v1.80.0

-- Redo Export Snirf feature for Exporting derived data to SNIRF file.
-- Add SnirfClass functionality to plot derived data.
-- Fix Spline SG MakeFilter.m with Teresa Girolamo  Group dataset. The message for her data set keeps displaying the warning "Filter parameters exceed Nyquist frequency" during processing that ties up user clicking OK to message box messages for each channel of data time series.  Fix by instead displaying a message dialog once for each file or option to quit processing and throw error exception.
-- Fix issue with menu threowing exception error

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

because we change parent units for screen to 'normalized'. Fix is to make sure to always set the monitor units back to 'pixels'.

Author: jayd1860

DataTree/AcquiredData/AcqDataClass.m

@@ -49,6 +49,9 @@
         % ---------------------------------------------------------
         s         = GetStims(obj, t)
 
+        % ---------------------------------------------------------
+        s         = GetStim(obj)
+
         % ---------------------------------------------------------
         CondNames = GetConditions(obj)
 

DataTree/AcquiredData/Nirs/NirsClass.m

@@ -770,6 +770,12 @@ function SetStims_MatInput(obj, s, ~, ~)
         end
 
 
+        % ---------------------------------------------------------
+        function s = GetStim(obj)
+            s = obj.s;
+        end
+        
+        
         % ----------------------------------------------------------------------------------
         function SetConditions(obj, CondNames)
             if nargin==1

DataTree/AcquiredData/Snirf/SnirfClass.m

@@ -16,6 +16,7 @@
         nirsdatanum
         nirs_tb
         stim0
+        hFig
     end
 
     methods
@@ -78,6 +79,8 @@
             obj.SetFileFormat('hdf5');
             obj.location = '/nirs';
             obj.nirsdatanum = 1;
+            obj.hFig = [-1; -1];
+
 
             %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
             % Between 1 and 4 arguments covers the following syntax variants
@@ -1005,8 +1008,17 @@ function SetData(obj, val)
         end
 
         % ---------------------------------------------------------
-        function val = GetData(obj)
-            val = obj.data;
+        function [val, t] = GetData(obj, iBlk)
+            val = [];
+            t = [];
+            if ~exist('iBlk','var') || isempty(iBlk)
+                iBlk = 1;
+            end
+            if isempty(obj) || isempty(obj.data)
+                return;
+            end
+            val = obj.data(iBlk);
+            t = obj.data(iBlk).time;
         end
 
         % ---------------------------------------------------------
@@ -1886,9 +1898,261 @@ function Info(obj)
                 MenuBox(msg);
             end
         end
+
+
+
+        % ----------------------------------------------------------------------------------
+        function hAxes = GenerateStandaloneAxes(obj, datatype, iChs)
+            k = find(obj.hFig(1,:)==-1);
+            obj.hFig(1,k(1)) = figure;
+            hAxes = gca;
+            plotname = sprintf('"%s";   %s data ;   channels idxs: [%s]', obj.GetFilename(),  datatype, num2str(iChs'));
+            namesize = uint32(length(plotname)/3);
+            set(obj.hFig(1,k(1)), 'units','characters');
+            p1 = get(obj.hFig(1,k(1)), 'position');
+            set(obj.hFig(1,k(1)), 'name',plotname, 'menubar','none', 'NumberTitle','off', 'position',[p1(1)/2, p1(2), p1(3)+namesize, p1(4)]);
+            obj.hFig(:,k(1)+1) = -1;
+        end
+           
 
+            
+        % ----------------------------------------------------------------------------------
+        function Plot(obj, sdPairs, iBlk)
+            %
+            % SYNTAX:
+            %   TreeNodeClass.Plot(iChs, iBlk)
+            % 
+            %
+            % DESCRIPTION:
+            %   Plot data from channels specified by 2d array where each row spoecifying a single channel
+            %   contains indices [source, detector, condition, wavelength]. In addtion to the data, this method 
+            %   plots any existing stims, and the probe associated with the SNIRF object from which the data 
+            %   was taken. NOTE: the args iBlk and hAxes can be ommitted and will default to 1 and current 
+            %   axes respectively.
+            %
+            %
+            % INPUT:
+            %   sdPairs - 2d array of channel indices where each row represents a channel consisting of the indices
+            %             [source, detector, condition, datatype]
+            %
+            %   iBlk - Optional argument (defaults = 1). In theory SNIRF data field is an array of data blocks. This argunment selects the 
+            %          data block from which the plot data is taken.
+            %   
+            %   hAxes - Optional argument (default is current axes or gca()), specifying the axes handle of the axes in which to plot the data.
+            %
+            %
+            
+            % Parse input args
+            if ~exist('sdPairs','var')
+                sdPairs = [1,1,0,1];
+            end
+            if ~exist('iBlk','var') || isempty(iBlk)
+                iBlk = 1;
+            end
+
+            
+            % Convert channels in the form of a list of sd pairs to a column vector of indices into the measurement list
+            iChs = obj.SdPairIdxs2vectorIdxs(sdPairs, iBlk);
+            
+            
+            % Extract SNIRF parameters for plotting:  probe, data, time, measuremntList and stim
+            d = obj.data(1).dataTimeSeries;
+            t = obj.data(1).time;
+            ml = obj.data(1).GetMeasurementList('matrix');
+            
+            % If there's no data to plot then exit
+            if isempty(d)
+                fprintf('No data to plot\n');
+                return;
+            end
+            
+            
+            % Set up standalone figure with axes for plotting data, if axes handle was not passed down from caller 
+            % in the last arg. There will be a separate figure displaying the probe associated with this data plot. 
+            % a few lines down in DisplayProbe.
+            hAxes = obj.GenerateStandaloneAxes('HRF', iChs);            
+                        
+            % Plot data
+            hold on
+            chSelect = [];
+            for ii = 1:length(iChs)
+                hdata(ii) = plot(hAxes, t, d(:,iChs(ii)), 'linewidth',2);
+                chSelect(ii,:) = [ml(iChs(ii),1), ml(iChs(ii),2), ml(iChs(ii),3), ml(iChs(ii),4), get(hdata(ii), 'color')]; 
+            end
+            set(hAxes, 'xlim', [t(1), t(end)]);                        
+            
+            % Display probe in separate figure
+            if isempty(chSelect)
+                fprintf('ERROR: no valid channels were selelcted\n');
+                obj.DisplayProbe();
+            else
+                obj.DisplayProbe(chSelect(:,1:2), chSelect(:,5:7));
+            end
+            
+            
+            % Wrap up before exiting
+            drawnow;
+            pause(.1);
+            hold off
+        end
 
 
+        % ----------------------------------------------------------------------------------
+        function iChs = SdPairIdxs2vectorIdxs(obj, sdPairs, iBlk)
+            iChs = [];
+            if ~exist('sdPairs','var')
+                sdPairs = [1,1,0,1];
+            end            
+            if ~exist('iBlk','var') || isempty(iBlk)
+                iBlk = 1;
+            end
+            
+            % Error Checking
+            if size(sdPairs, 2)>1 && size(sdPairs, 2)~=4
+                fprintf('ERROR: invalid sdPair. sdPair has to be a Nx4 2D array\n');
+                return;
+            end
+            
+            
+            % If sdPairs argument is a column vector then we are done because channels are 
+            % already specified in the output format i.e., as single number indices. 
+            if size(sdPairs, 2)==1
+                iChs = sdPairs;
+                return;
+            end            
+                        
+            ml = obj.data(1).GetMeasurementList('matrix', iBlk);
+            
+            % Error checking
+            if isempty(ml)
+                return
+            end
+            
+            for ii = 1:size(sdPairs,1)
+                k = find(ml(:,1)==sdPairs(ii,1)  &  ml(:,2)==sdPairs(ii,2)  &  ml(:,3)==sdPairs(ii,3)  &  ml(:,4)==sdPairs(ii,4));
+                if isempty(k)
+                    continue;
+                end
+                iChs(ii,1) = k;
+            end
+        end
+        
+        
+        
+        % ----------------------------------------------------------------------------------
+        function sdPairs = VectorIdxs2SdPairIdxs(obj, iChs, iBlk)
+            if ~exist('iChs','var')
+                iChs = 1;
+            end            
+            if ~exist('iBlk','var') || isempty(iBlk)
+                iBlk = 1;
+            end
+            
+            % If sdPairs argument is not a column vector then we are done;  because the 
+            % channels are already specified in the output format i.e., as a 2d array. 
+            if size(iChs, 2)>1
+                sdPairs = iChs;
+                return;
+            end
+            
+            ml = obj.data(1).GetMeasurementList('matrix', iBlk);
+            
+            % Remove any invalid indices
+            iChs(iChs==0) = [];
+            iChs(iChs>size(ml,1)) = [];
+            
+            sdPairs = ml(iChs,:);
+        end
+        
+        
+        
+        % ----------------------------------------------------------------------------------
+        function hAxes = DisplayProbe(obj, chSelect, chSelectColors, hAxes)
+            % Parse args
+            if ~exist('chSelect','var')
+                chSelect = [];
+            end
+            if ~exist('chSelectColors','var')                
+                chSelectColors = repmat([1.0, 0.5, 0.2], size(chSelect,1),1);
+            end
+            if ~exist('hAxes','var')
+                hAxes = [];
+            end
+            
+            % If chSelect is in the form of a column vector rather than sd pairs
+            % then convert to sd pairs
+            chSelect = obj.VectorIdxs2SdPairIdxs(chSelect);            
+            
+            freememoryflag = false;
+            if ~isempty(obj) && obj.IsEmpty()
+                obj.acquired.Load();
+                freememoryflag = true;
+            end
+            
+            % Set up the axes
+            bbox = obj.GetSdgBbox();
+            if isempty(hAxes)
+                k = find(obj.hFig(2,:)==-1);
+                
+                % See if there's a data plot associated with this probe display
+                % If there is get its name and use it to name this figure
+                plotname = '';
+                if ishandle(obj.hFig(1,k(1)))
+                    plotname = get(obj.hFig(1,k(1)), 'name');
+                end
+                obj.hFig(2,k(1)) = figure('menubar','none', 'NumberTitle','off', 'name',plotname);
+                hAxes = gca;
+            end
+
+            axis(hAxes, [bbox(1), bbox(2), bbox(3), bbox(4)]);
+            gridsize = get(hAxes, {'xlim', 'ylim', 'zlim'});
+            if ismac() || islinux()
+                fs = 18;
+            else
+                fs = 11;
+            end
+
+            % Get probe paramaters
+            probe = obj.GetProbe();
+            srcpos = probe.sourcePos2D;
+            detpos = probe.detectorPos2D;
+            ml = obj.GetMeasurementList('matrix');
+            lstSDPairs = find(ml(:,4)==1);
+            
+            % Draw all channels
+            for ii = 1:length(lstSDPairs)
+                hCh(ii) = line2(srcpos(ml(lstSDPairs(ii),1),:), detpos(ml(lstSDPairs(ii),2),:), [], gridsize, hAxes);
+                col = [1.00 1.00 1.00] * 0.85;
+                if ~isempty(chSelect)
+                    k = find(chSelect(:,1)==ml(lstSDPairs(ii),1) & chSelect(:,2)==ml(lstSDPairs(ii),2));
+                    if ~isempty(k)
+                        col = chSelectColors(k(1),:);
+                    end
+                end
+                set(hCh(ii), 'color',col, 'linewidth',2, 'linestyle','-', 'userdata',ml(lstSDPairs(ii),1:2));
+            end
+            
+            % ADD SOURCE AND DETECTOR LABELS
+            for iSrc = 1:size(srcpos,1)
+                if ~isempty(find(ml(:,1)==iSrc)) %#ok<*EFIND>
+                    hSD(iSrc) = text( srcpos(iSrc,1), srcpos(iSrc,2), sprintf('%d', iSrc), 'fontsize',fs, 'fontweight','bold', 'color','r' );
+                    set(hSD(iSrc), 'horizontalalignment','center', 'edgecolor','none', 'Clipping', 'on');
+                end
+            end
+            for iDet = 1:size(detpos,1)
+                if ~isempty(find(ml(:,2)==iDet))
+                    hSD(iDet+iSrc) = text( detpos(iDet,1), detpos(iDet,2), sprintf('%d', iDet), 'fontsize',fs, 'fontweight','bold', 'color','b' );
+                    set(hSD(iDet+iSrc), 'horizontalalignment','center', 'edgecolor','none', 'Clipping', 'on');
+                end
+            end
+            
+            if freememoryflag
+                obj.FreeMemory();
+            end            
+        end        
+        
+        
+
     end
 
 

DataTree/GroupClass.m

@@ -709,6 +709,15 @@ function Save(obj, hwait)
                 obj.logger.Write(ME.message);
             end            
             obj.initsaveflag = true;
+
+            % Clean up folder of .error files
+            if exist([pwd, '/.error'],'file')
+                try
+                    delete([pwd, '/.error'])
+                catch
+                end
+            end
+
         end
 
 

DataTree/ProcStream/ProcInputClass.m

@@ -198,6 +198,12 @@ function SaveAcquiredData(obj)
     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     methods
 
+        % ----------------------------------------------------------------------------------
+        function stim = GetStim(obj)
+            stim = obj.acquired.GetStim();
+        end
+        
+        
         % ----------------------------------------------------------------------------------
         function vals = GetStimValSettings(obj)
             vals = obj.stimValSettings;

DataTree/ProcStream/ProcResultClass.m

@@ -660,6 +660,26 @@ function SetNtrials(obj, val)
         end
 
 
+        % ----------------------------------------------------------------------------------
+        function s = GetData(obj, datatype)
+            if nargin==1
+                t = [];
+            end
+            s = obj.GetVar('s');
+            if isempty(s)
+                if isempty(obj.dod) || ~isa(obj.dod, 'DataClass')
+                    return;
+                end
+                stim = obj.GetVar('stim');
+                if isempty(stim)
+                    return;
+                end
+                snirf = SnirfClass(obj.dod, stim);
+                s = snirf.GetStims(t);
+            end
+        end
+        
+        
         % ----------------------------------------------------------------------------------
         function val = GetTincAuto(obj, iBlk)
             val = {};