Commit 2d2d322c authored by Jay Dubb's avatar Jay Dubb
Browse files

v1.25.5 

-- Modify hmrR_tCCA() to produce a filter per subject rather than only 1 per group. Add subject index argument to identify which subject.
-- Change default value for user parameter ss_ch_inx from 0 to array [1 2 3 4 5] in hmrR_tCCA()
-- Move processOpt_tcca.cfg from unit test folder to user function tcca folder.
-- Remove isdir for dir() output warning for incorrectly using isdir as a boolean function rather than just as a boolean scalar.
parent df400382

FuncRegistry/FindUserFuncDir.m

+1 −1
Original line number Diff line number Diff line
@@ -5,7 +5,7 @@ dirnameApp = getAppDir(); 
userfuncdir{1} = [dirnameApp, 'FuncRegistry/UserFunctions/'];

dirs = dir([userfuncdir{1}, '*']);

for ii = 1:length(dirs)

    if ~dirs(ii).isdir()

    if ~dirs(ii).isdir

        continue

    elseif strcmp(dirs(ii).name, '..') || strcmp(dirs(ii).name, '.')

        continue

FuncRegistry/UserFunctions/tcca_glm/hmrR_tCCA.m

+8 −7
Original line number Diff line number Diff line 
% SYNTAX:

% [Aaux, rcMap] = hmrR_tCCA(data, aux, probe, runIdx, flagtCCA, tCCAparams, tCCAaux_inx, rhoSD_ssThresh, ss_ch_inx, runIdxResting, tResting)

% [Aaux, rcMap] = hmrR_tCCA(data, aux, probe, runIdx, subjIdx, flagtCCA, tCCAparams, tCCAaux_inx, rhoSD_ssThresh, ss_ch_inx, runIdxResting, tResting)

%

% UI NAME:

% hmrR_tCCA
@@ -17,6 +17,7 @@ 
% aux - SNIRF aux type where dataTimeCourse is aux time course data (See SNIRF Spec for more details)

% probe - SNIRF probe type containing source/detector geometry data (See SNIRF Spec for more details)

% runIdx - the index of the run in a multi-run session

% subjIdx - the index of the subject in a group 

% flagtCCA - turns the function on / off

% tCCAparams - These are the parameters for tCCA function

%            1 - 1 timelag [s]
@@ -41,8 +42,8 @@ 
%           Only relevant when flagICRegressors = 1.

%

% USAGE OPTIONS:

% hmrR_tCCA_Concentration_Data: [Aaux, rcMap] = hmrR_tCCA(dc, aux, probe, iRun, flagtCCA, tCCAparams, tCCAaux_inx, rhoSD_ssThresh, ss_ch_inx, runIdxResting, tResting)

% hmrR_tCCA_OD_Data: [Aaux, rcMap] = hmrR_tCCA(dod, aux, probe, iRun, flagtCCA, tCCAparams, tCCAaux_inx, rhoSD_ssThresh, ss_ch_inx, runIdxResting, tResting)

% hmrR_tCCA_Concentration_Data: [Aaux, rcMap] = hmrR_tCCA(dc, aux, probe, iRun, iSubj, flagtCCA, tCCAparams, tCCAaux_inx, rhoSD_ssThresh, ss_ch_inx, runIdxResting, tResting)

% hmrR_tCCA_OD_Data: [Aaux, rcMap] = hmrR_tCCA(dod, aux, probe, iRun, iSubj, flagtCCA, tCCAparams, tCCAaux_inx, rhoSD_ssThresh, ss_ch_inx, runIdxResting, tResting)

%

%

% PARAMETERS:
@@ -50,11 +51,11 @@ 
% tCCAparams: [3 0.08 0.3]

% tCCAaux_inx: [1 2 3 4 5 6 7 8]

% rhoSD_ssThresh: 15.0

% ss_ch_inx: 0

% ss_ch_inx: [1 2 3 4 5]

% runIdxResting: 1

% tResting: [30 210]

%

function [Aaux, rcMap] = hmrR_tCCA(data, aux, probe, runIdx, flagtCCA, tCCAparams, tCCAaux_inx, rhoSD_ssThresh, ss_ch_inx, runIdxResting, tResting)

function [Aaux, rcMap] = hmrR_tCCA(data, aux, probe, runIdx, subjIdx, flagtCCA, tCCAparams, tCCAaux_inx, rhoSD_ssThresh, ss_ch_inx, runIdxResting, tResting)



%% COMMENTS/THOUGHTS/QUESTIONS ALEX

% 2) Output canonical correlation coefficients as quality metric?
@@ -160,8 +161,8 @@ if flagtCCA 
        param.NumOfEmb = ceil(timelag*fq / tCCAparams(2));

        

        %% DO THE TCCA WORK

        filterFilename = sprintf('./tCCAfilter_%d_%d.txt', iBlk, chksm);

        tCCAexists = isfile(sprintf('./tCCAfilter_%d_%d.txt', iBlk, chksm));

        filterFilename = sprintf('./tCCAfilter_%d_%d_%d.txt', subjIdx, iBlk, chksm);

        tCCAexists = isfile(sprintf('./tCCAfilter_%d_%d_%d.txt', subjIdx, iBlk, chksm));

        isTrainingRun = runIdxResting == runIdx;

        if ~tCCAexists && isTrainingRun

            dotCCA = 'train';

UnitTests/Example6_GrpTap/processOpt_tcca.cfg→FuncRegistry/UserFunctions/tcca_glm/processOpt_tcca.cfg

+1 −1
Original line number Diff line number Diff line
@@ -15,7 +15,7 @@ 
@ hmrR_BandpassFilt dod (dod hpf %0.3f 0 lpf %0.3f 0.5

@ hmrR_BandpassFilt aux (aux hpf %0.3f 0 lpf %0.3f 0.5

@ hmrR_OD2Conc_new dc (dod,probe ppf %0.1f_%0.1f 1_1

@ hmrR_tCCA [Aaux,rcMap] (dc,aux,probe,iRun flagtCCA %d 1 tCCAparams %d_%0.2f_%0.1f 3_0.08_0.3 tCCAaux_inx %d_%d_%d_%d_%d_%d_%d_%d 1_2_3_4_5_6_7_8 rhoSD_ssThresh %0.1f 15 ss_ch_inx %d 0 runIdxResting %d 1 tResting %d_%d 30_210

@ hmrR_tCCA [Aaux,rcMap] (dc,aux,probe,iRun,iSubj flagtCCA %d 1 tCCAparams %d_%0.2f_%0.1f 3_0.08_0.3 tCCAaux_inx %d_%d_%d_%d_%d_%d_%d_%d 1_2_3_4_5_6_7_8 rhoSD_ssThresh %0.1f 15 ss_ch_inx %d_%d_%d_%d_%d_%d 1_2_3_4_5 runIdxResting %d 1 tResting %d_%d 30_210

@ hmrR_GLM [dcAvg,dcAvgStd,nTrials,dcNew,dcResid,dcSum2,beta,R] (dc,stim,probe,mlActAuto,Aaux,tIncAuto,rcMap trange %0.1f_%0.1f -2_20 glmSolveMethod %d 1 idxBasis %d 2 paramsBasis %0.1f_%0.1f_%0.1f_%0.1f_%0.1f_%0.1f 0.1_3_10_1.8_3_10 rhoSD_ssThresh %0.1f 15 flagNuisanceRMethod %d 1 driftOrder %d 3 flagMotionCorrect %d 0

UnitTests/FindUnitTestsFolders.m

+1 −1
Original line number Diff line number Diff line
@@ -8,7 +8,7 @@ dirs = mydir([rootpath, '/UnitTests/*']); 
groupFolders = cell(length(dirs),1);

kk=1;

for ii=1:length(dirs)

    if ~dirs(ii).isdir()

    if ~dirs(ii).isdir

        continue;

    end

    pathfull = [rootpath, '/UnitTests/', dirs(ii).name];

Utils/getVernum.m

+1 −1
Original line number Diff line number Diff line
@@ -2,5 +2,5 @@ function vrnnum = getVernum() 


vrnnum{1} = '1';   % Major version #

vrnnum{2} = '25';  % Major sub-version #

vrnnum{3} = '4';   % Minor version #

vrnnum{3} = '5';   % Minor version #

vrnnum{4} = '0';   % Minor sub-version # or patch #: 'p1', 'p2', etc

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