Unverified Commit 5db986c0 authored by jayd1860's avatar jayd1860 Committed by GitHub
Browse files

Fix error loading SNIRF stim caused by previous fix to aux that broke stim loading (#129) 

* v1.36.0

-- Fix issues with building and running Homer3 executable.
-- Add logging of Homer3 input arguments.
-- Fix a performance issue in fullpath.m discovered when loading large data set.

* v1.36.1

-- Fix another issue in executable of not finding data files in subject folder.

* v1.36.2

-- Fix for error loading SNIRF aux.name field didn't work for ALL cases. Added code in HDF5 transpose code to handle all cases.
-- Added error handling in AuxClass

* -- Fix syncSubmodules attempted syncing with empty submodule
parent b000659a

DataTree/AcquiredData/DataFiles/DataFilesClass.m

+9 −2
Original line number Diff line number Diff line
@@ -217,10 +217,13 @@ classdef DataFilesClass < handle 
            parentdir = filesepStandard(parentdir);

            pattern = obj.dirFormats.choices{iFormat}{iPattern};

            

            dirs = mydir([parentdir, pattern]);

            dirs = mydir([parentdir, pattern], obj.rootdir);

            

            dirnamePrev = '';

            for ii = 1:length(dirs)

                if dirs(ii).IsEmpty()

                    continue;

                end

                if dirs(ii).IsFile()

                    if strcmp(pattern, '*')

                        continue
@@ -257,7 +260,7 @@ classdef DataFilesClass < handle 
                if obj.SearchLookupTable(pathrel2)

                    continue;

                end

                obj.files(end+1) = FileClass([obj.rootdir, '/', pathrel2]);

                obj.files(end+1) = FileClass([obj.rootdir, '/', pathrel2], obj.rootdir);

                obj.AddLookupTable(obj.files(end).name)

            end

        end
@@ -455,6 +458,8 @@ classdef DataFilesClass < handle 
            end

            

            % Try to create object of data filetype and load data into it

            msg = 'Please wait while we check group folder for valid data files ...';

            hwait = waitbar_improved(0, msg);

            dataflag = false;

            for ii = 1:length(obj.files)

                if obj.files(ii).isdir
@@ -468,6 +473,7 @@ classdef DataFilesClass < handle 
                else

                    dataflag = true;

                end

                hwait = waitbar_improved(ii/length(obj.files), hwait, msg);

            end

            if dataflag==false

                obj.files = FileClass.empty();
@@ -479,6 +485,7 @@ classdef DataFilesClass < handle 
            	obj.files(errorIdxs) = [];

                obj.nfiles = obj.nfiles - length(errorIdxs);

            end

            close(hwait);

        end

DataTree/AcquiredData/DataFiles/FileClass.m

+4 −4
Original line number Diff line number Diff line
@@ -62,7 +62,7 @@ classdef FileClass < matlab.mixin.Copyable 
            else

                file.rootdir = pwd;

            end

            file.rootdir = filesepStandard(file.rootdir);            

            file.rootdir = filesepStandard(file.rootdir, 'full');            

            

            obj.Add(file);

        end
@@ -78,15 +78,15 @@ classdef FileClass < matlab.mixin.Copyable 
            end

            

            if isproperty(obj2, 'folder')

                rootdir = [filesepStandard(obj2.folder), obj2.name]; %#ok<*PROPLC>

                rootpath = [filesepStandard(obj2.folder), obj2.name]; %#ok<*PROPLC>

            else

                rootdir = [filesepStandard(obj2.rootdir), obj2.name];                

                rootpath = [filesepStandard(obj2.rootdir), obj2.name];                

            end

            

            obj.idx          = obj.idx+1;

            obj.isdir        = obj2.isdir;

            obj.filename     = obj2.name;

            obj.name         = getPathRelative(rootdir, obj2.rootdir);

            obj.name         = getPathRelative(rootpath, obj2.rootdir);

            obj.rootdir 	 = obj2.rootdir;

            obj.err          = 0;          % Set error to NO ERROR            

        end

DataTree/AcquiredData/DataFiles/Hdf5/HDF5_Transpose.m

+9 −6
Original line number Diff line number Diff line
@@ -7,12 +7,15 @@ end 
% Matlab stores contiguous muti-dimensional arrays in column-major order.

% HDF5 stores them in row-major order. We want to transpose the data to agree

% with the file format's storage order.

if ~isrow(val) && ~iscolumn(val)            % Matrices

    val = permute(val, ndims(val):-1:1);

% elseif ischar(val)                          % 1D char strings 

%     val = permute(val, ndims(val):-1:1);

elseif ~isempty(findstr('multidim', options))   % Force multi-dimensional even if vector

if (~isrow(val) && ~iscolumn(val))              || ...      % Matrices

     ~isempty(findstr('multidim', options))      || ...      % Force multi-dimensional even if vector

     ~isempty(findstr('2D', options))                        % Force 2D even if vector

    

    val = permute(val, ndims(val):-1:1);

elseif ~isempty(findstr('2D', options))         % Force 2D even if vector

    

elseif iscolumn(val) && ischar(val)

    

    val = permute(val, ndims(val):-1:1);

    

end

DataTree/AcquiredData/DataFiles/mydir.m

+1 −1
Original line number Diff line number Diff line
@@ -77,7 +77,7 @@ if ~exist('pathname','var') || isempty(pathname) 
    pathname = pwd;

end

if ~exist('pathroot','var') || isempty(pathroot)

    pathroot = pwd;

    pathroot = fileparts(pathname);

end



if ispathvalid(pathname, 'dir') && ~includes(pathname, '*')

DataTree/AcquiredData/Snirf/AuxClass.m

+4 −0
Original line number Diff line number Diff line
@@ -256,6 +256,10 @@ classdef AuxClass < FileLoadSaveClass 
                err = -4;

                return

            end

            if ~ischar(obj.name)

                err = -5;

                return

            end

        end

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