Unverified Commit 31d98b44 authored by jayd1860's avatar jayd1860 Committed by GitHub
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Change TreeNodeClass.Plot method accept source/detector/datatype instead of... 

Change TreeNodeClass.Plot method accept source/detector/datatype instead of single number index  (#151)

v1.64.0

-- Fix DataTree/setpaths not deleting other DataTree repos from path.
-- Change TreeNodeClass.Plot method accept source/detector/datatype instead of single number index vector, and handle multiple plot figures.
-- Reorganize and add documentation for TreeNodeClass plotting methods under separate methods section.
-- Redo LoadRunPlotExample (rename from LoadRunPlotExample1.m and delete LoadRunPlotExample2.m)  to display multiple plot figures.
parent f487f7cc

DataTree/AcquiredData/Snirf/DataClass.m

+5 −3
Original line number Diff line number Diff line
@@ -494,8 +494,10 @@ classdef DataClass < FileLoadSaveClass 
            %                        will follow this order in linear form. That is, the order of ml will index the columns 

            %                        of d squeezed into 2 dimensions d(:,:)

            %       

            %           'matrix'   - dataTimeSeries will not be modified but ml will be returned as a 2D matrix instead of a 

            %                        MeasListClass structure. It's rows will have the same order as the structure elements. 

            %           'matrix'   - This options refers to the measurement list type: if 'matrix' keyword is in the options 

            %                        then ml will be returned as a 2D matrix instead of a MeasListClass object (that is the 

            %                        object representing the measurementList SNIRF field). The rows of the 2d array will have 

            %                        the same order as the original MeasListClass object elements. 

            %       

            %           'datatype' - used in combination with reshape. dataTimeSeries will be reshaped as above but the 

            %                        slowest dimensions to change will be reversed from left-to-right, that is,
@@ -510,7 +512,7 @@ classdef DataClass < FileLoadSaveClass 
            %       %%%% dc is a DataClass object containing concentration data, with 4 sources, 8 detectors, 9 sd pairs, and 3 Hb data types:  hbo, hbr, and hbt. 

            %

            %

            %       % Example 1:  Return OD dataTimeSeries, time and  measurementList unchanged.

            %       % Example 1:  Return OD dataTimeSeries, time and  measurementList (ml) unchanged, that is, as a MeasListClass object instead of Nx4 2D array.

            %       [d, t, ml, order] = dod.GetDataTimeSeries();

            %

            %

DataTree/AcquiredData/Snirf/SnirfClass.m

+13 −2
Original line number Diff line number Diff line
@@ -507,6 +507,11 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
        

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

        function err = LoadProbe(obj, fileobj, ~)

            % metaDataTags is a prerequisite for load probe, so check to make sure its already been loaded

            if isempty(obj.metaDataTags)

                obj.LoadMetaDataTags(fileobj);

            end

                

            % get lenth unit through class method

            LengthUnit = obj.metaDataTags.Get('LengthUnit');

            obj.probe = ProbeClass();
@@ -1070,11 +1075,17 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
            if ~exist('iBlk','var') || isempty(iBlk)

                iBlk = 1;

            end

            freememory = false;

            if isempty(obj.data)

                obj.LoadData(obj.GetFilename());

                freememory = true;

            end

            if iBlk>length(obj.data)

                return;

            end

            for ii = 1:length(iBlk)

                ml = [ml; obj.data(ii).GetMeasurementList(matrixMode)];

            ml = obj.data(iBlk).GetMeasurementList(matrixMode);

            if freememory 

                obj.FreeMemory(obj.GetFilename());

            end

        end

DataTree/Examples/EditStimExample.m

+28 −4
Original line number Diff line number Diff line
@@ -69,21 +69,25 @@ logger = Logger('DataTreeClass'); 
cfg = ConfigFileClass();



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

% 1. Plot raw data for current element for channels 1 and 2

% 1. Plot raw data for current element for channel 2

% 2. Export stim for the current element

% 3. Edit stim in the events TSV file

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

obj = dataTree.currElem;

obj.Load();

obj.Plot('raw',[1,2]);

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

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



obj.ExportStim();



pause(2);



EditEventsTsvFile_InMatlabEditor(obj, dataSetDir);



obj.ReloadStim();

obj.Plot('raw',[1,2]);

obj.ClosePlots();

dataTree.ReloadStim();

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

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





%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -118,3 +122,23 @@ editorTab.makeActive; 
MenuBox('Please edit TSV stim file and save it, then click the ''OK'' button.');









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

function repositionFigures(h,i)

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

    i = 1;

end

k = find(h(1,:)==-1)-1;

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

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

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

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

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

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

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

+168 −0
Original line number Diff line number Diff line 
function LoadRunPlotExample1(dataSetDir)

function LoadRunPlotExample(dataSetDir)



%

%   Syntax:

%       LoadRunPlotExample1(dataSetDir)

%       LoadRunPlotExample(dataSetDir)

%

%   Description:

%       This script does the following:
@@ -22,7 +22,7 @@ function LoadRunPlotExample1(dataSetDir) 
%

%   Examples:

%       cd <local_path>/DataTree

%       LoadRunPlotExample1('./Examples/Example4_twNI')

%       LoadRunPlotExample('./Examples/Example4_twNI')

%
@@ -31,7 +31,7 @@ function LoadRunPlotExample1(dataSetDir) 
% Parse arguments

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

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

    f = which('LoadRunPlotExample1');

    f = which('LoadRunPlotExample');

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

end
@@ -67,44 +67,77 @@ logger = Logger('DataTreeClass'); 




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

% Plot raw data for current element for channels 6 nd 7

% 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();

obj.Plot('raw',[6,7]);

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

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

pause(2);







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

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

% and 1st group for channels 6 nd 7

% and 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();

obj.Plot('raw',[6,7]);

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

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

pause(2);







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

% Run processing stream for current element and plot 

% concentration HRF for channels 2,3 and 4

% 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();

obj.Plot('conc hrf',[2,3,4]);

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

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

pause(2);







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

% Run processing stream for the first group and plot it's

% concentration HRF for channels 2,3 and 4

% 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();

obj.Plot('conc hrf', [2,3,4]);

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

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

pause(2);
@@ -112,4 +145,24 @@ obj.Plot('conc hrf', [2,3,4]); 
% Close open log files

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

obj.logger.Close();

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

obj.ClosePlots('all')









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

function repositionFigures(h,i)

k = find(h(1,:)==-1)-1;

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

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

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

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

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

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

DataTree/Examples/LoadRunPlotExample2.m

deleted100644 → 0
+0 −178
Original line number Diff line number Diff line 
function LoadRunPlotExample2(dataSetDir)



%

%   Syntax:

%       LoadRunPlotExample2(dataSetDir)

%

%   Description:

%       LoadRunPlotExample2 does the exast same thing as it accesses snirf objects directly without any methods 

%       and then plots them directly in the script to show user how snirf objects work. 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

%       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/Eaxmple4_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





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

% This step is NOT essential, but is a good idea in order to

% set up logging. Since we are running data tree standalone 

% initilize logger here which would have been done by parent 

% gui like Homer3 

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

global logger

logger = Logger('DataTreeClass');





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

% Plot raw data for current element for channels 6 nd 7

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

obj = dataTree.currElem;

obj.Load();

t = obj.acquired.data(1).time;

d = obj.acquired.data(1).dataTimeSeries;

id = [obj.iGroup, obj.iSubj, obj.iSess, obj.iRun];

stim = [];

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

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

end

hfig = Plot(t, d, stim, [6,7], obj.GetName(), 'raw', id);

pause(2);







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

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

% and 1st group for channels 6 nd 7

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

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

obj.Load();

t = obj.acquired.data(1).time;

d = obj.acquired.data(1).dataTimeSeries;

stim = [];

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

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

end

hfig = Plot(t, d, stim, [6,7], id, obj.GetName(), 'raw', hfig);

pause(2);







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

% Run processing stream for current element and plot 

% concentration HRF for channels 2,3 and 4

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

obj = dataTree.currElem;

obj.Calc();

t = obj.procStream.output.dcAvg.time;

d = obj.procStream.output.dcAvg.dataTimeSeries;

stim = [];

id = [obj.iGroup, obj.iSubj, obj.iSess, obj.iRun];

hfig = Plot(t, d, stim, [2,3,4], id, obj.GetName(), 'conc hrf', hfig);

pause(2);







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

% Run processing stream for the first group and plot it's

% concentration HRF for channels 2,3 and 4

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

obj = dataTree.groups(1);

obj.Calc();

t = obj.procStream.output.dcAvg.time;

d = obj.procStream.output.dcAvg.dataTimeSeries;

stim = [];

id = [obj.iGroup, obj.iSubj, obj.iSess, obj.iRun];

Plot(t, d, stim, [2,3,4], id, obj.GetName(), 'conc hrf', hfig);







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

% Close open log file

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

obj.logger.Close();









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

function hfig = Plot(t, d, stim, iChs, id, name, datatype, hfig)

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

    hfig = [];

end

if ishandles(hfig)

    close(hfig);

end

hfig = figure;

figname = sprintf('PROCESSING ELEMENT: "%s" (ID = [%s]) ;   DATATYPE: "%s";   CHANNELS: [ %s ]', name, ...

    num2str(id), datatype, num2str(iChs));

namesize = uint32(length(figname)/2);

set(hfig, 'units','characters');

p1 = get(hfig, 'position');

set(hfig, 'name',figname, 'menubar','none', 'NumberTitle','off', 'position',[p1(1)/2, p1(2), p1(3)+namesize, p1(4)]);



% Plot data

plot(t, d(:, iChs));

hAxes = gca;

set(hAxes, 'xlim', [t(1), t(end)]);



% Plot stims

hold on

if ~isempty(stim)

    ylim = get(hAxes, 'ylim');

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

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

    CondColTbl = distinguishable_colors(10);

    for jj = 1:length(stim)

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

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

        end

    end

end

hold off

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