Commit 150061c6 authored by jayd1860's avatar jayd1860
Browse files

v1.47.0 

-- Fix mlAct in hmrR_tCCA.m
-- In PlotProbeGUI get condition dynamically from parent gui, that is MainGUI
-- In PlotProbeGUI.m add back ability to display OD HRF and also any data type that is currently selected in MainGUI
parent 5d3d66e0

DataTree/AcquiredData/Snirf/DataClass.m

+4 −1
Original line number Diff line number Diff line
@@ -616,6 +616,9 @@ classdef DataClass < FileLoadSaveClass 
        

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

        function SetInactiveChannelData(obj)

            if obj.IsEmpty()

                return

            end

            for iMeas = 1:size(obj.dataTimeSeries,2)

                % We set the criteria for deciding if a channel is inactive if ALL it's 

                % data points are zero. Is this a safe assumption? Maybe we should create

FuncRegistry/UserFunctions/mlAct_Initialize.m

+5 −1
Original line number Diff line number Diff line
@@ -12,7 +12,11 @@ elseif isvector(mlAct0) && (length(mlAct0) > length(k)) 
elseif size(mlAct0,1) == length(k)

    mlAct = mlAct0;

elseif size(ml,2) == 2

    if ~isempty(mlAct0)

        mlAct = mlAct0;

    else

        mlAct = [ ml(k,1:2), ones(size(ml(k,:),1),2) ];

    end        

else

    mlAct = [ ml(k,1:2), ones(size(ml(k,:),1),1), ml(k,4) ];

end

FuncRegistry/UserFunctions/tcca_glm/hmrR_tCCA.m

+3 −7
Original line number Diff line number Diff line
@@ -126,13 +126,9 @@ if flagtCCA 
        fq = 1/(t(2)-t(1));

                

        % get  a list of active channels

        if isempty(mlActMan{iBlk})

            mlActMan{iBlk} = ones(size(ml,1)*2,1);

        end

        if isempty(mlActAuto{iBlk})

            mlActAuto{iBlk} = ones(size(ml,1)*2,1);

        end

        MeasListAct = mlActMan{iBlk} & mlActAuto{iBlk};

        mlActMan{iBlk} = mlAct_Initialize(mlActMan{iBlk}, ml);

        mlActAuto{iBlk} = mlAct_Initialize(mlActAuto{iBlk}, ml);

        MeasListAct = mlActMan{iBlk}(:,3) & mlActAuto{iBlk}(:,3);

        

        %% find the list of short and long distance channels

        lst = 1:size(ml,1);

MainGUI/GetDatatype.m

+1 −0
Original line number Diff line number Diff line
@@ -30,4 +30,5 @@ elseif plotConcVal && ~plotHRFVal 
elseif plotConcVal && plotHRFVal

    datatype      = c.CONC_HRF;

end

maingui.datatype = datatype;

PlotProbeGUI/PlotProbeGUI.m

+78 −130
Original line number Diff line number Diff line
@@ -46,10 +46,15 @@ plotprobe.condition = []; 
plotprobe.pos = [];



% Rest of the parameters 

plotprobe.datatypeVals = struct('RAW',1, 'RAW_HRF',2, 'OD',4, 'OD_HRF',8, 'CONC',16, 'CONC_HRF',32);

plotprobe.datatype = [];

plotprobe.datatypeVals = [];

plotprobe.name = 'plotprobe';

plotprobe.y = {};

plotprobe.yStd = {};

plotprobe.t = {};

plotprobe.ml = {};

plotprobe.SD = [];



SetGuiControls(handles)



setGuiFonts(handles.figure);
@@ -66,11 +71,49 @@ plotprobe.tMarkShow = get(handles.radiobuttonShowTimeMarkers, 'value'); 
plotprobe.tMarkUnits  = str2num(get(handles.textTimeMarkersAmpUnits, 'string'));







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

function ParseArgs(args)

function InheritParentGuiParams()

global plotprobe

global maingui



% Now whichever of the above parameters weren't assigned values

% obtain values either from parent gui or assign default value

if isempty(maingui)

    if isempty(plotprobe.groupDirs)

        plotprobe.groupDirs = filesepStandard({pwd});

    end

    if isempty(plotprobe.format)

        plotprobe.format = 'snirf';

    end

    if isempty(plotprobe.condition)

        plotprobe.condition = 1;

    end

    if isempty(plotprobe.datatypeVals)

        plotprobe.datatypeVals = struct('RAW',1, 'RAW_HRF',2, 'OD',4, 'OD_HRF',8, 'CONC',16, 'CONC_HRF',32);

    end

    if isempty(plotprobe.datatype)

        plotprobe.datatype = plotprobe.datatypeVals.CONC_HRF;

    end

else

    if isempty(plotprobe.groupDirs)

        plotprobe.groupDirs = maingui.groupDirs;

    end

    if isempty(plotprobe.format)

        plotprobe.format = maingui.format;

    end

    plotprobe.condition = maingui.condition;

    plotprobe.datatypeVals = maingui.buttonVals;

    plotprobe.datatype = maingui.datatype;

end









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

function ParseArgs(args)

global plotprobe



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

    return;

end
@@ -152,32 +195,7 @@ elseif length(varargin)==5 
    plotprobe.pos       = varargin{5};                      % PlotProbeGUI(groupDirs, format, datatype, condition, pos)

end



% Now whichever of the above parameters weren't assigned values

% obtain values either from parent gui or assign default value

if isempty(maingui)

    if isempty(plotprobe.groupDirs)

        plotprobe.groupDirs = filesepStandard({pwd});

    end

    if isempty(plotprobe.format)

        plotprobe.format = 'snirf';

    end

    if isempty(plotprobe.condition)

        plotprobe.condition = 1;

    end

else

    if isempty(plotprobe.groupDirs)

        plotprobe.groupDirs = maingui.groupDirs;

    end

    if isempty(plotprobe.format)

        plotprobe.format = maingui.format;

    end

    if isempty(plotprobe.condition)

        plotprobe.condition = maingui.condition;

    end

end

if isempty(plotprobe.datatype)

    plotprobe.datatype = plotprobe.datatypeVals.CONC_HRF;

end

InheritParentGuiParams()
@@ -310,8 +328,6 @@ set(handles.axes1, 'xlim', [0,1], 'ylim', [0,1]); 
cla(handles.axes1); 

axis off;



condition = plotprobe.condition;

datatype  = plotprobe.datatype;

currElem  = plotprobe.dataTreeHandle.currElem;



% Load current element data from file
@@ -323,27 +339,7 @@ SetWindowTitle(handles) 


% Clear axes of previous data, before redisplaying it

ClearAxesData(handles);



hold on

nDataBlks = plotprobe.dataTreeHandle.currElem.GetDataBlocksNum();

plotprobe.y = cell(nDataBlks,1);

plotprobe.t = cell(nDataBlks,1);

for iBlk=1:nDataBlks

    if datatype == plotprobe.datatypeVals.OD_HRF

        plotprobe.y{iBlk} = currElem.GetDodAvg(condition, iBlk);

        plotprobe.ystd{iBlk} = plotprobe.dataTree.currElem.GetDodAvgStd(condition, iBlk);

        plotprobe.t{iBlk} = currElem.GetTHRF();

        plotprobe.tMarkUnits='(AU)';

    elseif datatype == plotprobe.datatypeVals.CONC_HRF

        plotprobe.y{iBlk} = currElem.GetDcAvg(condition, iBlk);

        plotprobe.ystd{iBlk} = plotprobe.dataTree.currElem.GetDcAvgStd(condition, iBlk);

        plotprobe.t{iBlk} = currElem.GetTHRF();

        plotprobe.tMarkAmp = plotprobe.tMarkAmp/1e6;

        plotprobe.tMarkUnits = '(micro-molars)';

    end

    plotProbeAndSetProperties(handles, iBlk);

end

hold off

plotProbeAndSetProperties(handles);
@@ -363,10 +359,7 @@ plotprobe.axScl = foo; 
ClearAxesData(handles);



set(hObject,'string', sprintf('%0.1f %0.1f', plotprobe.axScl) );

nDataBlks = plotprobe.dataTreeHandle.currElem.GetDataBlocksNum();

for iBlk=1:nDataBlks

    plotProbeAndSetProperties(handles, iBlk);

end

plotProbeAndSetProperties(handles);
@@ -381,11 +374,8 @@ set(hEditScl,'string', sprintf('%0.1f %0.1f', plotprobe.axScl) ); 


% Clear axes of previous data, before redisplaying it

ClearAxesData(handles);

plotProbeAndSetProperties(handles);



nDataBlks = plotprobe.dataTreeHandle.currElem.GetDataBlocksNum();

for iBlk=1:nDataBlks

    plotProbeAndSetProperties(handles, iBlk);

end
@@ -400,11 +390,7 @@ set(hEditScl,'string', sprintf('%0.1f %0.1f', plotprobe.axScl) ); 


% Clear axes of previous data, before redisplaying it

ClearAxesData(handles);



nDataBlks = plotprobe.dataTreeHandle.currElem.GetDataBlocksNum();

for iBlk=1:nDataBlks

    plotProbeAndSetProperties(handles, iBlk);

end

plotProbeAndSetProperties(handles);
@@ -418,11 +404,7 @@ set(hEditScl,'string', sprintf('%0.1f %0.1f', plotprobe.axScl) ); 


% Clear axes of previous data, before redisplaying it

ClearAxesData(handles);



nDataBlks = plotprobe.dataTreeHandle.currElem.GetDataBlocksNum();

for iBlk=1:nDataBlks

    plotProbeAndSetProperties(handles, iBlk);

end

plotProbeAndSetProperties(handles);
@@ -434,30 +416,29 @@ hEditScl = handles.editPlotProbeAxScl; 


plotprobe.axScl(1) = plotprobe.axScl(1) + 0.1;

set(hEditScl,'string', sprintf('%0.1f %0.1f', plotprobe.axScl) );

nDataBlks = plotprobe.dataTreeHandle.currElem.GetDataBlocksNum();



% Clear axes of previous data, before redisplaying it

ClearAxesData(handles);

plotProbeAndSetProperties(handles);



for iBlk=1:nDataBlks

    plotProbeAndSetProperties(handles, iBlk);

end







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

function radiobuttonShowTimeMarkers_Callback(hObject, ~, handles)

global plotprobe



data = getappdata(handles.figure, 'data');

plotprobe.tMarkShow = get(hObject,'value');

nDataBlks = plotprobe.dataTreeHandle.currElem.GetDataBlocksNum();

for iBlk = 1:nDataBlks

    for iSD = 1:size(data{iBlk},1)

        k = find(data{iBlk}(iSD,4:end)>0);

        if ~isempty(data{iBlk})

            if plotprobe.tMarkShow

            set(data{iBlk}(:,4:end), 'visible', 'on');    

                set(data{iBlk}(iSD,4+k-1), 'visible', 'on');

            else

            set(data{iBlk}(:,4:end), 'visible', 'off');    

                set(data{iBlk}(iSD,4+k-1), 'visible', 'off');

            end

        end

    end

end
@@ -468,21 +449,14 @@ end 
function editPlotProbeTimeMarkersAmp_Callback(hObject, ~, handles)

global plotprobe



datatype     = plotprobe.datatype;

datatypeVals = plotprobe.datatypeVals;



plotprobe.tMarkAmp = str2num(get(hObject,'string'));

if datatype == datatypeVals.CONC_HRF

if plotprobe.datatype == plotprobe.datatypeVals.CONC_HRF

    plotprobe.tMarkAmp = plotprobe.tMarkAmp/1e6;

end



% Clear axes of previous data, before redisplaying it

ClearAxesData(handles);



nDataBlks = plotprobe.dataTreeHandle.currElem.GetDataBlocksNum();

for iBlk=1:nDataBlks

    plotProbeAndSetProperties(handles, iBlk);

end

plotProbeAndSetProperties(handles);
@@ -505,11 +479,7 @@ set(hObject,'string', sprintf('%0.1f ',plotprobe.tMarkInt) ); 


% Clear axes of previous data, before redisplaying it

ClearAxesData(handles);



nDataBlks = plotprobe.dataTreeHandle.currElem.GetDataBlocksNum();

for iBlk = 1:nDataBlks

    plotProbeAndSetProperties(handles, iBlk);

end

plotProbeAndSetProperties(handles);
@@ -550,10 +520,7 @@ uicontrol('parent',figures(iNew), 'style','text', 'string',hname.String, 'units' 
uipanel('parent',figures(iNew), 'units',hdiv.Units, 'position',hdiv.Position, 'bordertype',hdiv.BorderType);

       

% Display data

nDataBlks = plotprobe.dataTreeHandle.currElem.GetDataBlocksNum();

for iBlk=1:nDataBlks

    plotProbeAndSetProperties(handles, iBlk, length(figures));

end

plotProbeAndSetProperties(handles, length(figures));

rePositionGuiWithinScreen(figures(iNew));
@@ -686,36 +653,16 @@ axes(handles.axes1); 
SetWindowTitle(handles)

SetTextFilename(handles);



condition = plotprobe.condition;

datatype  = plotprobe.datatype;



% Load current element data from file

if plotprobe.dataTreeHandle.currElem.IsEmpty()

    plotprobe.dataTreeHandle.currElem.Load();

end



nDataBlks = plotprobe.dataTreeHandle.currElem.GetDataBlocksNum();

plotprobe.y = cell(nDataBlks,1);

plotprobe.t = cell(nDataBlks,1);



tMarkAmp = str2num(get(handles.editPlotProbeTimeMarkersAmp, 'string'));

for iBlk = 1:nDataBlks

    if datatype == plotprobe.datatypeVals.OD_HRF

        plotprobe.y{iBlk} = plotprobe.dataTreeHandle.currElem.GetDodAvg(condition, iBlk);

        plotprobe.t{iBlk} = plotprobe.dataTreeHandle.currElem.GetTHRF();

        plotprobe.tMarkUnits='(AU)';

    elseif datatype == plotprobe.datatypeVals.CONC_HRF

        plotprobe.y{iBlk} = plotprobe.dataTreeHandle.currElem.GetDcAvg(condition, iBlk);

        plotprobe.t{iBlk} = plotprobe.dataTreeHandle.currElem.GetTHRF();

        plotprobe.tMarkAmp = tMarkAmp/1e6;

        plotprobe.tMarkUnits = '(micro-molars)';

    end

    

% Clear axes of previous data, before redisplaying it

ClearAxesData(handles);

plotProbeAndSetProperties(handles);

figure(handles.figure)

end
@@ -781,9 +728,14 @@ end 
% Set name of current processing element and the length of the text box

% framing it

if ~isempty(CondNames)

    if plotprobe.datatype == plotprobe.datatypeVals.CONC_HRF || ...

       plotprobe.datatype == plotprobe.datatypeVals.OD_HRF

        name = sprintf('   %s,    condition: ''%s''', treeNodeName, CondNames{plotprobe.condition});

    else

    name = sprintf('   %s,    condition:  none', treeNodeName, CondNames{plotprobe.condition});

        name = sprintf('   %s,    condition:  N/A', treeNodeName);

    end

else

    name = sprintf('   %s,    condition:  N/A', treeNodeName);

end

n = length(name) + 0.5*length(name);

set(handles.textFilename, 'units','characters');
@@ -795,7 +747,6 @@ p1 = get(handles.textFilename, 'position'); 
set(handles.textFilenameFrame, 'units','characters');

p2 = get(handles.textFilenameFrame, 'position');

set(handles.textFilenameFrame, 'position',[p2(1), p2(2), p1(3)+(2.5*abs(p1(1)-p2(1))), p2(4)]);

p2 = get(handles.textFilenameFrame, 'position');



% Return to normalized units for textbox

set(handles.textFilename, 'units','normalized');
@@ -836,9 +787,6 @@ end 


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

function radiobuttonShowStd_Callback(~, ~, handles)

global plotprobe

ClearAxesData(handles);

nDataBlks = plotprobe.dataTreeHandle.currElem.GetDataBlocksNum();

for iBlk=1:nDataBlks

    plotProbeAndSetProperties(handles, iBlk);

end
 
plotProbeAndSetProperties(handles);

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