Commit 694d1b6f authored by jayd1860's avatar jayd1860
Browse files

v1.20.4 

-- Change current supported snirf version to 1.1. This is NOT OFFICIAL yet. This is what I'm advocating needs to happen because we are changing SNIRF format.
-- Add forward compatibility for snirf in ProbeClass. New snirf tentatively version 1.1, sourcePos2D and detectorPos2D have 2 columns but we convert to 3 columns to be compatible with Homer3 application
-- Change GroupClass version to 1.1 to account for the change in acquisition layer changes (Snirf format changed)
-- Update python application SnirfClass.py and add AuxClass
parent 043e67d6

DataTree/AcquiredData/Snirf/ProbeClass.m

+26 −9
Original line number Diff line number Diff line
@@ -5,7 +5,7 @@ classdef ProbeClass < FileLoadSaveClass 
        wavelengthsEmission

        sourcePos2D

        detectorPos2D

        frequency

        frequencies

        timeDelay

        timeDelayWidth

        momentOrder
@@ -31,7 +31,7 @@ classdef ProbeClass < FileLoadSaveClass 
                    obj.wavelengthsEmission  = [];

                    obj.sourcePos2D  = SD.SrcPos;

                    obj.detectorPos2D  = SD.DetPos;

                    obj.frequency  = 1;

                    obj.frequencies  = 1;

                    obj.timeDelay  = 0;

                    obj.timeDelayWidth  = 0;

                    obj.momentOrder = [];
@@ -52,7 +52,7 @@ classdef ProbeClass < FileLoadSaveClass 
                obj.wavelengthsEmission  = [];

                obj.sourcePos2D  = [];

                obj.detectorPos2D  = [];

                obj.frequency  = 1;

                obj.frequencies  = 1;

                obj.timeDelay  = 0;

                obj.timeDelayWidth  = 0;

                obj.momentOrder = [];
@@ -65,6 +65,18 @@ classdef ProbeClass < FileLoadSaveClass 


        

        

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

        function ForwardCompatibility(obj)

            if size(obj.sourcePos2D,2)<3

                obj.sourcePos2D       = [obj.sourcePos2D, zeros(size(obj.sourcePos2D,1), 1)];

            end

            if size(obj.detectorPos2D,2)<3

                obj.detectorPos2D     = [obj.detectorPos2D, zeros(size(obj.detectorPos2D,1), 1)];

            end

        end



        

        

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

        function err = LoadHdf5(obj, fileobj, location)

            err = 0;
@@ -101,13 +113,13 @@ classdef ProbeClass < FileLoadSaveClass 
                obj.wavelengthsEmission       = HDF5_DatasetLoad(gid, 'wavelengthsEmission');

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

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

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

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

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

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

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

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

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

                obj.sourceLabels              = HDF5_DatasetLoad(gid, 'sourceLabels', obj.sourceLabels); %#ok<*PROPLC>

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

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

                                

                % Close group
@@ -116,6 +128,11 @@ classdef ProbeClass < FileLoadSaveClass 
                err=-1;

                return;

            end

            

            % Call method to change future current and future versions of

            % SNIRF data to Homer3 compatible structure

            obj.ForwardCompatibility();

            

        end
@@ -139,9 +156,9 @@ classdef ProbeClass < FileLoadSaveClass 
            end     

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

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

            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, '/sourcePos2D'], obj.sourcePos2D(:,1:2), 'rw:2D');

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

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

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

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

            hdf5write_safe(fileobj, [location, '/momentOrder'], obj.momentOrder);
@@ -187,7 +204,7 @@ classdef ProbeClass < FileLoadSaveClass 
            if ~all(obj.detectorPos2D(:)==obj2.detectorPos2D(:))

                return;

            end

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

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

                return;

            end

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

DataTree/AcquiredData/Snirf/SnirfClass.m

+11 −4
Original line number Diff line number Diff line
@@ -64,7 +64,7 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
            %

             

            % Initialize properties from SNIRF spec 

            obj.formatVersion = '1.0';

            obj.formatVersion = '1.1';

            obj.metaDataTags   = MetaDataTagsClass().empty();

            obj.data           = DataClass().empty();

            obj.stim           = StimClass().empty();
@@ -344,7 +344,14 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
                [obj.gid, obj.fid] = HDF5_GroupOpen(fileobj, '/');

                

                %%%% Load formatVersion

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

                formatVersionFile = HDF5_DatasetLoad(obj.gid, 'formatVersion'); %#ok<*PROPLC>

                formatVersionFile = str2double(formatVersionFile);

                formatVersionCurr = str2double(obj.formatVersion); 

                if formatVersionFile < formatVersionCurr

                    fprintf('Warning: Current SNIRF version is %0.1f. Cannot load older version (%0.1f) file. Backward compatibility not yet implemented ...\n', formatVersionCurr, formatVersionFile)

                    err = -2;

                    return 

                end

            

                %%%% Load metaDataTags

                obj.LoadMetaDataTags(obj.fid);
@@ -432,7 +439,7 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
            

            % Save formatVersion

            if isempty(obj.formatVersion)

                obj.formatVersion = '1.10';

                obj.formatVersion = '1.1';

            end

            hdf5write_safe(fileobj, '/formatVersion', obj.formatVersion);

DataTree/AcquiredData/Snirf/SnirfClass.py

+56 −8
Original line number Diff line number Diff line
@@ -11,6 +11,19 @@ sys.path.append(rootpath) 
from DataFiles.Hdf5.hdf5lib import h5getstr





# ---------------------------------------------------------------------------

def PrintArraySize(v, vname):

    if len(v.shape)==1:

        nrows = v.shape[0]

        ncols = 1

    elif len(v.shape)==2:

        nrows = v.shape[0]

        ncols = v.shape[1]

    sys.stdout.write('%s = [%d x %d]\n'% (vname, nrows, ncols))









############################################################

class ErrorClass:

    # -----------------------------------------------------------
@@ -55,9 +68,8 @@ class DataClass(ErrorClass): 


    # -----------------------------------------------------------

    def Print(self):

        sys.stdout.write('  dataTimeSeries = [%d x %d]\n'% (self.dataTimeSeries.shape[0], self.dataTimeSeries.shape[1]))

        sys.stdout.write('  time = %d\n'% self.time.shape[0])



        PrintArraySize(self.dataTimeSeries, '  dataTimeSeries')

        PrintArraySize(self.time, '  time')





############################################################
@@ -70,14 +82,14 @@ class ProbeClass(ErrorClass): 
        self.wavelengthsEmission  = fid.get(location + '/wavelengthsEmission')

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

        self.timeDelay  = 0

        self.timeDelayWidth  = 0

        self.momentOrder = []

        self.correlationTimeDelay = 0

        self.correlationTimeDelayWidth = 0

        self.sourceLabels = h5getstr(fid, location + '/sourceLabels')

        self.detectorLabels = h5getstr(fid, location + '/detectorLabels')

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

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



        ErrorClass.__init__(self)
@@ -92,7 +104,7 @@ class ProbeClass(ErrorClass): 
        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('  frequencies = %s\n'% self.frequencies)

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

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

        sys.stdout.write('  momentOrder = %s\n'% self.momentOrder)
@@ -130,6 +142,31 @@ class StimClass(ErrorClass): 






###########################################################

class AuxClass(ErrorClass):



    # -----------------------------------------------------------

    def __init__(self, fid, location):

        self.name  = h5getstr(fid, location + '/name')

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

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

        ErrorClass.__init__(self)



    # -----------------------------------------------------------

    def Print(self):

        sys.stdout.write('  name: %s\n'% self.name)

        PrintArraySize(self.dataTimeSeries, '  dataTimeSeries')

        PrintArraySize(self.time, '  time')



    # -----------------------------------------------------------

    def IsEmpty(self):

        if ((self.time.all()==None) or (len(self.time)==0)) and \

            ((self.dataTimeSeries.all()==None) or (len(self.dataTimeSeries)==0)):

            return True

        return False







############################################################

class MetaDataTagsClass(ErrorClass):
@@ -189,6 +226,13 @@ class SnirfClass(ErrorClass): 


        # aux

        self.aux = []

        ii = 1

        while 1:

            temp = AuxClass(fid, '/nirs/aux' + str(ii))

            if temp.GetError() < 0:

                break

            self.aux.append(temp)

            ii = ii+1



        fid.close()
@@ -212,6 +256,10 @@ class SnirfClass(ErrorClass): 
        sys.stdout.write('probe:\n')

        self.probe.Print()



        for ii in range(0, len(self.aux)):

            sys.stdout.write('aux[%d]:\n'% ii)

            self.aux[ii].Print()





# -----------------------------------------------------------

if __name__ == "__main__":
@@ -223,7 +271,7 @@ if __name__ == "__main__": 


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

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

        sys.stdout.write('Loading data from %s\n'% filenames[ii])

        sys.stdout.write('Loading data from %s\n\n'% filenames[ii])

        snirf = SnirfClass(filenames[ii])

        snirf.Print()

        sys.stdout.write('\n')

DataTree/GroupClass.m

+5 −1
Original line number Diff line number Diff line
@@ -73,9 +73,13 @@ classdef GroupClass < TreeNodeClass 
        

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

        function SetVersion(obj, vernum)

            % Version number should be incremented whenever properties are added, deleted or changed in 

            % GroupClass, SubjectClass, RunClass OR acquisition class, like AcqDataClass, SnirfClass and 

            % its sub-classes or NirsClass 

            

            if nargin==1

                obj.version{1} = '1';   % Major version #

                obj.version{2} = '0';   % Major sub-version #

                obj.version{2} = '1';   % Major sub-version #

                obj.version{3} = '0';   % Minor version #

                obj.version{4} = '0';   % Minor sub-version # or patch #: 'p1', 'p2', etc

            elseif iscell(vernum)

Utils/getVernum.m

+1 −1
Original line number Diff line number Diff line
@@ -2,5 +2,5 @@ function vrnnum = getVernum() 


vrnnum{1} = '1';   % Major version #

vrnnum{2} = '20';  % Major sub-version #

vrnnum{3} = '3';   % Minor version #

vrnnum{3} = '4';   % Minor version #

vrnnum{4} = '0';   % Minor sub-version # or patch #: 'p1', 'p2', etc

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