iData: fix in save images (ndims=2 'data' get raw image/no axes)

Objects/@iData/private/iData_private_cleannaninf.m

@@ -1,17 +1,18 @@
-function s=iData_private_cleannaninf(s)
+function s=iData_private_cleannaninf(s, ratio)
 % iData_private_cleannaninf: clean NaNs and Infs from a numerical field
 %
 
+if nargin < 2, ratio=10; end
 if isa(s,'iData')
   if numel(s) > 1
     a = [];
     for index=1:numel(s)
-      a = [ a ; feval(mfilename, s(index)) ];
+      a = [ a ; feval(mfilename, s(index), ratio) ];
     end
     s = a;
   else
-    s=set(s,'Signal',iData_private_cleannaninf(get(s,'Signal')));
-    s=set(s,'Error', iData_private_cleannaninf(get(s,'Error')));
+    s=set(s,'Signal',iData_private_cleannaninf(get(s,'Signal'), ratio));
+    s=set(s,'Error', iData_private_cleannaninf(get(s,'Error'), ratio));
   end
   return
 end
@@ -26,12 +27,12 @@
 
   S(isnan(S)) = 0;
   if ~isempty(mins)
-    if mins<0, S(find(S == -Inf)) = mins*100;
-    else       S(find(S == -Inf)) = mins/100; end
+    if mins<0, S(find(S == -Inf)) = mins*ratio;
+    else       S(find(S == -Inf)) = mins/ratio; end
   end
   if ~isempty(maxs)
-    if maxs>0, S(find(S == +Inf)) = maxs*100;
-    else       S(find(S == +Inf)) = maxs/100; end
+    if maxs>0, S(find(S == +Inf)) = maxs*ratio;
+    else       S(find(S == +Inf)) = maxs/ratio; end
   end
   s = double(reshape(S, size(s)));
 end

Objects/@iData/private/iData_private_saveas_analyze.m

@@ -19,6 +19,7 @@
 dim=size(a);
 siz=zeros(size(dim));
 
+a = iData_private_cleannaninf(a);
 x=getaxis(a,1);
 y=getaxis(a,2);
 z=getaxis(a,3);

Objects/@iData/private/iData_private_saveas_html.m

@@ -121,7 +121,13 @@
   % create output from the figure: png pdf fig
   basename     = fullfile(target, 'img', [ 'iFit_DataSet_' a.Tag ]);
   basename_img = fullfile('img', [ 'iFit_DataSet_' a.Tag ]);
-  saveas(f, basename, 'png');
+  if ndims(a) == 2
+    saveas(a, basename, 'png data');  % just the image for 2D data sets, else getframe
+  elseif ndims(a) == 3
+    saveas(a, basename, 'png', 'tight view3');
+  else
+    saveas(a, basename, 'png', 'tight');
+  end
 
   % only export when not in 'data' mode (flat HTML with minimal content)
   if isempty(strfind(format, 'data')) && isempty(strfind(format, 'flat'))
@@ -132,18 +138,19 @@
 
   % export object into a number of usable formats
   % 1D: mat dat/data hdf5/mantid png json      xml      yaml      nc fig pdf svg
-  % 2D: mat dat/data hdf5/mantid png json      xml      yaml      nc fig pdf svg 
+  % 2D: mat dat/data hdf5/mantid png json      xml      yaml      nc fig pdf svg  fits
   % 3D: mat dat/data hdf5/mantid png json/data xml/data yaml/data nc fig pdf vtk mrc nc   
   % nD: mat dat/data hdf5/mantid png json/data xml/data yaml/data nc
-  export       = {'mat','dat data','hdf mantid', 'json','xml','yaml','nc' };
+  export       = {'mat','dat data','hdf mantid', 'json','xml','yaml','nc','tiff' };
   export_label = { ...
   'Matlab binary file. Open with Matlab or <a href="http://ifit.mccode.org">iFit</a>.', ...
   'Flat text file which contains axes and the data set. You will have to reshape the matrix after reading the contents. View with any text editor.', ...
   '<a href="http://www.hdfgroup.org/">NeXus/HDF5</a> data file, to be opened with e.g. <a href="http://www.mantidproject.org/Main_Page">Mantid</a>, <a href="http://www.hdfgroup.org/hdf-java-html/hdfview">hdfview</a> or <a href="http://ifit.mccode.org">iFit</a>.', ...
   '<a href="http://en.wikipedia.org/wiki/JSON">JavaScript Object Notation</a>, to be opened with e.g. JSONView Chrome/Firefox plugin and text editors.', ...
   '<a href="http://www.w3.org/XML/">Extensible Markup Language</a> file, to be opened with e.g. Chrome/Firefox and text editors.', ...
   '<a href="http://en.wikipedia.org/wiki/YAML">YAML</a> interchange format, to be viewed with e.g. text editors.', ...
-  '<a href="http://www.unidata.ucar.edu/software/netcdf/">NetCDF</a> binary file, to be viewed with <a href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html">ncview</a> and <a href="http://www.hdfgroup.org/hdf-java-html/hdfview">hdfview</a>.'};
+  '<a href="http://www.unidata.ucar.edu/software/netcdf/">NetCDF</a> binary file, to be viewed with <a href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html">ncview</a> and <a href="http://www.hdfgroup.org/hdf-java-html/hdfview">hdfview</a>.', ...
+  '<a href="https://en.wikipedia.org/wiki/TIFF">TIFF</a> image file, to be viewed with e.g. <a href="http://rsb.info.nih.gov/ij/">ImageJ</a>, <a href="http://www.gimp.org/">GIMP.</a>.'};
 
   % add 'data' keyword when the object memory size is larger than 10 Mb
   w = whos('a');
@@ -165,6 +172,11 @@
       'Extensible Web page with embeded viewer (X3DOM), to be viewed with Chrome/Firefox.', ...
       'X3D Geometry Scene for <a href="http://castle-engine.sourceforge.net/view3dscene.php">view3dscene</a>, <a href="http://www.instantreality.org/">InstantPlayer</a>, <a href="http://freewrl.sourceforge.net/">FreeWRL</a>' ];
   end
+  if ndims(a) == 2
+    export = [ export 'fits' ];
+    export_label = [ export_label ...
+      'Flexible Image Transport System (<a href="https://fits.gsfc.nasa.gov/fits_home.html">FITS</a>) image, which can be viewed with e.g. <a href="http://rsb.info.nih.gov/ij/">ImageJ</a>, <a href="http://www.gimp.org/">GIMP.</a>.' ];
+  end
   if isempty(strfind(format, 'data')) && isempty(strfind(format, 'flat'))
     for index=1:numel(export)
       f = export{index};
@@ -190,6 +202,9 @@
     fprintf(fid, '<div style="text-align: center;"><a href="%s"><img src="%s" align="middle"></a><br>\n<i>Data: %s</i><br></div>\n', ...
       [ basename_img '.png' ], ...
       [ basename_img '.png' ], titl);
+    if ndims(a) == 2
+      fprintf(fid, '(try the <a href="%s">TIFF file</a> in case the axes are not shown)<br>\n', [ basename_img '.tiff' ]);
+    end
     if ~isempty(m)
       fprintf(fid, '<div style="text-align: center;"><i>Model: %s</i><br></div>\n', m.Name);
     end

Objects/@iData/private/iData_private_saveas_nii.m

@@ -5,7 +5,7 @@
 % Jimmy Shen 23 Oct 2005 (Updated 22 Jan 2014)
 % make_nii, save_nii
 
-
+  a = iData_private_cleannaninf(a);
   nii = make_nii(getaxis(a, 0),[], [], [], char(a));
   % nii.hdr.hist.descrip = char(a);
   save_nii(nii, filename);

Objects/@iData/private/iData_private_saveas_stl.m

@@ -2,6 +2,7 @@
   if ndims(a) == 1    iData_private_warning(mfilename,[ 'Object ' inputname(1) ' ' a.Tag ' 1D does not seem to be exportatble as a ' format ' file. Ignoring.' ]);
     return
   else
+    a = iData_private_cleannaninf(a);
     if ndims(a) == 2
       [x, xlab] = getaxis(a,2); x=double(x);
       [y, ylab] = getaxis(a,1); y=double(y);

Objects/@iData/private/iData_private_saveas_vtk.m

@@ -10,6 +10,7 @@
   return
 end
 
+a = iData_private_cleannaninf(a);
 str=char(a);
 
 if ndims(a) <= 2 && isvector(a) % line, 1D or 2D

Objects/@iData/private/iData_private_saveas_x3d.m

@@ -2,13 +2,15 @@
   % export as a X3D/XHTML file
   % option can contain: axes (display axes), auto to rescale axes in range [0,1]
   % for aspect ratio 1.
+
   titl = char(a);
   titl(titl=='<')='[';
   titl(titl=='>')=']';
   desc = evalc('disp(a)');
   desc(desc=='<')='[';
   desc(desc=='>')=']';
   a = reducevolume(a);
+  a = iData_private_cleannaninf(a);
   x1=min(a); x2=max(a);
   if ndims(a) <= 2
     f=figure('visible','off');

Objects/@iData/saveas.m

@@ -327,11 +327,11 @@
   case 'hdr'  % Analyze volume
     filename = iData_private_saveas_analyze(a, filename);
   case 'mrc'  % MRC map file
-    WriteMRC(getaxis(a,0),1,filename);  % in private
+    WriteMRC(getaxis(iData_private_cleannaninf(a),0),1,filename);  % in private
   case {'fits','fit','fts'} % FITS image
     if ndims(a) == 2
-      a = double(a);
-      fitswrite(a, filename);
+      b = real(double(iData_private_cleannaninf(a,1))); % Signal/Monitor
+      fitswrite(b', filename);
     else
       disp([ mfilename ': Export into ' format ' is only possible for 2D objects, not for ' num2str(ndims(a)) 'D. Use resize to change dimensionality. Ignoring.' ]) 
     end
@@ -340,9 +340,10 @@
   case 'csv'  % Spreadsheet comma separated values file format
     csvwrite(filename, double(a));
   case {'gif','bmp','pbm','pcx','pgm','pnm','ppm','ras','xwd','hdf4','tiff','png','art'}  % bitmap images
-    if ndims(a) == 2
-      b=getaxis(a,0); % Signal/Monitor
-      b=round((b-min(b(:)))/(max(b(:))-min(b(:)))*256);
+    if ndims(a) == 2 && ~isempty(root) % 'data' option
+      b = real(double(iData_private_cleannaninf(a,1)));
+      b = round((b-min(b(:)))/(max(b(:))-min(b(:)))*256);
+      b = flipud(b);
     else
       f = getframe(a,[],options);
       b = f.cdata;