Commit 4e55f850 authored by jayd1860's avatar jayd1860
Browse files

v1.80.3 

Utils, v1.7.2
-- Add ability to simulate workflow data with generateSimDataset() function:
1. probe.SD
2. probe.SD with spring registration
3. probe.SD with spring registration + data
4. digpts + probe.SD
5. digpts + probe.SD + data
3. data with landmark registration
parent e5a5a8ae

Utils/Shared/Version.txt

+1 −1
Original line number Diff line number Diff line 
1.7.1
 
 No newline at end of file
 
1.7.2
 
 No newline at end of file

Utils/Shared/simData/generateSimDataset.m

+196 −18
Original line number Diff line number Diff line 
function nirs = generateSimDataset(dirname, nSubj, nSess, nRuns, options)



function out = generateSimDataset(dirname, nSubj, nSess, nRuns, options)

%



nirs = [];

% Syntax:

%   out = generateSimDataset()

%   out = generateSimDataset(dirname)

%   out = generateSimDataset(dirname, nSubj)

%   out = generateSimDataset(dirname, nSubj, nSess)

%   out = generateSimDataset(dirname, nSubj, nSess, nRuns)

%   out = generateSimDataset(dirname, nSubj, nSess, nRuns, options)

%

% Description:

%   options - { {'probe'|'digpts}, 'springs', 'data' }  

%

% Examples:

%   out = generateSimDataset();

%   out = generateSimDataset(pwd);

%   out = generateSimDataset(pwd, [],[],[],'probe');

%   out = generateSimDataset(pwd, 3,3,3,'probe:data');

%   out = generateSimDataset(pwd, [],[],[],'probe:springs');

%   out = generateSimDataset(pwd, [],[],[],'probe:landmarks:data');

%   out = generateSimDataset(pwd, [],[],[],'probe:landmarks:data');

%   out = generateSimDataset(pwd, [],[],[],'digpts');

%   out = generateSimDataset(pwd, [],[],[],'digpts:data');

%

global atlasViewer

atlasViewer = [];

out = [];



t0 = tic;





if ~exist('dirname','var')

    dirname = filesepStandard(pwd);

if ~exist('dirname','var') || isempty(dirname)

    dirname = pwd;

end

if ~exist('nSubj','var')

if ~exist('nSubj','var') || isempty(nSubj)

    nSubj = 3;

end

if ~exist('nSess','var')

if ~exist('nSess','var') || isempty(nSess)

    nSess = 3;

end

if ~exist('nRuns','var')

if ~exist('nRuns','var') || isempty(nRuns)

    nRuns = 3;

end

if ~exist('options','var')

    options = 'probe:springs';

    options = 'probe:springs:data';

end



dirname = filesepStandard(dirname);



% Reset folder to known state

resetDataset();



% Create template data

setNamespace('AtlasViewerGUI');

dirnameAtlas = getAtlasDir();
@@ -31,7 +57,34 @@ if ~ispathvalid(dirnameAtlas) 
end

refpts = initRefpts();

refpts = getRefpts(refpts, dirnameAtlas);

SD = genProbeFromRefpts(refpts, 36, 2, options);



if optionExists(options, 'probe')

    genProbeFromRefpts(refpts, 36, 2, options);

elseif optionExists(options, 'digpts')

    genDigptsFromRefpts(refpts, 36, 2);

end



if optionExists(options, 'data')

    digpts = initDigpts();

    digpts = getDigpts(digpts);

    probe  = initProbe();

    probe  = getProbe(probe, dirname, digpts);

    genSimData(probe, dirname, nSubj, nSess, nRuns, t0);

    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];

        saveDigpts(digptsNew);

    end

    delete('./digpts*.txt');

end









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

function genSimData(probe, dirname, nSubj, nSess, nRuns, t0)

SD = convertProbe2SD(probe);

nirs = NirsClass(SD);



% Generate stims
@@ -48,10 +101,14 @@ for iC = 1:ncond 
    offset = offset+50;

end





%

% Generate data

for iSubj = 1:nSubj

    sname = sprintf('subj-%d', iSubj);

    if iSubj < 10

        iSubjName = sprintf('0%d', iSubj);

    else

        iSubjName = sprintf('%d', iSubj);

    end

    sname = sprintf('sub-%s', iSubjName);

    if ispathvalid([dirname, sname])

        rmdir([dirname, sname], 's')

    end
@@ -72,3 +129,124 @@ for iSubj = 1:nSubj 
    end

end







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

function resetDataset(dirname)

if ~exist('dirname','var')

    dirname = filesepStandard(pwd);

end



currdir = filesepStandard(pwd);

cd(dirname);



files = dir('*');

for ii = 1:length(files)

    if strcmpi(files(ii).name, '.')

        continue

    end

    if strcmpi(files(ii).name, '..')

        continue

    end

    if strcmpi(files(ii).name, 'anatomical')

        continue

    end

    if files(ii).isdir

        rmdir(files(ii).name,'s')

    else

        delete(files(ii).name)

    end

end

cd(currdir);









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

function digpts = movePts(digpts, r, s, t)

if ~exist('r','var')

    r = [0,0,0];

end

if ~exist('s','var')

    s = [1,1,1];

end

if ~exist('t','var')

    t = [0,0,0];

end



alpha = deg2rad(r(1));

beta  = deg2rad(r(2));

theta = deg2rad(r(3));



A = [ ...

    1            0             0    0;

    0   cos(alpha)   -sin(alpha)    0;

    0   sin(alpha)    cos(alpha)    0;

    0            0             0    1;

    ];



B = [ ...

    cos(beta)    0     sin(beta)     0;

    0            1             0     0;

   -sin(beta)    0     cos(beta)     0;

    0            0             0     1;

    ];



C = [ ...

    cos(theta)   -sin(theta)   0     0;

    sin(theta)    cos(theta)   0     0;

    0            0             1     0;

    0            0             0     1;

    ];



D = [ ...

    1            0             0     t(1);

    0            1             0     t(2);

    0            0             1     t(3);

    0            0             0     1;

    ];



S = [ ...

  s(1)           0             0     0;

    0           s(2)           0     0;

    0            0           s(3)    0;

    0            0             0     1;

    ];



T = S*D*C*B*A;



digpts.srcpos = xform_apply(digpts.srcpos, T);

digpts.detpos = xform_apply(digpts.detpos, T);

digpts.refpts.pos = xform_apply(digpts.refpts.pos, T);







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

function r = randNearOne(w, h, t0)

generateRandNumSeed(t0);

r = ones(w,h) + (rand(w,h) - 0.5) / 2;







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

function r = randNearZero(w, h, t0)

generateRandNumSeed(t0);

r = (rand(w,h) - 0.5) / 2;







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

function generateRandNumSeed(time0)

if time0 == 0

    x = uint32(100*rand);

    rng(x);

    y = uint32(100*rand);

    rng(y);

else

    s = 0;

    while s==0

        s = uint64(1e4*toc(time0));

    end    

    rng(s);

end

Version.txt

+1 −1
Original line number Diff line number Diff line 
1.80.2
 
 No newline at end of file
 
1.80.3
 
 No newline at end of file

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