Merge remote-tracking branch 'remotes/origin/development'

DataTree/AcquiredData/DataFiles/FileClass.m

@@ -20,6 +20,7 @@
         err
         logger
         errmsg
+        errcodeUnvalidated
     end
 
     methods
@@ -40,8 +41,8 @@
             obj.rootdir    = '';
             obj.errmsg     = '';          % Assume file is not loadable
             obj.logger     = InitLogger(logger);            
-            obj.errmsg    = '';
 
+            obj.errcodeUnvalidated = -9999;
 
             if nargin==0
                 return;
@@ -88,7 +89,13 @@ function Add(obj, obj2)
             obj.filename     = obj2.name;
             obj.name         = getPathRelative(rootpath, obj2.rootdir);
             obj.rootdir 	 = obj2.rootdir;
-            obj.err          = 0;          % Set error to NO ERROR            
+            obj.date         = obj2.date;
+            obj.datenum      = datestr2datenum(obj.date);
+            if obj.IsFile()
+                obj.err          = obj.errcodeUnvalidated;          % Set error to unvalidated
+            else
+                obj.err          = 0;
+            end
         end
 
 
@@ -434,7 +441,7 @@ function Loaded(obj)
             if isempty(obj.name)
                 return;
             end
-            if obj.err ~= 0
+            if (obj.err ~= 0)  &&  (obj.IsValidated)
                 return;
             end
             b = false;            
@@ -443,19 +450,22 @@ function Loaded(obj)
 
         % ----------------------------------------------------
         function err = ErrorCheckName(obj)
+            err = 0;
             [p1,f1] = fileparts(obj.name);
             [p2,f2] = fileparts(filesepStandard(obj.rootdir,'nameonly:file'));
             [~,f3]  = fileparts(p2);
             if strcmp(f1, p1)
-                obj.err = -1;
+                err = -1;
             end
             if strcmp(f1, f2)
-                obj.err = -2;
+                err = -2;
             end
             if strcmp(f1, f3)
-                obj.err = -3;
+                err = -3;
+            end
+            if err ~= 0
+                obj.err = err;
             end
-            err = obj.err;
         end
 
 
@@ -545,6 +555,7 @@ function NameConflictFixed(obj)
         % -----------------------------------------------------
         function SetError(obj, errmsg)
             obj.errmsg = errmsg;
+            obj.err = -1;
         end
 
 
@@ -553,6 +564,62 @@ function SetError(obj, errmsg)
             msg = obj.errmsg;
         end
 
+
+        % -----------------------------------------------------
+        function SetValid(obj)
+            obj.err = 0;
+        end
+
+
+        % -----------------------------------------------------
+        function SetErrorUnvalidated(obj)
+            obj.err = obj.errcodeUnvalidated;
+        end
+
+
+        % -----------------------------------------------------
+        function b = IsValidated(obj)
+            b = false;
+            if obj.err == obj.errcodeUnvalidated
+                return 
+            end
+            b = true;
+        end
+
+
+
+        % -----------------------------------------------------
+        function b = IsUnValidated(obj)
+            b = true;
+            if obj.err == obj.errcodeUnvalidated
+                return 
+            end
+            b = false;
+        end
+
+
+
+        % ----------------------------------------------------------
+        function b = eq(obj, obj2)
+            b = false;
+            if ~strcmp(obj.name, obj2.name)
+                return;
+            end
+            if ~strcmp(obj.date, obj2.date)
+                return;
+            end
+            if obj.isdir ~= obj2.isdir
+                return;
+            end
+            if obj.bytes ~= obj2.bytes
+                return;
+            end
+            if obj.datenum ~= obj2.datenum
+                return;
+            end
+            b = true;
+        end
+
     end
 
 end

DataTree/AcquiredData/DataFiles/Hdf5/HDF5_DatasetLoad.m

@@ -8,8 +8,20 @@
 end
 
 try
-    dsetid = H5D.open(gid, name);
 
+    if ~H5L.exists(gid, name, 'H5P_DEFAULT')
+        switch(class(val0))
+            case 'char'
+                val = '';
+            case 'cell'
+                val = {};
+            otherwise
+                val = [];
+        end
+        return
+    end
+
+    dsetid = H5D.open(gid, name);
     % NOTE: HDF5 stores contiguous muti-dimensional arrays in row-major order.
     % Matlab stores them in row-major order. We want to transpose the loaded data 
     % it back to Matlab's column-major storage order and thus get back the 
@@ -29,3 +41,5 @@
             val = [];
     end
 end
+
+

DataTree/AcquiredData/DataFiles/Hdf5/HDF5_Transpose.m

@@ -1,16 +1,16 @@
-function val = HDF5_Transpose(val, options)
+function val = HDF5_Transpose(val, option)
 
-if ~exist('options','var')
-    options = '';
+if ~exist('option','var')
+    option = '';
 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
-     ~isempty(findstr('multidim', options))     || ...      % Force multi-dimensional even if vector
-     ~isempty(findstr('2D', options))           || ...      % Force 2D even if vector
-     ~isempty(findstr('3D', options))                       % Force 3D even if vector
+     ~isempty(findstr('multidim', option))     || ...      % Force multi-dimensional even if vector
+     ~isempty(findstr('2D', option))           || ...      % Force 2D even if vector
+     ~isempty(findstr('3D', option))                       % Force 3D even if vector
 
     val = permute(val, ndims(val):-1:1);
 

DataTree/AcquiredData/DataFiles/Hdf5/hdf5write_safe.m

@@ -1,18 +1,18 @@
 function err = hdf5write_safe(fileobj, name, val, options)
 err = -1;
-if isempty(val)
+if ~exist('val','var')
     return;
 end
 if ~exist('options','var')
     options = '';
 end
 
-force_scalar = false;
 force_array = false;
+force_vector = false;
 if any(strcmp(options, 'array'))
     force_array = true;
-elseif any(strcmp(options, 'scalar'))
-    force_scalar = true;
+elseif any(strcmp(options, 'vector'))
+    force_vector = true;
 end
 
 % Identify type of val and use SNIRF v1.1-compliant write function
@@ -32,25 +32,21 @@
 
 % Create dataset
 if iscell(val) || isstring(val)
-    if length(val) > 1 && ~force_scalar || force_array  % Returns true for single strings, believe it or not
+    if (length(val) > 1) || force_array  % Returns true for single strings, believe it or not
         write_string_array(fid, name, val);
     else
         write_string(fid, name, val);
     end
 elseif ischar(val)
     write_string(fid, name, val);
-elseif isfloat(val)
-    if length(val) > 1 && ~force_scalar || force_array
+elseif isfloat(val) || isinteger(val)
+    if force_vector
+        write_numeric_vector(fid, name, val);
+    elseif (length(val) > 1) || force_array
         write_numeric_array(fid, name, val);
     else
         write_numeric(fid, name, val);
     end
-elseif isinteger(val)
-    if length(val) > 1 && ~force_scalar || force_array
-        write_numeric_array(fid, name, val);  % As of now, no integer arrays exist
-    else
-        write_integer(fid, name, val);
-    end
 else
     warning(['An unrecognized variable was saved to ', name])
 end
@@ -82,50 +78,76 @@
 
 
 
+
 % -----------------------------------------------------------------
 function err = write_numeric(fid, name, val)
-tid = H5T.copy('H5T_NATIVE_DOUBLE');
+warning off;  % Suppress the int truncation warning
+hdftype = convert_to_hdf5_type(val);
+tid = H5T.copy(hdftype);
 sid = H5S.create('H5S_SCALAR');
 dsid = H5D.create(fid, name, tid, sid, 'H5P_DEFAULT');
 H5D.write(dsid, tid, 'H5S_ALL', 'H5S_ALL', 'H5P_DEFAULT', val);
 err = 0;
+warning on;
+
 
 
 
 % -----------------------------------------------------------------
-function err = write_integer(fid, name, val)
-warning off;  % Suppress the int truncation warning
-tid = H5T.copy('H5T_NATIVE_ULONG');
-sid = H5S.create('H5S_SCALAR');
-dsid = H5D.create(fid, name, tid, sid, 'H5P_DEFAULT');
-H5D.write(dsid, tid, 'H5S_ALL', 'H5S_ALL', 'H5P_DEFAULT', int32(val));
+function err = write_numeric_array(fid, name, data)
 err = 0;
-warning on;
+data = HDF5_Transpose(data, '2D');
+sizedata = size(data);
+n = sizedata;
+
+tid = -1;
+sid = -1;
+gid = -1;
+dsid = -1;
+
+maxdims = n;
+
+hdftype = convert_to_hdf5_type(data);
+
+try
+
+    sid = H5S.create_simple(numel(n), fliplr(n), fliplr(maxdims));
+    gid = HDF5_CreateGroup(fid, fileparts(name));
+    dsid = H5D.create(gid, name, hdftype, 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 err = write_numeric_array(fid, name, data)
+function err = write_numeric_vector(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
+data = HDF5_Transpose(data, '2D');
+sizedata = length(data);
+n = sizedata;
 
 tid = -1;
 sid = -1;
 gid = -1;
 dsid = -1;
 
 maxdims = n;
+hdftype = convert_to_hdf5_type(data);
 try
 
-    sid = H5S.create_simple(numel(n), fliplr(n), fliplr(maxdims));   
+    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');
+    dsid = H5D.create(gid, name, hdftype, sid, 'H5P_DEFAULT');
     H5D.write(dsid, 'H5ML_DEFAULT', 'H5S_ALL', 'H5S_ALL', 'H5P_DEFAULT', data);
 
 catch
@@ -140,6 +162,7 @@
 
 
 
+
 % ------------------------------------------------------
 function cleanUp(tid, sid, gid, dsid)
 if ~isnumeric(tid)
@@ -156,3 +179,30 @@ function cleanUp(tid, sid, gid, dsid)
 end
 
 
+
+
+% -------------------------------------------------------
+function hdftype = convert_to_hdf5_type(val)
+hdftype = '';
+switch class(val)
+    case 'int8'
+        hdftype = 'H5T_STD_8LE';
+    case 'uint8'
+        hdftype = 'H5T_STD_U8LE';
+    case 'int16'
+        hdftype = 'H5T_STD_16LE';
+    case 'uint16'
+        hdftype = 'H5T_STD_U16LE';
+    case 'int32'
+        hdftype = 'H5T_STD_32LE';
+    case 'uint32'
+        hdftype = 'H5T_STD_U32LE';
+    case 'int64'
+        hdftype = 'H5T_STD_64LE';
+    case 'uint64'
+        hdftype = 'H5T_STD_U64LE';
+    case 'double'
+        hdftype = 'H5T_NATIVE_DOUBLE';
+end
+
+