Hmr r block avg #208
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…or export of proc stream mlActMan (BUNPC#162) Merge v1.72.0: Fix for ar_glm_final.m stepwise error in GLM and fix for export of proc stream mlActMan
…ing: commit 1680519 Author: jayd1860 <[email protected]> Date: Tue Apr 11 14:49:33 2023 -0400 -- Sync setpaths in DataTree with DataTree library commit 0f5428e Author: jayd1860 <[email protected]> Date: Tue Apr 4 16:30:29 2023 -0400 v1.76.0 -- Update DataTree shared lib submodule (BUNPC#168) * v1.75.4 * DataTree, v1.11.1 -- Fix error when loading some probes in NirsClass check that NirsClass.GetChannelsMeanDistance() is error checking size of SrcPos3D and DetPos3D against meas list indices. * Utils, v1.4.4 -- Change font size in MenuBox. -- Adjust button width to slightly wider. * v1.75.5 -- Fix font size for MAC for MenuBox.m and configSettingsGUI.m * v1.75.6 -- Utils, 1.4.6 -- Tweak size of MenuBox text gap. * v1.76.0 -- Update DataTree shared lib submodule * DataTree, 1.12.0 -- Change AcqDataClass GetSrcPos and GetDetPos methods to ignore '2D' and instead automatically try to retrieve 3D optodes if available otherwise it retrieves 2D. This fixes the problem of retrieving non existent or artificially generated 2D optodes that do not agree with the 'LengthUnit' which is a problem when doing image reconstruction and using a non-zero SD separation to exclude channels (possibbly end up exluding ALL chaqnnels if units apply to the wrong optodes). -- Update NirsClass so SDgui matches GrommetRot being changed back to cell array type instead of numeric array. commit 4974adb Author: Meryem Ayşe Yücel <[email protected]> Date: Mon Apr 3 12:02:43 2023 -0400 Dev may2 (BUNPC#167) * Update ar_fit.m Fixing bug in filename stepwise->stepwisefit, and the relevant extracted output. * Update ar_glm_final.m Reducing the number of max iterations to 10 for the sake of computational time. * Update ar_glm_final.m fix Pmax 10->100 * AR p order Order was hardcoded, changed it be 2 X sampling frequency. commit d0fac4b Author: jayd1860 <[email protected]> Date: Thu Mar 23 02:10:45 2023 -0400 v1.75.6 -- Fix font size in MenuBox on MAC (BUNPC#166) * v1.75.4 * DataTree, v1.11.1 -- Fix error when loading some probes in NirsClass check that NirsClass.GetChannelsMeanDistance() is error checking size of SrcPos3D and DetPos3D against meas list indices. * Utils, v1.4.4 -- Change font size in MenuBox. -- Adjust button width to slightly wider. * v1.75.5 -- Fix font size for MAC for MenuBox.m and configSettingsGUI.m * v1.75.6 -- Utils, 1.4.6 -- Tweak size of MenuBox text gap. commit f583645 Author: jayd1860 <[email protected]> Date: Tue Mar 21 21:52:42 2023 -0400 v1.75.3 -- Fix issue with setpaths error on MAC when setting file persmissions and logging it global logger not declared. -- Clean up addremove argument to setpaths and add option (addremove=2) to exclusively load only the current repo while excluding search paths for all other similar repos commit d2c3873 Author: jayd1860 <[email protected]> Date: Tue Mar 21 15:31:33 2023 -0400 v1.75.2 -- Sync with shared libraries (submodules). * DataTree, v1.11.0 -- Change NirsClass.ProbeEqual() to consider measurement lists in different orders but same set of SD pairs to be equal. SO SDgui doesn't think edits were made when they weren't. -- Add NirsClass.GetChannelsMeanDistance() method same as in SnirfClass * Utils, v1.4.2 -- Make another tweak in MenuBox - character size doesn't quite equal character units so we compensate by multiplying by scaling factor for button width and height. * Utils, v1.4.1 -- Fix some size and position issues with radiobutton style MenuBox. Another attempt to simplify size and position calculations. commit a44aeed Author: sreekanthkura7 <[email protected]> Date: Tue Mar 21 14:25:14 2023 -0400 Add plotProbe2 display commit 27a642e Author: jayd1860 <[email protected]> Date: Sat Mar 18 00:49:19 2023 -0400 Fix SpatialUnit scaling in SD NirsClass (BUNPC#165) * v1.75.0 -- In syncSubmodules.m add option to ignore last revision dates of the parent repo and submodules and instead force the direction of copying changes from parent repo to submodules ('parent2submodules') or submodules to parent repo ('submodules2parent'). * DataTree, v1.9.0, v1.8.3 -- Fix wrong probe scaling converting units in SnirfClass.ProbeClass and NirsClass -- Add m (meter) to SpatialUnits NirsClass add appropriate scaling. When changing units in SDgui ask iof fixing incorrect units or simply changing units and associated coordinates. * Utils, v1.4.0, v1.3.5 -- Remove non-class method convert_optodepos_to_circlular_2D_pos.m from ProbeClass to Utils. -- Add missing function pretty_print_struct.m used in DataTree to Utils library -- Fix bug in last commit having to do with the MenuBox radiobutton dialog selction of spatial unit change: either a) correcting them and changing units ONLY or b) changing units and coordinates. -- Add radiobutton selection style option to MenuBox.m -- Fix some issues with MenuBox.m including issue with MenuBox disappearing outside of screen when run standalone with no parent GUI. * v1.75.1 -- DataTree, v1.10.0, Fix error in probe registration loading SD file where anchor points are not copied correctly. commit 4544f60 Author: jayd1860 <[email protected]> Date: Wed Mar 8 13:23:12 2023 -0500 v1.74.3 -- Sync with latest shared libraries * DataTree, v1.8.1 -- Fix error when trying to retrieve ppf param during image recon because dataTree.currElem.procStream.fcalls being empty. This is because of using GroupClass.CompareVersions caused procstream fcalls from groupResults not to load (it was deemed too old) which is clearly not what we want. Removed for now the comparison (CompareVersions for now always returns 0) until we can figure out best way to handle old versions of groupResults. -- Provide ProbeClass.GetScaleFactor() method to retrieve private scaling field -- In ExportProcStreamDependencies get rid of the *_Library_Version suffix next to each library name in the JSON output * FuncRegistry, v1.2.2 -- Fix issue with converting mlACt vector to 2D array with mlAct_Initialize.m during image recon. * Utils, v1.3.2 -- Add ability to versionstr2num to process version arguments in the form of 3 numbers rather than a string for backward compatability with DataTree GroupClass to get old style version. commit 104e17c Author: jayd1860 <[email protected]> Date: Tue Mar 7 11:53:01 2023 -0500 v1.74.1 -- Fix Logger.Write issue when getting cell array of strings input. -- Remove redundant copy of jsonlab library which has been moved to Utils shared library files from jsonlab library. -- Utils, v1.3.1: Remove unnecessary files from jsonlab library. License looks like it allows modification as long as you include the license itself in the distribution. -- FuncRegistry, v1.2.1: Update version number after Meryem's changes to ar_glm_final.m. commit 349a96d Author: jayd1860 <[email protected]> Date: Sun Mar 5 14:41:52 2023 -0500 v1.74.0 -- Move updateVersions and supporting function out of Utils/submodules to Utils/Shared in DataTree standalone mode to update repo versions. -- Move JSON library from Utils to Utils/Shared for use in DataTree standalone mode to write JSON files when expoerting proc stream. * DataTree, v1.8.0 -- Fix issue of DataTree in standalone mode not getting the right value for config parameter "Export Processing Stream Functions". -- Remove reliance on static method TreeNodeClass.ExportProcStreamFunctions to get value of config parameter which tells you if code should export processing stream. Instead switch to getting the value directly from the ConfigFileClass global variable cfg which is automatically updated when changes are made to any config parameters through the configSettingsGUI. * Utils, v1.3.0 -- Add JSON library so that export of procesaswing stream to JSON files can work in DataTree in standalone mode. -- Add repoManagement/updateVersions.m and supporting function so that use can use the script to update versions in DataTree in standalone mode. -- When saving config parameters in configSettingsGUI update global ConfigFileClass variable cfg so that DataTree in standalone mode has immediate access to changes in config params without having to rerun dataTree. commit d86615d Author: Meryem Ayşe Yücel <[email protected]> Date: Sun Mar 5 14:35:03 2023 -0500 Dev may2 (BUNPC#163) * Update ar_fit.m Fixing bug in filename stepwise->stepwisefit, and the relevant extracted output. * Update ar_glm_final.m Reducing the number of max iterations to 10 for the sake of computational time. * Update ar_glm_final.m fix Pmax 10->100 * AR p order Order was hardcoded, changed it be 2 X sampling frequency. --------- Co-authored-by: jayd1860 <[email protected]> commit c3a2f13 Author: jayd1860 <[email protected]> Date: Sat Mar 4 23:04:36 2023 -0500 v1.73.1 -- Fix issue where you get error in getVernum.m when namespace isn't set. commit 222f6e0 Author: jayd1860 <[email protected]> Date: Sat Mar 4 00:57:24 2023 -0500 v1.73.0 -- Separate ApplicationName into ApplicationName and Version when exporting processing stream to JSON file. -- Change default for config parameter Export Processing Stream Functions from No to Yes. -- Add library version numbers to JSON file generated by export processing stream utility -- Add utility updateVersions.m to Utils/submodules to automatically generate new version numbers for main application and shared library depedencies -- Fix issue with copying probe in NirsClass.CopyProbe when concerting from .nirs to .snirf. Also use NirsClass constructor rather than load() to load .nirs data when converting from .nirs to .snirf. commit 16a3aae Merge: 9991e1d 40bb3ca Author: jayd1860 <[email protected]> Date: Fri Mar 3 00:46:55 2023 -0500 Merge branch 'master' into development commit 9991e1d Author: jayd1860 <[email protected]> Date: Fri Mar 3 00:28:17 2023 -0500 -- Update version numbers for DataTree and FuncRegistry after new fixes commit 592a42f Author: Meryem Ayşe Yücel <[email protected]> Date: Fri Mar 3 00:23:21 2023 -0500 Update ar_fit.m (BUNPC#161) * Update ar_fit.m Fixing bug in filename stepwise->stepwisefit, and the relevant extracted output. * Update ar_glm_final.m Reducing the number of max iterations to 10 for the sake of computational time. commit a383a3f Author: jayd1860 <[email protected]> Date: Thu Mar 2 23:43:34 2023 -0500 v1.72.0 -- Fix error when exporting processing stream to JSON files because of bug in extracting mlActMan - since it is no longer a vector but a 2D array of sd pairs plus data type. commit bf948c0 Author: jayd1860 <[email protected]> Date: Tue Feb 28 23:28:38 2023 -0500 # Conflicts: # DataTree/AcquiredData/Nirs/NirsClass.m # DataTree/AcquiredData/Snirf/ProbeClass.m # DataTree/GroupClass.m # DataTree/Version.txt # FuncRegistry/UserFunctions/iWLS/ar_glm_final.m # FuncRegistry/Version.txt # Utils/Shared/Version.txt # Utils/Shared/versionstr2num.m # Version.txt
Date: 5/11/2023 3:06:37 PM v1.79.3 -- Add more standalone startup function to setpaths.m to be able to independent of any startup code search paths except current folder -- Chnage default value of config param Load Stim From TSV File from no to yes. * DataTree, v1.14.2 -- Fix events TSV file naming bug. Add TSV file name method TreeNode.GetStimTsvFilename() to use for all events TSV file naming. -- Fixes to setpaths for running DataTree standalone * Utils, v1.6.0 -- Fix some bugs in events TSV stim loading error handling. Add config param "Replace TSV File Tabs with Spaces" to handle events TSV errors when file is a mix of spaces and tabs. -- Add method ConfigFileClass.GetValueOptions for getting all available value options for a param. Date: 5/10/2023 10:52:19 AM v1.79.1 -- Fix Homer3 displaying probe in 3D rather than 2D. (BUNPC#177) * DataTree, v1.14.0 -- Fix Homer3 displaying probe in 3D rather than 2D. Back out changes that default to 3D in ProbeClass and NirsClass GetSrcPos and GetDetPos for ALL cases. The way it's supposed to work is probe is supposed to use 2D coordinates ONLY when being displayed in Homer3. Rest of the time default to 3D if it exists. Reason for original change is misunderstanding of what the purpose of 2D coord was which is ONLY for display * Utils, v1.5.1 -- Add ability to simulate full dataset (generateSimData.m, simulateDataTimeSeries.m) to be able to eventually do workflow unit and system tests Date: 5/3/2023 12:38:30 PM v1.78.1 -- Fix error when displaying data, remove unnecessary call to get file descriptor: obj.fid = HDF5_GetFileDescriptor(fileobj); (BUNPC#174) Date: 5/3/2023 10:52:24 AM -- Forgot to include HDF5_GetFileDescriptor.m in v1.78.0 commit. (BUNPC#173) Date: 5/3/2023 10:13:49 AM v1.78.0 -- Improve saving performance of SNIRF files by using low level HDF5 library. (BUNPC#172) * DataTree, v1.13.0 -- Comprehensive solution to improving the save performance of SNIRF files by using low-level HDF5 calls and limiting the number of HDF5 open and create calls that are made for file, group and dataset. Date: 4/14/2023 1:59:38 AM 1.77.0 -- Fix stim events TSV issue with conditions names with spaces - we should be able to handle that. (BUNPC#170) Utils, v1.5.0 -- Fix stim events TSV issue with conditions names with spaces - we should be able to handle that. Change rule to handle spaces and how error reporting is done in readTsv. DataTree, v1.12.1 -- Don't load events TSV files twice - once in SnirfClass and once in AcqDataClass its superclass. Date: 4/11/2023 2:49:33 PM -- Sync setpaths in DataTree with DataTree library
-- 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.
Update code for OD block average for compatibility with current SNIRF format
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Update code for OD block average for compatibility with current SNIRF format. No change to concentration calculation.