v1.80.4 (9fe13dd9) · Commits · github_fork / Homer3

Utils/Shared/Version.txt

+1 −1

Original line number	Diff line number	Diff line
		1.7.2
		No newline at end of file
		1.7.3
		No newline at end of file

Utils/Shared/simData/generateSimDataset.m

+82 −25

Original line number	Diff line number	Diff line
		@@ -12,18 +12,57 @@ function out = generateSimDataset(dirname, nSubj, nSess, nRuns, options)
		% 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 @@ if ~exist('nSubj','var') \|\| isempty(nSubj)
		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 @@ if optionExists(options, 'data')
		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);
		@@ -108,11 +151,25 @@ for iSubj = 1:nSubj
		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 iSess = 1:nSess
		if iSess < 10
		iSessName = sprintf('0%d', iSess);
		else
		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)
		@@ -120,15 +177,15 @@ for iSubj = 1:nSubj
		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);
		runNameFull = sprintf('%s%s_%s_run0%d.snirf', sessNameFull, subjName, sessName, iRun);
		else
		rname = sprintf('%s%s/%s_run%d.snirf', dirname, sname, sname, iRun);
		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



		% -----------------------------------------------------------------

Version.txt

+1 −1

Original line number	Diff line number	Diff line
		1.80.3
		No newline at end of file
		1.80.4
		No newline at end of file

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