alignment
…validation Argument validation
-- Fix checking for latest updates. Move checkForAtlasViewerUpdates.m to the more general checkForUpdates.m and fix the problems which stopped working after getVernum changes. -- Streamline executable installation code * DataTree, v1.15.2 -- Fix error in DataFilesClass.FindDataSet() if the pattern that found acquisition file has no extension that means this pattern is meant ONLY for folders. Therefore any file matches should be skipped. -- Update SNIRF fields of MeasListClass with latest from spec. * Utils, v1.7.4 -- Fix checking for latest updates. Move checkForHomerUpdates.m to the more general checkForUpdates.m and fix the problems which stopped working after getVernum changes.
-- Fix issue on MAC where simple conversion from .nirs to .snirf files at launch time causes a MATLAB exception. This has been the case since speeding up dataset loading and saving using Matlab's low level HDF5 library. Problem that was fixed was that writing integers in hdf5write_safe() --> write_integer(), the call to H5T.copy creating space for the integer was using type H5T_NATIVE_ULONG the size of which depends on the platform - 32 bits on Windows, 64 bits on MAC. On MAC the size conflicted with the hard-coded size inside write_integer() of 32 bits (int32(val)). -- Improve launch performance by speeding up check of last time any of the user functions were modified to know if Registry.mat needs to be re-saved and re-loaded DataTree, v1.15.4 -- Fix snirf write issue where the created HDF5 dataset data type/size does not match the type/size of value being stored FuncRegistry, v1.4.1 -- Improve launch performance by speeding up check of last time any of the user functions were modified to know if Registry.mat needs to be re-saved and re-loaded
DataTree, v1.16.1, v1.16.0 -- Fix SnirfClass.Save() not saving 3D landmarks and labels. Reproduce with fullhead_56x144_v2.SD. The conversion from SD to Snirf is getting confused: In the SD file the SD.Landmarks3D is empty, which is why it is making the Snirf probe.landmarksPos3D empty. (That is, it is assigning probe.landmarksPos3D from SD.Landmarks3D) However: SD.Landmarks have the actual 3D coordinates. Added code to look for 3D positions (checking that they are actually 3D and not 2D) in SD.Landmarks if SD.Landmarks3D is empty. -- Fix error in NirsClass equal compare where ProbeEqual method is not checking size of SD.MeasList fields before comparing content causing exception when SD.MeasList is not same sizes -- Fix aux conversion from SNIRF aux with different time bases to NirsClass aux Utils, 1.8.0 -- Avoid looking in Install folder for the AppSettings.cfg files
# Conflicts: # FuncRegistry/UserFunctions/Archive/hmrS_SessAvgStd2_oldversion_nirs.m # FuncRegistry/UserFunctions/hmrG_SubjAvg.m # FuncRegistry/UserFunctions/hmrR_BlockAvg.m # FuncRegistry/UserFunctions/hmrR_MotionArtifact.m # FuncRegistry/UserFunctions/hmrR_MotionArtifactByChannel.m # FuncRegistry/UserFunctions/hmrR_MotionCorrectPCA.m # FuncRegistry/UserFunctions/hmrR_PCAFilter.m # FuncRegistry/UserFunctions/hmrS_SessAvgStd.m
…rk correctly in hmrMotionArtifact.m. (BUNPC#187) * v1.81.3 -- Fix failure to load full head probe fullhead_56x144_v3.SD or ninjaNIRS2022_2023-09-19-18-26-16.snirf files because SnirfClass.GetAuxDataMatrix gets an error when resampling with Matlab's resample function which does not handle a huge difference between aux sample rate and the data sample rate. To fix added local resample function resamplee.m to avoid this issue. DataTree, v1.17.3 -- Fix failure to load full head probe fullhead_56x144_v3.SD or ninjaNIRS2022_2023-09-19-18-26-16.snirf files because SnirfClass.GetAuxDataMatrix gets an error when resampling with Matlab's resample function which does not handle a huge difference between aux sample rate and the data sample rate. To fix added local resample function resamplee.m to avoid this issue. Utils, v1.8.1 -- Fix in ImageRecon error when setting timerange, such that it is more than or less that tHRF. Fix is to get tHRF when ImageRecon GUI launches and use ceiln and floorn for min and max tHRF to make sure it is not out of range. Added floorn.m and ceiln.m to fix this. -- Fix failure to load full head probe fullhead_56x144_v3.SD or ninjaNIRS2022_2023-09-19-18-26-16.snirf files because SnirfClass.GetAuxDataMatrix gets an error when resampling with Matlab's resample function which does not handle a huge difference between aux sample rate and the data sample rate. To fix added local resample function resamplee.m to avoid this issue. * v1.81.4 -- Fix issue found by Meryem, where prune channels doesn't work correctly in hmrMotionArtifact.m because combining mlActAuto and mlActMan isn't done correctly such that manual prunning is erased by auto pruning. Add function mlAct_CombineIndexLists to solve issue. Same issue in hmrR_MotionArtifactByChannel.m and hmrR_MotionCorrectWavelet.m. -- Make hmrR_PruneChannels.m user parameters drange and SNRthresh greater precision FuncRegistry, v1.4.2 -- Fix issue found by Meryem, where prune channels doesn't work correctly in hmrMotionArtifact.m because combining mlActAuto and mlActMan isn't done correctly such manual prunning is erased by auto pruning. Same issue in hmrR_MotionArtifactByChannel.m and hmrR_MotionCorrectWavelet.m. -- Make hmrR_PruneChannels.m user parameters drange and SNRthresh greater precision DataTree, v1.17.4 -- Fix probe not displaying in Homer3 because probe.sourcePos2D and probe.detectorPos2D are all zeros (which signifies empty but is not detected as empty) instead of actually empty. Also try to make units for generated 2D probe same as 3D by calling new method ProbeClass.ScaleProjection2D() -- Fix AuxClass eq function to check for different dataTimeSeries sizes when checking if 2 AuxClass objects are equal
Changed the default mode to quite mode on. Changed StimClass default value of "more" to 1 from []. [] wasa breaking the code at line 471: " obj.data = [obj.data; tPts, duration, amp, more];"
quite mode and stimClass
fix plotprob2 bugs 1)typo 2)conditions mismatch error
…ipts Two livescript examples
SplineSG has mlActAuto as an input. Due to the changes in homer3, mlActAuto containes only the first wavelength. SplineSG thus failed to clean the data from the second wavelength. Note for homer2 users: This was working properly for homer2. Note for homer3 users: Please reconsider running your pipeline with this version and up.
Critical bug fix SplineSG mlAct
New function hmrR_TaskNorm
…tation_update Documentation update
Fixed the issue of propagation of excluded channel indices from first wavelength to the second. Added sanity check/test to confirm it is working.
Updated PlotProbe2 and GUI to have short separation fade option. Also has different color plotting features for different conditions.
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Updated PlotProbe2 and GUI to have short separation fade option. Also has different color plotting features for different conditions.