v1.80.4

Utils, v1.7.3
-- Add session to simulated data. Copy generated SD file with spring registration to subject folders.

Author: jayd1860

Utils/Shared/Version.txt

@@ -1 +1 @@
-1.7.2
+1.7.3

Utils/Shared/simData/generateSimDataset.m

@@ -9,21 +9,60 @@
 %   out = generateSimDataset(dirname, nSubj, nSess, nRuns, options)
 %
 % Description:
-%   options - { {'probe'|'digpts}, 'springs', 'data' }  
+%   options - { {'probe'|'digpts}, 'springs', 'data' }
 %
 % Examples:
+%
+%   %%%%% Change current folder to <root groups test folder>
+%   emptyGroupTestDir = 'c:/users/public/groups/emptyGroupTestDir';
+%   if ~exist(emptyGroupTestDir,'dir'), mkdir(emptyGroupTestDir); end
+%   cd(emptyGroupTestDir);
+%
+%   %%%%% Now generate probe and/or digitized points and/or raw/unprocessed dataTree data.
+%   %%%%% These 9 examples covers all the major AtlasViewer + Homer3 workflows
+%
+%   % Example 1: probe file in SD format with spring registration and
+%   % raw/unprocessed dataTree data with 3 subjects, 3 sessions each, and 3 runs each.
+%   out = generateSimDataset(pwd, 3, 3, 3, 'probe:springs:data');
+%
+%   % Example 2: probe file in SD format with spring registration and
+%   % raw/unprocessed dataTree data with 3 subjects, 3 sessions each with 3 runs each.
 %   out = generateSimDataset();
+%
+%   % Example 3: probe file in SD format with spring registration and
+%   % acquisition data with 3 subjects, 1 session each, and 3 runs each.
 %   out = generateSimDataset(pwd);
+%
+%   % Example 4: probe file in SD format with spring registration and acquisition data
+%   % with 2 subjects with 1 session each, and each session with 5 runs each.
+%   out = generateSimDataset(pwd, 2, 1, 5);
+%
+%   % Example 5: probe file in SD format with NO registration and NO acquisition data
 %   out = generateSimDataset(pwd, [],[],[],'probe');
-%   out = generateSimDataset(pwd, 3,3,3,'probe:data');
+%
+%   % Example 6: probe file in SD format with spring registration and NO data
 %   out = generateSimDataset(pwd, [],[],[],'probe:springs');
+%
+%   % Example 7: Unprocessed dataTree data with 3 subjects, 3 sessions, and 3 runs each
+%   % and with acquisition files containing probe with landmark registration.
+%   % with 3 subjects with 1 session each, and each session with 3 runs each.
 %   out = generateSimDataset(pwd, [],[],[],'probe:landmarks:data');
-%   out = generateSimDataset(pwd, [],[],[],'probe:landmarks:data');
+%
+%   % Example 8: Digpts file with associated probe file in SD format containing measurement list
+%   % and NO acquisition data
 %   out = generateSimDataset(pwd, [],[],[],'digpts');
-%   out = generateSimDataset(pwd, [],[],[],'digpts:data');
+%
+%   % Example 9: Digpts file with associated probe file in SD format containing measurement list
+%   % and data with 1 subject with 2 sessions each, and each session with 4 runs each.
+%   out = generateSimDataset(pwd, 1, 2, 4, 'digpts:data');
+%
 %
 global atlasViewer
+global probeFilename
+
 atlasViewer = [];
+probeFilename = 'newfile1.SD';
+
 out = [];
 
 t0 = tic;
@@ -35,7 +74,7 @@
     nSubj = 3;
 end
 if ~exist('nSess','var') || isempty(nSess)
-    nSess = 3;
+    nSess = 1;
 end
 if ~exist('nRuns','var') || isempty(nRuns)
     nRuns = 3;
@@ -73,15 +112,19 @@
     subjDirs = dir('sub-*');
     for ii = 1:length(subjDirs)
         digptsNew = movePts(digpts, randNearZero(1,3,t0), randNearOne(1,3,t0), randNearZero(1,3,t0));
-        digptsNew.pathname = [filesepStandard(pwd), subjDirs(ii).name];
+        digptsNew.pathname = [filesepStandard(dirname), subjDirs(ii).name];
         saveDigpts(digptsNew);
+        if ispathvalid([dirname, probeFilename])
+            if optionExists(options, 'springs')
+                copyfile([dirname, probeFilename], [filesepStandard(dirname), subjDirs(ii).name, '/', probeFilename]);
+            end
+        end
     end
     delete('./digpts*.txt');
 end
 
 
 
-
 % ----------------------------------------------
 function genSimData(probe, dirname, nSubj, nSess, nRuns, t0)
 SD = convertProbe2SD(probe);
@@ -108,29 +151,43 @@ function genSimData(probe, dirname, nSubj, nSess, nRuns, t0)
     else
         iSubjName = sprintf('%d', iSubj);
     end
-    sname = sprintf('sub-%s', iSubjName);
-    if ispathvalid([dirname, sname])
-        rmdir([dirname, sname], 's')
+    subjName = sprintf('sub-%s', iSubjName);
+    subjNameFull = filesepStandard([dirname, subjName], 'dir:nameonly');
+    if ispathvalid(subjNameFull)
+        rmdir(subjNameFull, 's')
     end
-    mkdir([dirname, sname]);
+    mkdir(subjNameFull);
 
-    for iRun = 1:nRuns
-        for iM = 1:size(nirs.SD.MeasList,1)
-            [nirs.t, nirs.d(:,iM)] = simulateDataTimeSeries(ntpts, 1, .4, t0);
-        end
-        snirf = SnirfClass(nirs.d, nirs.t, nirs.SD, [], nirs.s, nirs.CondNames);
-        if iRun<10
-            rname = sprintf('%s%s/%s_run0%d.snirf', dirname, sname, sname, iRun);
+    for iSess = 1:nSess
+        if iSess < 10
+            iSessName = sprintf('0%d', iSess);
         else
-            rname = sprintf('%s%s/%s_run%d.snirf', dirname, sname, sname, iRun);
+            iSessName = sprintf('%d', iSess);
+        end
+        sessName = sprintf('ses-%s', iSessName);
+        sessNameFull = filesepStandard([subjNameFull, sessName], 'dir:nameonly');
+        if ispathvalid(sessNameFull)
+            rmdir(sessNameFull, 's')
+        end
+        mkdir(sessNameFull);
+        
+        for iRun = 1:nRuns
+            for iM = 1:size(nirs.SD.MeasList,1)
+                [nirs.t, nirs.d(:,iM)] = simulateDataTimeSeries(ntpts, 1, .4, t0);
+            end
+            snirf = SnirfClass(nirs.d, nirs.t, nirs.SD, [], nirs.s, nirs.CondNames);
+            if iRun<10
+                runNameFull = sprintf('%s%s_%s_run0%d.snirf', sessNameFull, subjName, sessName, iRun);
+            else
+                runNameFull = sprintf('%s%s_%s_run%d.snirf', sessNameFull, subjName, sessName, iRun);
+            end
+            snirf.Save(runNameFull);
+            fprintf('Created run %s\n', runNameFull);
         end
-        snirf.Save(rname);
-        fprintf('Created run %s\n', rname);
     end
 end
 
 
-
 % -----------------------------------------------------------------
 function resetDataset(dirname)
 if ~exist('dirname','var')
@@ -188,7 +245,7 @@ function resetDataset(dirname)
 B = [ ...
     cos(beta)    0     sin(beta)     0;
     0            1             0     0;
-   -sin(beta)    0     cos(beta)     0;
+    -sin(beta)    0     cos(beta)     0;
     0            0             0     1;
     ];
 
@@ -207,7 +264,7 @@ function resetDataset(dirname)
     ];
 
 S = [ ...
-  s(1)           0             0     0;
+    s(1)           0             0     0;
     0           s(2)           0     0;
     0            0           s(3)    0;
     0            0             0     1;
@@ -246,7 +303,7 @@ function generateRandNumSeed(time0)
     s = 0;
     while s==0
         s = uint64(1e4*toc(time0));
-    end    
+    end
     rng(s);
 end
 

Version.txt

@@ -1 +1 @@
-1.80.3
+1.80.4