Merge v1.70.1: Fix menu item "Load Stim from TSV" file. (#154)

* v1.70.1

-- Fix menu item "Load Stim from TSV" file.
-- Fix ProbeClass converting SD probe data to ProbeClass - instead of SD.refpts it should be SD.Landmarks

* -- Sync with v1.1.1 Utils library: add some diagnostic data simulation scripts to Utils/Shared library which can add data time course to for instance probe.SD for testing AtlasViewer probe registration

Author: jayd1860

DataTree/AcquiredData/Nirs/NirsClass.m

@@ -220,19 +220,19 @@ function SortData(obj)
                 err = 0;
             end
 
-            if isproperty(fdata,'t')
+            if isproperty(fdata,'t') && isproperty(fdata,'d') 
                 obj.t = fdata.t;
                 if ~isempty(obj.t)
                     obj.errmargin = min(diff(obj.t))/10;
                 elseif err == 0
                     err = -3;
                 end
+                if length(fdata.t) ~= size(fdata.d,1) && err == 0
+                    err = -3;
+                end
             elseif err == 0
                 err = -3;
             end
-            if length(fdata.t) ~= size(fdata.d,1) && err == 0
-                err = -3;
-            end
         end
 
 

DataTree/AcquiredData/Snirf/ProbeClass.m

@@ -55,12 +55,15 @@
                     else
                         obj.detectorPos3D  = SD.DetPos;
                     end
-                    if isfield(SD,'refpts')
-                        obj.landmarkPos3D = SD.refpts.pos;
-                        obj.landmarkLabels = SD.refpts.labels;
-                        if isfield(SD,'refpts2D')
-                            obj.landmarkPos2D = SD.refpts2D.pos;
+                    if isfield(SD,'Landmarks3D')
+                        obj.landmarkPos3D = SD.Landmarks3D.pos;
+                        obj.landmarkLabels = SD.Landmarks3D.labels;
+                        if isfield(SD,'Landmarks2D')
+                            obj.landmarkPos2D = SD.Landmarks2D.pos;
                         end
+                    else
+                        obj.landmarkPos3D = SD.DummyPos;
+                        obj.landmarkLabels = SD.Landmarks3D.labels;
                     end
                     obj.frequencies  = 1;
                     obj.timeDelays  = 0;

DataTree/Version.txt

@@ -1 +1 @@
-1.3.0
+1.3.1

MainGUI/MainGUI.m

@@ -2195,11 +2195,8 @@ function menuItemExportStim_Callback(~, ~, ~)
 
 
 % --------------------------------------------------------------------
-function menuItemReloadStim_Callback(~, ~, handles)
+function menuItemReloadStim_Callback(hObject, ~, handles)
 global maingui
-[iGroup, iSubj, iSess, iRun] = maingui.dataTree.GetCurrElemIndexID();
 maingui.dataTree.ReloadStim();
-Update('DataTreeClass',[iGroup, iSubj, iSess, iRun]);
-DisplayStim(handles);
-
+DisplayData(handles, hObject);
 

Utils/Shared/Version.txt

@@ -1 +1 @@
-1.1.0
+1.1.1

Utils/Shared/simData/generateSimData.m

@@ -0,0 +1,56 @@
+function generateSimData(dirname, format)
+if ~exist('dirname','var')
+    dirname = pwd;
+end
+if ~exist('format','var')
+    format = '.snirf';
+end
+dirname = filesepStandard(dirname);
+
+files = DataFilesClass(dirname, format, 'standalone').files;
+for ii = 1:length(files)
+    if ~isempty(findstr(files(ii).name, '_sim'))
+        continue;
+    end
+    obj = generateSimDataOneFile([files(ii).rootdir, files(ii).name]);
+    
+    [p,f,e] = fileparts([files(ii).rootdir, files(ii).name]);
+    fname = [filesepStandard(p),f,'_sim',e];
+    fprintf('Saving simulated data in %s\n', fname);
+    obj.Save(fname);
+end
+
+
+
+
+% ---------------------------------------------------------------
+function obj = generateSimDataOneFile(obj)
+d = [];
+if ischar(obj)
+    obj = SnirfClass(obj);
+    d = obj.data;
+elseif isa(obj, 'SnirfClass')
+    d = obj.data;
+elseif isa(obj, 'DataClass')
+    d = obj;
+    obj = SnirfClass(d);
+end
+ml = d.GetMeasurementList('matrix');
+for iBlk = length(d)
+    nTpts = size(d(iBlk).dataTimeSeries,1);
+    for iM = 1:length(d(iBlk).measurementList)
+        data = ml(iM,:);
+        stepsize = floor(nTpts / length(data));
+        for iDt = 1:length(data)
+            y = data(iDt);
+            iTptS = (iDt-1) * stepsize + 1;
+            iTptE = iTptS + stepsize - 1;            
+            if nTpts-iTptE < stepsize
+                iTptE = nTpts;
+            end
+            d(iBlk).dataTimeSeries(iTptS:iTptE, iM) = y;
+        end
+    end
+end
+obj.data = d;
+

Utils/Shared/simData/simulateDataTimeSeries.m

@@ -0,0 +1,29 @@
+function [t, y] = simulateDataTimeSeries(N, alpha, sigma)
+
+if ~exist('N','var')
+    N = 1e3; 
+end
+if ~exist('alpha','var')
+    alpha = 1;
+end
+if ~exist('sigma','var')
+    sigma = .4; 
+end
+
+% generate time
+nTpts = N;
+sampleRate = 10;
+timeTotal = 1/sampleRate * nTpts;
+t = 0:1/sampleRate:timeTotal;
+t(N+1:end) = [];
+
+% Generate data
+
+y = zeros(N, 1); 
+y(1) = randn; % Initialize
+fprintf('Rand = %0.4f\n', y(1));
+
+for k = 2:N
+    y(k) = alpha*y(k-1) + randn*sigma;
+end
+

Utils/Shared/simData/simulateProbeData.m

@@ -0,0 +1,22 @@
+function snirf = simulateProbeData(probefile, ntpts)
+snirf = SnirfClass.empty();
+if ~exist('probefile','var')
+    return;
+end
+if ~exist('ntpts','var')
+    ntpts = 1e3;
+end
+
+if ~ispathvalid(probefile)
+    return;
+end
+
+nirs = NirsClass(probefile);
+for iM = 1:length(nirs.SD.MeasList)
+    [nirs.t, nirs.d(:,iM)] = simulateDataTimeSeries(ntpts);
+end
+snirf = SnirfClass(nirs.d, nirs.t, nirs.SD, [], []);
+[p,f] = fileparts(probefile);
+snirf.Save(['./',f,'.snirf']);
+
+

Version.txt

@@ -1 +1 @@
-1.70.0
+1.70.1