Models: Phonons: better HTML rendering. Display % remaining.

Scripts/Models/Factory/private/sqw_phon.m

@@ -685,7 +685,7 @@
       seconds   = floor(remaining-hours*3600-minutes*60);
       enddate   = addtodate(now, ceil(remaining), 'second');
 
-      options.status = [ 'ETA ' sprintf('%i:%02i:%02i', hours, minutes, seconds) ', ending on ' datestr(enddate) ];
+      options.status = [ 'ETA ' sprintf('%i:%02i:%02i', hours, minutes, seconds) ', ending on ' datestr(enddate) ' [' num2str(round(move*100.0/size(displacements,1))) '%]' ];
       disp([ mfilename ': ' options.status ]);
       sqw_phonons_htmlreport('', 'status', options);
     end

Scripts/Models/Factory/private/sqw_phonons_get_forces.m

@@ -222,6 +222,11 @@
         [st, result] = system([ precmd 'python ' fullfile(target,'sqw_phonons_forces_iterate.py') ]);
       end
       disp(result)
+      % get how many steps have been computed: name is 'phonon.N[xyz][+-].pckl'
+      move_update = dir(fullfile(target,'phonon.*.pckl'));
+      if numel(move_update) > move
+        move = numel(move_update);
+      end
       if move <= nb_of_steps
         % display ETA. There are nb_of_steps steps.
         % up to now we have done 'move' and it took etime(clock, t)
@@ -235,7 +240,7 @@
         seconds   = floor(remaining-hours*3600-minutes*60);
         enddate   = addtodate(now, ceil(remaining), 'second');
 
-        options.status = [ 'ETA ' sprintf('%i:%02i:%02i', hours, minutes, seconds) ', ending on ' datestr(enddate) '. move ' num2str(move) '/' num2str(nb_of_steps) ];
+        options.status = [ 'ETA ' sprintf('%i:%02i:%02i', hours, minutes, seconds) ', ending on ' datestr(enddate) '. move ' num2str(move) '/' num2str(nb_of_steps) ' [' num2str(round(move*100.0/nb_of_steps)) '%]'];
         disp([ mfilename ': ' options.status ]);
         sqw_phonons_htmlreport('', 'status', options);
       end

Scripts/Models/Factory/private/sqw_phonons_htmlreport.m

@@ -174,16 +174,20 @@ function sqw_phonons_htmlreport_table(fid, options, name)
   '.vtk Visualization Toolkit (VTK) file which can be viewed with <a href="http://www.paraview.org/">ParaView</a>, <a href="http://code.enthought.com/projects/mayavi/">Mayavi2</a>, <a href="https://wci.llnl.gov/simulation/computer-codes/visit/executables">VisIt</a>, <a href="https://www.slicer.org/">Slicer4</a>' ...
   '.mrc MRC Electron density map, to be visualized with <a href="http://www.pymol.org/">PyMol</a>, <a href="http://www.ks.uiuc.edu/Research/vmd/">VMD</a>, <a href="http://www.cgl.ucsf.edu/chimera/">Chimera</a>, <a href="http://www.yasara.org/">Yasara</a>, <a href="http://mem.ibs.fr/VEDA/">VEDA</a>' ...
   '.xhtml Extensible Web page. You can rotate the object (left mouse button), zoom (right mouse button), and pan (middle mouse button).', ...
+  '.fits 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>.', ...
+  '.tiff <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>.' ...
     }
 
     [index1, index2] = strtok([ name index{1} ]);
     if ~isempty(dir(fullfile(options.target,index1)))
       % the file exists
       if strcmp(index1, [ name '.png' ])
-        fprintf(fid, '<div style="text-align:center"><a href="%s"><img src="%s" align="middle" title="%s"></a></div><br>\n', index1, index1, index1);
+        fprintf(fid, '<div style="text-align:center"><a href="%s"><img src="%s" align="middle" title="%s"></a><br>(try the <a href="%s">TIFF file</a> in case the axes are not shown)</div><br>\n', index1, index1, index1, [ name '.tiff' ]);
       elseif strcmp(index1, [ name '.html' ])
+        % embed a frame
         fprintf(fid, '<div style="text-align:center"><iframe src="%s" align="middle" width="480" height="480"></iframe><br>%s<br>(<a href="%s" target=_blank>open in external window</a>)<br></div><br>\n', index1, index2, index1);
       elseif strcmp(index1, [ name '.xhtml' ])
+        % embed an x3dom frame
         fprintf(fid, [ '<div style="text-align:center"><iframe src="%s" align="middle" width="700" height="850"></iframe><br>\n' ...
         '%s<br>(<a href="%s" target=_blank>open in external window</a>)<br>\n' ...
         'The <font color="blue">blue</font> axis is the Energy (meV), the <font color="red">red</font> axis is QK (rlu), the <font color="green">green</font> axis is QL (rlu).<br>\n' ...
@@ -390,7 +394,9 @@ function sqw_phonons_htmlreport_error(fid, options, message)
     fprintf(fid, '<h3><a name="kpath"></a>The dispersion along principal directions</h3>\n');
     fprintf(fid, 'The dispersion curves along the principal axes is shown in log10 scale.<br>\n');
     builtin('save', fullfile(options.target, 'Phonon_kpath.mat'), 'Phonon_kpath');
-    save(Phonon_kpath, fullfile(options.target, 'Phonon_kpath.png'), 'png', 'view2 tight');
+    save(Phonon_kpath, fullfile(options.target, 'Phonon_kpath.png'), 'png data');
+    save(Phonon_kpath, fullfile(options.target, 'Phonon_kpath.fits'), 'fits');
+    save(Phonon_kpath, fullfile(options.target, 'Phonon_kpath.tiff'), 'tiff');
     save(Phonon_kpath, fullfile(options.target, 'Phonon_kpath.dat'), 'dat data');
     save(Phonon_kpath, fullfile(options.target, 'Phonon_kpath.svg'), 'svg', 'view2 tight');
     save(Phonon_kpath, fullfile(options.target, 'Phonon_kpath.pdf'), 'pdf', 'view2 tight');
@@ -471,7 +477,9 @@ function sqw_phonons_htmlreport_eval_3D(fid, options, object)
   fprintf(fid, 'The powder average S(q,w) is shown below:<br>\n');
 
   builtin('save', fullfile(options.target, 'Phonon_powder.mat'), 'Phonon_powder');
-  saveas(log_Phonon_powder, fullfile(options.target, 'Phonon_powder.png'),'png','tight view2');
+  saveas(log_Phonon_powder, fullfile(options.target, 'Phonon_powder.png'),'png data');
+  saveas(log_Phonon_powder, fullfile(options.target, 'Phonon_powder.fits'),'fits');
+  saveas(log_Phonon_powder, fullfile(options.target, 'Phonon_powder.tiff'),'tiff');
   saveas(log_Phonon_powder, fullfile(options.target, 'Phonon_powder.fig'), 'fig', 'tight');
   saveas(Phonon_powder, fullfile(options.target, 'Phonon_powder.dat'), 'dat data');
   saveas(log_Phonon_powder, fullfile(options.target, 'Phonon_powder.pdf'), 'pdf', 'tight view2');

Scripts/Models/Factory/sqw_phonons.m

@@ -317,6 +317,7 @@
     options.duration = 0;
   end
   Phonon_Model = signal;
+  if ~isdir(options.target), mkdir(options.target); end
   builtin('save', fullfile(options.target, 'Phonon_Model.mat'), 'Phonon_Model');
 
   sqw_phonons_htmlreport('', 'create_atoms', options);