fixing a bug in alignment of external image due to autoscaling

new LANS version from now on
alignment gui still needs to be updated for the windows version of LANS.

src/fnc/align2images.m

@@ -1,5 +1,6 @@
 %function [im1_out,im2_xyscale,rgb,f101]=align2images(v1,v2,im1,im2,im1_xyscale,im2_xyscale,log_flag1,log_flag2)
-function [im1_out,im2_xyscale,f101]=align2images(v1,v2,im1,im2,im1_xyscale,im2_xyscale,log_flag1,log_flag2,symb_col)
+function [im1_out,im2_xyscale,f101]=align2images(v1,v2,im1,im2,im1_vscale,im2_vscale,...
+ im1_xyscale,im2_xyscale,log_flag1,log_flag2,symb_col)
 
 N = size(v1,2);
 
@@ -60,7 +61,8 @@
 % main_GUI:Preferences->Additional Output Options
 %sc1 = find_image_scale(im1(im1>0),0,additional_settings.autoscale_quantiles, log_flag1,0);
 % autoscale image based on min/max values
-sc1 = find_image_scale(im1(im1>0),1,additional_settings.autoscale_quantiles, log_flag1,0);
+% sc1 = find_image_scale(im1(im1>0),1,additional_settings.autoscale_quantiles, log_flag1,0);
+sc1 = im1_vscale;
 
 % warp the image, using the maximum as the FillValues (usually maximum is
 % white in the BW images, which is a reasonable choice)
@@ -151,7 +153,8 @@
 % transform output images before passing them for display
 
 % first the nanosims image
-sc2 = find_image_scale(im2,0,additional_settings.autoscale_quantiles, log_flag2,0);
+%sc2 = find_image_scale(im2,0,additional_settings.autoscale_quantiles, log_flag2,0);
+sc2 = im2_vscale;
 if log_flag2
  im2 = log10(im2);
  sc2 = log10(sc2);

src/fnc/align2images_2points.m

@@ -1,10 +1,11 @@
-function [ext5,im1_xyscale,rgb,f100]=align2images_2points(v1,v2,im1,im2,im1_xyscale,im2_xyscale,log_flag1,log_flag2,tflag)
+function [ext5,im1_xyscale,rgb,f100]=align2images_2points(v1,v2,im1,im2,im1_vscale,im2_vscale,...
+ im1_xyscale,im2_xyscale,log_flag1,log_flag2,tflag)
 
 % align im1 to im2 based on two points
 
 global additional_settings;
 
-if nargin>8
+if nargin>10
  fill_v = 1*(tflag>0);
 else
  fill_v = quantile(im1(:),additional_settings.autoscale_quantiles(1));
@@ -196,7 +197,8 @@
 rgb = zeros(size(im2,1),size(im2,2),3);
 
 im1 = ext5;
-sc1 = find_image_scale(im1(im1>0),0,additional_settings.autoscale_quantiles, log_flag1,0);
+%sc1 = find_image_scale(im1(im1>0),0,additional_settings.autoscale_quantiles, log_flag1,0);
+sc1 = im1_vscale;
 if log_flag1
  im1 = log10(im1);
  sc1 = log10(sc1);
@@ -208,7 +210,8 @@
 meanv1 = (meanv1-sc1(1))/diff(sc1);
 
 im2 = nanosimsimage;
-sc2 = find_image_scale(im2,0,additional_settings.autoscale_quantiles, log_flag2,0);
+%sc2 = find_image_scale(im2,0,additional_settings.autoscale_quantiles, log_flag2,0);
+sc2 = im2_vscale;
 if log_flag2
  im2 = log10(im2);
  sc2 = log10(sc2);

src/fnc/align_exernal_nanosims.m

@@ -498,6 +498,11 @@ function show_alignment_Callback(hObject, eventdata, handles)
 log_flag1 = get(handles.checkbox1,'value');
 log_flag2 = get(handles.checkbox2,'value');
 
+ext_vscale = str2num([get(handles.min_ext,'String'), ...
+ ' ', get(handles.max_ext,'String')]);
+ns_vscale = str2num([get(handles.min_ns,'String'), ...
+ ' ', get(handles.max_ns,'String')]);
+
 if hObject == handles.show_alignment4
  % set flags
  set(handles.show_alignment4,'Checked','on');
@@ -506,9 +511,10 @@ function show_alignment_Callback(hObject, eventdata, handles)
  align_type = 4;
  % align based on multiple (>4) points
  v1 = round(handles.extplist');
- v2 = round(handles.nanosimsplist');
+ v2 = round(handles.nanosimsplist'); 
  [ext_aligned, ext_aligned_xyscale, f_aligned] = ...
  align2images(v1,v2,handles.extimage,handles.nanosimsimage,...
+ ext_vscale, ns_vscale,...
  handles.extimage_xyscale,handles.nanosimsimage_xyscale,...
  log_flag1,log_flag2,handles.points_color_symbol); 
 
@@ -543,7 +549,9 @@ function show_alignment_Callback(hObject, eventdata, handles)
  s2 = size(im2,2);
  end
  [ext_aligned, ext_aligned_xyscale, rgb_aligned, f_aligned] = ...
- align_interactively(im1,im2,s1,s2,log_flag1,log_flag2);
+ align_interactively(im1,im2,...
+ ext_vscale, ns_vscale,...
+ s1,s2,log_flag1,log_flag2);
 
 elseif hObject == handles.show_alignment2
  % set flags
@@ -575,6 +583,7 @@ function show_alignment_Callback(hObject, eventdata, handles)
  extimage_xyscale = handles.extimage_xyscale * size(im1,2)/size(handles.extimage,2);
  [ext_aligned, ext_aligned_xyscale, rgb_aligned, f_aligned] = ...
  align2images_2points(v1,v2,im1,im2,...
+ ext_vscale, ns_vscale,...
  extimage_xyscale,handles.nanosimsimage_xyscale,...
  log_flag1,log_flag2);
 
@@ -630,6 +639,10 @@ function export_aligned_external_Callback(hObject, eventdata, handles)
  % rescale it first to 0->255
  im1 = handles.ext_aligned;
  sc1 = find_image_scale(im1(im1>0),0,additional_settings.autoscale_quantiles,0,0);
+ min1 = str2num(get(handles.min_ext,'String'));
+ max1 = str2num(get(handles.max_ext,'String'));
+ if isnumeric(min1), sc1(1)=min1; end
+ if isnumeric(max1), sc1(2)=max1; end
  im1 = (im1-sc1(1))/diff(sc1);
  im1(im1<0)=0;
  im1(im1>1)=1;
@@ -800,6 +813,10 @@ function load_external_image_Callback(hObject, eventdata, handles)
  a.mag_factor_used = 1;
  end
  mag_factor_used = a.mag_factor_used;
+ if isfield(a,'vscale')
+ set(handles.min_ext,'String',num2str(a.vscale(1)));
+ set(handles.max_ext,'String',num2str(a.vscale(2)));
+ end 
 else
  im=double(imread(handles.extimagefile));
  xyscale = size(im,2);
@@ -821,6 +838,10 @@ function load_external_image_Callback(hObject, eventdata, handles)
  %global additional_settings;
  %sc=quantile(double(im(:)),additional_settings.autoscale_quantiles);
  sc = find_image_scale(double(im));
+ min1 = str2num(get(handles.min_ext,'String'));
+ max1 = str2num(get(handles.max_ext,'String'));
+ if isnumeric(min1), sc(1)=min1; end
+ if isnumeric(max1), sc(2)=max1; end
  imagesc(im,sc);
  global additional_settings;
  colormap(get_colormap(additional_settings.colormap));
@@ -872,6 +893,8 @@ function load_nanosims_image_Callback(hObject, eventdata, handles)
  image(im);
 else
  sc=vscale;
+ set(handles.min_ns,'String',num2str(vscale(1)));
+ set(handles.max_ns,'String',num2str(vscale(2))); 
  imagesc(im,sc);
  colormap(get_colormap(additional_settings.colormap));
 end
@@ -1186,6 +1209,10 @@ function update_points_Callback(hObject, eventdata, handles)
  if ~isempty(im)
  axes(ax); hold off
  sc = find_image_scale(im,0,additional_settings.autoscale_quantiles, log_flag,0);
+ min1 = str2num(get(handles.min_ext,'String'));
+ max1 = str2num(get(handles.max_ext,'String'));
+ if isnumeric(min1), sc(1)=min1; end
+ if isnumeric(max1), sc(2)=max1; end
  if size(im,3)>1
  if log_flag
  im = log10(im);
@@ -1199,6 +1226,10 @@ function update_points_Callback(hObject, eventdata, handles)
  if log_flag
  im = log10(im);
  sc = log10(sc);
+ if isinf(sc(1)), sc(1)=sc(2)-3; end
+ end
+ if contains(get(hObject,'Tag'),'min_') || contains(get(hObject,'Tag'),'max_') 
+ fprintf(1,'Ext image scale set to [%.2e, %.2e]\n', sc); 
  end
  imagesc(im, sc);
  colormap(get_colormap(additional_settings.colormap));
@@ -1231,6 +1262,10 @@ function update_points_Callback(hObject, eventdata, handles)
  if ~isempty(im)
  axes(ax); hold off;
  sc = find_image_scale(im,0,additional_settings.autoscale_quantiles, log_flag,0);
+ min1 = str2num(get(handles.min_ns,'String'));
+ max1 = str2num(get(handles.max_ns,'String'));
+ if isnumeric(min1), sc(1)=min1; end
+ if isnumeric(max1), sc(2)=max1; end
  if size(im,3)>1
  if log_flag
  im = log10(im);
@@ -1244,6 +1279,10 @@ function update_points_Callback(hObject, eventdata, handles)
  if log_flag
  im = log10(im);
  sc = log10(sc);
+ if isinf(sc(1)), sc(1)=sc(2)-3; end
+ end
+ if contains(get(hObject,'Tag'),'min_') || contains(get(hObject,'Tag'),'max_')
+ fprintf(1,'Nanosims image scale set to [%.2e, %.2e]\n', sc); 
  end
  imagesc(im, sc);
  colormap(get_colormap(additional_settings.colormap));

src/fnc/align_interactively.m

@@ -1,4 +1,5 @@
-function [im_out,im1_xyscale,rgb,f102] = align_interactively(im1,im2,im1_xyscale,im2_xyscale,log_flag1,log_flag2,tflag)
+function [im_out,im1_xyscale,rgb,f102] = align_interactively(im1,im2,im1_vscale,im2_vscale,...
+ im1_xyscale,im2_xyscale,log_flag1,log_flag2,tflag)
 
 % default output
 im_out = [];
@@ -16,10 +17,11 @@
 
 global additional_settings;
 
-if nargin>6
+if nargin>8
  fill_v = 1*(tflag>0);
 else
- fill_v = quantile(im1(:),additional_settings.autoscale_quantiles(1));
+ %fill_v = quantile(im1(:),additional_settings.autoscale_quantiles(1));
+ fill_v = im1_vscale(1);
 end
 
 % rescale image im1 so that it matches true dimensions of im2
@@ -74,7 +76,8 @@
  fprintf(1,'ERROR: Sizes of the external and nanosims images are not in proportion.\n');
  fprintf(1,'Please zoom in the external image to correct this.\n');
 else
- sc1 = find_image_scale(im1s(im1s>0),0,additional_settings.autoscale_quantiles, log_flag1,0);
+ %sc1 = find_image_scale(im1s(im1s>0),0,additional_settings.autoscale_quantiles, log_flag1,0);
+ sc1 = im1_vscale;
  if log_flag1
  im1s = log10(im1s);
  sc1 = log10(sc1);
@@ -83,7 +86,8 @@
  im1s(im1s<0)=0;
  im1s(im1s>1)=1;
 
- sc2 = find_image_scale(im2s,0,additional_settings.autoscale_quantiles, log_flag2,0);
+ %sc2 = find_image_scale(im2s,0,additional_settings.autoscale_quantiles, log_flag2,0);
+ sc2 = im2_vscale;
  if log_flag2
  im2s = log10(im2s);
  sc2 = log10(sc2);

src/fnc/display_RGB_image.m

@@ -8,7 +8,7 @@
 global additional_settings;
 
 
-if ~isempty(rgb7) | ~isempty(rgb8)
+if ~isempty(rgb7) || ~isempty(rgb8)
 
  for ii=1:2
  if ii==1
@@ -17,7 +17,7 @@
  else
  rgb=rgb8;
  plotopt=opt1(8);
- end;
+ end
 
  if plotopt
 
@@ -101,51 +101,51 @@
 
  % export RGB image (as eps and tif)
  if(opt1(11)) 
- if(~isempty(xl) & ~isempty(yl) & ~isempty(zl))
+ if(~isempty(xl) && ~isempty(yl) && ~isempty(zl))
  xyfile0=[xl,'-vs-',yl,'-vs-',zl];
  else
  if(isempty(xl))
  xyfile0=[yl,'-vs-',zl];
- end;
+ end
  if(isempty(yl))
  xyfile0=[xl,'-vs-',zl];
- end;
+ end
  if(isempty(zl))
  xyfile0=[xl,'-vs-',yl];
- end;
- end;
+ end
+ end
  if(ii==1)
  ext='-rgb';
  ext_cmyk = '-cmyk';
  else
  ext='-rgba';
  ext_cmyk = '-cmyka';
- end;  
+ end 
  xyfile=convert_string_for_texoutput([xyfile0,ext]);
  xyfile=[xyfile,'.eps'];
  xyfile=[p.fdir,'eps',delimiter,xyfile];
  epsdir = fileparts(xyfile);
- if(~isdir(epsdir))
+ if(~isfolder(epsdir))
  mkdir(epsdir);
  fprintf(1,'Directory %s did not exist, so it was created.\n',epsdir);
- end;
+ end
  print_figure(mf,xyfile,additional_settings.print_factors(1));
  outfname = mepstopdf(xyfile,'epstopdf');
  outfname = regexprep(outfname,'\','/');
  if ii==1
  rgb7_fname = outfname;
  else
  rgb8_fname = outfname; 
- end;
+ end
  xyfile=convert_string_for_texoutput([xyfile0,ext]);
  xyfile=[xyfile, '.tif'];
  xyfile_cmyk=convert_string_for_texoutput([xyfile0,ext_cmyk]);
  xyfile_cmyk=[xyfile_cmyk, '.tif'];
  tifdir=[p.fdir, 'tif'];
- if(~isdir(tifdir))
+ if(~isfolder(tifdir))
  mkdir(tifdir);
  fprintf(1,'Directory %s did not exist, so it was created.\n',tifdir);
- end;
+ end
  xyfile=[p.fdir,'tif',delimiter,xyfile];
  xyfile_cmyk=[p.fdir,'tif',delimiter,xyfile_cmyk];
  Nbits = 8;
@@ -158,7 +158,8 @@
  % also save the image as CMYK
  outprof = iccread('USSheetfedCoated.icc'); 
  inprof = iccread('sRGB.icm');
- C = makecform('icc',inprof,outprof); 
+ C = makecform('icc',inprof,outprof); 
+ rgb(isnan(rgb(:)))=0; % set NaN to 0
  cmyk = applycform(rgb, C);
  imwrite(cmyk, xyfile_cmyk);
  %a = 0;

src/lookatnanosims.m

@@ -202,6 +202,7 @@
  % counts, and the corresponding ion count ratios,
  % will be calculated by accumulating only the
  % specified planes.
+LANS_version = '2024-01-18'; % Bugs in align_external_image due to autoscale fixed.
 
 % name of the external image file (empty by default)
 EXTERNAL_IMAGEFILE = '';
@@ -219,7 +220,7 @@
  fprintf(1,'Written by Lubos Polerecky <lpolerec (at) mpi-bremen.de>\n')
  fprintf(1,'(2008-2012) Max-Planck Institute for Marine Microbiology, Bremen\n')
  fprintf(1,'Updates by Lubos Polerecky <l.polerecky (at) uu.nl>\n')
- fprintf(1,'(2013-2023) Utrecht University\n')
+ fprintf(1,'(2013-2024) Utrecht University\n')
  fprintf(1,'More info: http:https://nanosims.geo.uu.nl/LANS\n')
  fprintf(1,'================================================================\n')
  fprintf(1,'Enjoy your work!\n')