Update setpaths for generalizability #64
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Updated to be more generalizable to different path formats. For example some paths have '\\' at the beginning and previous setpaths did not support such paths. This one should support all paths supported by matlab via fullfile() function.
removed filesepStandard_startup() function from working on other parts of setpaths as it is not general enough compared to fullfile()
…caused by inconsistent meas list channel order. (BUNPC#65) * 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. * v2.48.1 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
Brain and scalp option was referring two old variable names. This fix is replacing them with activeChLst_SDpairs variable.
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).
…ter importing a new MRI anatomy
Update Transformation matrix mcspace to mni space after importing a new MRI anatomy
Fix merging error
* 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"
-- 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.
-- 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.
-- 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
-- Fix bug saving wrong format indicating what folder format is associated with saved dataset. This leads to not finding ANY data files when reloading dataset next time Homer is launched. To reproduce comment out the fix and add ONE "error" snirf file (such as probe.snirf) which will not be loaded AND are in a different folder format than the valid dataset. Exit Homer and restart it. Homer will not find ANY data files when relaunching. DataTree, v1.22.0 -- Fix bug saving wrong format indicating what folder format is associated with saved dataset. This leads to not finding ANY data files when reloading dataset next time Homer is launched. To reproduce comment out the fix and add ONE "error" snirf file (such as probe.snirf) which will not be loaded AND are in a different folder format than the valid dataset. Exit Homer and restart it. Homer will not find ANY data files when relaunching.
need to handle the special case of ppf = 1 as we do in hmrR_OD2Conc.m
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Updated to be more generalizable to different path formats. For example some paths have '\' at the beginning and previous setpaths did not support such paths. This one should support all paths supported by matlab via fullfile() function.
Still requires testing on Mac and Linux.