Commit c4fea3e2 authored by jayd1860's avatar jayd1860
Browse files

v1.65.0 

-- Add LoadRunPlotExample2 to DataTree examples. It does exactly same as LoadRunPlotExample1 but more transparently plotting without using TreeNodes.Plot()
parent 1a144a7f

DataTree/AcquiredData/AcqDataClass.m

+4 −25
Original line number Diff line number Diff line
@@ -216,32 +216,11 @@ classdef AcqDataClass < matlab.mixin.Copyable 
        % ---------------------------------------------------------

        function bbox = GetSdgBbox(obj)

            bbox = [];

            

            optpos = [obj.GetSrcPos('2D'); obj.GetDetPos('2D')];

            if isempty(optpos)

                return

            end

            

            xmax = max(optpos(:,1));

            ymax = max(optpos(:,2));



            xmin = min(optpos(:,1));

            ymin = min(optpos(:,2));

            

            width = xmax-xmin;

            height = ymax-ymin;

            

            if width==0

                width = 1;

            end

            if height==0

                height = 1;

            if isa(obj, 'SnirfClass')

                bbox = obj.probe.GetSdgBbox();

            elseif isa(obj, 'NirsClass')

                bbox = obj.SD.GetSdgBbox();

            end

            

            px = width * 0.05; 

            py = height * 0.05; 



            bbox = [xmin-px, xmax+px, ymin-py, ymax+py];

        end

DataTree/AcquiredData/Snirf/ProbeClass.m

+34 −0
Original line number Diff line number Diff line
@@ -523,6 +523,40 @@ classdef ProbeClass < FileLoadSaveClass 
            b = true;

        end

        

        

        

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

        function bbox = GetSdgBbox(obj)

            bbox = [];

            

            optpos = [obj.GetSrcPos('2D'); obj.GetDetPos('2D')];

            if isempty(optpos)

                return

            end

            

            xmax = max(optpos(:,1));

            ymax = max(optpos(:,2));



            xmin = min(optpos(:,1));

            ymin = min(optpos(:,2));

            

            width = xmax-xmin;

            height = ymax-ymin;

            

            if width==0

                width = 1;

            end

            if height==0

                height = 1;

            end

            

            px = width * 0.05; 

            py = height * 0.05; 



            bbox = [xmin-px, xmax+px, ymin-py, ymax+py];

        end

        

        

    end

    

end

DataTree/AcquiredData/Snirf/SnirfClass.m

+2 −1
Original line number Diff line number Diff line
@@ -1284,6 +1284,7 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
        

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

        function probe = GetProbe(obj)

            obj.LoadProbe(obj.GetFilename());

            probe = obj.probe;

        end

DataTree/Examples/LoadRunPlotExample.m→DataTree/Examples/LoadRunPlotExample1.m

+8 −4
Original line number Diff line number Diff line
@@ -78,7 +78,8 @@ logger = Logger('DataTreeClass'); 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

obj = dataTree.currElem;

obj.Load();

h = obj.Plot('raw',[2,3,0,1; 3,5,0,1; 4,6,0,1]);

sdPairsSelect = [2,3,0,1; 3,5,0,1; 4,6,0,1];  % Channels to plot: 2d array where each channel row is [source idx, detector idx, condition idx, datatype idx]

h = obj.Plot('raw', sdPairsSelect);

repositionFigures(h,1);         % Local function to reposition figures so they can be all be seen on screen at once

pause(2);
@@ -96,7 +97,8 @@ pause(2); 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

obj = dataTree.groups(1).subjs(2).sess(1).runs(3);

obj.Load();

h = obj.Plot('raw',[2,3,0,2; 3,5,0,2; 4,6,0,2]);

sdPairsSelect = [2,3,0,2; 3,5,0,2; 4,6,0,2];  % Channels to plot: 2d array where each channel row is [source idx, detector idx, condition idx, datatype idx]

h = obj.Plot('raw', sdPairsSelect);

repositionFigures(h,2);          % Local function to reposition figures so they can be all be seen on screen at once

pause(2);
@@ -116,7 +118,8 @@ pause(2); 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

obj = dataTree.currElem;

obj.Calc();

h = obj.Plot('conc hrf',[2,3,1,2; 3,5,1,2; 4,6,1,2]);

sdPairsSelect = [2,3,1,2; 3,5,1,2; 4,6,1,2];  % Channels to plot: 2d array where each channel row is [source idx, detector idx, condition idx, datatype idx]

h = obj.Plot('conc hrf', sdPairsSelect);

repositionFigures(h,3);         % Local function to reposition figures so they can be all be seen on screen at once

pause(2);
@@ -135,7 +138,8 @@ pause(2); 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

obj = dataTree.groups(1);

obj.Calc();

h = obj.Plot('conc hrf',[3,6,2,3; 4,8,2,3]);

sdPairsSelect = [3,6,2,3; 4,8,2,3];  % Channels to plot: 2d array where each channel row is [source idx, detector idx, condition idx, datatype idx]

h = obj.Plot('conc hrf', sdPairsSelect);

repositionFigures(h,4);         % Local function to reposition figures so they can be all be seen on screen at once

pause(2);

DataTree/Examples/LoadRunPlotExample2.m

0 → 100644
+367 −0
Original line number Diff line number Diff line 
function LoadRunPlotExample2(dataSetDir)



%

%   Syntax:

%       LoadRunPlotExample2(dataSetDir)

%

%   Description:

%       This script does the following:

%

%       1. If starting from scratch, first download the DataTree repo from

%          github

%

%           a) git clone  -b <branch_name>   https://github.com/<username>/DataTree  <local_path>/DataTree

%           b) cd <local_path>/DataTree

%           c) setpaths

%

%       2. Change folder to dataSetDir (1st arg)

%       3. Load data set

%       4. Plot raw data for various dataTree elements

%       5. Run processing stream

%       6. Plot HRF for various dataTree elements

%

%   Examples:

%       cd <local_path>/DataTree

%       LoadRunPlotExample2('./Examples/Example4_twNI')

%



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

% Parse arguments

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

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

    f = which('LoadRunPlotExample2');

    dataSetDir = [fileparts(f), '/Example4_twNI'];

end





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

% a) Change current folder to a data set folder,

% b) Load dataset

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

if ~exist(dataSetDir,'dir')

    mkdir(dataSetDir);

end

cd(dataSetDir)

if exist([dataSetDir, '/derivatives']','dir')

    rmdir([dataSetDir, '/derivatives'], 's')

end

dataTree = DataTreeClass();

if dataTree.IsEmpty()

    MenuBox('No data set was loaded',{'OK'});

    return

end





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

% Plot raw data for current element, for  1st wavelength of 3 source/detector pairs , [2,3], [3,5] and [4,6]:

% (NOTE: for non-HRF, raw, and OD, condition is 0 and datatype refers to wavelength)

%        for non-HRF, concentration, condition is 0 and datatype refers to Hb type)

%

%    ch A:      source idx = 2, detector idx = 3,  condition idx = 0,   datatype idx = 1

%    ch B:      source idx = 3, detector idx = 5,  condition idx = 0,   datatype idx = 1

%    ch C:      source idx = 4, detector idx = 6,  condition idx = 0,   datatype idx = 1

%

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

obj = dataTree.currElem;

obj.Load();



[time, dataTimeSeries, measurementList, stim, probe] = GetAcquiredData(obj);

sdPairsSelect = [2,3,0,1; 3,5,0,1; 4,6,0,1];  % Channels to plot: 2d array where each channel row is [source idx, detector idx, condition idx, datatype idx]

plotname = sprintf('"%s" (%s);   raw data', obj.GetName(), num2str([obj.iGroup, obj.iSubj, obj.iSess, obj.iRun]));

h(1,:) = Plot(time, dataTimeSeries, measurementList, stim, probe, sdPairsSelect, plotname);

repositionFigures(h);

pause(2);





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

% Plot raw data for 3rd run of the 1st session, 3rd subject, 1st group,  

% for 2nd wavelength of 3 source/detector pairs, [2,3], [3,5] and [4,6]:

% (NOTE: for non-HRF, raw, and OD, condition is 0 and datatype refers to wavelength)

%        for non-HRF, concentration, condition is 0 and datatype refers to Hb type)

%

%    ch A:      source idx = 2, detector idx = 3,  condition idx = 0,   datatype idx = 2

%    ch B:      source idx = 3, detector idx = 5,  condition idx = 0,   datatype idx = 2

%    ch C:      source idx = 4, detector idx = 6,  condition idx = 0,   datatype idx = 2

%

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

obj = dataTree.groups(1).subjs(2).sess(1).runs(3);

obj.Load();



[time, dataTimeSeries, measurementList, stim, probe] = GetAcquiredData(obj);

sdPairsSelect = [2,3,0,2; 3,5,0,2; 4,6,0,2];  % Channels to plot: 2d array where each channel row is [source idx, detector idx, condition idx, datatype idx]

plotname = sprintf('"%s" (%s);   raw data', obj.GetName(), num2str([obj.iGroup, obj.iSubj, obj.iSess, obj.iRun]));

h(2,:) = Plot(time, dataTimeSeries, measurementList, stim, probe, sdPairsSelect, plotname);

repositionFigures(h);

pause(2);





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

% Run processing stream for current element and plot concentration HRF for HbR of condition 1,

% for 3 channels with source/detector pairs, [2,3], [3,5] and [4,6]:

%

% (NOTE: for HRF data OD, condition is > 0 and datatype refers to wavelength)

%        for HRF data concentration, condition is > 0 and datatype refers to Hb type)

%

%    ch A:      source idx = 2, detector idx = 3,  condition idx = 1,   datatype idx = 2

%    ch B:      source idx = 3, detector idx = 5,  condition idx = 1,   datatype idx = 2

%    ch C:      source idx = 4, detector idx = 6,  condition idx = 1,   datatype idx = 2

%

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

obj = dataTree.currElem;

obj.Calc();



[time, dataTimeSeries, measurementList, stim, probe] = GetDerivedData(obj, 'conc hrf');

sdPairsSelect = [2,3,1,2; 3,5,1,2; 4,6,1,2];  % Channels to plot: 2d array where each channel row is [source idx, detector idx, condition idx, datatype idx]

plotname = sprintf('"%s" (%s);   conc hrf', obj.GetName(), num2str([obj.iGroup, obj.iSubj, obj.iSess, obj.iRun]));

h(3,:) = Plot(time, dataTimeSeries, measurementList, stim, probe, sdPairsSelect, plotname);

repositionFigures(h);

pause(2);





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

% Run processing stream for group 1 and plot concentration HRF for HbT of condition 2,

% for 2 channels with source/detector pairs, [3,6] and [4,8]:

%

% (NOTE: for HRF data OD, condition is > 0 and datatype refers to wavelength)

%        for HRF data concentration, condition is > 0 and datatype refers to Hb type)

%

%    ch A:      source idx = 3, detector idx = 6,  condition idx = 2,   datatype idx = 3

%    ch B:      source idx = 4, detector idx = 8,  condition idx = 2,   datatype idx = 3

%

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

obj = dataTree.groups(1);

obj.Calc();



[time, dataTimeSeries, measurementList, stim, probe] = GetDerivedData(obj, 'conc hrf');

sdPairsSelect = [3,6,2,3; 4,8,2,3];     % Channels to plot: 2d array where each channel row is [source idx, detector idx, condition idx, datatype idx]

plotname = sprintf('"%s" (%s);   conc hrf', obj.GetName(), num2str([obj.iGroup, obj.iSubj, obj.iSess, obj.iRun]));

h(4,:) = Plot(time, dataTimeSeries, measurementList, stim, probe, sdPairsSelect, plotname);

repositionFigures(h);

pause(2);





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

% Close open log files

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

obj.logger.Close();

MenuBox('When done, click okay button to close all plots','OK');

for ii = 1:length(h(:))

    if ishandles(h(ii))

        close(h(ii))

    end

end







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

function [time, dataTimeSeries, measurementList, stim, probe] = GetAcquiredData(obj)

snirfObj = obj.acquired;



time            = snirfObj.data(1).time;

dataTimeSeries  = snirfObj.data(1).dataTimeSeries;

measurementList = snirfObj.data(1).measurementList;

stim            = snirfObj.stim;

probe           = snirfObj.probe;







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

function [time, dataTimeSeries, measurementList, stim, probe] = GetDerivedData(obj, datatype)



% Get probe and stim from derived input 

probe  = obj.GetProbe();

if ~isempty(obj.procStream.input.acquired)

    stim   = obj.procStream.input.acquired.stim;

else

    stim = [];

end



% Get data from derived output 

switch(lower(datatype))

    case 'od'

        data       = obj.procStream.output.dod;

    case 'conc'

        data       = obj.procStream.output.dod;

    case 'od hrf'

        data       = obj.procStream.output.dodAvg;

    case 'conc hrf'

        data       = obj.procStream.output.dcAvg;

end

time            = data(1).time;

dataTimeSeries  = data(1).dataTimeSeries;

measurementList = data(1).measurementList;







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

function hFig = Plot(time, dataTimeSeries, measurementList, stim, probe, sdPairs, plotname)

if isempty(dataTimeSeries)

    fprintf('No data to plot\n');

    return;

end



ml = ConvertMeasurementListToMatrix(measurementList);



% Convert channels specified by SD pairs to single number vector containing channel indices into the measurement list

iChs = [];

for kk = 1:size(sdPairs,1)

    ii = find( (ml(:,1)==sdPairs(kk,1)) & (ml(:,2)==sdPairs(kk,2)) & (ml(:,3)==sdPairs(kk,3)) & (ml(:,4)==sdPairs(kk,4)));

    if isempty(ii)

        continue;

    end

    iChs = [iChs; ii];

end



% Create figure for plotting

plotname = sprintf('%s ;  channels idxs: [%s]', plotname, num2str(iChs'));

hFig(1) = figure('menubar','none', 'NumberTitle','off', 'name',plotname);

hAxes = gca;





% Plot data

hold on

chSelect = [];

for ii = 1:length(iChs)

    hdata(ii) = plot(hAxes, time, dataTimeSeries(:,iChs(ii)), 'linewidth',2);

    chSelect(ii,:) = [ml(iChs(ii),1), ml(iChs(ii),2), ml(iChs(ii),3), ml(iChs(ii),4), get(hdata(ii), 'color')];

end

set(hAxes, 'xlim', [time(1), time(end)]);



% Plot stim

if ~isempty(stim)

    CondNames = {};

    hCond = [];

    iCond = [];

    kk = 1;    

    ylim = get(hAxes, 'ylim');

    d = (1e-4)*(ylim(2)-ylim(1));

    yrange = [ylim(1)+d, ylim(2)-d];

    stimColorsTable = [1.0,0.0,0.0; 0.0,1.0,0.0; 0.0,0.0,1.0; 1.0,1.0,0.0; 1.0,0.0,1.0; 0.0,1.0,1.0; 1.0,0.5,0.0; 1.0,0.0,0.5; 0.5,1.0,0.0; 0.5,0.0,1.0];

    for jj = 1:length(stim)

        h = [];

        for ii = 1:size(stim(jj).data,1)

            if isempty(stim(jj).data)

                continue

            end

            h = plot(hAxes, stim(jj).data(ii,1)*[1,1], yrange, 'color',stimColorsTable(jj,:));

        end

        CondNames{jj} = stim(jj).name;

        if ~isempty(h)

            hCond(kk) = h;

            iCond(kk) = jj;

            kk = kk+1;

        end

    end

    if ishandles(hCond)

        legend(hAxes, hCond, CondNames(iCond));

    end

end



% Display probe in separate figure

if isempty(chSelect)

    fprintf('ERROR: no valid channels were selelcted');

    hFig(2) = DisplayProbe(probe, sdPairs);

else

    hFig(2) = DisplayProbe(probe, chSelect(:,1:2), chSelect(:,5:7), ml, plotname);

end



% Wrap up before exiting

drawnow;

pause(.1);

hold off







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

function hFig = DisplayProbe(probe, chSelect, chSelectColors, ml, plotname)

% Parse args

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

    chSelect = [];

end

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

    chSelectColors = repmat([1.0, 0.5, 0.2], size(chSelect,1),1);

end



% Set up the axes

bbox = probe.GetSdgBbox();

    

% See if there's a data plot associated with this probe display

% If there is get its name and use it to name this figure

hFig = figure('menubar','none', 'NumberTitle','off', 'name',plotname);

hAxes = gca;



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

gridsize = get(hAxes, {'xlim', 'ylim', 'zlim'});

if ismac() || islinux()

    fs = 18;

else

    fs = 11;

end



% Get probe paramaters

srcpos = probe.sourcePos2D;

detpos = probe.detectorPos2D;

lstSDPairs = find(ml(:,4)==1);



% Draw all channels

for ii = 1:length(lstSDPairs)

    hCh(ii) = line2(srcpos(ml(lstSDPairs(ii),1),:), detpos(ml(lstSDPairs(ii),2),:), [], gridsize, hAxes);

    col = [1.00 1.00 1.00] * 0.85;

    if ~isempty(chSelect)

        k = find(chSelect(:,1)==ml(lstSDPairs(ii),1) & chSelect(:,2)==ml(lstSDPairs(ii),2));

        if ~isempty(k)

            col = chSelectColors(k(1),:);

        end

    end

    set(hCh(ii), 'color',col, 'linewidth',2, 'linestyle','-', 'userdata',ml(lstSDPairs(ii),1:2));

end



% ADD SOURCE AND DETECTOR LABELS

for iSrc = 1:size(srcpos,1)

    if ~isempty(find(ml(:,1)==iSrc)) %#ok<*EFIND>

        hSD(iSrc) = text( srcpos(iSrc,1), srcpos(iSrc,2), sprintf('%d', iSrc), 'fontsize',fs, 'fontweight','bold', 'color','r' );

        set(hSD(iSrc), 'horizontalalignment','center', 'edgecolor','none', 'Clipping', 'on');

    end

end

for iDet = 1:size(detpos,1)

    if ~isempty(find(ml(:,2)==iDet))

        hSD(iDet+iSrc) = text( detpos(iDet,1), detpos(iDet,2), sprintf('%d', iDet), 'fontsize',fs, 'fontweight','bold', 'color','b' );

        set(hSD(iDet+iSrc), 'horizontalalignment','center', 'edgecolor','none', 'Clipping', 'on');

    end

end







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

function ml = ConvertMeasurementListToMatrix(measurementList)

ml = zeros(length(measurementList),4);

hbTypes = {'hbo','hbr','hbt'};

for ii = 1:length(measurementList)

    k = 0;

    for jj = 1:length(hbTypes)

        if ~isempty(strfind(lower(measurementList(ii).dataTypeLabel), hbTypes{jj}))

            k = jj;

            break;

        end

    end

    if measurementList(ii).wavelengthIndex > 0

        ml(ii,:) = [measurementList(ii).sourceIndex, measurementList(ii).detectorIndex, measurementList(ii).dataTypeIndex, measurementList(ii).wavelengthIndex];

    elseif k > 0

        ml(ii,:) = [measurementList(ii).sourceIndex, measurementList(ii).detectorIndex, measurementList(ii).dataTypeIndex, k];

    end

end







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

function repositionFigures(h)

n = size(h,1);

set(h(n,1), 'units','normalized')

set(h(n,2), 'units','normalized')

p1 = get(h(n,1), 'position');

p2 = get(h(n,2), 'position');

set(h(n,1), 'position',[p1(1)-(p1(1)/2),  1.0-(p1(4)+n/10),  p1(3),  p1(4)])

set(h(n,2), 'position',[p2(1)+(p2(1)/2),  1.0-(p2(4)+n/10),  p2(3),  p2(4)])

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