Unverified Commit 2774c2ad authored by stephen scott tucker's avatar stephen scott tucker Committed by GitHub
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User function fixes and changes (#56) 

* prevented ArgClass Extract from indexing into empty list

* FuncCallClass GetInputs and GetOutputs convenience function for returning strings

* GetProcInputs method returns all properties of ProcInputClass for use with proc stream checking

* Processing stream is only run if Check returns zero, else an error msg is raised

* Changed uses of properties to propnames in ProcInputClass GetProcInputs

* tCCAaux_inx is a list again as variable length parameters are supported

* Standardized tIncMan, mlActAuto in code

* Properly generate the tIncCh matrix if it is not provided

* Include mlActAuto and tIncAuto in PCA motion correction

* recurse updated to work with new function inputs

* mlActMan and mlActAuto both used for wavelet correction

* OD2Conc wavelength restriction removed

* Phase out old GLM for new stim GLM, suppress a line in errchk

* Prevent stim amps getter from crashing on empty data

* Removed registry from PR
parent 3a11afd5

DataTree/AcquiredData/Snirf/SnirfClass.m

+6 −4
Original line number Diff line number Diff line
@@ -1061,6 +1061,7 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
            s = zeros(length(t), length(obj.stim));

            for ii=1:length(obj.stim)

                data = obj.stim.GetData();

                if ~isempty(data)

                    [~, k] = nearest_point(t, data(:, 1));

                    if isempty(k)

                        continue;
@@ -1068,6 +1069,7 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
                    s(k,ii) = data(:, 3);

                end

            end

        end

        

        

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

FuncRegistry/UserFunctions/Registry.mat

deleted100644 → 0
−106 KiB

File deleted.

View file

FuncRegistry/UserFunctions/hmrR_GLM.m

+54 −54
Original line number Diff line number Diff line
@@ -95,7 +95,7 @@ 
% trange: [-2.0, 20.0]

% glmSolveMethod: 1

% idxBasis: 1

% paramsBasis: [1.0 1.0 0.0 0.0 0.0 0.0], maxnum: 6

% paramsBasis: [1.0 1.0 0.0 0.0]

% rhoSD_ssThresh: 15.0

% flagNuisanceRMethod: 1

% driftOrder: 3
@@ -131,8 +131,9 @@ end 
% GetStims method to convert stim to the s vector that this function needs.

snirf = SnirfClass(data_y, stim);

t = snirf.GetTimeCombined();

s = snirf.GetStims(t);

nTrials = repmat({zeros(1, size(s,2))}, length(data_y), 1);

stimStates = snirf.GetStims(t);

stimAmps = snirf.GetStimAmps(t);

nTrials = repmat({zeros(1, size(stimStates,2))}, length(data_y), 1);



for iBlk=1:length(data_y)
@@ -227,19 +228,33 @@ for iBlk=1:length(data_y) 
    end

    

    %%%%%%%%%%%%%%%%

    % Prune good stim

    % Prune good stim, generate onset matrix

    %%%%%%%%%%%%%%%%

    % handle case of conditions with 0 trials

    lstCond = find(sum(s>0,1)>0);

    nCond = length(lstCond); %size(s,2);

    onset = zeros(nT,nCond);

    % Get only indices of conditions with any stimStates that are 1

    lstCond = find(sum(stimStates == 1, 1) > 0);

    nCond = length(lstCond); % size(stimStates,2);

    nTrials{iBlk} = zeros(nCond,1);

    onset = zeros(nT, nCond);

    for iCond = 1:nCond

        lstT = find(s(:,lstCond(iCond))==1);

        lstp = find((lstT+nPre)>=1 & (lstT+nPost)<=nTpts);

        lstT = find(stimStates(:, lstCond(iCond)) == 1);  % Indices of stims enabled (== 1)

        lstp = find((lstT+nPre) >= 1 & (lstT+nPost) <= nTpts);  % Indices of stims not clipped by signal

        lst = lstT(lstp);

        nTrials{iBlk}(iCond) = length(lst);

        onset(lst+nPre,iCond) = 1;

        % Generate basis boxcars of stim amplitude and duration

        starts = lst+nPre;

        if ~isempty(stim(iCond).data)

            durations = stim(iCond).data(:, 2);

            amplitudes = stim(iCond).data(:, 3);

            for i = 1:length(starts)

                if idxBasis == 1  % Gaussian has no duration T (yet)

                   pulse_duration = 1; 

                else

                   pulse_duration = round(durations(i) / dt); 

                end

                pulse = (amplitudes(i) / pulse_duration) * ones(pulse_duration, 1);

                onset(starts(i):starts(i) + pulse_duration - 1, iCond) = pulse;

            end

        end

    end

     

    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -254,19 +269,22 @@ for iBlk=1:length(data_y) 
        tbasis = zeros(ntHRF,nB);

        for b=1:nB

            tbasis(:,b) = exp(-(tHRF-(trange(1)+b*gms)).^2/(2*gstd.^2));

            tbasis(:,b) = tbasis(:,b)./max(tbasis(:,b)); %normalize to 1

            tbasis(:,b) = tbasis(:,b)./max(tbasis(:,b));

        end

        

    elseif idxBasis==2

        % Modified Gamma

        if length(paramsBasis)==2

            nConc = 1;

        else

            nConc = 2;

        end

            

        nB = 1;

        tbasis = zeros(ntHRF,nB,nConc);

        for iConc = 1:nConc

            tau = paramsBasis((iConc-1)*3+1);

            sigma = paramsBasis((iConc-1)*3+2);

            T = paramsBasis((iConc-1)*3+3);

            tau = paramsBasis((iConc-1)*2+1);

            sigma = paramsBasis((iConc-1)*2+2);

            

            tbasis(:,1,iConc) = (exp(1)*(tHRF-tau).^2/sigma^2) .* exp( -(tHRF-tau).^2/sigma^2 );

            lstNeg = find(tHRF<0);
@@ -276,28 +294,21 @@ for iBlk=1:length(data_y) 
                tbasis(1:round((tau-tHRF(1))/dt),1,iConc) = 0;

            end

            

            if T>0

                for ii=1:nB

                    foo = conv(tbasis(:,ii,iConc),ones(round(T/dt),1)) / round(T/dt);

                    tbasis(:,ii,iConc) = foo(1:ntHRF,1);

                end

            end

        end

        

    elseif idxBasis==3

        % Modified Gamma and Derivative

        if length(paramsBasis)==3

        if length(paramsBasis)==2

            nConc = 1;

        elseif length(paramsBasis)==6

        else

            nConc = 2;

        end

        

        nB = 2;

        tbasis=zeros(ntHRF,nB,nConc);

        for iConc = 1:nConc

            tau = paramsBasis((iConc-1)*3+1);

            sigma = paramsBasis((iConc-1)*3+2);

            T = paramsBasis((iConc-1)*3+3);

            tau = paramsBasis((iConc-1)*2+1);

            sigma = paramsBasis((iConc-1)*2+2);

            

            tbasis(:,1,iConc) = (exp(1)*(tHRF-tau).^2/sigma^2) .* exp( -(tHRF-tau).^2/sigma^2 );

            tbasis(:,2,iConc) = 2*exp(1)*( (tHRF-tau)/sigma^2 - (tHRF-tau).^3/sigma^4 ) .* exp( -(tHRF-tau).^2/sigma^2 );
@@ -306,19 +317,13 @@ for iBlk=1:length(data_y) 
                tbasis(1:round((tau-tHRF(1))/dt),1:2,iConc) = 0;

            end

            

            if T>0

                for ii=1:nB

                    foo = conv(tbasis(:,ii,iConc),ones(round(T/dt),1)) / round(T/dt);

                    tbasis(:,ii,iConc) = foo(1:ntHRF,1);

                end

            end

        end

        

    elseif idxBasis==4

        % AFNI Gamma function

        if length(paramsBasis)==3

        if length(paramsBasis)==2

            nConc = 1;

        elseif length(paramsBasis)==6

        else

            nConc = 2;

        end
@@ -326,16 +331,11 @@ for iBlk=1:length(data_y) 
        tbasis=zeros(ntHRF,nB,nConc);

        for iConc = 1:nConc

            

            p = paramsBasis((iConc-1)*3+1);

            q = paramsBasis((iConc-1)*3+2);

            T = paramsBasis((iConc-1)*3+3);

            p = paramsBasis((iConc-1)*2+1);

            q = paramsBasis((iConc-1)*2+2);

            

            tbasis(:,1,iConc) = (tHRF/(p*q)).^p.* exp(p-tHRF/q);

            

            if T>0

                foo = conv(tbasis(:,1,iConc),ones(round(T/dt),1)) / round(T/dt);

                tbasis(:,1,iConc) = foo(1:ntHRF,1);

            end

        end

        

    end
@@ -577,19 +577,19 @@ for iBlk=1:length(data_y) 
                    yresid = zeros(size(y));

                    

                    foo = nTrials{iBlk};

                    nTrials{iBlk} = zeros(1,size(s,2));

                    nTrials{iBlk} = zeros(1,size(stimAmps,2));

                    nTrials{iBlk}(lstCond) = foo;

                    

                    foo = yavg;

                    yavg = zeros(size(foo,1),size(foo,2),size(foo,3),size(s,2));

                    yavg = zeros(size(foo,1),size(foo,2),size(foo,3),size(stimAmps,2));

                    yavg(:,:,:,lstCond) = foo;

                    

                    foo = yavgstd;

                    yavgstd = zeros(size(foo,1),size(foo,2),size(foo,3),size(s,2));

                    yavgstd = zeros(size(foo,1),size(foo,2),size(foo,3),size(stimAmps,2));

                    yavgstd(:,:,:,lstCond) = foo;

                    

                    foo = ysum2;

                    ysum2 = zeros(size(foo,1),size(foo,2),size(foo,3),size(s,2));

                    ysum2 = zeros(size(foo,1),size(foo,2),size(foo,3),size(stimAmps,2));

                    ysum2(:,:,:,lstCond) = foo;

                    

                    beta = [];
@@ -732,23 +732,23 @@ for iBlk=1:length(data_y) 
    end

    

    foo = nTrials{iBlk};

    nTrials{iBlk} = zeros(1,size(s,2));

    nTrials{iBlk} = zeros(1,size(stimAmps,2));

    nTrials{iBlk}(lstCond) = foo;

    

    foo = yavg;

    yavg = zeros(size(foo,1),size(foo,2),size(foo,3),size(s,2));

    yavg = zeros(size(foo,1),size(foo,2),size(foo,3),size(stimAmps,2));

    yavg(:,:,:,lstCond) = foo;

    

    foo = yavgstd;

    yavgstd = zeros(size(foo,1),size(foo,2),size(foo,3),size(s,2));

    yavgstd = zeros(size(foo,1),size(foo,2),size(foo,3),size(stimAmps,2));

    yavgstd(:,:,:,lstCond) = foo;

    

    foo = ysum2;

    ysum2 = zeros(size(foo,1),size(foo,2),size(foo,3),size(s,2));

    ysum2 = zeros(size(foo,1),size(foo,2),size(foo,3),size(stimAmps,2));

    ysum2(:,:,:,lstCond) = foo;

    

    foo = tb;

    beta = zeros(size(foo,1),size(foo,2),size(foo,3),size(s,2));

    beta = zeros(size(foo,1),size(foo,2),size(foo,3),size(stimAmps,2));

    beta(:,:,:,lstCond) = foo;

    

    %%%%%%%%%%%%%%%%%%%%%%%%%

FuncRegistry/UserFunctions/hmrR_GLM_errchk.m

+1 −1
Original line number Diff line number Diff line
@@ -14,7 +14,7 @@ function errmsg = hmrR_GLM_errchk(trange, glmSolveMethod, idxBasis, paramsBasis, 
       errmsg = 'Select a valid basis function (0-4)';

       return

    elseif glmSolveMethod > 2 || glmSolveMethod < 1

       errmsg = 'Select a valid solve method (1-2)'

       errmsg = 'Select a valid solve method (1-2)';

       return

    end

end
 
 No newline at end of file

FuncRegistry/UserFunctions/hmrR_GLM_new.m→FuncRegistry/UserFunctions/hmrR_GLM_old.m

+232 −86

File changed and moved.

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