Changeset 950 for trunk/src/series

Timestamp:

Jun 11, 2016, 9:32:29 PM (8 years ago)

Author:

sommeria

Message:

various updates

Location:

trunk/src/series

Files:

• civ_series.m (modified) (5 diffs)
• sub_background.m (modified) (4 diffs)

trunk/src/series/civ_series.m

@@ -283 +283 @@
 if iview_A~=0
     XmlFileName=find_imadoc(RootPath_A,SubDir_A,RootFile_A,FileExt_A);
-    time=[];
+    Time=[];
     if ~isempty(XmlFileName)
         XmlData=imadoc2struct(XmlFileName);
         if isfield(XmlData,'Time')
-            time=XmlData.Time;
+            Time=XmlData.Time;
             TimeSource='xml';
         end
@@ -302 +302 @@
         end
     end
-    if isempty(time) && ~isempty(find(strcmp(FileType_A,{'mmreader','video'})))% case of video input
-        time=zeros(FileInfo_A.NumberOfFrames+1,2);
-        time(:,2)=(0:1/FileInfo_A.FrameRate:(FileInfo_A.NumberOfFrames)/FileInfo_A.FrameRate)';
+    if isempty(Time) && ~isempty(find(strcmp(FileType_A,{'mmreader','video'})))% case of video input
+        Time=zeros(FileInfo_A.NumberOfFrames+1,2);
+        Time(:,2)=(0:1/FileInfo_A.FrameRate:(FileInfo_A.NumberOfFrames)/FileInfo_A.FrameRate)';
         TimeSource='video';
         ColorType='truecolor';
     end
-    if isempty(time)% time = index i +0.001 index j by default
+    if isempty(Time)% Time = index i +0.001 index j by default
         %MinIndex_i=min(i1_series_Civ1);
         MaxIndex_i=max(i2_series_Civ1);
         %MinIndex_j=min(j1_series_Civ1);
         MaxIndex_j=max(j2_series_Civ1);
-        time=(1:MaxIndex_i)'*ones(1,MaxIndex_j);
-        time=time+0.001*ones(MaxIndex_i,1)*(1:MaxIndex_j);
-        time=[zeros(1,MaxIndex_j);time];% insert a first line of zeros
-        time=[zeros(MaxIndex_i+1,1) time];% insert a first column of zeros
+        Time=(1:MaxIndex_i)'*ones(1,MaxIndex_j);
+        Time=Time+0.001*ones(MaxIndex_i,1)*(1:MaxIndex_j);
+        Time=[zeros(1,MaxIndex_j);Time];% insert a first line of zeros
+        Time=[zeros(MaxIndex_i+1,1) Time];% insert a first column of zeros
     end
     
@@ -438 +438 @@
             end
             if strcmp(Param.ActionInput.ListCompareMode,'displacement')
-                Data.Civ1_Time=time(i2+1,j2+1);% the time is the time of the secodn image
-                Data.Civ1_Dt=1;% time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading
+                Data.Civ1_Time=Time(i2+1,j2+1);% the Time is the Time of the secodn image
+                Data.Civ1_Dt=1;% Time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading
             else
-            Data.Civ1_Time=(time(i2+1,j2+1)+time(i1+1,j1+1))/2;% the time is the time at the middle of the image pair
-            Data.Civ1_Dt=time(i2+1,j2+1)-time(i1+1,j1+1);
+            Data.Civ1_Time=(Time(i2+1,j2+1)+Time(i1+1,j1+1))/2;% the Time is the Time at the middle of the image pair
+            Data.Civ1_Dt=Time(i2+1,j2+1)-Time(i1+1,j1+1);
             end
             for ilist=1:length(list_param)
@@ -736 +736 @@
                 Civ2_Dt=1;
             else
-                Civ2_Dt=time(i2_civ2+1,j2_civ2+1)-time(i1_civ2+1,j1_civ2+1);
+                Civ2_Dt=Time(i2_civ2+1,j2_civ2+1)-Time(i1_civ2+1,j1_civ2+1);
             end
         end
@@ -761 +761 @@
             Data.Civ2_ImageB=ImageName_B;
              if strcmp(Param.ActionInput.ListCompareMode,'displacement')
-                Data.Civ2_Time=time(i2_civ2+1,j2_civ2+1);% the time is the time of the secodn image
-                Data.Civ2_Dt=1;% time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading
+                Data.Civ2_Time=Time(i2_civ2+1,j2_civ2+1);% the Time is the Time of the secodn image
+                Data.Civ2_Dt=1;% Time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading
              else
-            Data.Civ2_Time=(time(i2_civ2+1,j2_civ2+1)+time(i1_civ2+1,j1_civ2+1))/2;
+            Data.Civ2_Time=(Time(i2_civ2+1,j2_civ2+1)+Time(i1_civ2+1,j1_civ2+1))/2;
             Data.Civ2_Dt=Civ2_Dt;
              end

trunk/src/series/sub_background.m

@@ -340 +340 @@
         if Param.ActionInput.CheckLevelTransform
             C=levels(Acor);
-            imwrite(C,newname,'BitDepth',8); % save the new image
+            imwrite(C,newname,'BitDepth',16); % save the new image
         else
             if isequal(FileInfo{1}.BitDepth,16)
@@ -393 +393 @@
                 if Param.ActionInput.CheckLevelTransform
                     C=levels(Acor);
-                    imwrite(C,newname,'BitDepth',8); % save the new image
+                    imwrite(C,newname,'BitDepth',16); % save the new image
                 else
                     if isequal(FileInfo{1}.BitDepth,16)
@@ -421 +421 @@
         if Param.ActionInput.CheckLevelTransform
             C=levels(Acor);
-            imwrite(C,newname,'BitDepth',8); % save the new image
+            imwrite(C,newname,'BitDepth',16); % save the new image
         else
             if isequal(FileInfo{1}.BitDepth,16)
@@ -435 +435 @@
 end
 
-
 function C=levels(A)
-%whos A;
-B=double(A(:,:,1));
-windowsize=round(min(size(B,1),size(B,2))/20);
-windowsize=floor(windowsize/2)*2+1;
-ix=1/2-windowsize/2:-1/2+windowsize/2;%
-%del=np/3;
-%fct=exp(-(ix/del).^2);
-fct2=cos(ix/(windowsize-1)/2*pi/2);
-%Mfiltre=(ones(5,5)/5^2);
-%Mfiltre=fct2';
-Mfiltre=fct2'*fct2;
-Mfiltre=Mfiltre/(sum(sum(Mfiltre)));
-
-C=filter2(Mfiltre,B);
-C(:,1:windowsize)=C(:,windowsize)*ones(1,windowsize);
-C(:,end-windowsize+1:end)=C(:,end-windowsize+1)*ones(1,windowsize);
-C(1:windowsize,:)=ones(windowsize,1)*C(windowsize,:);
-C(end-windowsize+1:end,:)=ones(windowsize,1)*C(end-windowsize,:);
-C=tanh(B./(2*C));
-[n,c]=hist(reshape(C,1,[]),100);
-% figure;plot(c,n);
-
-[m,i]=max(n);
-c_max=c(i);
-[dummy,index]=sort(abs(c-c(i)));
-n=n(index);
-c=c(index);
-i_select = find(cumsum(n)<0.95*sum(n));
-if isempty(i_select)
-    i_select = 1:length(c);
-end
-c_select=c(i_select);
-n_select=n(i_select);
-cmin=min(c_select);
-cmax=max(c_select);
-C=(C-cmin)/(cmax-cmin)*256;
-C=uint8(C);
+
+nblock_y=100;%2*Param.TransformInput.BlockSize;
+nblock_x=100;%2*Param.TransformInput.BlockSize;
+[npy,npx]=size(A);
+[X,Y]=meshgrid(1:npx,1:npy);
+
+%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
+fctblock= inline('median(x(:))');
+Backg=blkproc(A,[nblock_y nblock_x],fctblock);% take the median in  blocks
+fctblock= inline('mean(x(:))');
+B=imresize(Backg,size(A),'bilinear');% interpolate to the initial size image
+A=(A-B);%substract background
+AMean=blkproc(A,[nblock_y nblock_x],fctblock);% take the mean in  blocks
+fctblock= inline('var(x(:))');
+AVar=blkproc(A,[nblock_y nblock_x],fctblock);% take the mean in  blocks
+Avalue=AVar./AMean% typical value of particle luminosity
+Avalue=imresize(Avalue,size(A),'bilinear');% interpolate to the initial size image
+C=uint16(1000*tanh(A./(2*Avalue)));
+%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
+% function C=levels(A)
+% %whos A;
+% B=double(A(:,:,1));
+% windowsize=round(min(size(B,1),size(B,2))/20);
+% windowsize=floor(windowsize/2)*2+1;
+% ix=1/2-windowsize/2:-1/2+windowsize/2;%
+% %del=np/3;
+% %fct=exp(-(ix/del).^2);
+% fct2=cos(ix/(windowsize-1)/2*pi/2);
+% %Mfiltre=(ones(5,5)/5^2);
+% %Mfiltre=fct2';
+% Mfiltre=fct2'*fct2;
+% Mfiltre=Mfiltre/(sum(sum(Mfiltre)));
+% 
+% C=filter2(Mfiltre,B);
+% C(:,1:windowsize)=C(:,windowsize)*ones(1,windowsize);
+% C(:,end-windowsize+1:end)=C(:,end-windowsize+1)*ones(1,windowsize);
+% C(1:windowsize,:)=ones(windowsize,1)*C(windowsize,:);
+% C(end-windowsize+1:end,:)=ones(windowsize,1)*C(end-windowsize,:);
+% C=tanh(B./(2*C));
+% [n,c]=hist(reshape(C,1,[]),100);
+% % figure;plot(c,n);
+% 
+% [m,i]=max(n);
+% c_max=c(i);
+% [dummy,index]=sort(abs(c-c(i)));
+% n=n(index);
+% c=c(index);
+% i_select = find(cumsum(n)<0.95*sum(n));
+% if isempty(i_select)
+%     i_select = 1:length(c);
+% end
+% c_select=c(i_select);
+% n_select=n(i_select);
+% cmin=min(c_select);
+% cmax=max(c_select);
+% C=(C-cmin)/(cmax-cmin)*256;
+% C=uint8(C);