LANS-2017-12-10-matlab2017b

src/fnc/LANS.m

@@ -56,7 +56,7 @@ function LANS_OpeningFcn(hObject, eventdata, handles, varargin)
 
 set(handles.figure1,'Name',['Look@NanoSIMS (version ',LANS_version,')'])
 fp=get(handles.figure1,'Position');
- 
+
 h = load_settings(handles,get_ini_file('r'));
 handles.dtc = h.dtc;
 

src/fnc/display_RGB_image.m

@@ -1,11 +1,9 @@
-function display_RGB_image(rgb7, rgb8, p, opt1, tit, xl, yl, zl,h)
+function [rgb7_fname, rgb8_fname] = display_RGB_image(rgb7, rgb8, p, opt1, tit, xl, yl, zl, cw)
 % display the rgb image, with some simple formating, and export it as eps
 % and 16-bit tif
-if matversion==2015
-defFontSize=10;
-else
-defFontSize=14;
-end;
+
+rgb7_fname=[];
+rgb8_fname=[];
 
 global additional_settings;
 
@@ -25,24 +23,21 @@ function display_RGB_image(rgb7, rgb8, p, opt1, tit, xl, yl, zl,h)
  set(gca,'DataAspectRatio',[1 1 1],'xtick',[],'ytick',[]);
  % include title, if requested
  if opt1(15)
+ xlab=['R=',xl,'; G=',yl,'; B=',zl];
  if(~isempty(tit))
- tit2=[tit];
- xlab=['R=',xl,'; G=',yl,'; B=',zl];
- if(length(tit2)>38)
- tit2=['...',tit2([(length(tit2)-38):length(tit2)])];
+ tit2=[tit]; 
+ if(length(tit)>additional_settings.title_length)
+ tit=['...',tit([(length(tit)-additional_settings.title_length):length(tit)])];
  end;
- xlabel(tit2,'interpreter','none','fontweight','normal','FontSize',additional_settings.defFontSize);
- title(xlab,'interpreter','none','fontweight','normal','FontSize',additional_settings.defFontSize);
- else
- title(['R=',xl,'; G=',yl,'; B=',zl],'interpreter','none','fontweight','normal','FontSize',additional_settings.defFontSize);
- %xl=xlabel('');
- %delete(xl);
+ title(tit,'interpreter','none','fontweight','normal',...
+ 'FontSize',additional_settings.defFontSize);
  end;
+ xlabel(xlab,'interpreter','none','fontweight','normal',...
+ 'FontSize',additional_settings.defFontSize);
  end;
 
  % add scale line
- cw=get(h.edit62,'string');
- if(isempty(cw))
+ if isempty(cw)
  cw = 'w';
  end;
  add_scale_line(p.scale,rgb7(:,:,1),cw);
@@ -85,7 +80,12 @@ function display_RGB_image(rgb7, rgb8, p, opt1, tit, xl, yl, zl,h)
  end;
  print_figure(mf,xyfile,additional_settings.print_factors(1));
  %fprintf(1,'RGB image saved as %s\n', xyfile);
- mepstopdf(xyfile,'epstopdf');
+ outfname = mepstopdf(xyfile,'epstopdf');
+ if ii==1
+ rgb7_fname = outfname;
+ else
+ rgb8_fname = outfname; 
+ end;
  xyfile=convert_string_for_texoutput([xyfile0,ext]);
  xyfile=[xyfile, '.tif'];
  tifdir=[p.fdir,'tif'];

src/fnc/display_masses_through_mask.m

@@ -1,137 +1,137 @@
-function display_masses_through_mask(handles)
-
-p = load_masses_parameters(handles);
-
-global additional_settings;
-
-[opt1,opt3,opt4]=load_options(handles,1);
-
-% if Maskimg was not defined yet, set it to zero here
-if ~isfield(p,'Maskimg')
- p.Maskimg=zeros(size(p.im{1},1),size(p.im{1},2));
-else
- % always load it from the last saved cells file
- global CELLSFILE MAT_EXT;
- p.Maskimg = load_cells_from_disk(handles,0,[CELLSFILE MAT_EXT]);
-end;
-
-% find out the title of the graph
-if(isempty(my_get(handles.edit63,'string')))
- tit=fixdir(p.fdir);
-else
- tit = my_get(handles.edit63,'string');
-end;
-
-if opt1(3) | opt1(6) | opt1(10) | opt1(5) | opt1(13) | opt1(14)
-
- if ~p.planes_aligned
-
- fprintf(1,'*** Warning: Accummulate planes first before displaying mass images!\n');
-
- else
-
- % get the filename with the classification of cells, so that the
- % histograms can be displayed separately for each cell class
- if opt1(3)
- cellfile = select_classification_file(p); 
- else 
- cellfile=[]; 
- end; 
-
- % display selected images, and export data if requested
- for ii=1:min([length(p.accu_im) length(opt4)])
-
- % display accummulated mass image
- if (opt1(6) | opt1(3)) & opt4(ii) 
-
- % if log10-transformation reqested, make sure min(scale) is
- % not 0
- if opt1(4) 
- if p.imscale{ii}(1)==0
- p.imscale{ii}(1)=1;
- fprintf(1,'*** Warning: minimum scale was 0, but was set to 1 due to logarithm scaling of the image.\n');
- end;
- %p.imscale{ii}=log10(p.imscale{ii});
- end;
-
- plotImageCells(ii,p.accu_im{ii},p.Maskimg,p.fdir,p.mass{ii},...
- [my_get(handles.edit62,'string'),'-'],p.imscale{ii},...
- opt1,opt3(ii),1,p.scale,tit,cellfile,p.images{ii},p.planes);
-
- % export image as EPS
- if opt1(6) & opt1(11) 
- exportImageCells(ii,p.fdir,p.mass{ii},p.ext,...
- additional_settings.print_factors(1));
- end;
-
- end;
-
- end;
-
- % export data as ASCII file
- if opt1(10) | opt1(13)
-
- out=get_Cell_pos_size(p.Maskimg,p.scale);
-
- if opt1(10)
- [m2, dm2]=accumulate_masses_in_cells(p.accu_im,p.Maskimg,p.im,p.images);
-
- for ii=1:min([length(p.accu_im) length(opt4)])
- if opt4(ii) 
- if isempty(out)
- fprintf(1,'*** WARNING: No ROIs have been defined, so no data can be exported.\n');
- else
- o = [out(:,1:3) m2{ii} dm2{ii} 100*dm2{ii}./m2{ii} out(:,4:6)];
- export_ascii_data_for_ROIS(o, p.fdir, p.mass{ii}, '.dac', 'd');
- end;
- end;
- end;
- end;
-
- end;
-
- % produce RGB from 3 selected mass images and display it
- if opt1(5)
-
- opt1(9)=0; opt1(8)=0; 
- [rgb7, rgb8, xl, yl, zl] = ...
- construct_RGB_image(handles,p.mass,p.imscale,p.Maskimg,p.accu_im,p.accu_im,opt1);
-
- display_RGB_image(rgb7, rgb8, p, opt1, tit, xl, yl, zl,handles);
-
- end;
-
- % display depth profiles
- if opt1(13)
-
- % accumulate masses in cells over all pixels, but separately in each plane
- [m2, dm2]=accumulate_masses_in_cells(p.im,p.Maskimg,p.im,p.images);
-
- % normalize accumulated masses to cell size (divide by pixel
- % number)
- if 0
- for jj=1:length(m2)
- csize = out(:,5)*ones(1,size(m2{jj},2));
- m2{jj} = m2{jj}./csize;
- dm2{jj} = dm2{jj}./csize;
- end;
- end;
-
- % display depth profiles of masses for all cells
- plot_export_masses_depth(m2, dm2, p.images,p.planes, ...
- opt1, opt4, p.mass, p.fdir, ...
- additional_settings.print_factors(3));
-
- fprintf(1,'Plotting/exporting depth profiles ... Done.\n');
-
- end;
-
- % display lateral profiles
- if opt1(14)
- lateral_profile_gui(p.accu_im,p.imscale,p.mass,p.fdir,p.scale,...
- additional_settings.print_factors(4));
- end;
-
- end;
-
-end;
+function display_masses_through_mask(handles)
+
+p = load_masses_parameters(handles);
+
+global additional_settings;
+
+[opt1,opt3,opt4]=load_options(handles,1);
+
+% if Maskimg was not defined yet, set it to zero here
+if ~isfield(p,'Maskimg')
+ p.Maskimg=zeros(size(p.im{1},1),size(p.im{1},2));
+else
+ % always load it from the last saved cells file
+ global CELLSFILE MAT_EXT;
+ p.Maskimg = load_cells_from_disk(handles,0,[CELLSFILE MAT_EXT]);
+end;
+
+% find out the title of the graph
+if(isempty(my_get(handles.edit63,'string')))
+ tit=fixdir(p.fdir);
+else
+ tit = my_get(handles.edit63,'string');
+end;
+
+if opt1(3) | opt1(6) | opt1(10) | opt1(5) | opt1(13) | opt1(14)
+
+ if ~p.planes_aligned
+
+ fprintf(1,'*** Warning: Accummulate planes first before displaying mass images!\n');
+
+ else
+
+ % get the filename with the classification of cells, so that the
+ % histograms can be displayed separately for each cell class
+ if opt1(3)
+ cellfile = select_classification_file(p); 
+ else 
+ cellfile=[]; 
+ end; 
+
+ % display selected images, and export data if requested
+ for ii=1:min([length(p.accu_im) length(opt4)])
+
+ % display accummulated mass image
+ if (opt1(6) | opt1(3)) & opt4(ii) 
+
+ % if log10-transformation reqested, make sure min(scale) is
+ % not 0
+ if opt1(4) 
+ if p.imscale{ii}(1)==0
+ p.imscale{ii}(1)=1;
+ fprintf(1,'*** Warning: minimum scale was 0, but was set to 1 due to logarithm scaling of the image.\n');
+ end;
+ %p.imscale{ii}=log10(p.imscale{ii});
+ end;
+
+ plotImageCells(ii,p.accu_im{ii},p.Maskimg,p.fdir,p.mass{ii},...
+ [my_get(handles.edit62,'string'),'-'],p.imscale{ii},...
+ opt1,opt3(ii),1,p.scale,tit,cellfile,p.images{ii},p.planes);
+
+ % export image as EPS
+ if opt1(6) & opt1(11) 
+ exportImageCells(ii,p.fdir,p.mass{ii},p.ext,...
+ additional_settings.print_factors(1));
+ end;
+
+ end;
+
+ end;
+
+ % export data as ASCII file
+ if opt1(10) | opt1(13)
+
+ out=get_Cell_pos_size(p.Maskimg,p.scale);
+
+ if opt1(10)
+ [m2, dm2]=accumulate_masses_in_cells(p.accu_im,p.Maskimg,p.im,p.images);
+
+ for ii=1:min([length(p.accu_im) length(opt4)])
+ if opt4(ii) 
+ if isempty(out)
+ fprintf(1,'*** WARNING: No ROIs have been defined, so no data can be exported.\n');
+ else
+ o = [out(:,1:3) m2{ii} dm2{ii} 100*dm2{ii}./m2{ii} out(:,4:6)];
+ export_ascii_data_for_ROIS(o, p.fdir, p.mass{ii}, '.dac', 'd');
+ end;
+ end;
+ end;
+ end;
+
+ end;
+
+ % produce RGB from 3 selected mass images and display it
+ if opt1(5)
+
+ opt1(9)=0; opt1(8)=0; 
+ [rgb7, rgb8, xl, yl, zl] = ...
+ construct_RGB_image(handles,p.mass,p.imscale,p.Maskimg,p.accu_im,p.accu_im,opt1);
+
+ display_RGB_image(rgb7, rgb8, p, opt1, tit, xl, yl, zl,get(handles.edit62,'string'));
+
+ end;
+
+ % display depth profiles
+ if opt1(13)
+
+ % accumulate masses in cells over all pixels, but separately in each plane
+ [m2, dm2]=accumulate_masses_in_cells(p.im,p.Maskimg,p.im,p.images);
+
+ % normalize accumulated masses to cell size (divide by pixel
+ % number)
+ if 0
+ for jj=1:length(m2)
+ csize = out(:,5)*ones(1,size(m2{jj},2));
+ m2{jj} = m2{jj}./csize;
+ dm2{jj} = dm2{jj}./csize;
+ end;
+ end;
+
+ % display depth profiles of masses for all cells
+ plot_export_masses_depth(m2, dm2, p.images,p.planes, ...
+ opt1, opt4, p.mass, p.fdir, ...
+ additional_settings.print_factors(3));
+
+ fprintf(1,'Plotting/exporting depth profiles ... Done.\n');
+
+ end;
+
+ % display lateral profiles
+ if opt1(14)
+ lateral_profile_gui(p.accu_im,p.imscale,p.mass,p.fdir,p.scale,...
+ additional_settings.print_factors(4));
+ end;
+
+ end;
+
+end;