"zero outside ROIs" is now implemented also for RGB overlay images

src/fnc/construct_RGB_image.m

@@ -1,4 +1,5 @@
-function [rgb7, rgb8, xl, yl, zl, xs, ys, zs, rgb_true] = construct_RGB_image(handles, p_name, p_scale, R, Raim, opt1, Rconf)
+function [rgb7, rgb8, xl, yl, zl, xs, ys, zs, rgb_true] = ...
+ construct_RGB_image(handles, p_name, p_scale, R, Raim, opt1, Rconf, Maskimg)
 % Construct RGB image from R and Raim images. Return also names and scales of the
 % masses that are in the R, G and B channels.
 
@@ -14,7 +15,7 @@
  i1=str2num(my_get(handles.edit59,'string'));
  i2=str2num(my_get(handles.edit60,'string'));
  i3=str2num(my_get(handles.edit61,'string'));
-end;
+end
 xl=[]; yl=[]; zl=[]; xs=[]; ys=[]; zs=[];
 
 % check whether the settings for the RGB display/calculation match with
@@ -23,19 +24,19 @@
 isum=sum([ i1>0 i2>0 i3>0 ]);
 c1 = (isum <= psl);
 if length(R)>=isum
- if(i1>0), c1 = (c1 & ~isempty(R{i1})); end;
- if(i2>0), c1 = (c1 & ~isempty(R{i2})); end;
- if(i3>0), c1 = (c1 & ~isempty(R{i3})); end;
+ if(i1>0), c1 = (c1 & ~isempty(R{i1})); end
+ if(i2>0), c1 = (c1 & ~isempty(R{i2})); end
+ if(i3>0), c1 = (c1 & ~isempty(R{i3})); end
 else 
  c1=0;
-end;
+end
 
 % continue if everything is fine
 if c1
 
- if(i1>0), xl=p_name{i1}; xs=p_scale{i1}; end;
- if(i2>0), yl=p_name{i2}; ys=p_scale{i2}; end;
- if(i3>0), zl=p_name{i3}; zs=p_scale{i3}; end;
+ if(i1>0), xl=p_name{i1}; xs=p_scale{i1}; end
+ if(i2>0), yl=p_name{i2}; ys=p_scale{i2}; end
+ if(i3>0), zl=p_name{i3}; zs=p_scale{i3}; end
 
  Nx = 0;
  Ny = 0;
@@ -53,6 +54,12 @@
  else
  Rc = [];
  end
+ if nargin>7 % Maskimg takes precedence over Rconf 
+ if sum(Maskimg(:))>0 && opt1(2) % zero values outside ROIs
+ Rc = ones(Ny,Nx);
+ Rc(Maskimg==0) = 0;
+ end
+ end
  [r7, r8, r] = fill_channel_rgb(R,Raim,Rc,Nx,Ny,i1,p_scale,xl,opt1);
  i=1; rgb7(:,:,i) = r7; rgb8(:,:,i) = r8; rgb_true(:,:,i) = r;
  [g7, g8, g] = fill_channel_rgb(R,Raim,Rc,Nx,Ny,i2,p_scale,yl,opt1);
@@ -64,8 +71,10 @@
  % apply a hack to remove blue from pixels where r+g are sufficiently
  % high, and modify yellow to orange 
  % (implemented for the Mycobacterium paper, LP 24-08-2022)
- factor = 0.85;
- i=3; rgb7(:,:,i) = b7*factor; rgb8(:,:,i) = b8*factor; rgb_true(:,:,i) = b*factor;
+ if 0
+ factor = 0.85;
+ i=3; rgb7(:,:,i) = b7*factor; rgb8(:,:,i) = b8*factor; rgb_true(:,:,i) = b*factor;
+ end
 
  if 0
  thresh = 0.5;
@@ -79,6 +88,7 @@
  %b7(ind) = 0;
  i=3; rgb7(:,:,i) = 1-b7; rgb8(:,:,i) = b8; rgb_true(:,:,i) = b;
  end
+
  if 0
  [r7, r8, r] = fill_channel_rgb(R,Raim,Rc,Nx,Ny,i1,p_scale,xl,opt1);
  i=1; rgb7(:,:,i) = r7; rgb8(:,:,i) = r8; rgb_true(:,:,i) = r;
@@ -145,7 +155,7 @@
  rgb7(rgb7>1) = 1;
  rgb8(rgb8<0) = 0;
  rgb8(rgb8>1) = 1; 
- if ~isempty(Rconf)
+ if ~isempty(Rconf) 
  % apply the hue correction. it does not make analytical sense,
  % but it does help the RGB image to look better by removing all
  % the potentially noisy pixels 

src/fnc/display_ratios_through_mask.m

@@ -111,7 +111,7 @@ function display_ratios_through_mask(handles, export_graphics_flag, accum_flag,
  %% display RGB image constructed from 3 selected ratio images
  if opt1(5)
  [rgb7, rgb8, xl, yl, zl, xs, ys, zs, rgb_true] = ...
- construct_RGB_image(handles,p.special,p.special_scale,R,Raim,opt1,Rconf); 
+ construct_RGB_image(handles,p.special,p.special_scale,R,Raim,opt1,Rconf,p.Maskimg);
  display_RGB_image(rgb7, rgb8, p, opt1, tit, xl, yl, zl, get(handles.edit62,'string')); 
  end