rename modified xmltree to avoid collision, reduce excess whitespace

@xmltree/branch.m → @xmltreemod/branch.m

@@ -17,7 +17,7 @@
     error('[XMLTree] Invalid UID.');
 end
 
-subtree = xmltree;
+subtree = xmltreemod;
 subtree = set(subtree,root(subtree),'name',tree.tree{uid}.name);
 %- fix by Piotr Dollar to copy attributes for the root node:
 subtree = set(subtree,root(subtree),'attributes',tree.tree{uid}.attributes); 

@xmltree/private/struct2xml.m → @xmltreemod/private/struct2xml.m

@@ -24,7 +24,7 @@
 end
 
 % Create an empty XML tree
-tree = xmltree;
+tree = xmltreemod;
 
 % Root element is the input argument name
 tree = set(tree,root(tree),'name',rootname);

@xmltree/xmltree.m → @xmltreemod/xmltreemod.m

@@ -1,4 +1,4 @@
-function tree = xmltree(varargin)
+function tree = xmltreemod(varargin)
 % XMLTREE/XMLTREE Constructor of the XMLTree class
 % FORMAT tree = xmltree(varargin)
 % 
@@ -25,9 +25,9 @@
         'parent',[],...
         'uid',1);
     tree.filename = '';
-    tree = class(tree,'xmltree');
+    tree = class(tree,'xmltreemod');
 
-elseif isa(varargin{1},'xmltree')
+elseif isa(varargin{1},'xmltreemod')
     tree = varargin{1};
 
 elseif ischar(varargin{1})
@@ -47,7 +47,7 @@
         tree.tree = xml_parser(xmlstr);
         tree.filename = varargin{1};
     end
-    tree = class(tree,'xmltree');
+    tree = class(tree,'xmltreemod');
 
 elseif isstruct(varargin{1})
     if nargin > 1

cifti_write.m

@@ -17,7 +17,7 @@ function cifti_write(cifti, filename, varargin)
     %   >> cifti.cdata = outdata;
     %   >> cifti.diminfo{2} = cifti_diminfo_make_scalars(size(outdata, 2));
     %   >> cifti_write(cifti, 'ciftiout.dscalar.nii');
-    libversion = '2.0.0';
+    libversion = '2.0.1';
     options = myargparse(varargin, {'stacklevel', 'disableprovenance', 'keepmetadata'}); %stacklevel is an implementation detail, don't add to help
     if isempty(options.stacklevel) %stacklevel is so that so it doesn't get "ciftisave" all the time
         options.stacklevel = 2;

private/cifti_parse_xml.m

@@ -5,7 +5,7 @@
     if any(nulls)
         bytes = bytes(1:(find(nulls, 1) - 1));
     end
-    tree = xmltree(bytes);
+    tree = xmltreemod(bytes);
     setfilename(tree, filename);%probably helps with error messages for malformed XML?
     attrs = myattrs(tree);
     for attr = attrs

private/cifti_write_xml.m

@@ -6,7 +6,7 @@
             cifti.metadata = cifti_metadata_set(cifti.metadata, 'ParentProvenance', prov);
         end
     end
-    tree = xmltree();
+    tree = xmltreemod();
     root_uid = root(tree);
     tree = set(tree, root_uid, 'name', 'CIFTI');
     tree = attributes(tree, 'add', root_uid, 'Version', '2');
@@ -79,7 +79,7 @@
                 tree = attributes(tree, 'add', model_uid, 'ModelType', 'CIFTI_MODEL_TYPE_SURFACE');
                 tree = attributes(tree, 'add', model_uid, 'SurfaceNumberOfVertices', num2str(model{1}.numvert));
                 [tree, vert_uid] = add(tree, model_uid, 'element', 'VertexIndices');
-                tree = add(tree, vert_uid, 'chardata', matrix2str(model{1}.vertlist(:)')); %NOTE: 0-based vertex indices
+                tree = add(tree, vert_uid, 'chardata', matrix2str_int(model{1}.vertlist(:)')); %NOTE: 0-based vertex indices
             case 'vox'
                 if size(model{1}.voxlist, 1) == model{1}.count && size(model{1}.voxlist, 2) == 3
                     warning('model voxel list appears to be transposed');
@@ -96,7 +96,7 @@
                 end
                 tree = attributes(tree, 'add', model_uid, 'ModelType', 'CIFTI_MODEL_TYPE_VOXELS');
                 [tree, vox_uid] = add(tree, model_uid, 'element', 'VoxelIndicesIJK');
-                tree = add(tree, vox_uid, 'chardata', matrix2str(model{1}.voxlist'));
+                tree = add(tree, vox_uid, 'chardata', matrix2str_int(model{1}.voxlist'));
             otherwise
                 error(['unrecignized brain model type "' model{1}.type '"']);
         end
@@ -167,7 +167,24 @@
     tree = add(tree, tfm_uid, 'chardata', matrix2str(modsform));
 end
 
-%TODO: num2str(..., 6) on a matrix adds a *lot* of whitespace, fix?
+%num2str(..., 6) on a matrix adds a *lot* of whitespace, so make a version for integers
+function outstring = matrix2str_int(input)
+    %matlab 2016a doesn't have join(), so we can't write a one-liner
+    matchar = num2str(input);
+    expectedlength = length(matchar(:)) + size(matchar, 1);
+    outstring = char(zeros(1, expectedlength, 'int8'));
+    curpos = 1;
+    for i = 1:size(matchar, 1)
+        addstring = [char(10) matchar(i, :)]; %hack: xml looks better with a newline before the matrix
+        outstring(curpos:(curpos + length(addstring) - 1)) = addstring;
+        curpos = curpos + length(addstring);
+    end
+    if any(outstring == 0) %check for bad length computation
+        warning('internal problem in cifti xml matrix2str()');
+        outstring(outstring == 0) = []; %delete the nulls
+    end
+end
+
 function outstring = matrix2str(input)
     %matlab 2016a doesn't have join(), so we can't write a one-liner
     matchar = num2str(input, 6); %6 significant figures for float improves round-trip consistency
@@ -216,7 +233,7 @@
                 error('invalid voxlist content in cifti struct');
             end
             [tree, vox_uid] = add(tree, parcel_uid, 'element', 'VoxelIndicesIJK');
-            tree = add(tree, vox_uid, 'chardata', matrix2str(map.parcels(i).voxlist'));
+            tree = add(tree, vox_uid, 'chardata', matrix2str_int(map.parcels(i).voxlist'));
         end
         for j = 1:length(map.parcels(i).surfs)
             numverts = -1;
@@ -234,7 +251,7 @@
             end
             [tree, vert_uid] = add(tree, parcel_uid, 'element', 'Vertices');
             tree = attributes(tree, 'add', vert_uid, 'BrainStructure', friendly_to_cifti_structure(map.parcels(i).surfs(j).struct));
-            tree = add(tree, vert_uid, 'chardata', matrix2str(map.parcels(i).surfs(j).vertlist));
+            tree = add(tree, vert_uid, 'chardata', matrix2str_int(map.parcels(i).surfs(j).vertlist));
         end
     end
 end