Commit 24fee309 authored by Jay Dubb's avatar Jay Dubb
Browse files

v1.20.5 

-- Update MetaDataTagsClass to agree with latest SNIRF spec adding new required field FrequencyUnit.
-- Instead of formatVersion use metaDataTags required field FrequencyUnit to determine whether old SnirfDataSet is being loaded.
-- Update probe to match latest Spec, add landmarkPos3D and it's alias landmarkPos, sourcePos3D and detectorPos3D, aliases sourcePos and detectorPos to stand for sourcePos2D and detectorPos2D
-- Allow both /nirs and /nirs1, /nirs2, etc to be root HDF5 groups of multiple SNIRF subject datasets.
-- Update GroupClass version because groupResults should change when acquired data format changes
parent b71f10e1

DataTree/AcquiredData/DataFiles/Hdf5/HDF5_GroupOpen.m

+1 −1
Original line number Diff line number Diff line
@@ -9,7 +9,7 @@ end 
try

    gid = H5G.open(fid, location);

catch

    gid = -1;

    gid.double = -1;

end

DataTree/AcquiredData/Snirf/MetaDataTagsClass.m

+24 −0
Original line number Diff line number Diff line
@@ -16,6 +16,9 @@ classdef MetaDataTagsClass < FileLoadSaveClass 
            obj.tags.MeasurementTime = datestr(now,'hh:mm:ss');

            obj.tags.LengthUnit = 'mm';

            obj.tags.TimeUnit = 'unknown';

            obj.tags.FrequencyUnit = 'unknown';

            obj.tags.AppName  = 'snirf-homer3';

            obj.tags.SnirfDraft = '3';

            

            if nargin==1

                obj.filename = varargin{1};
@@ -56,6 +59,8 @@ classdef MetaDataTagsClass < FileLoadSaveClass 
            %%%%%%%%%%%% Ready to load from file



            try

                % Reset tags

                obj.tags = struct();

                

                % Open group

                [gid, fid] = HDF5_GroupOpen(fileobj, location);
@@ -68,6 +73,9 @@ classdef MetaDataTagsClass < FileLoadSaveClass 
                

                HDF5_GroupClose(fileobj, gid, fid);



                % Detect old or invalid metadatatag data

                assert(obj.IsValid());

                

            catch

                

                err = -1;
@@ -102,6 +110,22 @@ classdef MetaDataTagsClass < FileLoadSaveClass 
        end

        

        

        

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

        function b = IsValid(obj)

            b = false;

            

            % Use latest required fields to determine if we're loading old

            % metaDataTag format version of SNIRF spec

            if ~isproperty(obj.tags, 'FrequencyUnit')

                return;

            end

            

            b = true;

        end



        

        

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

        function B = eq(obj, obj2)

            B = false;

DataTree/AcquiredData/Snirf/ProbeClass.m

+45 −3
Original line number Diff line number Diff line
@@ -5,6 +5,9 @@ classdef ProbeClass < FileLoadSaveClass 
        wavelengthsEmission

        sourcePos2D

        detectorPos2D

        landmarkPos2D

        sourcePos3D

        detectorPos3D

        frequencies

        timeDelay

        timeDelayWidth
@@ -13,6 +16,7 @@ classdef ProbeClass < FileLoadSaveClass 
        correlationTimeDelayWidth

        sourceLabels

        detectorLabels

        landmarkLabels

    end
@@ -31,6 +35,8 @@ classdef ProbeClass < FileLoadSaveClass 
                    obj.wavelengthsEmission  = [];

                    obj.sourcePos2D  = SD.SrcPos;

                    obj.detectorPos2D  = SD.DetPos;

                    obj.sourcePos3D  = [];

                    obj.detectorPos3D  = [];

                    obj.frequencies  = 1;

                    obj.timeDelay  = 0;

                    obj.timeDelayWidth  = 0;
@@ -52,6 +58,8 @@ classdef ProbeClass < FileLoadSaveClass 
                obj.wavelengthsEmission  = [];

                obj.sourcePos2D  = [];

                obj.detectorPos2D  = [];

                obj.sourcePos3D  = [];

                obj.detectorPos3D  = [];

                obj.frequencies  = 1;

                obj.timeDelay  = 0;

                obj.timeDelayWidth  = 0;
@@ -77,6 +85,21 @@ classdef ProbeClass < FileLoadSaveClass 


        

        

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

        function BackwardCompatibility(obj)

            if isempty(obj.sourcePos2D)

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

            end

            if isempty(obj.detectorPos2D)

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

            end

            if isempty(obj.landmarkPos2D)

                obj.landmarkPos2D = HDF5_DatasetLoad(gid, 'landmarkPos', [], '2D');

            end

        end



        

        

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

        function err = LoadHdf5(obj, fileobj, location)

            err = 0;
@@ -113,6 +136,9 @@ classdef ProbeClass < FileLoadSaveClass 
                obj.wavelengthsEmission       = HDF5_DatasetLoad(gid, 'wavelengthsEmission');

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

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

                obj.landmarkPos2D             = HDF5_DatasetLoad(gid, 'landmarkPos2D', [], '2D');

                obj.sourcePos3D               = HDF5_DatasetLoad(gid, 'sourcePos3D', [], '2D');

                obj.detectorPos3D             = HDF5_DatasetLoad(gid, 'detectorPos3D', [], '2D');

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

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

                obj.timeDelayWidth            = HDF5_DatasetLoad(gid, 'timeDelayWidth');
@@ -121,6 +147,7 @@ classdef ProbeClass < FileLoadSaveClass 
                obj.correlationTimeDelayWidth = HDF5_DatasetLoad(gid, 'correlationTimeDelayWidth');

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

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

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

                                

                % Close group

                HDF5_GroupClose(fileobj, gid, fid);
@@ -136,6 +163,7 @@ classdef ProbeClass < FileLoadSaveClass 
        end



        

        

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

        function SaveHdf5(obj, fileobj, location)

            % Arg 1
@@ -251,6 +279,20 @@ classdef ProbeClass < FileLoadSaveClass 
            end

        end

        

        

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

        function b = IsEmpty(obj)

            b = true;

            if isempty(obj.wavelengths)

                return;

            end

            if isempty(obj.sourcePos2D) && isempty(obj.detectorPos2D) && ...

                    isempty(obj.sourcePos3D) && isempty(obj.detectorPos3D) 

                return;

            end

            b = false;

        end

        

    end

    

end

DataTree/AcquiredData/Snirf/SnirfClass.m

+71 −16
Original line number Diff line number Diff line
@@ -13,6 +13,7 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
        fid

        gid

        location

        nirsdatanum

        nirs_tb;        

    end
@@ -64,7 +65,7 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
            %

             

            % Initialize properties from SNIRF spec 

            obj.formatVersion = '1.1';

            obj.formatVersion = '1.0';

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

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

            obj.stim           = StimClass().empty();
@@ -73,6 +74,7 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
            

            % Set class properties NOT part of the SNIRF format

            obj.fileformat = 'hdf5';

            obj.nirsdatanum = 1;

            obj.location = '/nirs';

            

            % See if we're loading .nirs data format
@@ -91,7 +93,6 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
            % because of all the variations of calling this class constructor but 

            % there should be a simpler way to do this 

            

            % The basic 5 of a .nirs format in a struct

            if nargin==1 || (nargin==2 && isa(varargin{2}, 'double'))

                if isa(varargin{1}, 'SnirfClass')

                    obj.Copy(varargin{1});
@@ -100,7 +101,12 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
                

                if ischar(varargin{1})

                    obj.filename = varargin{1};

                    if nargin==2

                        obj.nirsdatanum = varargin{2};

                    end

                    obj.Load(varargin{1});

                    

                % The basic 5 of a .nirs format in a struct

                elseif isstruct(varargin{1}) || isa(varargin{1}, 'NirsClass')

                    tfactors = 1;    % Debug simulation parameter

                    if nargin==2
@@ -229,6 +235,40 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
        end

        

        

        

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

        function err = SetLocation(obj)

            err = 0;

            gid1 = HDF5_GroupOpen(obj.fid, sprintf('%s%d', obj.location, obj.nirsdatanum));

            gid2 = HDF5_GroupOpen(obj.fid, obj.location);

            

            if gid1.double > 0

                obj.location = sprintf('%s%d', obj.location, obj.nirsdatanum);

                return;

            elseif gid2.double > 0

                return;

            end

            err = -1;

        end

        

        

        



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

        function err = LoadFormatVersion(obj)

            err = 0;

            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

        end

        

        

        

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

        function err = LoadMetaDataTags(obj, fileobj)

            err = 0;
@@ -294,6 +334,7 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
        end

        

        

        

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

        function err = LoadAux(obj, fileobj)

            err = 0;
@@ -315,6 +356,7 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
        end

        

        

        

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

        function err = LoadHdf5(obj, fileobj, ~)

            err = 0;
@@ -343,30 +385,43 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
                % Open group

                [obj.gid, obj.fid] = HDF5_GroupOpen(fileobj, '/');

                

                if obj.SetLocation() < 0

                    err = -1;

                    return

                end

                

                %%%% Load 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)

                if obj.LoadFormatVersion() < 0

                    err = -2;

                    return 

                    return;

                end

                

                %%%% Load metaDataTags

                obj.LoadMetaDataTags(obj.fid);

                if obj.LoadMetaDataTags(obj.fid) < 0

                    err = -3;

                    return;

                end

                

                %%%% Load data

                obj.LoadData(obj.fid);

                if obj.LoadData(obj.fid) < 0

                    err = -4;

                end

                

                %%%% Load stim

                obj.LoadStim(obj.fid);

                if obj.LoadStim(obj.fid)

                    err = -5;

                end

                

                %%%% Load probe

                obj.LoadProbe(obj.fid);

                if obj.LoadProbe(obj.fid)

                    err = -6;

                end

                

                %%%% Load aux

                obj.LoadAux(obj.fid);

                if obj.LoadAux(obj.fid)

                    err = -7;

                end

                    

            

                % Close group

                HDF5_GroupClose(fileobj, obj.gid, obj.fid);
@@ -1072,10 +1127,10 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
            if isempty(obj)

                return;

            end

            if isempty(obj.data)

            if isempty(obj.data) || (isa(obj.data, 'DataClass') && obj.data(1).IsEmpty())

                return;

            end

            if isempty(obj.probe)

            if isempty(obj.data) || (isa(obj.probe, 'ProbeClass') && obj.probe.IsEmpty())

                return;

            end

            b = false;

DataTree/AcquiredData/Snirf/SnirfClass.py

+2 −2
Original line number Diff line number Diff line
@@ -266,8 +266,8 @@ if __name__ == "__main__": 
    if len(sys.argv) > 1:

        filenames[0] =  sys.argv[1]

    else:

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

        # 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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