Fix merging error #68
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jayd1860
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May 2, 2024
… v2.50.2
v2.50.2
-- Sync with shared libraries
-- Fix issue with installation of build (because of faulty getAppDir.m when deployed is used) when no previous homer3 installation exists
DataTree, v1.21.1
-- Change name of sample data folder from SubjDataSample to SampleData.
Utils, v1.8.3
-- Fix issue with installation of build (because of faulty getAppDir.m when deployed is used) when no previous homer3 installation exists
v2.50.1
-- Fix error in FileClass.ErrorCheckName() causing the reporting of a false warning a: "The current file [***] has the same name as the folder containing it. All files should have a different name than the folder containing them ...". To reproduce take a dataset with a flat file structure, and generate a corrupt stim(1).data which causes an error to be detected but then also a false warning.
DataTree, v1.21.0
-- Fix error in FileClass.ErrorCheckName() causing the reporting of a false warning a: "The current file [***] has the same name as the folder containing it. All files should have a different name than the folder containing them ...". To reproduce take a dataset with a flat file structure, and generate a corrupt stim(1).data which causes an error to be detected but then also a false warning.
v2.50.0
-- Fix very slow loading of datasets on MAC OS because H5D.open() is very slow error handling when loading optional, i.e., nonexistent fields. Fix is to using a fast check to see if dataset exists using H5L.exist() before attempting to load with H5D.open(). This also greatly speeds up loading time on Wionodws as well.
-- Reduce the amount of print statements to console. Provide WriteFileOnly method in Logger class.
-- Remove needless statement to fix matlab exception when syncing with submodules using syncSubmodules.m
DataTree, v1.20.0
-- Fix very slow loading of datasets on MAC OS because H5D.open() is very slow error handling when loading optional, i.e., nonexistent fields. Fix is to using a fast check to see if dataset exists using H5L.exist() before attempting to load with H5D.open(). This also greatly speeds up loading time on Windows as well.
-- Reduce the amount of print statements to console. Remove 'Initializing empty derived data output file ...' and 'Attempting to load ***-level proc stream from ...' and 'Saving group ...'
Utils, v1.8.2
-- Reduce the amount of print statements to console. Provide WriteFileOnly method in Logger class.
v2.49.0
DataTree, v1.19.0
-- Building on last commit to improve DataTree launch performance by caching DataFilesClass object in ./derivatives/homer/DatasetFiles_snirf.mat - this time add smart loading of ./derivatives/homer/DatasetFiles_snirf.mat containing cached DataFilesClass object which takes a long time to build. Rather than just crudely rebuilding DataFilesClass object from scratch if anything in the current files differs from saved data; rebuild ONLY those parts of the dataset that have changes and add those changes to saved object.
DataTree, v1.18.1
-- Changes to improve startup performance when launching Homer. It takes a lot of time to build and check the set of valid data files out of which the dataTree is built. changes to BUNPC/development. It will save the object with the vetted dataset files list (that's what slows things down) in the BIDS derived folder
derivatives / homer / DatasetFiles.mat
It will do it once if the saved file isn't there OR if something about the dataset has changed since last save - i.e. data file added, deleted, moved or edited. Otherwise it quickly loads and copies it which is a lot faster.
-- Fix issue with incorrect folder structure report in DataFilesClass.m and incorrect counting of number of files and folders. Test case is TaskA
-- Fix ProbeClass.IsValid validation not checking mandatory dimensions of sourcePos and detectorPos os having minimum of 2 and 3 columns.
DataTree, 1.18.0
-- Fix for "Stim Rejection not working for auto/manual time exclusion"
Add unit test script to test DataFilesClass with simulated dataset
Merge pull request #68 from sreekanthkura7/development
Fix merging error
Merge pull request #67 from sreekanthkura7/development
Update Transformation matrix mcspace to mni space after importing a new MRI anatomy
update code to add transformation matrix from mcspace to mni space after importing a new MRI anatomy
Fix isProbeAlreadyRegistered issue
-- Update showReducedMesh.m
Previously, if the user opted for the original mesh, it was still reducing the mesh. Cleaned up to code to provide both options (reduced and orig mesh).
Update ImageRecon.m
Brain and scalp option was referring two old variable names. This fix is replacing them with activeChLst_SDpairs variable.
FIx a bug in probe design in AV
v2.48.1, Fix image reconstruction generating bad image that might be caused by inconsistent meas list channel order. (#65)
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
v2.48.0
-- Fix image reconstruction generating bad image that might be caused by inconsistent meas list channel order. Found by Meryem. Issue looks like in hmrConc2OD.m
-- Fix issue in probe registration where AV does not detect presence of spring registration when it calls compatibleProbes.m from getProbe.m at load time.
-- Fix issue in probe loading when searching SD files for compatible probes and it is not detected because of faulty algorithm in compatibleProbes.m.
-- 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.
-- Add 2nd wavelength to get_tiss_prop.m to be the default rather than one wavelength and set default tiss ptop values for 760 nm and 850 nm as published in Sensors. 13 February 2023: "Impact of Anatomical Variability on Sensitivity Profile in fNIRS–MRI Integration"
-- 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, 1.8.1
-- 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.
Fix bug in tranforming brain vol to head space in import MRI anatomy utility
Fix an issue while changing Atlas
Fix probe registartion issue to avoid slight modifications for the probes developed in 3D probe design, Fix runMCXlab issue to use Imgvol instead fluedata to find inside tissue point, Fix a variable name issue on ImageReacon
v2.47.0
-- If probe is already registered when pulling to surface with pullProbeToHeadsurf then don't re-register it.
-- Fix issue with 3D sources and detectors not being copied correctly in NirsClass because IsFlatProbe() had a bug in it.
-- Add NirsClass.ProbeSimilar() method which to use in getProbe() --> findUniqueProbeFiles() so that unique set of probe files can be found
-- Change displayProbe() when re-registering do that there's no gap in display that is so the probe doesn't disappear and then re-appear, instead going smoothly from one registration to the next.
DataTree, v1.17.2
-- Fix issue with 3D sources and detectors not being copied correctly in NirsClass because IsFlatProbe() had a bug in it.
-- Add NirsClass.ProbeSimilar() method which to use in getProbe() --> findUniqueProbeFiles() so that unique set of probe files can be found
v2.45.1
-- 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.
v2.46.1
DataTree, v1.17.1
-- Fix convertBintoSnirfv2 from SD to NirsClass generating error in IsProbeFlat() method.
v2.46.0
-- Fix Homer3 generated snirf files not passing pysnirf2 validation.
-- Minor change to ImportMriAnatomy.fig to be resizeable to allow user to exapnd GUI to see long files paths.
-- When saving probe from the file menu check that there's a probe to save and display warning if there isn't
DataTree, v1.17.0
-- Fix Homer3 generated snirf files not passing pysnirf2 validation.
-- update runMCXlab to fix the issue when GUP mcxlab returen zero flue.data when an optode is very close to the tissue boundary
v2.45.0
-- Fix bug in 3D probe design when adding dummy optodes the spring list adds invalid springs where optode indices in the spring are the same.
-- Got rid of probe.filename_to_save field for saving probe to simplify things. You are now ALWAYS asked name to save to instead of keeping track what i the 'current' probe file associated with the probe.
-- Clean up redundant 3D probe design code + some minor code text formatting
-- Add ability to getProbe.m loadFromSDFiles() to read .snirf files. This could be done from dataTree but if no data is available only .SD files were looked at and .snirf files were ignored. Now .snirf is included in the list of file type3s from which probe data could be loaded.
-- Fix import probe which was broken
-- Fix issue head orientation changing after head size registration
-- Fix issue with measurement list not being saved in SDgui when saving to .snirf file. Even though data should be empty the measlist should still be saved.
-- Make cfg variable global in SDgui so that it's not constantly reinitialized every time the code needs to access a config variable. Instead initialize and use global cfg for instace in GetGrommetChoices
DataTree, 1.16.0
-- 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, 1.8.1
-- Avoid looking in Install folder for the AppSettings.cfg files
v2.44.1
-- Sync with latest DataTree libraries.
-- 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, v1.15.4
-- Fix snirf write issue where the created HDF5 dataset data type/size does not match the type/size of value being stored
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.
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Fixing a merging error that happened during previous pull request.