Commit c4126bb7 authored by jayd1860's avatar jayd1860
Browse files

v1.34.1 

-- Fix Stim saving not working properly because of HDF5's not allowing to overwrite string data. Instead of saving only stim, have to save whole file.
-- Add LoadTime method to DataTree to fix bug related to incorrectly displaying active conditions in MainGUI (to reproduce have first run in subject not have all conditions while the rest of the runs have all conditions and for condition that first runs doesn't have the subject display of conditions in MainGUI will also think the condition is not active when selecting it in the listbox even though other runs have that condition so on the subject level it should be active).
parent 1f599d14

DataTree/AcquiredData/Nirs/NirsClass.m

+7 −0
Original line number Diff line number Diff line
@@ -185,6 +185,13 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass 
        

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

        function err = LoadTime(obj, fdata, err)

            if nargin == 1

                fdata.t = load(obj.GetFilename(),'-mat', 't');

                err = 0;

            elseif nargin == 2

                err = 0;                

            end

            

            if isproperty(fdata,'t')

                obj.t = fdata.t;

                if ~isempty(obj.t)

DataTree/AcquiredData/Snirf/DataClass.m

+56 −1
Original line number Diff line number Diff line
@@ -164,6 +164,50 @@ classdef DataClass < FileLoadSaveClass 
        end

        

        

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

        function err = LoadTime(obj, fileobj, location)

            err = 0;

                       

            % Arg 1

            if ~exist('fileobj','var') || (ischar(fileobj) && ~exist(fileobj,'file'))

                fileobj = '';

            end

                      

            % Arg 2

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

                location = '/nirs/data1';

            elseif location(1)~='/'

                location = ['/',location];

            end

                      

            % Error checking            

            if ~isempty(fileobj) && ischar(fileobj)

                obj.SetFilename(fileobj);

            elseif isempty(fileobj)

                fileobj = obj.GetFilename();

            end

            if isempty(fileobj)

               err = -1;

               return;

            end

            

            

            try

                % Open group

                [gid, fid] = HDF5_GroupOpen(fileobj, location);

                

                obj.time = HDF5_DatasetLoad(gid, 'time');

                                   

                % Close group

                HDF5_GroupClose(fileobj, gid, fid);

            catch ME

                err = -1;

            end

            

            err = ErrorCheck(obj, err, {'time'});

        end

        

        

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

        function SaveHdf5(obj, fileobj, location)

            if ~exist('fileobj', 'var') || isempty(fileobj)
@@ -207,7 +251,11 @@ classdef DataClass < FileLoadSaveClass 
        

        

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

        function err = ErrorCheck(obj, err)

        function err = ErrorCheck(obj, err, params)

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

                params = propnames(obj);

            end

            if ismember('dataTimeSeries',params)

            if obj.IsEmpty()

                err = -1;

            end
@@ -218,6 +266,12 @@ classdef DataClass < FileLoadSaveClass 
                err = -1;

            end

        end

            if ismember('time',params)

                if isempty(obj.time)

                    err = -1;

                end

            end

        end

        

    end
@@ -302,6 +356,7 @@ classdef DataClass < FileLoadSaveClass 
        

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

        function t = GetTime(obj)

            

            t = obj.time;

        end

DataTree/AcquiredData/Snirf/ProbeClass.m

+4 −8
Original line number Diff line number Diff line
@@ -227,15 +227,11 @@ classdef ProbeClass < FileLoadSaveClass 
            end     

            hdf5write_safe(fileobj, [location, '/wavelengths'], obj.wavelengths);

            hdf5write_safe(fileobj, [location, '/wavelengthsEmission'], obj.wavelengthsEmission);

            if ~isempty(obj.sourcePos2D)

            hdf5write_safe(fileobj, [location, '/sourcePos2D'], obj.sourcePos2D(:,1:2), 'rw:2D');

            hdf5write_safe(fileobj, [location, '/detectorPos2D'], obj.detectorPos2D(:,1:2), 'rw:2D');

            end

            hdf5write_safe(fileobj, [location, '/landmarkPos2D'], obj.landmarkPos2D, 'rw:2D');

            if ~isempty(obj.sourcePos3D)

            hdf5write_safe(fileobj, [location, '/sourcePos3D'], obj.sourcePos3D, 'rw:3D');

            hdf5write_safe(fileobj, [location, '/detectorPos3D'], obj.detectorPos3D, 'rw:3D');

            end

            hdf5write_safe(fileobj, [location, '/landmarkPos3D'], obj.landmarkPos3D, 'rw:3D');

            hdf5write_safe(fileobj, [location, '/frequencies'], obj.frequencies);

            hdf5write_safe(fileobj, [location, '/timeDelays'], obj.timeDelays);

DataTree/AcquiredData/Snirf/SnirfClass.m

+13 −3
Original line number Diff line number Diff line
@@ -387,6 +387,17 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
        

        

        

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

        function err = LoadTime(obj)

            err = 0;

            if isempty(obj.data)

                obj.data = DataClass();

                err = obj.data.LoadTime(obj.GetFilename(), [obj.location, '/data1']);

            end

        end

        

        

        

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

        function err = LoadData(obj, fileobj)

            err = 0;
@@ -671,8 +682,7 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
            flags = zeros(length(obj.stim), 1);

            

            % Load stim from file and update it

            snirfFile = SnirfClass();

            snirfFile.LoadStim(fileobj);

            snirfFile = SnirfClass(fileobj);

            

            % Update stims from file with edited stims

            for ii = 1:length(obj.stim)
@@ -697,7 +707,7 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
            % If stims were edited then update snirf file with new stims

            changes = sum(flags);

            if changes > 0

                snirfFile.SaveStim(fileobj);

                snirfFile.Save();

            end

            stimFromFile = snirfFile.stim;

        end

DataTree/GroupClass.m

+6 −2
Original line number Diff line number Diff line
@@ -768,7 +768,7 @@ classdef GroupClass < TreeNodeClass 
            

            % Create ExportTable initialized with the filled in 2D TableCell array. 

            % ExportTable object is what actually does the exporting to a file. 

            ExportTable(obj.name, 'HRF mean', tblcells);

            ExportTable([obj.path, obj.outputDirname, obj.name], 'HRF mean', tblcells);

        end
@@ -1061,7 +1061,11 @@ classdef GroupClass < TreeNodeClass 
        % ----------------------------------------------------------------------------------

        function BackwardCompatability(obj)

            if ispathvalid([obj.path, 'groupResults.mat'])

                try

                    g = load([obj.path, 'groupResults.mat']);

                catch ME

                    g = [];

                end

                

                % Do not try to restore old data older than Homer3

                if isempty(g)

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