Unverified Commit 10832b7e authored by Christian Arthur's avatar Christian Arthur Committed by GitHub
Browse files

CSV Stim Tools (#58) 



* Updated DesignNotes.ppt

* Update 1
Added Zoom and Pan functionality to axesSDG (probe display) on the MainGUI with additional buttons in the GUI

* Update 1.1
Minor Zoom adjustments

* 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

* Added removal and addition of stim data columns and interface in StimEditGUI; added dialog box for setting amp, duration, and values for new stims

* Added rename column interface

* GUI updates: column interface changed, rename condition moved to menubar -> tools

* Tooltip to manual edit, exit condition for value entry prompt

* Callback Added for CSV Read/Write

* Script Addition
- CSV Write to StimEditGUI
- CSV Read from StimEditGUI

* Stim CSV Reader and Write Update
- Integrated into StimEditGUI.fig

* StimEditGUI.fig Update
- Added StimCSV_Read and StimCSV_Write to the Menu Bar

* StimEditGUI.fig Update
- Normalized objects (with two errors(?))

* Added sample .csv file for stims

* Session level GLM

Adding hmrS_GLM which gets all run level data from a single subject and concatenates them. The new design matrix has HRF regressors common to all runs but have separate regressors for the rest of the model (e.g. drift, short separation).

* Update hmrS_GLM.m

Fix on contrast estimation from the concatenated GLM.

* Update hmrS_GLM.m

Updating the help of the function

* tstats for iRML

Adding tstats per condition and per contrast for the iterative restricted maximum likelihood method from Barker, BOE, 2013.

* Stim GUI interface changes (#47)

* 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

* Added removal and addition of stim data columns and interface in StimEditGUI; added dialog box for setting amp, duration, and values for new stims

* Added rename column interface

* GUI updates: column interface changed, rename condition moved to menubar -> tools

* Tooltip to manual edit, exit condition for value entry prompt

* Generate filters with butter interface, error checking

* Logic to prevent button presses when no conditions are present

* Removed rename cond and add/delete/rename column GUI options because they result in undefined behavior

* User function improvements (#53)

* 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

* Synced the Stim CSV Reader and Writer
- Added menu button for saving and loading CSV files

* Re-Update
- Added CSV Stim Read and Write tools to StimEdit GUI

* Clean Up
- Adjusted SubjClass.m, hmrR_GLM.m to sync with the development branch
- Deleted the previously pulled hmrS_GLM.m (from a reverted merge)

Co-authored-by: default avatarsstucker <sstucker@bu.edu>
Co-authored-by: default avatarMeryem Ayse Yucel <49535526+mayucel@users.noreply.github.com>
parent a6798fa1

Docs/ex_stimCSV.csv

0 → 100644
+29 −0
Original line number Diff line number Diff line 
Stim 1 Name,,,,

Onset,Duration,Amplitude,Extra1,Extra2

31.1984,10,1,5,20

61.1969,10,1,10,40

91.1953,10,1,15,60

121.1938,10,1,20,80

151.1923,10,1,25,100

181.1907,10,1,30,120

211.1892,10,1,35,140

241.1877,10,1,40,160

271.1861,10,1,45,180

300.1846,10,1,50,200

331.1831,10,1,55,220

361.1815,10,1,60,240

,,,,

Stim 2 Name,,,,

Onset,Duration,Amplitude,Extra1,Extra2

40,10,1,20,5

70,10,1,40,10

100,10,1,60,15

130,10,1,80,20

160,10,1,100,25

190,10,1,120,30

220,10,1,140,35

250,10,1,160,40

280,10,1,180,45

310,10,1,200,50

340,10,1,220,55

370,10,1,240,60

StimEditGUI/StimEditGUI.fig

−13.7 KiB (50.6 KiB)

File changed.

No diff preview for this file type.

View original file
View changed file

StimEditGUI/StimEditGUI.m

+41 −1
Original line number Diff line number Diff line
@@ -1025,7 +1025,6 @@ end 


labels = stimEdit.dataTreeHandle.currElem.GetStimDataLabels(icond);

stimdata = stimEdit.dataTreeHandle.currElem.GetStimData(icond);



if ~isempty(stimdata)

    [tpts, idx] = sort(stimdata(:,1));

    stimdata_sorted = stimdata(idx,:);
@@ -1313,3 +1312,44 @@ stimEdit.dataTreeHandle.currElem.AddStimColumn(name, value); 
Display(handles);







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

function StimCSV_Read_Callback(hObject, eventdata, handles)

% hObject    handle to StimCSV_Read (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    structure with handles and user data (see GUIDATA)

global stimEdit

[conds,labels,stimData] = StimCSV_Reader();

for j = 1:length(labels{1})

    stimEdit.dataTreeHandle.currElem.AddStimColumn(labels{1}{j},1);

end

for i = 1:length(stimData)

    onsets = str2double(stimData{i}(:,1));

    dur = str2double(stimData{i}(:,2));

    amp = str2double(stimData{i}(:,3));

    if size(stimData{i},2) > 3

        other = str2double(stimData{i}(:,4:end));

    else

        other = [];

    end

    for k = 1:size(stimData{i},1)

        stimEdit.dataTreeHandle.currElem.AddStims(onsets(k), conds{i}{1}, dur(k), amp(k), other(k,:));

    end

end

iG = stimEdit.locDataTree.GetCurrElemIndexID();

stimEdit.locDataTree.groups(iG).SetConditions();

Display(handles);





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

function StimCSV_Write_Callback(hObject, eventdata, handles)

% hObject    handle to CSV_Write (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    structure with handles and user data (see GUIDATA)

global stimEdit

conds = stimEdit.dataTreeHandle.currElem.GetConditions();

for i = 1:length(conds)

    stimData{:,i} = stimEdit.dataTreeHandle.currElem.GetStimData(i);

    stimLabels{:,i} = stimEdit.dataTreeHandle.currElem.GetStimDataLabels(i);

end

StimCSV_Write(conds,stimLabels,stimData);

Utils/StimCSV_Reader.m

0 → 100644
+61 −0
Original line number Diff line number Diff line 
function [conds,labels,stimData] = StimCSV_Reader()

    %Open File

%     filename = "StimCSV_Sample_Error.csv";

    [file,path,~] = uigetfile({'*.csv','CSV File (*.csv)'});

    filename = [path file];

    stimFileID = fopen(filename);

    

    %Initial Variables

    i = 1;

    stimNameIndicator = true;

    stimLabelIndicator = true;

    labels = cell(1,1);

    data = [];

    stimData = cell(1,1);

    

    %Get Line

    linestr = fgetl(stimFileID);

    

    while(linestr ~= -1)

        strCell = strsplit(linestr,',');

        strCell = strCell(~cellfun(@isempty,strCell));

        if isempty(strCell) %Update Stim (Finalize)

            try

                stimData{:,i} = data;

            catch

                errordlg('Invalid Stim CSV Syntax. Please check reference file for guidance');

                return;

            end

            i = i+1;

            stimNameIndicator = true;

            stimLabelIndicator = true;

            data = [];

        elseif stimNameIndicator %Update Stim Name

            try

                conds{i} = strCell(1);

            catch

                errordlg('Invalid Stim CSV Syntax. Please check reference file for guidance');

                return;

            end

            stimNameIndicator = false;

        elseif stimLabelIndicator %Update Stim Label

            labels{i} = strCell;

            stimLabelIndicator = false;

        else %Update Stim Data

            try

                data = [data; strCell];

            catch

                errordlg('Invalid Stim CSV Syntax. Please check reference file for guidance');

                return;

            end

        end

        %Read Next Line

        linestr = fgetl(stimFileID);

    end

    

    %Final Stim Update

    stimData{:,i} = data;

    

    %Close File

    fclose(stimFileID);

end
 
 No newline at end of file

Utils/StimCSV_Write.m

0 → 100644
+46 −0
Original line number Diff line number Diff line 
function StimCSV_Write(conds,stimLabels,stimData)

%     filename = 'test.csv';

%     stimvar = importStim;

    [file,path,~] = uiputfile({'*.csv','CSV File (*.csv)'});

    filename = [path file];

    

    fid = fopen(filename,'w');

    

    for i = 1:length(conds)

        for j = 1:size(stimData{i},1)+2

            linestr = [];

            for k = 1:size(stimLabels{i},2)

                if j == 1

                    if k == 1

                        linestr = sprintf('%s,', conds{i});

                        linediv = sprintf(',');

                    elseif k == size(stimLabels{i},2)

                        % Done

                        linediv = sprintf('%s\n', linediv);

                    else

                        linestr = sprintf('%s,', linestr);

                        linediv = sprintf('%s,', linediv);

                    end

                elseif j == 2

                    if k == size(stimLabels{i},2)

                        linestr = sprintf('%s%s', linestr, stimLabels{i}{k});

                    else

                        linestr = sprintf('%s%s,', linestr, stimLabels{i}{k});

                    end

                else

                    if k == size(stimLabels{i},2)

                        linestr = sprintf('%s%f', linestr, stimData{i}(j-2,k));

                    else

                        linestr = sprintf('%s%f,', linestr, stimData{i}(j-2,k));

                    end

                end

            end

            linestr = sprintf('%s\n', linestr);

            fprintf(fid,linestr);

        end

        fprintf(fid,linediv);

    end

    

    fclose(fid);



end

CRA Git | Maintained and supported by SUSTech CRA and CCSE