Commit a28e66fa authored by Jay Dubb's avatar Jay Dubb
Browse files

v1.22.0 

-- Some code clean up for processing stream calculation - remove loading SDRuns in SubjClass and GroupClass and replace with derived parameter mlAct. SDRuns is not needed and doesn't follow the Homer3 proc stream model of using derived parameters. Change definition of hmrS_RunAvg_Nirs.m user function accordingly and the accompanying unit test config files processOpt_default_homer3_nirs.cfg and processOpt_motionArtifact_homer3_nirs.cfg.

-- Fix small bug in passing empty parameter to Homer3

-- Close all GUIs before running unit test in clean up function
parent 344f659e

DataTree/GroupClass.m

+0 −1
Original line number Diff line number Diff line
@@ -410,7 +410,6 @@ classdef GroupClass < TreeNodeClass 
            obj.outputVars.dcAvgStdSubjs{s.iSubj}  = s.procStream.output.GetVar('dcAvgStd');

            obj.outputVars.tHRFSubjs{s.iSubj}      = s.procStream.output.GetTHRF();

            obj.outputVars.nTrialsSubjs{s.iSubj}   = s.procStream.output.GetVar('nTrials');

            obj.outputVars.SDSubjs{s.iSubj}        = s.GetMeasList();

            

            s.FreeMemory();

        end

DataTree/ProcStream/ProcStreamClass.m

+2 −2
Original line number Diff line number Diff line
@@ -585,7 +585,7 @@ classdef ProcStreamClass < handle 
            %              name: 'hmrS_RunAvg'

            %            nameUI: 'hmrS_RunAvg'

            %            argOut: '[dcAvg,dcAvgStd,tHRF,nTrials]'

            %             argIn: '(dcAvgRuns,dcAvgStdRuns,dcSum2Runs,tHRFRuns,SDRuns,nTrialsRuns'

            %             argIn: '(dcAvgRuns,dcAvgStdRuns,dcSum2Runs,tHRFRuns,mlActRuns,nTrialsRuns'

            %           paramIn: [0x0 ParamClass]

            %              help: '  Calculate the block average for all subjects, for all common stimuli'

            %
@@ -725,7 +725,7 @@ classdef ProcStreamClass < handle 
            %          '@ hmrG_SubjAvg [dcAvg,dcAvgStd,nTrials,grpAvgPass] (dcAvgSubjs,dcAvgStdSubjs,SDSubjs,nTrialsSubjs tRange %0.1f'

            %         }

            %     S = {

            %          '@ hmrS_RunAvg [dcAvg,dcAvgStd,nTrials] (dcAvgRuns,dcAvgStdRuns,dcSum2Runs,SDRuns,nTrialsRuns'

            %          '@ hmrS_RunAvg [dcAvg,dcAvgStd,nTrials] (dcAvgRuns,dcAvgStdRuns,dcSum2Runs,mlActRuns,nTrialsRuns'

            %         }

            %     R = {

            %         '@ hmrR_Intensity2OD dod (d'

DataTree/SubjClass.m

+3 −4
Original line number Diff line number Diff line
@@ -204,9 +204,8 @@ classdef SubjClass < TreeNodeClass 
            obj.outputVars.dcAvgStdRuns{r.iRun}  = r.procStream.output.GetVar('dcAvgStd');

            obj.outputVars.dcSum2Runs{r.iRun}    = r.procStream.output.GetVar('dcSum2');

            obj.outputVars.tHRFRuns{r.iRun}      = r.procStream.output.GetTHRF();

            obj.outputVars.nTrialsRuns{r.iRun}   = r.procStream.output.GetVar('nTrials');

            obj.outputVars.mlActRuns{r.iRun}     = r.procStream.output.GetVar('mlActAuto');

            obj.outputVars.SDRuns{r.iRun}        = r.GetMeasList();

            obj.outputVars.nTrialsRuns{r.iRun}   = r.procStream.output.GetVar('nTrials');

            obj.outputVars.stimRuns{r.iRun}      = r.GetVar('stim');

            

            % Free run memory
@@ -243,11 +242,11 @@ classdef SubjClass < TreeNodeClass 
            

            

            % Load all the variables that might be needed by procStream.Calc() to calculate proc stream for this subject

            obj.outputVars = struct();

            for iRun = 1:length(r)

                obj.LoadVars(r(iRun), tHRF_common);

            end

            

            

            % Make variables in this subject available to processing stream input

            obj.procStream.input.LoadVars(obj.outputVars);

FuncRegistry/UserFunctions/Archive/hmrS_RunAvg_Nirs.m

+30 −23
Original line number Diff line number Diff line 
function [yAvg, yAvgStd, tHRF, nTrials] = hmrS_RunAvg_Nirs(yAvgRuns, yAvgStdRuns, ySum2Runs, tHRFRuns, SDRuns, nTrialsRuns)

% SYNTAX:

% [yAvg, yAvgStd, tHRF, nTrials] = hmrS_RunAvg_Nirs(yAvgRuns, yAvgStdRuns, ySum2Runs, tHRFRuns, SDRuns, nTrialsRuns)

% [yAvg, yAvgStd, tHRF, nTrials] = hmrS_RunAvg_Nirs(yAvgRuns, yAvgStdRuns, ySum2Runs, tHRFRuns, mlActRuns, nTrialsRuns)

%

% UI NAME:

% Run_Average
@@ -12,7 +11,7 @@ function [yAvg, yAvgStd, tHRF, nTrials] = hmrS_RunAvg_Nirs(yAvgRuns, yAvgStdRuns 
% yAvgRuns:

% yAvgStdRuns:

% tHRFRuns: 

% SDRuns:

% mlActRuns:

% nTrialsRuns:

% trange: defines the range for the block average

% thresh: Threshold for excluding channels if it's data deviates too much
@@ -25,15 +24,18 @@ function [yAvg, yAvgStd, tHRF, nTrials] = hmrS_RunAvg_Nirs(yAvgRuns, yAvgStdRuns 
% nTrials: the number of trials averaged for each condition across all runs

%

% USAGE OPTIONS:

% Run_Average_on_Concentration_Data:  [dcAvg, dcAvgStd, tHRF, nTrials]    = hmrS_RunAvg_Nirs(dcAvgRuns, dcAvgStdRuns, dcSum2Runs, tHRFRuns, SDRuns, nTrialsRuns)

% Run_Average_on_Delta_OD_Data:       [dodAvg, dodAvgStd, tHRF, nTrials]  = hmrS_RunAvg_Nirs(dodAvgRuns, dodAvgStdRuns, dodSum2Runs, tHRFRuns, SDRuns, nTrialsRuns)

% Run_Average_on_Concentration_Data:  [dcAvg, dcAvgStd, tHRF, nTrials]    = hmrS_RunAvg_Nirs(dcAvgRuns, dcAvgStdRuns, dcSum2Runs, tHRFRuns, mlActRuns, nTrialsRuns)

% Run_Average_on_Delta_OD_Data:       [dodAvg, dodAvgStd, tHRF, nTrials]  = hmrS_RunAvg_Nirs(dodAvgRuns, dodAvgStdRuns, dodSum2Runs, tHRFRuns, mlActRuns, nTrialsRuns)

%



function [yAvg, yAvgStd, tHRF, nTrials] = hmrS_RunAvg_Nirs(yAvgRuns, yAvgStdRuns, ySum2Runs, tHRFRuns, mlActRuns, nTrialsRuns)



yAvg = [];

yAvgStd = [];

tHRF = [];

nTrials_tot = [];

grp1=[];



for iRun = 1:length(yAvgRuns)

    

    yAvg      = yAvgRuns{iRun};
@@ -41,7 +43,7 @@ for iRun = 1:length(yAvgRuns) 
    ySum2     = ySum2Runs{iRun};

    tHRF      = tHRFRuns{iRun};

    nTrials   = nTrialsRuns{iRun};

    SD        = SDRuns{iRun};    

    mlAct     = mlActRuns{iRun};

    

    if isempty(yAvg)

        break;
@@ -51,6 +53,10 @@ for iRun = 1:length(yAvgRuns) 
    

    if ndims(yAvg) == (3-(nCond<2))

        

        if isempty(mlAct)

            mlAct = 1:size(yAvg,2);

        end

        

        % grab tHRF to make common for group average

        if iRun==1

            grp1 = zeros(size(yAvg,1), size(yAvg,2), nCond);
@@ -58,19 +64,18 @@ for iRun = 1:length(yAvgRuns) 
            nTrials_tot = zeros(size(yAvg,2), nCond);

        end

        

        lstChInc = find(SD.MeasListActAuto==1);

        for iC = 1:nCond

            nT = nTrials(iC);            

            if nT>0

                if iRun==1

                    grp1(:,lstChInc,iC) = yAvg(:,lstChInc,iC) * nT;

                    grp1Sum2(:,lstChInc,iC) = ySum2(:,lstChInc,iC);

                    nTrials_tot(lstChInc,iC) = nT;

                    grp1(:,mlAct,iC) = yAvg(:,mlAct,iC) * nT;

                    grp1Sum2(:,mlAct,iC) = ySum2(:,mlAct,iC);

                    nTrials_tot(mlAct,iC) = nT;

                else

                    for iCh=1:length(lstChInc) %size(yAvg,2)

                        grp1(:,lstChInc(iCh),iC) = grp1(:,lstChInc(iCh),iC) + interp1(tHRF,yAvg(:,lstChInc(iCh),iC),tHRF(:)) * nT;

                        grp1Sum2(:,lstChInc(iCh),iC) = grp1Sum2(:,lstChInc(iCh),iC) + interp1(tHRF,ySum2(:,lstChInc(iCh),iC),tHRF(:));

                        nTrials_tot(lstChInc(iCh),iC) = nTrials_tot(lstChInc(iCh),iC) + nT;

                    for iCh=1:length(mlAct) %size(yAvg,2)

                        grp1(:,mlAct(iCh),iC) = grp1(:,mlAct(iCh),iC) + interp1(tHRF,yAvg(:,mlAct(iCh),iC),tHRF(:)) * nT;

                        grp1Sum2(:,mlAct(iCh),iC) = grp1Sum2(:,mlAct(iCh),iC) + interp1(tHRF,ySum2(:,mlAct(iCh),iC),tHRF(:));

                        nTrials_tot(mlAct(iCh),iC) = nTrials_tot(mlAct(iCh),iC) + nT;

                    end

                end

            end
@@ -97,6 +102,10 @@ for iRun = 1:length(yAvgRuns) 
        

    elseif ndims(yAvg) == (4-(nCond<2))

        

        if isempty(mlAct)

            mlAct = 1:size(yAvg,3);

        end

        

        % grab tHRF to make common for group average

        if iRun==1

            grp1 = zeros(size(yAvg,1), size(yAvg,2), size(yAvg,3), nCond);
@@ -104,22 +113,20 @@ for iRun = 1:length(yAvgRuns) 
            nTrials_tot = zeros(size(yAvg,3), nCond);

        end

        

        lst1 = find(SD.MeasList(:,4)==1);

        lstChInc = find(SD.MeasListActAuto(lst1)==1);

        for iC = 1:1:nCond

            nT = nTrials(iC);

            if nT>0

                if iRun==1

                    grp1(:,:,lstChInc,iC) = yAvg(:,:,lstChInc,iC) * nT;

                    grp1Sum2(:,:,lstChInc,iC) = ySum2(:,:,lstChInc,iC);

                    nTrials_tot(lstChInc,iC) = nT;

                    grp1(:,:,mlAct,iC) = yAvg(:,:,mlAct,iC) * nT;

                    grp1Sum2(:,:,mlAct,iC) = ySum2(:,:,mlAct,iC);

                    nTrials_tot(mlAct,iC) = nT;

                else

                    for iCh=1:length(lstChInc) %size(yAvg,3)

                    for iCh=1:length(mlAct) %size(yAvg,3)

                        for iHb=1:size(yAvg,2)

                            grp1(:,iHb,lstChInc(iCh),iC) = grp1(:,iHb,lstChInc(iCh),iC) + interp1(tHRF,yAvg(:,iHb,lstChInc(iCh),iC),tHRF(:)) * nT;

                            grp1Sum2(:,iHb,lstChInc(iCh),iC) = grp1Sum2(:,iHb,lstChInc(iCh),iC) + interp1(tHRF,ySum2(:,iHb,lstChInc(iCh),iC),tHRF(:));

                            grp1(:,iHb,mlAct(iCh),iC) = grp1(:,iHb,mlAct(iCh),iC) + interp1(tHRF,yAvg(:,iHb,mlAct(iCh),iC),tHRF(:)) * nT;

                            grp1Sum2(:,iHb,mlAct(iCh),iC) = grp1Sum2(:,iHb,mlAct(iCh),iC) + interp1(tHRF,ySum2(:,iHb,mlAct(iCh),iC),tHRF(:));

                        end

                        nTrials_tot(lstChInc(iCh),iC) = nTrials_tot(lstChInc(iCh),iC) + nT;

                        nTrials_tot(mlAct(iCh),iC) = nTrials_tot(mlAct(iCh),iC) + nT;

                    end

                end

            end

Homer3.m

+2 −4
Original line number Diff line number Diff line
@@ -14,12 +14,10 @@ logger = Logger('Homer3'); 


logger.CurrTime();



if nargin==0

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

    groupDirs = convertToStandardPath(pwd);

end

if nargin<2

    inputFileFormat='snirf';

elseif nargin==1 && isempty(inputFileFormat)

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

    inputFileFormat='snirf';

end

cfg = ConfigFileClass();

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