Commit a82e33e3 authored by Jay Dubb's avatar Jay Dubb
Browse files

v.1.23.1 

-- Step 2 in allowing acquired file data such as stimulus conditions to be modified through a separate save procedure. Finished implementing this feature.
-- Add HDF5_DatasetWrite which allows overwriting of chunked datasets. This is what allows tims to be updated in a SNIF file after file creation.
-- Consolidate StimEditGUI file into one file (StimEditGUI.m).
-- Add small button to upper right corner of MainGUI.fig to easily shrink or expand GUI to fixed standard sizes, without having to resize by dragging mouse.
parent a0260163

AppSettings.cfg

+4 −0
Original line number Diff line number Diff line
@@ -23,4 +23,8 @@ on 
% Data Storage Scheme

file



% Auto Save Acquisition Files

Yes





% END

DataTree/AcquiredData/DataFiles/Hdf5/HDF5_DatasetWrite.m

0 → 100644
+101 −0
Original line number Diff line number Diff line 
function err = HDF5_DatasetWrite(fname, location, data)



if exist(fname,'file')

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

else

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

end

if fid<0

    err = -1;

    return;

end



% Create group where dataset is located

group = filesepStandard(fileparts(location), 'nameonly');

gid = CreateGroup(fid, group);

if gid < 0

    err = -1;

    return;

end



% Update dataset

err = WriteDataset(fid, location, data);









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

function gid = CreateGroup(fid, group)

if group == '/'

    gid = H5G.open(fid, '/');

    return;

end



try

    gid = H5G.open(fid, group);

catch

    [rootgroup, group] = filesepStandard(fileparts(group));

    gid = CreateGroup(fid, rootgroup);

    gid = H5G.create(gid, group, 'H5P_DEFAULT','H5P_DEFAULT','H5P_DEFAULT');

end







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

function err = WriteDataset(fid, location, data)



err = 0;



% data = HDF5_Transpose(data);

dims = size(data);

h5_dims = fliplr(dims);

unlimited = H5ML.get_constant_value('H5S_UNLIMITED');

h5_maxdims = [unlimited, unlimited];



if isnumeric(data)

    type_id = H5T.copy('H5T_NATIVE_DOUBLE');

elseif ischar(data)

    type_id = H5T.copy('H5T_C_S1'); 

else

    err = -1;

    return;

end



space_id = H5S.create_simple(2, h5_dims, h5_maxdims);

proplist_id = H5P.create('H5P_DATASET_CREATE');



% Open or create dataset

try

    dset_id = H5D.open(fid, location);

    H5D.set_extent(dset_id, h5_dims);

catch

    H5P.set_chunk(proplist_id, h5_dims);

    dset_id = H5D.create(fid, location, type_id, space_id, proplist_id);

end

file_space_id = H5D.get_space(dset_id);



% Write dataset

% H5D.write(dset_id, type_id, space_id, file_space_id, proplist_id, data);

H5D.write(dset_id, type_id, space_id, file_space_id, 'H5P_DEFAULT', data);



% Close space, type, dataset and file

H5S.close(space_id);

H5T.close(type_id);

H5D.close(dset_id);

H5F.close(fid);







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

function [dset_id, type_id, space_id, proplist_id] = CreateDataset(fid, location, h5_dims)



h5_maxdims = h5_dims;



type_id = H5T.copy('H5T_NATIVE_DOUBLE');

space_id = H5S.create_simple(2, h5_dims, h5_maxdims);

proplist_id = H5P.create('H5P_DATASET_CREATE');

H5P.set_chunk(proplist_id, [h5_dims(1), h5_dims(2)]);



dset_id = H5D.create(fid, location, type_id, space_id, proplist_id);

DataTree/AcquiredData/DataFiles/Hdf5/HDF5_WriteStrings.m→DataTree/AcquiredData/DataFiles/Hdf5/HDF5_DatasetWriteStrings.m

+1 −1
Original line number Diff line number Diff line 
function HDF5_WriteStrings(fname, location, data)

function HDF5_DatasetWriteStrings(fname, location, data)



if ~exist(fname, 'file')

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

DataTree/AcquiredData/DataFiles/Hdf5/hdf5write_safe.m

+2 −13
Original line number Diff line number Diff line
@@ -9,23 +9,12 @@ if ~exist('options','var') 
end



if iscell(val)

    HDF5_WriteStrings(fname, name, val)

    HDF5_DatasetWriteStrings(fname, name, val)

else

    val = HDF5_Transpose(val, options);

    try

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

            try

                % For datasets that are writeable AFTER they are created

                % there's we need to have a separte create step where we can provide the

                % dimensions and chunk size. Since there's no way to test to see if dataset

                % already exists, we use try/catch by attempting to create the data set

                % and no harm done if it exists and we catch the exception.

                dims = size(val);

                h5create(fname, name, [dims(1), Inf], 'ChunkSize',[dims(1), 64]);

            catch

                % Dataset already exists. move on...

            end

            h5write(fname, name, val, [1,1], dims);

            HDF5_DatasetWrite(fname, name, val);

        else

            hdf5write(fname, name, val, 'WriteMode','append');

        end

DataTree/AcquiredData/Snirf/SnirfClass.m

+163 −154
Original line number Diff line number Diff line
@@ -9,12 +9,13 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
        aux

    end

    

    properties (Access = private)

    properties (Access = public)

        fid

        gid

        location

        nirsdatanum

        nirs_tb;

        stim0

    end

    

    methods
@@ -240,6 +241,8 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
            obj.stim           = StimClass().empty();

            obj.probe          = ProbeClass().empty();

            obj.aux            = AuxClass().empty();

            

            obj.stim0          = StimClass().empty();

        end
@@ -256,6 +259,11 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
            obj.stim          = CopyHandles(obj2.stim);

            obj.probe         = CopyHandles(obj2.probe);

            obj.aux           = CopyHandles(obj2.aux);

            

            try

                obj.stim0     = CopyHandles(obj2.stim0);

            catch

            end

        end
@@ -371,25 +379,15 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
        

        

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

        function err = LoadStim(obj, fileobj, options)

        function err = LoadStim(obj, fileobj)

            err = 0;

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

                options = '';

            end

            

            paramName = 'stim';

            if optionExists(options, 'original') || optionExists(options, 'orig')

                paramName = 'stim0';

            end

            

            % Since we want to load stims in sorted order (i.e., according to alphabetical order

            % of condition names), first load to temporary variable.

            ii=1;

            while 1

                if ii > length(obj.stim)

                    obj.stim(ii) = StimClass;

                end

                if obj.stim(ii).LoadHdf5(fileobj, [obj.location, '/', paramName, num2str(ii)]) < 0

                if obj.stim(ii).LoadHdf5(fileobj, [obj.location, '/stim', num2str(ii)]) < 0

                    obj.stim(ii).delete();

                    obj.stim(ii) = [];

                    if ii==1
@@ -400,6 +398,21 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
                ii=ii+1;

            end

            obj.SortStims();

            

            % Load original, unedited stims, if they exist

            ii=1;

            while 1

                if ii > length(obj.stim0)

                    obj.stim0(ii) = StimClass;

                end

                if obj.stim0(ii).LoadHdf5(fileobj, [obj.location, '/stim0', num2str(ii)]) < 0

                    obj.stim0(ii).delete();

                    obj.stim0(ii) = [];

                    break;

                end

                ii=ii+1;

            end

            

        end
@@ -435,7 +448,7 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
        

        

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

        function err = LoadHdf5(obj, fileobj, params)

        function err = LoadHdf5(obj, fileobj, ~)

            err = 0;

            

            % Arg 1
@@ -535,18 +548,15 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
        

        

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

        function SaveStim(obj, fileobj, options)

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

                options = '';

        function SaveStim(obj, fileobj)

            for ii=1:length(obj.stim)

                obj.stim(ii).SaveHdf5(fileobj, [obj.location, '/stim', num2str(ii)]);

            end

            

            paramName = 'stim';

            if optionExists(options, 'original') || optionExists(options, 'orig')

                paramName = 'stim0';

            if isempty(obj.stim0)

                obj.stim0 = obj.stim.copy();

                for ii=1:length(obj.stim0)

                    obj.stim0(ii).SaveHdf5(fileobj, [obj.location, '/stim0', num2str(ii)]);

                end



            for ii=1:length(obj.stim)

                obj.stim(ii).SaveHdf5(fileobj, [obj.location, '/', paramName, num2str(ii)]);

            end

        end
@@ -606,28 +616,19 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
        

        

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

        function [changes, stim0] = UpdateStim(obj, fileobj)

        function [stimFromFile, changes] = UpdateStim(obj, fileobj)

            flags = zeros(length(obj.stim), 1);

            

            % Load original unedited stim, rename it and save it if it

            % doesn't already exist

            snirf = SnirfClass();

            snirf.LoadStim(fileobj, 'orig');

            if snirf.stim.Error()<0  

                obj.stim.SaveStim('orig');

            end

            

            % Now load current stim from file and update it

            snirf.LoadStim(fileobj);

            stim0 = snirf.stim;

            % Load stim from file and update it

            snirfFile = SnirfClass();

            snirfFile.LoadStim(fileobj);

            

            % Update original stims from file with edited stims

            % Update stims from file with edited stims

            for ii = 1:length(obj.stim)

                for jj = 1:length(stim0)

                    if strcmp(obj.stim(ii).GetName(), stim0(jj).GetName())

                        if obj.stim(ii) ~= stim0(jj)

                            stim0(jj).Copy(obj.stim(ii));

                            stim0(jj).SaveHdf5(fileobj, [obj.location, '/stim', num2str(jj)]);

                for jj = 1:length(snirfFile.stim)

                    if strcmp(obj.stim(ii).GetName(), snirfFile.stim(jj).GetName())

                        if obj.stim(ii) ~= snirfFile.stim(jj)

                            snirfFile.stim(jj).Copy(obj.stim(ii));

                        end

                        flags(ii) = 1;

                        break;
@@ -636,30 +637,36 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
                if ~flags(ii)

                    % We have new stimulus condition added

                    if ~obj.stim(ii).IsEmpty()

                        stim0(jj+1) = StimClass(obj.stim(ii));

                        stim0(jj+1).SaveHdf5(fileobj, [obj.location, '/stim', num2str(jj+1)]);

                        snirfFile.stim(jj+1) = StimClass(obj.stim(ii));

                    end

                end

            end

            

            % If stims were edited then update snirf file with new stims

            changes = sum(flags);

            if changes

                snirfFile.SaveStim(fileobj);

            end

            stimFromFile = snirfFile.stim;

        end

        

        

        

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

        function changes = StimChangesMade(obj)

            % Load original unedited stims from file

            snirf = SnirfClass();

            snirf.LoadStim(obj.filename);

            stim0 = snirf.stim;

            

            flags = zeros(length(obj.stim), 1);

            

            % Update original stims from file with edited stims

            % Load stims from file

            snirf = SnirfClass();

            snirf.LoadStim(obj.filename);

            stimFromFile = snirf.stim;

            

            % Update stims from file with edited stims

            for ii = 1:length(obj.stim)

                for jj = 1:length(stim0)

                    if strcmp(obj.stim(ii).GetName(), stim0(jj).GetName())

                        if obj.stim(ii) ~= stim0(jj)

                for jj = 1:length(stimFromFile)

                    if strcmp(obj.stim(ii).GetName(), stimFromFile(jj).GetName())

                        if obj.stim(ii) ~= stimFromFile(jj)

                            flags(ii) = 1;

                        else

                            flags(ii) = -1;
@@ -692,6 +699,7 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
            if isempty(obj)

                return

            end

            

            % Arg 1

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

                fileobj = '';
@@ -1287,6 +1295,7 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
        end

        

        

        

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

        function vals = GetStimValues(obj, icond)

            if icond>length(obj.stim)

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