Merge with SPM changes

gllmflndn · Nov 8, 2023 · d270f75 · d270f75
1 parent 6ce36fd
commit d270f75
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Showing 6 changed files with 62 additions and 40 deletions.
diff --git a/@gifti/gifti.m b/@gifti/gifti.m
@@ -21,8 +21,8 @@
             this = varargin{1};
 
         elseif isstruct(varargin{1})
-            f       = {'faces', 'face', 'tri' 'vertices', 'vert', 'pnt', 'cdata', 'indices'};
-            ff      = {'faces', 'faces', 'faces', 'vertices', 'vertices', 'vertices', 'cdata', 'indices'};
+            f       = {'faces', 'face', 'tri' 'vertices', 'vert', 'pnt', 'pos', 'cdata', 'indices'};
+            ff      = {'faces', 'faces', 'faces', 'vertices', 'vertices', 'vertices', 'vertices', 'cdata', 'indices'};
             [c, ia] = intersect(f,fieldnames(varargin{1}));
             if ~isempty(c)
                 this = gifti;

diff --git a/@gifti/private/Makefile b/@gifti/private/Makefile
@@ -1,15 +1,13 @@
 #!/usr/bin/env make -f
 # GIfTI Makefile
 #
-# Copyright (C) 2015 Wellcome Trust Centre for Neuroimaging
-#
-# $Id: Makefile 6704 2016-01-29 17:23:13Z guillaume $
+# Copyright (C) 2008-2023 Wellcome Centre for Human Neuroimaging
 
 include Makefile.var
 
-SPMMEX = zstream.$(SUF) xml_parser.$(SUF) base64.$(SUF)
+SPMMEX = zstream.$(MEXEXT) xml_parser.$(MEXEXT) base64.$(MEXEXT)
 
-ifeq (mex,$(SUF))
+ifeq (mex,$(MEXEXT))
   export CFLAGS = $(shell $(MEX) -p CFLAGS) -std=c99
 else
   ifeq (windows,$(PLATFORM))
@@ -34,8 +32,8 @@ install:
 tarball: all
 	$(TAR) cf spm_mex.tar $(SPMMEX)
 
-%.$(SUF) : %.c
+%.$(MEXEXT) : %.c
 	$(MEX) $< $(MEXEND)
 
-xml_parser.$(SUF): xml_parser.c yxml.c yxml.h
+xml_parser.$(MEXEXT): xml_parser.c yxml.c yxml.h
 	$(MEX) $< yxml.c $(MEXEND)
diff --git a/@gifti/private/Makefile.var b/@gifti/private/Makefile.var
@@ -41,25 +41,25 @@ MOVE           = mv -f
 TAR            = tar
 ZIP            = gzip -f
 
-ifndef SUF
+ifndef MEXEXT
   ifndef PLATFORM
     PLATFORM   = $(shell $(UNAME))
   endif
   ##### Linux #####
   ifeq (Linux,$(PLATFORM))
-    SUF        = mexa64
+    MEXEXT     = mexa64
   endif
   ##### MacOS #####
   ifeq (Darwin,$(PLATFORM))
-    SUF        = mexmaci64
+    MEXEXT     = mexmaci64
   endif
   ##### Windows #####
   ifeq (MINGW32,$(word 1,$(subst _, ,$(PLATFORM)))) # MSC
     override PLATFORM = windows
     ifeq (x86,$(PROCESSOR_ARCHITECTURE))
-      SUF      = mexw32
+      MEXEXT   = mexw32
     else
-      SUF      = mexw64
+      MEXEXT   = mexw64
     endif
     MEXBIN     = cmd /c "mex.bat
     MEXOPTS   += -DSPM_WIN32
@@ -68,19 +68,19 @@ ifndef SUF
     AR         = lib.exe /out:
   endif
   ifeq (MSYS,$(word 1,$(subst _, ,$(PLATFORM)))) # GCC
-    SUF        = mexw64
+    MEXEXT     = mexw64
     MEXOPTS   += -DSPM_WIN32
     MOSUF      = obj
   endif
   #### Octave ####
   ifeq (octave,$(PLATFORM))
     MEXBIN     = mkoctfile
     MEXOPTS    = --mex
-    SUF        = mex
+    MEXEXT     = mex
     override PLATFORM = $(shell $(UNAME))
   endif
   #### Otherwise ####
-  ifndef SUF
+  ifndef MEXEXT
     $(error Unknowm platform $(PLATFORM))
   endif
 endif

diff --git a/@gifti/private/gifti_read.m b/@gifti/private/gifti_read.m
@@ -203,6 +203,10 @@
             % special case that does not require permuting
             d = reshape(d,s.Dim);
         else
+            if isa(d,'file_array')
+                %warning('Memory-mapped data are loaded into memory');
+                d = subsref(d,substruct('()',repmat({':'},1,numel(d.dim))));
+            end
             d = permute(reshape(d,fliplr(s.Dim)),length(s.Dim):-1:1);
         end
     case 'ColumnMajorOrder'

diff --git a/@gifti/private/obj_read.m b/@gifti/private/obj_read.m
@@ -40,7 +40,7 @@
                 otherwise
                     v = sscanf(l(2:end),'%f %f %f');
                     if numel(v) > 3, v = v(1:3); end
-                    M.vertices(size(M.vertices,1)+1,:) = v;
+                    M.vertices(:,size(M.vertices,2)+1) = v;
             end
         case 'f'
             f = sscanf(l(2:end),'%d %d %d');
@@ -64,8 +64,8 @@
                 end
             end
             i = find(f<0);
-            if isempty(i), f(i) = size(M.vertices,1) + f(i); end
-            M.faces(size(M.faces,1)+1,:) = f;
+            if isempty(i), f(i) = size(M.vertices,2) + f(i); end
+            M.faces(:,size(M.faces,2)+1) = f;
         case 'o'
             fprintf('Ignoring named objects.\n');
         case 'g'
@@ -82,3 +82,6 @@
 end
 
 fclose(fid);
+
+M.vertices = M.vertices';
+M.faces = M.faces';
diff --git a/@gifti/save.m b/@gifti/save.m
@@ -1,11 +1,14 @@
-function save(this,filename,encoding)
+function save(this,filename,encoding,ordering)
 % Save GIfTI object in a GIfTI format file
 % FORMAT save(this,filename,encoding)
 % this      - GIfTI object
 % filename  - name of GIfTI file to be created [Default: 'untitled.gii']
 % encoding  - optional argument to specify encoding format, among
 %             ASCII, Base64Binary, GZipBase64Binary, ExternalFileBinary.
 %             [Default: 'GZipBase64Binary']
+% ordering  - optional argument to specify array element ordering, among
+%             ColumnMajorOrder, RowMajorOrder
+%             [Default: 'ColumnMajorOrder']
 %__________________________________________________________________________
 
 % Guillaume Flandin
@@ -24,6 +27,24 @@ function save(this,filename,encoding)
 end
 filename = fullfile(p,[f e]);
 
+% Check encoding
+%--------------------------------------------------------------------------
+if nargin < 3 || isempty(encoding), encoding = 'GZipBase64Binary'; end
+switch encoding
+    case {'ASCII','Base64Binary','GZipBase64Binary','ExternalFileBinary'}
+    otherwise
+        error('Unknown encoding.');
+end
+
+% Check order
+%--------------------------------------------------------------------------
+if nargin < 4 || isempty(ordering), ordering = 'ColumnMajorOrder'; end
+switch ordering
+    case {'ColumnMajorOrder','RowMajorOrder'}
+    otherwise
+        error('Unknown ordering.');
+end
+
 % Open file for writing
 %--------------------------------------------------------------------------
 fid = fopen(filename,'wt');
@@ -33,23 +54,17 @@ function save(this,filename,encoding)
 
 % Write file
 %--------------------------------------------------------------------------
-if nargin < 3, encoding = 'GZipBase64Binary'; end
-switch encoding
-    case {'ASCII','Base64Binary','GZipBase64Binary','ExternalFileBinary'}
-    otherwise
-        error('Unknown encoding.');
-end
-fid = save_gii(fid,this,encoding);
+fid = save_gii(fid,this,encoding,ordering);
 
 % Close file
 %--------------------------------------------------------------------------
 fclose(fid);
 
 
 %==========================================================================
-% function fid = save_gii(fid,this,encoding)
+% function fid = save_gii(fid,this,encoding,ordering)
 %==========================================================================
-function fid = save_gii(fid,this,encoding)
+function fid = save_gii(fid,this,encoding,ordering)
 
 % Defaults for DataArray's attributes
 %--------------------------------------------------------------------------
@@ -81,8 +96,7 @@ function save(this,filename,encoding)
     for j=1:length(d)
         this.data{i}.attributes.(sprintf('Dim%d',j-1)) = num2str(d(j));
     end
-    % Enforce some conventions
-    this.data{i}.attributes.ArrayIndexingOrder = 'ColumnMajorOrder';
+    this.data{i}.attributes.ArrayIndexingOrder = ordering;
     if ~isfield(this.data{i}.attributes,'DataType') || ...
         isempty(this.data{i}.attributes.DataType)
         warning('DataType set to default: %s', def.DataType);
@@ -206,7 +220,7 @@ function save(this,filename,encoding)
         fprintf(fid,'%s</CoordinateSystemTransformMatrix>\n',o(2));
     end
 
-    % Data (saved using MATLAB's ColumnMajorOrder)
+    % Data
     %----------------------------------------------------------------------
     fprintf(fid,'%s<Data>',o(2));
     tp = getdict;
@@ -215,21 +229,24 @@ function save(this,filename,encoding)
     catch
         error('[GIFTI] Unknown DataType.');
     end
+    dat = this.data{i}.data;
+    if isa(dat,'file_array')
+        dat = subsref(dat,substruct('()',repmat({':'},1,numel(dat.dim))));
+    end
+    if strcmp(this.data{i}.attributes.ArrayIndexingOrder,'RowMajorOrder')
+        dat = dat.';
+    end
     switch this.data{i}.attributes.Encoding
         case 'ASCII'
-            fprintf(fid, [tp.format ' '], this.data{i}.data);
+            fprintf(fid, [tp.format ' '], dat);
         case 'Base64Binary'
-            fwrite(fid,base64('encode',typecast(this.data{i}.data(:),'uint8')),'uint8');
+            fprintf(fid,base64encode(typecast(dat(:),'uint8')));
             % uses native machine format
         case 'GZipBase64Binary'
-            fwrite(fid,base64('encode',zstream('C',typecast(this.data{i}.data(:),'uint8'))),'uint8');
+            fprintf(fid,base64encode(zstream('C',typecast(dat(:),'uint8'))));
             % uses native machine format
         case 'ExternalFileBinary'
             extfilename = this.data{i}.attributes.ExternalFileName;
-            dat = this.data{i}.data;
-            if isa(dat,'file_array')
-                dat = subsref(dat,substruct('()',repmat({':'},1,numel(dat.dim))));
-            end
             if ~def.offset
                 fide = fopen(extfilename,'w'); % uses native machine format
             else