Commit 1ac7f226 authored by Jay Dubb's avatar Jay Dubb
Browse files

v1.30.2 

-- Add functionality to allow unit testing of MainGUI and add unit test that launches MainGUI and generates HRF for group. The biggest change is in MainGUI and supporting graphics functions to always specify the axes handle for built-in axes display functions such plot, hold, xlim, ylim, xlabel, ylabel, legend, etc. rather than letting the axes defalt to gca.

-- Add UnitTestsAll_MainGUI to UnitTestsAll to run some basic checks on MainGUI.

-- Fix broken unit tests because the user function hmrR_Intensity2OD was changed to prompt user for input if input data was negative. Changed hmrR_Intensity2OD to detect when it is being run in unit test and with global UNIT_TEST variable and to not accept user input in that case if it is set to true.
parent 1cafc060

DataTree/DataTreeClass.m

+8 −0
Original line number Diff line number Diff line
@@ -579,6 +579,14 @@ classdef DataTreeClass < handle 
        end

        

        

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

        function ResetAll(obj)

            for ii = 1:length(obj.groups)

                obj.groups(ii).Reset()

            end

        end

        

        

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

        function b = IsEmpty(obj)

            b = true;

FuncRegistry/UserFunctions/hmrR_Intensity2OD.m

+36 −0
Original line number Diff line number Diff line
@@ -23,6 +23,9 @@ dod = DataClass().empty(); 
for ii=1:length(intensity)

    dod(ii) = DataClass();

    d = intensity(ii).GetDataTimeSeries();

 

    d = ErrorCheck(d);

 

    dm = mean(abs(d),1);

    nTpts = size(d,1);

    dod(ii).SetTime(intensity(ii).GetTime());
@@ -30,3 +33,36 @@ for ii=1:length(intensity) 
    dod(ii).SetMl(intensity(ii).GetMl());

    dod(ii).SetDataTypeDod();

end







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

function d = ErrorCheck(d)

global UNIT_TEST



if ~isempty(UNIT_TEST) && UNIT_TEST

    return;

end



% Optional (user prompt): Adding dc offset if intensity (d) has negative values

if ~isempty(d(d<=0))

    quest = {'Intensity signal has negative values. If you would like to add a dc offset, please click YES. If you would like to proceed with negative values, hit CANCEL.'};

    dlgtitle = 'Warning';

    btn1 = 'YES';

    btn2 = 'CANCEL';

    detbtn = btn1;

    answer = questdlg(quest,dlgtitle,btn1,btn2,detbtn);

    switch answer

        case 'YES'

            for j = 1:size(d,2)

                foo = d(:,j);

                if ~isempty(foo<0)

                    d(:,j) = foo + abs(min(foo));

                    foo = d(:,j);

                end

                if ~isempty(foo == 0)

                    d(:,j) = foo + min(foo(foo > 0));

                end

            end

    end

end

Homer3.m

+17 −11
Original line number Diff line number Diff line 
function Homer3(groupDirs, inputFileFormat)

function unitTest = Homer3(groupDirs, inputFileFormat, unitTest)



%  Syntax:

%       Homer3(groupDirs, inputFileFormat)

%       unitTest = Homer3(groupDirs, inputFileFormat)

%   

%  Examples:

%
@@ -10,9 +10,6 @@ function Homer3(groupDirs, inputFileFormat) 
%



global logger

logger = Logger('Homer3');



logger.CurrTime();



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

    groupDirs = filesepStandard(pwd);
@@ -20,15 +17,24 @@ end 
if ~exist('inputFileFormat','var') || isempty(inputFileFormat)

    inputFileFormat = '.snirf';

end

cfg = ConfigFileClass();

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

    unitTest = [];

end



if isempty(unitTest)

    logger = Logger('Homer3');

elseif unitTest.IsEmpty()

    logger = InitLogger(logger);

else

    return;

end

logger.CurrTime();

cfg = ConfigFileClass();

if strcmp(cfg.GetValue('Logging'), 'off')

    logger.SetDebugLevel(logger.Null());

end



PrintSystemInfo(logger, 'Homer3');

checkForHomerUpdates();



logger.Write(sprintf('Opened application config file %s\n', cfg.filename))

gdir = cfg.GetValue('Last Group Folder');

if isempty(gdir)
@@ -38,11 +44,11 @@ if isempty(gdir) 
end



try

    MainGUI(groupDirs, inputFileFormat, logger, 'userargs');

    unitTest = MainGUI(groupDirs, inputFileFormat, unitTest, 'userargs');    

catch ME

    % Clean up in case of error make sure all open file handles are closed 

    % so we don't leave the application in a bad state

    logger.Close()

    rethrow(ME)

    logger.Close();

    rethrow(ME);

end

MainGUI/DisplayAxesSDG.m

+18 −7
Original line number Diff line number Diff line
@@ -36,8 +36,9 @@ 




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

function DisplayAxesSDG(hAxes)

function DisplayAxesSDG(handles)

global maingui

global UNIT_TEST



tic;
@@ -45,8 +46,13 @@ tic; 
% Command line call:

% plotAxes_SDG(guidata(gcbo),bool);

%

if nargin<1

    hAxes   = maingui.axesSDG.handles.axes;

if nargin==0

    return;

end

if ~ishandles(handles)

    hAxes = handles.axesSDG;

else

    hAxes = handles;    

end

iCh         = maingui.axesSDG.iCh;

iSrcDet     = maingui.axesSDG.iSrcDet;
@@ -65,8 +71,10 @@ end 
if ~ishandles(hAxes)

    return;

end



% Set gca to be SDG axes

axes(hAxes);



% Delete all channel lines drawn

if ishandles(maingui.axesSDG.handles.ch)

    delete(maingui.axesSDG.handles.ch)
@@ -77,6 +85,7 @@ if isfield(maingui.axesSDG, 'xlim') 
else

    axis(hAxes, [bbox(1), bbox(2), bbox(3), bbox(4)]);

end



%set(hAxes, 'xticklabel','', 'yticklabel','', 'xgrid','off, ygrid','off')

set(hAxes, 'xticklabel','')

bttndownfcn = get(hAxes,'ButtonDownFcn');
@@ -115,7 +124,7 @@ hCh = zeros(length(lstML),1); 


% Draw all channels

for ii = 1:length(lstML)

    hCh(ii) = line2(SD.SrcPos(ml(lstML(ii),1),:), SD.DetPos(ml(lstML(ii),2),:), [], gridsize);

    hCh(ii) = line2(SD.SrcPos(ml(lstML(ii),1),:), SD.DetPos(ml(lstML(ii),2),:), [], gridsize, hAxes);

    if ismember(ii,lstExclAuto)

        % Draw auto-excluded channel

        col = [1.00 0.6 0.6];
@@ -148,7 +157,7 @@ if ~isempty(iSrcDet) && iSrcDet(1,1)~=0 
    

    for idx = 1:size(iSrcDet,1)

        lwidth = 3;

        hCh(idx+ii) = line2(SD.SrcPos(iSrcDet(idx,1),:), SD.DetPos(iSrcDet(idx,2),:), [], gridsize);

        hCh(idx+ii) = line2(SD.SrcPos(iSrcDet(idx,1),:), SD.DetPos(iSrcDet(idx,2),:), [], gridsize, hAxes);

        % Attach toggle callback to the selected channels for function on

        % second click

        set(hCh(idx+ii),'color',color(idx,:), 'ButtonDownFcn',sprintf('toggleLinesAxesSDG_ButtonDownFcn(gcbo,[%d],guidata(gcbo))',idx), 'linewidth',2);
@@ -198,7 +207,9 @@ else 
end



% Turn off zoom but only for SDG axes

h=zoom;

h = zoom(hAxes);

if isempty(UNIT_TEST) || ~UNIT_TEST

    setAllowAxesZoom(h, hAxes, 0);

end



% fprintf('DisplayAxesSDG: Elapsed Time - %0.3f\n', toc);

MainGUI/DisplayDataConc.m

+3 −3
Original line number Diff line number Diff line 
function DisplayDataConc(t, d, dStd, hbType, ch, chLst, nTrials, condition, linecolor, linestyle)

function DisplayDataConc(hAxes, t, d, dStd, hbType, ch, chLst, nTrials, condition, linecolor, linestyle)



% Parse args

if ~exist('t','var')
@@ -44,7 +44,7 @@ end 
for iHb=1:length(hbType)

    for ii=length(ch(chLst)):-1:1

        dHbMl = squeeze(d(:, hbType(iHb), ch(chLst(ii))));

        h     = plot(t, dHbMl);

        h     = plot(hAxes, t, dHbMl);

        

        % fprintf('Plotting channel: %d, color: [%0.1f, %0.1f, %0.1f]\n', chLst(ii), linecolor(chLst(ii),:));

        set(h, 'color', linecolor(chLst(ii),:));
@@ -55,7 +55,7 @@ for iHb=1:length(hbType) 
            dHbMlStd    = squeeze(dStd( :, hbType(iHb), ch(chLst(ii)) ));

            dHbMlStdErr = dHbMlStd./sqrt(nTrials(condition));

            idx         = [1:10:length(t)];

            h2          = errorbar(t(idx), dHbMl(idx), dHbMlStdErr(idx),'.');

            h2          = errorbar(hAxes, t(idx), dHbMl(idx), dHbMlStdErr(idx),'.');

            set(h2,'color',linecolor(chLst(ii),:));

        end

    end

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