v1.70.0 -- Fix hmrR_PCAFilter mlAct channel order issue; Provide DataTree examples; Fix DataTree standalone issues. (#153)

* Update on AR-GLM code (#148)

* v1.59.0

-- Fix retrieving inactive channels in hmrR_PCAFilter.m using the new mlAct supporting user functions.
-- Update design doc to document new loading and exporting of stim from and to BIDS events TSV files.

* Make standalone DataTree work by supplying missing cell2str.m function to shared library

* v1.60.0

-- Include startup functions in setpaths to be able initialize search paths for DataTree.
-- Add examples folder with runProcessingStream.m on how to download and run processing stream in DataTree standalone.

* v1.61.0

-- Add initialization script to run after downloading DataTree which downloads dependencies Utils and FuncRegistry and runs setpaths for ease of standalone operation
-- Add submodules .gitmodules file to DataTree library to stream line process of downloading dependencies when running DataTree standalone
-- Provide plotting method for TreeNodeClass elements to run from command line
-- Fix typos in .gitmodules and add FuncRegistry as a third submodule/library that Homer3 uses
-- Provide LoadRunPlotExamples.m example of how to use DataTree from scratch.
-- Add missing description of input argument mlAct in hmrR_PCAFilter.m

* v1.61.1

-- Fix typo in DataTree/.gitmodules FuncRegistry entry. This was fixed in the parent (Homer3) .gitmodules but not DataTree.
-- In syncSubmodules.m add .gitmodules to the list of file types to search for when syncing parent and submodules

* v1.62.0

-- Sync with changes in DataTree and Utils shared libraries:

  DataTree:

      1. Rename LoadRunPlotExamples to LoadRunPlotExample1.m and LoadRunPlotExample2.m - LoadRunPlotExample1 uses TreeNodeClass methods to get access to data and time and plot them, while LoadRunPlotExample2.m does the same thing BUT accesses snirf objects directly without any methods and then plots them directly in the script to show user how snirf objects work. Add example data that goes with it Example4_twNI.

      2. Add another example EditStimExample.m which shows how to export and edit stim and conditions. Add example data that goes with it SubjDataSample.

      3. Fix bugs in StimClass methods for editing stims (adding, deleting, and changing condition of) based on an inclusive time points vector.

      4. Fix run/plot examples and remove the download and initialization parts as that is unnecessary and does not quite makes sense since you have to first download the repo before accessing the LoadRunPlotExamples.m script.  This part can simply be described in the comments.

      5. Simplify initialization by moving downloading of submodules to setpaths and get rid of initialize.m

   Utils:

      1. Add capability to readTsv.m to be able to load TSV file that is separated by spaces instead of tabs if it is can be clearly determined that spaces are separators (instead of say names of conditions). If spaces are detected then the file is written to correctly contain tab separators as is appropriate for the .tsv format.

      2. Add namespace DataTreeClass to setGuiFonts.m so that fonts can be set in a figure when DataTree standalone is running

      3. Return figure handle of MenuBox.m so that it can be repositioned after calling it

* v1.64.0

-- Fix DataTree/setpaths not deleting other DataTree repos from path.
-- Change TreeNodeClass.Plot method accept source/detector/datatype instead of single number index vector, and handle multiple plot figures.
-- Reorganize and add documentation for TreeNodeClass plotting methods under separate methods section.
-- Redo LoadRunPlotExample (rename from LoadRunPlotExample1.m and delete LoadRunPlotExample2.m)  to display multiple plot figures.

* Remove obsolete example - merge with bunpc missed this for some reason

* v1.67.0

-- Sync with shared libraries
   Add version number files to libaries.
   Add common functions getVernum.m and parseGitSubmodulesFile.m which can exist as generic non startup Utils functions
   Add logging to setpaths to setpaths.log (instead of the previous SystemInfo.log) so its clear where the log file came from.
   Remove extra log files created unintentionally in DataTree like History.log
   Return missing support functions to downloadDependencies.m

-- Add .csd files to list of files in syncSubmodules.m to sync with shared libraries

* v1.68.0

-- Sync with DataTree v1.1.0 shared library :
   Add error checking to TreeNodeClass.Plot() method when there no data.
   Clean up zombie figure handles from TreeNodeClass.Plot() method so that handles don't accumulate indefinitely in obj.hFig as more plots are displayed.
   Return single number indices of plotted channels in TreeNodeClass.Plot()
   Minor change to LoadRunPlotExample1.m to name the function same as file

* v1.69.0

-- Fix another exception in setpaths when removing path with setpaths(0), because Logger and printStack is no longer in path but is not empty.
-- Update NirsClass.m to be able to at least load .nirs data setpaths.m
-- Update archived user functions for .nirs dataset (hmrE_RunAvg_Nirs, hmrS_SessAvg, etc) for the new BIDS data structure (which has sessions)
-- Simplify and clean up initial saving of group structure file groupResults.mat also saving the function call chain which did not get saved initially at time of Homer3 launch. Added initsaveflag to GroupClass and moved call to Save out of Load method and into the calling method DataTreeClass.LoadGroup() after proc stream initialization/copying has been completed and after SetConditions has been called.

* -- Minor fix to setpaths logging plus added time stamp when setpaths completed. Sync with same fix in DataTree setpaths.

* v1.70.0

-- Sync with shared libraries and AtlasViewer v1.24.0: Replace calls to matlab's built-in function menu() with Utils MenuBox() to fix strange issue with direct use of menu where it generates this error in R2017b and R2020b (and maybe other matlab versions):

   Error using matlab.ui.Figure/set
   Error setting property 'Position' of class 'Figure':
   Width and height must be greater than or equal to 0

   Error in menu>local_GUImenu (line 239)
   set( menuFig, 'Position', [winLeftGap bottom winWide winHigh] );

   Error in menu (line 51)
      k = local_GUImenu( xHeader, ArgsIn );

---------

Co-authored-by: Meryem Ayşe Yücel <[email protected]>
Co-authored-by: Jay Dubb <[email protected]>

Author: 3 people

.gitmodules

@@ -1,6 +1,9 @@
 [submodule "Utils/Shared"]
 	path = Utils/Shared
 	url = https://github.com/BUNPC/Utils
-[submodule "Group/DataTree"]
+[submodule "DataTree"]
 	path = DataTree
 	url = https://github.com/BUNPC/DataTree
+[submodule "FuncRegistry"]
+	path = FuncRegistry
+	url = https://github.com/BUNPC/FuncRegistry

DataTree/.gitmodules

@@ -0,0 +1,6 @@
+[submodule "Utils"]
+	path = Utils
+	url = https://github.com/BUNPC/Utils
+[submodule "FuncRegistry"]
+	path = FuncRegistry
+	url = https://github.com/BUNPC/FuncRegistry

DataTree/AcquiredData/AcqDataClass.m

@@ -213,39 +213,6 @@ function FreeMemory(obj, filename)
 
 
 
-        % ---------------------------------------------------------
-        function bbox = GetSdgBbox(obj)
-            bbox = [];
-            
-            optpos = [obj.GetSrcPos('2D'); obj.GetDetPos('2D')];
-            if isempty(optpos)
-                return
-            end
-            
-            xmax = max(optpos(:,1));
-            ymax = max(optpos(:,2));
-
-            xmin = min(optpos(:,1));
-            ymin = min(optpos(:,2));
-            
-            width = xmax-xmin;
-            height = ymax-ymin;
-            
-            if width==0
-                width = 1;
-            end
-            if height==0
-                height = 1;
-            end
-            
-            px = width * 0.05; 
-            py = height * 0.05; 
-
-            bbox = [xmin-px, xmax+px, ymin-py, ymax+py];
-        end
-        
-        
-        
         % ----------------------------------------------------------------------------------
         function varval = GetVar(obj, varname)
             if ismethod(obj,['Get_', varname])

DataTree/AcquiredData/DataFiles/FindFiles.m

@@ -93,8 +93,8 @@
         case {'nirs','.nirs'}
             files = DataFilesClass(dirnameGroup, 'nirs');
         otherwise
-            q = menu(sprintf('Homer3 only supports file formats: {%s}. Please choose one.', cell2str(supportedFormats(:,1))), ...
-                    'OK','CANCEL');
+            q = MenuBox(sprintf('Homer3 only supports file formats: {%s}. Please choose one.', cell2str(supportedFormats(:,1))), ...
+                    {'OK','CANCEL'}); 
             if q==2
                 return;
             else

DataTree/AcquiredData/Nirs/NirsClass.m

@@ -185,7 +185,7 @@ function SortData(obj)
 
                 % Optional fields
                 err = obj.LoadAux(fdata, err);
-                err = obj.LoadStims(fdata, err);
+                err = obj.LoadStim(fdata, err);
 
             catch
 
@@ -261,7 +261,7 @@ function SortData(obj)
 
 
         % ---------------------------------------------------------
-        function err = LoadStims(obj, fdata, err)
+        function err = LoadStim(obj, fdata, err)
             if ischar(fdata)
                 fname = fdata;
 
@@ -399,6 +399,20 @@ function SaveMat(obj, fname, options)
 
 
 
+        % --------------------------------------------------------------------
+        function b = EqualStim(obj, obj2)
+            b = false;
+            if length(obj.s) ~= length(obj2.s)
+                return;
+            end
+            if ~all(obj.s(:) == obj2.s(:))
+                return;
+            end            
+            b = true;
+        end
+        
+        
+        
         % -------------------------------------------------------
         function B = eq(obj, obj2)
             B = false;
@@ -466,7 +480,7 @@ function SaveMat(obj, fname, options)
             % If we're working off the snirf file instead of loading everything into memory
             % then we have to load stim here from file before accessing it.
             if strcmpi(obj.GetDataStorageScheme(), 'files')
-                obj.LoadStims(obj.GetFilename(), 0);
+                obj.LoadStim(obj.GetFilename(), 0);
             end
 
             % Generate new instance of NirsClass
@@ -562,23 +576,41 @@ function SetDataTimeSeries(obj, val)
             obj.d = val;
         end
 
+        
         % ---------------------------------------------------------
-        function val = GetDataTimeSeries(obj, ~, iBlk)
-            val = [];
-            if ~exist('iBlk','var') || isempty(iBlk)
-                iBlk=1;
+        function [d, t, ml] = GetDataTimeSeries(obj, options, ~)
+            d = obj.d;
+            t = obj.t;
+            ml = obj.GetMeasurementList(options);
+        end        
+        
+            
+        % ---------------------------------------------------------
+        function ml = GetMeasurementList(obj, matrixMode, ~)
+            if ~exist('matrixMode','var')
+                matrixMode = '';
+            end
+            if strcmpi(matrixMode, 'matrix')
+                ml = obj.SD.MeasList;
+            else
+                ml = MeasListClass();
+                for ii = 1:size(obj.SD.MeasList,1)
+                    ml(ii).sourceIndex = obj.SD.MeasList(ii,1);
+                    ml(ii).detectorIndex = obj.SD.MeasList(ii,2);
+                    ml(ii).dataTypeIndex = 0;
+                    ml(ii).wavelengthIndex = obj.SD.MeasList(ii,4);
             end
-            if iBlk>1
-                return
             end
-            val = obj.d;
         end
 
+                
+                
         % ---------------------------------------------------------
         function SetTime(obj, val)
             obj.t = val;
         end
 
+        
         % ---------------------------------------------------------
         function val = GetTime(obj, iBlk)
             val = [];
@@ -588,26 +620,31 @@ function SetTime(obj, val)
             val = obj.t;
         end
 
+        
         % ---------------------------------------------------------
         function val = GetSD(obj)
             val = obj.SD;
         end
 
+        
         % ---------------------------------------------------------
         function SetS(obj, val)
             obj.s = val;
         end
 
+        
         % ---------------------------------------------------------
         function val = GetS(obj)
             val = obj.s;
         end
 
+        
         % ---------------------------------------------------------
         function SetAux(obj, val)
             obj.aux = val;
         end
 
+        
         % ---------------------------------------------------------
         function val = GetAux(obj, options)
             if ~exist('options','var')
@@ -627,17 +664,50 @@ function SetAux(obj, val)
         end
 
 
-        
         % ---------------------------------------------------------
         function SetCondNames(obj, val)
             obj.CondNames = val;
         end
 
+        
         % ---------------------------------------------------------
         function val = GetCondNames(obj)
             val = obj.CondNames;
         end
 
+        
+        % ---------------------------------------------------------
+        function bbox = GetSdgBbox(obj)
+            bbox = [];
+            
+            optpos = [obj.SD.SrcPos; obj.SD.DetPos];
+            % optpos = [obj.SD.SrcPos; obj.SD.DetPos; obj.SD.DummyPos];
+            if isempty(optpos)
+                return
+            end
+            
+            xmax = max(optpos(:,1));
+            ymax = max(optpos(:,2));
+
+            xmin = min(optpos(:,1));
+            ymin = min(optpos(:,2));
+            
+            width = xmax-xmin;
+            height = ymax-ymin;
+            
+            if width==0
+                width = 1;
+            end
+            if height==0
+                height = 1;
+            end
+            
+            px = width * 0.05; 
+            py = height * 0.05; 
+
+            bbox = [xmin-px, xmax+px, ymin-py, ymax+py];
+        end
+        
     end
 
 
@@ -669,17 +739,6 @@ function SetCondNames(obj, val)
         end
 
 
-        % ---------------------------------------------------------
-        function ml = GetMeasurementList(obj, ~, ~)
-            ml = MeasListClass();
-            for ii = 1:size(obj.SD.MeasList,1)
-                ml(ii).sourceIndex = obj.SD.MeasList(ii,1);
-                ml(ii).detectorIndex = obj.SD.MeasList(ii,2);
-                ml(ii).wavelengthIndex = obj.SD.MeasList(ii,4);
-            end
-        end
-        
-        
         % ---------------------------------------------------------
         function wls = GetWls(obj)
             wls = obj.SD.Lambda;
@@ -917,6 +976,7 @@ function SetStimDuration(~, ~, ~)
             return;
         end
 
+        
         % ----------------------------------------------------------------------------------
         function duration = GetStimDuration(~, ~)
             duration = [];
@@ -929,6 +989,7 @@ function SetStimAmplitudes(~, ~, ~)
         end
 
 
+        
         % ----------------------------------------------------------------------------------
         function vals = GetStimAmplitudes(obj, icond)
             vals = [];
@@ -951,6 +1012,8 @@ function RenameCondition(obj, oldname, newname)
             obj.SortStims();
         end
 
+        
+        
         % ----------------------------------------------------------------------------------
         function nbytes = MemoryRequired(obj)
             nbytes = 0;
@@ -1056,6 +1119,13 @@ function CopyProbe(obj, SD)
         end
 
 
+        % -------------------------------------------------------
+        function CopyStim(obj, obj2)
+            obj.s = obj2.s;
+            obj.CondNames = obj2.CondNames;
+        end        
+        
+        
         % ----------------------------------------------------------------------------------
         function b = CopyStruct(obj, s)            
             fields = propnames(obj);
@@ -1200,6 +1270,23 @@ function ErrorCheck(obj)
         end
 
 
+        % -------------------------------------------------------
+        function changes = StimChangesMade(obj)                        
+            % Load stims from file
+            nirs = NirsClass();
+            nirs.SetFilename(obj.GetFilename())
+            nirs.LoadStim(obj.GetFilename());
+            changes = ~obj.EqualStim(nirs);
+        end
+        
+        
+        
+        % -------------------------------------------------------
+        function b = DataModified(obj)
+            b = obj.StimChangesMade();
+        end
+                
+        
     end
 
     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

DataTree/AcquiredData/Snirf/DataClass.m

@@ -494,8 +494,10 @@ function SaveHdf5(obj, fileobj, location)
             %                        will follow this order in linear form. That is, the order of ml will index the columns 
             %                        of d squeezed into 2 dimensions d(:,:)
             %       
-            %           'matrix'   - dataTimeSeries will not be modified but ml will be returned as a 2D matrix instead of a 
-            %                        MeasListClass structure. It's rows will have the same order as the structure elements. 
+            %           'matrix'   - This options refers to the measurement list type: if 'matrix' keyword is in the options 
+            %                        then ml will be returned as a 2D matrix instead of a MeasListClass object (that is the 
+            %                        object representing the measurementList SNIRF field). The rows of the 2d array will have 
+            %                        the same order as the original MeasListClass object elements. 
             %       
             %           'datatype' - used in combination with reshape. dataTimeSeries will be reshaped as above but the 
             %                        slowest dimensions to change will be reversed from left-to-right, that is, 
@@ -510,7 +512,7 @@ function SaveHdf5(obj, fileobj, location)
             %       %%%% dc is a DataClass object containing concentration data, with 4 sources, 8 detectors, 9 sd pairs, and 3 Hb data types:  hbo, hbr, and hbt. 
             %
             %
-            %       % Example 1:  Return OD dataTimeSeries, time and  measurementList unchanged.
+            %       % Example 1:  Return OD dataTimeSeries, time and  measurementList (ml) unchanged, that is, as a MeasListClass object instead of Nx4 2D array.
             %       [d, t, ml, order] = dod.GetDataTimeSeries();
             %
             %

DataTree/AcquiredData/Snirf/ProbeClass.m

@@ -523,6 +523,40 @@ function SaveHdf5(obj, fileobj, location)
             b = true;
         end
 
+        
+        
+        % ---------------------------------------------------------
+        function bbox = GetSdgBbox(obj)
+            bbox = [];
+            
+            optpos = [obj.GetSrcPos('2D'); obj.GetDetPos('2D')];
+            if isempty(optpos)
+                return
+            end
+            
+            xmax = max(optpos(:,1));
+            ymax = max(optpos(:,2));
+
+            xmin = min(optpos(:,1));
+            ymin = min(optpos(:,2));
+            
+            width = xmax-xmin;
+            height = ymax-ymin;
+            
+            if width==0
+                width = 1;
+            end
+            if height==0
+                height = 1;
+            end
+            
+            px = width * 0.05; 
+            py = height * 0.05; 
+
+            bbox = [xmin-px, xmax+px, ymin-py, ymax+py];
+        end
+        
+        
     end
 
 end