Commit 043e67d6 authored by jayd1860's avatar jayd1860
Browse files

v1.20.4 

-- Update SnirfClass to match latest changes to SNIRF spec: sourcePos changed to sourcePos2D, detectorPos to detector2D, and a method to write/read HDF5 strings fields like sourceLabels/detectorLabels
parent ccc39212

DataTree/AcquiredData/DataFiles/Hdf5/HDF5_WriteStrings.m

0 → 100644
+33 −0
Original line number Diff line number Diff line 
function HDF5_WriteStrings(fname, location, data)



if ~exist(fname, 'file')

    fid = H5F.create(fname, 'H5F_ACC_TRUNC', 'H5P_DEFAULT', 'H5P_DEFAULT');

else

    fid = H5F.open(fname,'H5F_ACC_RDWR','H5P_DEFAULT');

end

data = cell2str_new(data);



filetype = H5T.copy('H5T_FORTRAN_S1'); 

H5T.set_size(filetype, size(data,2)); 

memtype = H5T.copy('H5T_C_S1'); 

H5T.set_size(memtype, size(data,2)); 



% Create dataspace. Setting maximum size to [] sets the maximum 

% size to be the current size. 

space = H5S.create_simple(1, size(data,1), []); 



% Create the dataset and write the string data to it. 

dset = H5D.create(fid, location, filetype, space, 'H5P_DEFAULT'); 



% Transpose the data to match the layout in the H5 file to match C 

% generated H5 file. 

H5D.write(dset, memtype, 'H5S_ALL', 'H5S_ALL', 'H5P_DEFAULT',  data'); 



% Close and release resources. 

H5D.close(dset); 

H5S.close(space); 

H5T.close(filetype); 

H5T.close(memtype); 

H5F.close(fid);

DataTree/AcquiredData/DataFiles/Hdf5/hdf5write_safe.m

+23 −21
Original line number Diff line number Diff line
@@ -8,8 +8,10 @@ if ~exist('options','var') 
    options = '';

end



if iscell(val)

    HDF5_WriteStrings(fname, name, val)

else

    val = HDF5_Transpose(val, options);



    try

        if ~isempty(findstr('rw', options))

            try
@@ -30,5 +32,5 @@ try 
    catch

        return;

    end



end

err = 0;
 
 No newline at end of file

DataTree/AcquiredData/Snirf/ProbeClass.m

+14 −14
Original line number Diff line number Diff line
@@ -3,8 +3,8 @@ classdef ProbeClass < FileLoadSaveClass 
    properties

        wavelengths

        wavelengthsEmission

        sourcePos

        detectorPos

        sourcePos2D

        detectorPos2D

        frequency

        timeDelay

        timeDelayWidth
@@ -29,8 +29,8 @@ classdef ProbeClass < FileLoadSaveClass 
                    SD = varargin{1};

                    obj.wavelengths = SD.Lambda;

                    obj.wavelengthsEmission  = [];

                    obj.sourcePos  = SD.SrcPos;

                    obj.detectorPos  = SD.DetPos;

                    obj.sourcePos2D  = SD.SrcPos;

                    obj.detectorPos2D  = SD.DetPos;

                    obj.frequency  = 1;

                    obj.timeDelay  = 0;

                    obj.timeDelayWidth  = 0;
@@ -50,8 +50,8 @@ classdef ProbeClass < FileLoadSaveClass 
            else

                obj.wavelengths          = [];

                obj.wavelengthsEmission  = [];

                obj.sourcePos  = [];

                obj.detectorPos  = [];

                obj.sourcePos2D  = [];

                obj.detectorPos2D  = [];

                obj.frequency  = 1;

                obj.timeDelay  = 0;

                obj.timeDelayWidth  = 0;
@@ -99,8 +99,8 @@ classdef ProbeClass < FileLoadSaveClass 
                % Load datasets

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

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

                obj.sourcePos                 = HDF5_DatasetLoad(gid, 'sourcePos', [], '2D');

                obj.detectorPos               = HDF5_DatasetLoad(gid, 'detectorPos', [], '2D');

                obj.sourcePos2D                 = HDF5_DatasetLoad(gid, 'sourcePos2D', [], '2D');

                obj.detectorPos2D               = HDF5_DatasetLoad(gid, 'detectorPos2D', [], '2D');

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

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

                obj.timeDelayWidth            = HDF5_DatasetLoad(gid, 'timeDelayWidth');
@@ -139,8 +139,8 @@ classdef ProbeClass < FileLoadSaveClass 
            end     

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

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

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

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

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

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

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

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

            hdf5write_safe(fileobj, [location, '/timeDelayWidth'], obj.timeDelayWidth);
@@ -162,13 +162,13 @@ classdef ProbeClass < FileLoadSaveClass 
        

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

        function srcpos = GetSrcPos(obj)

            srcpos = obj.sourcePos;

            srcpos = obj.sourcePos2D;

        end

        

        

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

        function detpos = GetDetPos(obj)

            detpos = obj.detectorPos;

            detpos = obj.detectorPos2D;

        end
@@ -181,10 +181,10 @@ classdef ProbeClass < FileLoadSaveClass 
            if ~all(obj.wavelengthsEmission(:)==obj2.wavelengthsEmission(:))

                return;

            end

            if ~all(obj.sourcePos(:)==obj2.sourcePos(:))

            if ~all(obj.sourcePos2D(:)==obj2.sourcePos2D(:))

                return;

            end

            if ~all(obj.detectorPos(:)==obj2.detectorPos(:))

            if ~all(obj.detectorPos2D(:)==obj2.detectorPos2D(:))

                return;

            end

            if ~all(obj.frequency(:)==obj2.frequency(:))

DataTree/AcquiredData/Snirf/SnirfClass.m

+1 −0
Original line number Diff line number Diff line
@@ -450,6 +450,7 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
            

            % Save aux

            obj.SaveAux(fileobj);            



        end

DataTree/AcquiredData/Snirf/SnirfClass.py

+10 −9
Original line number Diff line number Diff line
@@ -68,8 +68,8 @@ class ProbeClass(ErrorClass): 


        self.wavelengths          = np.array(fid.get(location + '/wavelengths'))

        self.wavelengthsEmission  = fid.get(location + '/wavelengthsEmission')

        self.sourcePos  = np.array(fid.get(location + '/sourcePos'))

        self.detectorPos  = np.array(fid.get(location + '/detectorPos'))

        self.sourcePos2D  = np.array(fid.get(location + '/sourcePos2D'))

        self.detectorPos2D  = np.array(fid.get(location + '/detectorPos2D'))

        self.frequency  = np.array(fid.get(location + '/frequency'))

        self.timeDelay  = 0

        self.timeDelayWidth  = 0
@@ -86,12 +86,12 @@ class ProbeClass(ErrorClass): 
    def Print(self):

        sys.stdout.write('  wavelengths = %s\n'% self.wavelengths)

        sys.stdout.write('  wavelengthsEmission = %s\n'% self.wavelengthsEmission)

        sys.stdout.write('  sourcePos:\n')

        for ii in range(0, self.sourcePos.shape[0]):

            sys.stdout.write('      %s\n'% self.sourcePos[ii])

        sys.stdout.write('  detectorPos:\n')

        for ii in range(0, self.detectorPos.shape[0]):

            sys.stdout.write('      %s\n'% self.detectorPos[ii])

        sys.stdout.write('  sourcePos2D:\n')

        for ii in range(0, self.sourcePos2D.shape[0]):

            sys.stdout.write('      %s\n'% self.sourcePos2D[ii])

        sys.stdout.write('  detectorPos2D:\n')

        for ii in range(0, self.detectorPos2D.shape[0]):

            sys.stdout.write('      %s\n'% self.detectorPos2D[ii])

        sys.stdout.write('  frequency = %s\n'% self.frequency)

        sys.stdout.write('  timeDelay = %s\n'% self.timeDelay)

        sys.stdout.write('  timeDelayWidth = %s\n'% self.timeDelayWidth)
@@ -218,7 +218,8 @@ if __name__ == "__main__": 
    if len(sys.argv) > 1:

        filenames[0] =  sys.argv[1]

    else:

        filenames = glob.glob('./Examples/*.snirf')

        filenames = glob.glob('../../../../snirf-samples/basic/*.snirf')

        # filenames = glob.glob('./Examples/*.snirf')



    for ii in range(0, len(filenames)):

        sys.stdout.write('======================================================================\n')

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