Changeset 906 for trunk/src/transform_field/ima_remove_background.m

Timestamp:

May 31, 2015, 7:49:31 PM (9 years ago)

Author:

sommeria

Message:

various bgu repairs and ima_remove_partices and ima_remove_background updated

File:

• trunk/src/transform_field/ima_remove_background.m (modified) (1 diff)

trunk/src/transform_field/ima_remove_background.m

@@ -27 +27 @@
 %=======================================================================
 
-function DataOut=remove_background(DataIn)
+function DataOut=remove_background(DataIn,Param)
 %------------------------------------------------------------------------
-DataOut=[];  %default  output field
-if strcmp(DataIn,'*')
+%% request input parameters
+if isfield(DataIn,'Action') && isfield(DataIn.Action,'RUN') && isequal(DataIn.Action.RUN,0)
+    prompt = {'radius'};
+    dlg_title = 'get the disk radius (pixels) used to calculate the regional minimum';
+    num_lines= 1;
+    def     = { '4'};
+    if isfield(Param,'TransformInput')&&isfield(Param.TransformInput,'DiskRadius')
+        def={num2str(Param.TransformInput.DiskRadius)};
+    end
+    answer = inputdlg(prompt,dlg_title,num_lines,def);
+    DataOut.TransformInput.DiskRadius=str2num(answer{1}); 
+    return
+end
+if ~isfield(DataIn,'A')
+    DataOut.Txt='remove_particles only valid for input images';
+    return
+end
+if ~exist('imerode','file');
+        DataOut.Txt='the function imerode from the image processing toolbox is needed';
     return
 end
 
-%parameters
-threshold=200
-nblock_x=30;%size of image subblocks for analysis
-nblock_y=30;
-%---------------------------------------------------------
+SE=strel('disk',Param.TransformInput.DiskRadius);
+%--------------------------------------------------------- 
 DataOut=DataIn;%default
+
+[npy,npx]=size(DataIn.A);
+[X,Y]=meshgrid(1:npx,1:npy);
 
 %BACKGROUND LEVEL
 Atype=class(DataIn.A);
-A=double(DataIn.A);
-Backg=zeros(size(A));
-Aflagmin=sparse(imregionalmin(A));%Amin=1 for local image minima
-Amin=A.*Aflagmin;%values of A at local minima
-% local background: find all the local minima in image subblocks
-sumblock= inline('sum(sum(x(:)))');
-Backg=blkproc(Amin,[nblock_y nblock_x],sumblock);% take the sum in  blocks
-Bmin=blkproc(Aflagmin,[nblock_y nblock_x],sumblock);% find the number of minima in blocks
-Backg=Backg./Bmin; % find the average of minima in blocks
-B=imresize(Backg,size(A),'bilinear');% interpolate to the initial size image
-ImPart=(A-B);
-DataOut.A=ImPart;
-%DataOut.A=ImPart.*(ImPart>threshold);
+Aerode=imerode(DataIn.A,SE);
+Aflagmin=find(DataIn.A==Aerode);
+Xmin=X(Aflagmin);
+Ymin=Y(Aflagmin);
+Amin=double(DataIn.A(Aflagmin));
+F = TriScatteredInterp([Xmin Ymin], Amin);
+DataOut.A=double(DataOut.A)-F(X,Y);
 DataOut.A=feval(Atype,DataOut.A);
+
+%BACKGROUND LEVEL
+% Atype=class(DataIn.A);
+% A=double(DataIn.A);
+% Backg=zeros(size(A));
+% Aflagmin=sparse(imregionalmin(A));%Amin=1 for local image minima
+% Amin=A.*Aflagmin;%values of A at local minima
+% % local background: find all the local minima in image subblocks
+% sumblock= inline('sum(sum(x(:)))');
+% Backg=blkproc(Amin,[nblock_y nblock_x],sumblock);% take the sum in  blocks
+% Bmin=blkproc(Aflagmin,[nblock_y nblock_x],sumblock);% find the number of minima in blocks
+% Backg=Backg./Bmin; % find the average of minima in blocks
+% B=imresize(Backg,size(A),'bilinear');% interpolate to the initial size image
+% ImPart=(A-B);
+% DataOut.A=ImPart;
+% %DataOut.A=ImPart.*(ImPart>threshold);
+% DataOut.A=feval(Atype,DataOut.A);