Debugged autoprocess_to_pdf.m and export_depth_profiles.m to ensure t…

…hat metafile processing with planes specified in the metafile works well.

src/fnc/export_data_from_input_files.m

@@ -13,7 +13,6 @@ function export_data_from_input_files(varnames, foutname, t1, t2)
 % filename of the final output
 fn = [foutname,'.dac']; 
 
-fprintf(1,'\nExporting data to %s ... \n',fn); 
 fid=fopen(fn,'w');
 %fid=1;
 
@@ -25,4 +24,5 @@ function export_data_from_input_files(varnames, foutname, t1, t2)
  fprintf(fid,fmt2, table2array(t2(ii,:)));
 end
 fclose(fid);
-fprintf(1,'Done.\n'); 
+
+fprintf(1,'NOTE: Complete data exported to %s\n',fn); 

src/fnc/getratiodata.m

@@ -87,7 +87,8 @@
 
  else
  % cells are not defined, so take data for all cells
- disp(['** Classification file ',fncells,' not found. All cells treated as equal (class "a").']);
+ fprintf(1, '** Classification file %s not found.\n', fncells);
+ fprintf(1, ' All cells treated as equal (class "a").\n');
  ii=1; d=[];
  d{ii} = r(:,4:5);
  cellid{ii}=r(:,1);

src/lookatnanosims.m

@@ -184,6 +184,24 @@
  % errors down the line (e.g., when one wanted
  % to display lateral profiles). This bug has
  % been fixed now.
+LANS_version = '2023-08-03'; % Bugs in export_depth_profiles.m fixed.
+ % Now it is again possible, without errors, to
+ % use metafile processing for plotting depth
+ % profiles of ion counts and ion count ratios
+ % in ROIs. By default, depth profiles in all
+ % planes selected during the processing of the
+ % individual datasets are plotted (and exported).
+ % One can change this behaviour by including a
+ % range of planes (e.g., [5:25]) for each
+ % individual dataset in the metafile. The range
+ % should be added at the end of the
+ % corresponding line. Note that this range is
+ % also used when doing Auto-process datasets
+ % during metafile processing. In this case,
+ % when the data is reprocessed, the total ion
+ % counts, and the corresponding ion count ratios,
+ % will be calculated by accumulating only the
+ % specified planes.
 
 % name of the external image file (empty by default)
 EXTERNAL_IMAGEFILE = '';

src/postprocess/autoprocess_to_pdf.m

@@ -16,7 +16,8 @@ function autoprocess_to_pdf(s, handles)
 
 % get instructions from the meta file
 all_cell_types = regexprep(s.cellclasses,' ','');
-[id,fname,tmnt,ct,xyz,nf,all,plot3d, basedir, image_range]=getmetainstructions(s.metafile, all_cell_types, s.plot3d);
+[id, fname, tmnt, ct, xyz, nf, all, plot3d, basedir, image_range] = ...
+ getmetainstructions(s.metafile, all_cell_types, s.plot3d);
 
 % the output filename will have the same base-name as the metafile
 if(~isempty(s.metafile))
@@ -105,13 +106,14 @@ function autoprocess_to_pdf(s, handles)
  % exist, do accumulation based on the information in the
  % main GUI.
  prefsfile = [s.base_dir fname{k} filesep s.prefsfile];
- if exist(prefsfile)
+ if exist(prefsfile,'file')
 
  a=load(prefsfile);
  fprintf(1,'Preferences loaded from %s\n',prefsfile);
 
  images=[];
  for j=1:length(p.mass)
+
  switch j
  case 1, ims = str2num(a.h.edit12.string); mname = a.h.edit3.string;
  case 2, ims = str2num(a.h.edit12.string); mname = a.h.edit4.string;
@@ -122,11 +124,29 @@ function autoprocess_to_pdf(s, handles)
  case 7, ims = str2num(a.h.edit12.string); mname = a.h.edit9.string;
  case 8, ims = str2num(a.h.edit12.string); mname = a.h.edit74.string;
  end
- images{j}=ims;
+
+ if isempty(ims)
+ images{j} = p.planes;
+ else
+ images{j}=ims;
+ end
+
+ % force image_range from the metafile, if not empty
+ b=eval(image_range{k});
+ if ~isempty(b)
+ if j==1
+ fprintf(1,'WARNING: Updating planes that will be accumulated based on the value in the metafile.\n')
+ fprintf(1,' Original: [%d:%d]\n', min(images{j}), max(images{j}));
+ fprintf(1,' Updated: %s\n', image_range{k});
+ end
+ images{j}=b;
+ end
+
  if ~strcmp(p.mass{j},mname)
  fprintf(1,'WARNING: Mass %s in the loaded IM file renamed to %s based on info in %s\n',p.mass{j},mname,prefsfile);
  p.mass{j} = mname;
  end
+
  end
 
  find_alignments = a.h.checkbox7.value;
@@ -137,7 +157,8 @@ function autoprocess_to_pdf(s, handles)
  if find_alignments
  xyalignfile = [s.base_dir fname{k} filesep s.xyalignfile];
 
- if exist(xyalignfile)
+ if exist(xyalignfile,'file')
+
  % load the previously calculated and stored alignment data
  b=load(xyalignfile);
  fprintf(1,'XY-alignment loaded from %s\n',xyalignfile);
@@ -146,8 +167,10 @@ function autoprocess_to_pdf(s, handles)
  end
  if isfield(b,'tforms')
  tforms = b.tforms;
- end 
+ end 
+
  else
+
  % if the xyalignfile does not exist, i.e., the im file has
  % never been processed or was processed but without image
  % alignment, autoalign images using the base mass 
@@ -162,28 +185,29 @@ function autoprocess_to_pdf(s, handles)
  [tforms, images, xyalign, ~, ~] = findimagealignments2(p.im{bm},[],[1:p.width],[1:p.height],0);
 
  end
+
  else
  images={str2num(a.h.edit12.string)};
  end
 
  % align only selected planes based on info in metafile
- if ~isempty(str2num(image_range{k}))
- for ik=1:length(images)
- images{ik} = str2num(image_range{k});
- end
- end
+ %if ~isempty(str2num(image_range{k}))
+ % for ik=1:length(images)
+ % images{ik} = str2num(image_range{k});
+ % end
+ %end
 
  % align and accumulate masses
- if ~p.planes_aligned && ~isempty(xyalign)
- if ~isempty(tforms)
- [p.accu_im, p.im]=accumulate_images2(p.im, tforms, p.mass, images, ones(1,length(p.mass)));
- else
- [p.accu_im, p.im]=accumulate_images(p.im, xyalign, p.mass, images, ones(1,length(p.mass)));
- end
- p.planes_aligned = 1;
- else
- [p.accu_im, p.im]=accumulate_images(p.im, xyalign, find_alignments, p.mass, images, zeros(1,length(p.mass)));
- end
+ %if ~p.planes_aligned && ~isempty(xyalign)
+ % if ~isempty(tforms)
+ % [p.accu_im, p.im]=accumulate_images2(p.im, tforms, p.mass, images, ones(1,length(p.mass)));
+ % else
+ % [p.accu_im, p.im]=accumulate_images(p.im, xyalign, p.mass, images, ones(1,length(p.mass)));
+ % end
+ % p.planes_aligned = 1;
+ %else
+ % [p.accu_im, p.im]=accumulate_images(p.im, xyalign, find_alignments, p.mass, images, zeros(1,length(p.mass)));
+ %end
 
  if isfield(a.h,'shift_columns_rows')
  shift_columns_rows = a.h.shift_columns_rows;
@@ -211,24 +235,39 @@ function autoprocess_to_pdf(s, handles)
  % [p.accu_im, p.im]=accumulate_images(p.im, xyalign, s.p.find_alignments, p.mass, {images}, ones(1,length(p.mass)));
 
  % align and accumulate masses
- if ~isempty(xyalign)
- if ~isempty(tforms)
- [p.accu_im, p.im]=accumulate_images2(p.im, tforms, p.mass, {images}, ones(1,length(p.mass)));
- %[p.accu_im, p.im]=accumulate_images2(p.im, tforms, p.mass, [], ones(1,length(p.mass)));
- else
- [p.accu_im, p.im]=accumulate_images(p.im, xyalign, p.mass, {images}, ones(1,length(p.mass)));
- %[p.accu_im, p.im]=accumulate_images(p.im, xyalign, p.mass, [], ones(1,length(p.mass)));
- end
- end
+ %if ~isempty(xyalign)
+ % if ~isempty(tforms)
+ % [p.accu_im, p.im]=accumulate_images2(p.im, tforms, p.mass, {images}, ones(1,length(p.mass)));
+ % %[p.accu_im, p.im]=accumulate_images2(p.im, tforms, p.mass, [], ones(1,length(p.mass)));
+ % else
+ % [p.accu_im, p.im]=accumulate_images(p.im, xyalign, p.mass, {images}, ones(1,length(p.mass)));
+ % %[p.accu_im, p.im]=accumulate_images(p.im, xyalign, p.mass, [], ones(1,length(p.mass)));
+ % end
+ %end
 
- shift_columns_rows = [0 0 0 0];
+ shift_columns_rows = s.p.shift_columns_rows;
 
  end 
 
  % shift columns or rows of the images, if needed, according to the
  % information stored in shift_columns_rows flags
  p.im = shift_columns_rows_images(p.im, shift_columns_rows);
- p.accu_im = shift_columns_rows_images(p.accu_im, shift_columns_rows); 
+ %p.accu_im = shift_columns_rows_images(p.accu_im, shift_columns_rows); 
+
+ % align and accumulate masses
+ if ~p.planes_aligned && ~isempty(xyalign) && ~isempty(tforms)
+ if isempty(tforms)
+ % old algorithm
+ [p.accu_im, p.im]=accumulate_images(p.im, xyalign, p.mass, images, ones(1,length(p.mass)));
+ else
+ % new algorithm
+ [p.accu_im, p.im]=accumulate_images2(p.im, tforms, p.mass, images, ones(1,length(p.mass)));
+ end
+ p.planes_aligned = 1;
+ else
+ % by default, use old algorithm
+ [p.accu_im, p.im]=accumulate_images2(p.im, xyalign, p.mass, images, zeros(1,length(p.mass)));
+ end
 
  else
 
@@ -254,7 +293,7 @@ function autoprocess_to_pdf(s, handles)
 
  % load cells from disk, if the file exists, otherwise set cells to zero
  cellfile = [s.base_dir fname{k} filesep s.cellfile];
- if exist(cellfile)
+ if exist(cellfile, 'file')
  a=load(cellfile);
  Maskimg = a.Maskimg;
  fprintf(1,'ROIs loaded from %s\n',cellfile);
@@ -269,6 +308,7 @@ function autoprocess_to_pdf(s, handles)
  fig173 = 173; % "random" figure number where all the images will be displayed
 
  % display and export all masses as PDF
+
  % because there is no general information about the right scale,
  % the images will be autoscaled in the same way as if the
  % auto-scale function is chosen from the menu in the GUI