Commit dedfe822 authored by jayd1860's avatar jayd1860
Browse files

Merge development into master 

Date: 5/11/2023 3:06:37 PM
v1.79.3

-- Add more standalone startup function to setpaths.m to be able to independent of any startup code search paths except current folder
-- Chnage default value of config param Load Stim From TSV File from no to yes.

* DataTree, v1.14.2
-- Fix events TSV file naming bug. Add TSV file name method TreeNode.GetStimTsvFilename() to use for all events TSV file naming.
-- Fixes to setpaths for running DataTree standalone

* Utils, v1.6.0
-- Fix some bugs in events TSV stim loading error handling. Add config param "Replace TSV File Tabs with Spaces" to handle events TSV errors when file  is a mix of spaces and tabs.
-- Add method ConfigFileClass.GetValueOptions for getting all available value options for a param.

Date: 5/10/2023 10:52:19 AM
v1.79.1 -- Fix Homer3 displaying probe in 3D rather than 2D. (#177)

* DataTree, v1.14.0
-- Fix Homer3 displaying probe in 3D rather than 2D. Back out changes that default to 3D in ProbeClass and NirsClass GetSrcPos and GetDetPos for ALL cases. The way it's supposed to work is probe is supposed to use 2D coordinates ONLY when being displayed in Homer3. Rest of the time default to 3D if it exists. Reason for original change is misunderstanding of what the purpose of 2D coord was which is ONLY for display

* Utils, v1.5.1
-- Add ability to simulate full dataset (generateSimData.m, simulateDataTimeSeries.m)  to be able to eventually do workflow unit and system tests

Date: 5/3/2023 12:38:30 PM
v1.78.1  -- Fix error when displaying data, remove unnecessary call to get file descriptor: obj.fid = HDF5_GetFileDescriptor(fileobj); (#174)

Date: 5/3/2023 10:52:24 AM
-- Forgot to include HDF5_GetFileDescriptor.m in v1.78.0 commit. (#173)

Date: 5/3/2023 10:13:49 AM
v1.78.0 -- Improve saving performance of SNIRF files by using low level HDF5 library. (#172)
* DataTree, v1.13.0
-- Comprehensive solution to improving the save performance of SNIRF files by using low-level HDF5 calls and limiting the number of HDF5 open and create calls that are made for file, group and dataset.

Date: 4/14/2023 1:59:38 AM
1.77.0 -- Fix stim events TSV issue with conditions names with spaces - we should be able to handle that.  (#170)

Utils, v1.5.0
-- Fix stim events TSV issue with conditions names with spaces - we should be able to handle that. Change rule to handle spaces and how error reporting is done in readTsv.

DataTree, v1.12.1
-- Don't load events TSV files twice - once in SnirfClass and once in AcqDataClass its superclass.

Date: 4/11/2023 2:49:33 PM
-- Sync setpaths in DataTree with DataTree library
parents e73d6502 f162f70a

DataTree/AcquiredData/AcqDataClass.m

+5 −2
Original line number Diff line number Diff line
@@ -92,7 +92,6 @@ classdef AcqDataClass < matlab.mixin.Copyable 
            if ~ischar(fileobj)

                fileobj = '';

            end

            obj.LoadBids(fileobj);           

        end
@@ -162,7 +161,11 @@ classdef AcqDataClass < matlab.mixin.Copyable 
            if isempty(file)

                return

            end

            obj.bids.stim = readTsv([filesepStandard(p), file(1).name],'numstr2num');

            [obj.bids.stim, err] = readTsv([filesepStandard(p), file(1).name],'numstr2num');

%             if err < 0

%                 obj.SetError(-8);

%                 return;

%             end

            if isempty(obj.bids.stim)

                return

            end

DataTree/AcquiredData/DataFiles/FileLoadSaveClass.m

+5 −0
Original line number Diff line number Diff line
@@ -63,6 +63,11 @@ classdef FileLoadSaveClass < matlab.mixin.Copyable 
                format = obj.fileformat;

            end

            

            p = fileparts(filename);

            if isempty(p)

                filename = ['./', filename];

            end

                       

            switch(lower(format))

                case obj.supportedFomats.matlab

                    if ismethod(obj, 'SaveMat')

DataTree/AcquiredData/DataFiles/Hdf5/HDF5_GetFileDescriptor.m

0 → 100644
+15 −0
Original line number Diff line number Diff line 
function fid = HDF5_GetFileDescriptor(fileobj)



% Either fileobj is a name of a file or a HDF5 file descriptor

if ischar(fileobj)

    if ispathvalid(fileobj,'file')

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

    else

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

    end

    if fid < 0

        return;

    end

else

    fid = fileobj;

end

DataTree/AcquiredData/DataFiles/Hdf5/hdf5write_safe.m

+142 −106
Original line number Diff line number Diff line 
function err = hdf5write_safe(fname, name, val, options)

    



function err = hdf5write_safe(fileobj, name, val, options)

err = -1;

if isempty(val)

    return;
@@ -16,13 +14,9 @@ function err = hdf5write_safe(fname, name, val, options) 
elseif any(strcmp(options, 'scalar'))

    force_scalar = true;

end

    % Identify type of val and use SNIRF v1.1-compliant write function



    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

% Identify type of val and use SNIRF v1.1-compliant write function

fid = HDF5_GetFileDescriptor(fileobj);

if fid < 0

    err = -1;

    return;
@@ -36,87 +30,129 @@ function err = hdf5write_safe(fname, name, val, options) 
    return;

end



% Create dataset

if iscell(val) || isstring(val)

    if length(val) > 1 && ~force_scalar || force_array  % Returns true for single strings, believe it or not

            write_string_array(fid, fname, name, val);

        write_string_array(fid, name, val);

    else

            write_string(fid, fname, name, val);

        write_string(fid, name, val);

    end

        return

elseif ischar(val)

        write_string(fid, fname, name, val);

        return

    write_string(fid, name, val);

elseif isfloat(val)

    if length(val) > 1 && ~force_scalar || force_array

            write_numeric_array(fname, name, val);

        write_numeric_array(fid, name, val);

    else

            write_numeric(fid, fname, name, val);

        write_numeric(fid, name, val);

    end

        return

elseif isinteger(val)

    if length(val) > 1 && ~force_scalar || force_array

            write_numeric_array(fid, fname, name, val);  % As of now, no integer arrays exist

        write_numeric_array(fid, name, val);  % As of now, no integer arrays exist

    else

            write_integer(fid, fname, name, val);

        write_integer(fid, name, val);

    end

        return

else

        warning(['An unrecognized variable was saved to ', name, ' in ', fname])

    warning(['An unrecognized variable was saved to ', name])

end



    H5F.close(fid);



end



function err = write_string(fid, fname, name, val)

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

function err = write_string(fid, name, val)

sid = H5S.create('H5S_SCALAR');

tid = H5T.copy('H5T_C_S1');

H5T.set_size(tid, 'H5T_VARIABLE');

did = H5D.create(fid, name, tid, sid, 'H5P_DEFAULT');

H5D.write(did, tid, 'H5S_ALL', 'H5S_ALL', 'H5P_DEFAULT', {val});

err = 0;

end



function err = write_string_array(fid, fname, name, val)





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

function err = write_string_array(fid, name, val)

val = HDF5_Transpose(val);

sid = H5S.create_simple(1, numel(val), H5ML.get_constant_value('H5S_UNLIMITED'));

tid = H5T.copy('H5T_C_S1');

H5T.set_size(tid, 'H5T_VARIABLE');

pid = H5P.create('H5P_DATASET_CREATE');

H5P.set_chunk(pid, 2);

    did = H5D.create(fid, name, tid, sid, pid);

    H5D.write(did, tid, 'H5S_ALL', 'H5S_ALL', 'H5P_DEFAULT', val);

dsid = H5D.create(fid, name, tid, sid, pid);

H5D.write(dsid, tid, 'H5S_ALL', 'H5S_ALL', 'H5P_DEFAULT', val);

err = 0;

end



function err = write_numeric(fid, fname, name, val)

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





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

function err = write_numeric(fid, name, val)

tid = H5T.copy('H5T_NATIVE_DOUBLE');

sid = H5S.create('H5S_SCALAR');

    H5D.create(fid, name, tid, sid, 'H5P_DEFAULT');

    h5write(fname, name, val);

dsid = H5D.create(fid, name, tid, sid, 'H5P_DEFAULT');

H5D.write(dsid, tid, 'H5S_ALL', 'H5S_ALL', 'H5P_DEFAULT', val);

err = 0;

end



function err = write_numeric_array(fname, name, val)

    val = HDF5_Transpose(val);

    sizeval = size(val);

    if sizeval(1) == 1 || sizeval(2) == 1

        n = length(val);

    else

        n = sizeval;

    end

    h5create(fname, name, n, 'Datatype', 'double');

    h5write(fname, name, val);

    err = 0;

end



function err = write_integer(fid, fname, name, val)



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

function err = write_integer(fid, name, val)

warning off;  % Suppress the int truncation warning

    tid = H5T.copy('H5T_NATIVE_INT');

tid = H5T.copy('H5T_NATIVE_ULONG');

sid = H5S.create('H5S_SCALAR');

    H5D.create(fid, name, tid, sid, 'H5P_DEFAULT');

    h5write(fname, name, val);

dsid = H5D.create(fid, name, tid, sid, 'H5P_DEFAULT');

H5D.write(dsid, tid, 'H5S_ALL', 'H5S_ALL', 'H5P_DEFAULT', int32(val));

err = 0;

warning on;







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

function err = write_numeric_array(fid, name, data)

err = 0;

data = HDF5_Transpose(data);

sizedata = size(data);

if sizedata(1) == 1 || sizedata(2) == 1

    n = length(data);

else

    n = sizedata;

end



tid = -1;

sid = -1;

gid = -1;

dsid = -1;



maxdims = n;

try

    

    sid = H5S.create_simple(numel(n), fliplr(n), fliplr(maxdims));   

    gid = HDF5_CreateGroup(fid, fileparts(name));

    dsid = H5D.create(gid, name, 'H5T_NATIVE_DOUBLE', sid, 'H5P_DEFAULT');

    H5D.write(dsid, 'H5ML_DEFAULT', 'H5S_ALL', 'H5S_ALL', 'H5P_DEFAULT', data);

    

catch

    

    % Clean up; Close everything

    cleanUp(tid, sid, gid, dsid);

    err = -1;

    return;

    

end

cleanUp(tid, sid, gid, dsid);







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

function cleanUp(tid, sid, gid, dsid)

if ~isnumeric(tid)

    H5T.close(tid);

end

if ~isnumeric(sid)

    H5S.close(sid);

end

if ~isnumeric(gid)

    H5G.close(gid);

end

if ~isnumeric(dsid)

    H5D.close(dsid);

end

DataTree/AcquiredData/DataFiles/SnirfFile2Tsv.m

+0 −7
Original line number Diff line number Diff line
@@ -48,11 +48,4 @@ else 
    writeTsv(dst, tsv);

end



% Remove stim from

% if optionExists(options, 'removeStim')

%     s.Load();

%     s.stim = StimClass().empty();

%     s.Save();

% end

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