Changeset 840

Timestamp:

Dec 10, 2014, 11:11:09 PM (10 years ago)

Author:

sommeria

Message:

 

Location:

trunk/src

Files:

• phys_ima.m (modified) (1 diff)
• series.m (modified) (1 diff)
• series/civ2vel_3C.m (modified) (3 diffs)
• series/extract_rdvision.m (modified) (5 diffs)

trunk/src/phys_ima.m

@@ -49 +49 @@
     Calib=XmlData{icell}.GeometryCalib;
     % rescaling of the image coordinates without change of the image array
-    if strcmp(Calib.CalibrationType,'rescale') && isequal(Calib,CalibIn{1})
+    if strcmp(Calib.CalibrationType,'rescale') && isequal(Calib,XmlData{1}.GeometryCalib)
         A_out{icell}=A{icell};%no transform
         Rangx=[0.5 npx-0.5];%image coordiantes of corners

trunk/src/series.m

@@ -1657 +1657 @@
             Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice;
         end
-        Param.InputTable{1}=regexprep(Param.InputTable{1},'\','/');%correct path name for PCWIN system
+        for ilist=1:size(Param.InputTable,1)
+        Param.InputTable{ilist,1}=regexprep(Param.InputTable{ilist,1},'\','/');%correct path name for PCWIN system
+        end
         % create, fill and save the xml parameter file
         t=struct2xml(Param);

trunk/src/series/civ2vel_3C.m

@@ -127 +127 @@
 [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
 
+%% grid of physical positions
+[x,y]=meshgrid(ObjectData.RangeX(1):ObjectData.DX:ObjectData.RangeX(2),ObjectData.RangeY(1):ObjectData.DY:ObjectData.RangeY(2));
+%camera coordinates:initialisation 2 cameras
+NbCamera=2;
+X=zeros(NbCamera,size(x,1),size(y,1));
+Y=zeros(NbCamera,size(x,1),size(y,1));
+for icamera=1:NbCamera
+%camera coordinates
+Calib=XmlData{1}.GeometryCalib;
+    xc=R(1)*Xphys+R(2)*Yphys+R(3)*Zphys+Calib.Tx_Ty_Tz(1);
+    yc=R(4)*Xphys+R(5)*Yphys+R(6)*Zphys+Calib.Tx_Ty_Tz(2);
+    zc=R(7)*Xphys+R(8)*Yphys+R(9)*Zphys+Calib.Tx_Ty_Tz(3);
+    
+    %undistorted image coordinates
+    X(icamera,:,:)=xc./zc;
+    Y(icamera,:,:)=yc./zc;
+end
+
+%% case of fixed planes (for moving interface, coeff need to be calculated for each field
+if isequal(size(InputTable),2)
+[S,D]=get_coeff(XmlData,X,Y);
+end
+
  %% MAIN LOOP ON FIELDS
 for index=1:NbField
@@ -154 +177 @@
         
         %% transform the input field (e.g; phys) if requested (no transform involving two input fields)
+            %camera coordinates
+        xc=R(1)*Xphys+R(2)*Yphys+R(3)*Zphys+Calib.Tx_Ty_Tz(1);
+        yc=R(4)*Xphys+R(5)*Yphys+R(6)*Zphys+Calib.Tx_Ty_Tz(2);
+        zc=R(7)*Xphys+R(8)*Yphys+R(9)*Zphys+Calib.Tx_Ty_Tz(3);
+
+        %undistorted image coordinates
+        Xu=xc./zc;
+        Yu=yc./zc;
         Data{iview}=phys(Data{iview},XmlData{iview});
         
@@ -346 +377 @@
 display([file_st ' written'])
 
-
+function [S,D]=get_coeff(XmlData,X,Y);
+Calib_a=XmlData{1}.GeometryCalib;
+R=(Calib_a.R)';%rotation matrix
+A(1,1)=R(1)-R(7)*X;
+A(1,2)=R(2)-R(8)*X;
+A(1,3)=R(3)-R(9)*X;
+A(2,1)=R(4)-R(7)*Y;
+A(2,2)=R(5)-R(8)*Y;
+A(2,3)=R(6)-R(9)*Y;
 
 %'pxcm_tsai': find differentials of the Tsai calibration

trunk/src/series/extract_rdvision.m

@@ -78 +78 @@
     check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files
     ListDir=ListCells(1,find(check_dir & ~check_bad));
-    InputTable=cell(numel(ListDir),5);
-    InputTable(:,2)=ListDir';
+    InputTable=cell(1,5);
+%    InputTable(:,2)=ListDir';
     isel=0;
     for ilist=1:numel(ListDir)
@@ -91 +91 @@
            isel=isel+1;
            InputTable{isel,1}=RootPath;
+           InputTable{isel,2}=ListDir{ilist};
             RootFile=regexprep(ListCellSub{1,seq_index},'.seq$','');
             InputTable{isel,3}=RootFile;
-        end
-        InputTable{isel,4}='*';
+                    InputTable{isel,4}='*';
         InputTable{isel,5}='.seq';
+        end
+
     end
     hseries=findobj(allchild(0),'Tag','series');% find the parent GUI 'series'
@@ -269 +271 @@
     [success,message]=copyfile(filexml,[filexml '~']);%make backup
     if success~=1
-        dips(['errror in xml file backup: ' message]);
+        displ(['errror in xml file backup: ' message]);
         return
     end
@@ -366 +368 @@
 BitDepth=8*SeqData.bytesperpixel;%needed to write images (8 or 16 bits)
 binrepertoire=fullfile(PathDir,SeqData.binrepertoire);
-tic
-OutputDir=fullfile(PathDir,SeqData.sequencename)
+OutputDir=fullfile(PathDir,SeqData.sequencename);
 if exist(OutputDir,'dir')
     errormsg=[OutputDir ' already exist, delete it first'];
@@ -376 +377 @@
     return%not able to create new image dir
 end
+fid=0;
 for ii=1:SeqData.nb_frames
-    fname=fullfile(binrepertoire,sprintf('%s%.5d.bin',SeqData.binfile,SqbData(ii).file_idx));
-    if ii==1 || ~strcmp(fname,fname_prev) % open the bin file if not in use
-        fid=fopen(fname,'rb');
+    OutputFile=fullfile_uvmat(PathDir,SeqData.sequencename,'img','.png',NomTypeNew,i1,[],j1);% TODO: set NomTypeNew from SeqData.mode
+    if ~exist(OutputFile,'file')
+        fname=fullfile(binrepertoire,sprintf('%s%.5d.bin',SeqData.binfile,SqbData(ii).file_idx));
+        if fid==0 || ~strcmp(fname,fname_prev) % open the bin file if not in use
+            if fid~=0
+                fclose(fid);%close the previous bin file
+            end
+            fid=fopen(fname,'rb');
+            fseek(fid,SqbData(ii).offset,-1);%look at the right starting place in the bin file
+            NbBinFile=NbBinFile+1;%counter of binary files (for checking purpose)
+            BinSize(NbBinFile)=0;% strat counter for new bin file
+        else
+            %
+            %         fid=fopen(fname,'rb');% open the new bin file
+%             fseek(fid,SqbData(ii).offset,-1);%look at the right starting place in the bin file
+        end
         fseek(fid,SqbData(ii).offset,-1);%look at the right starting place in the bin file
-        NbBinFile=NbBinFile+1;%counter of binary files (for checking purpose)
-        BinSize(NbBinFile)=0;% strat counter for new bin file
-    else
-        fclose(fid);%close the previous bin file
-        fid=fopen(fname,'rb');% open the new bin file
-        fseek(fid,SqbData(ii).offset,-1);%look at the right starting place in the bin file
-    end
-    fname_prev=fname;
-    A=reshape(fread(fid,SeqData.width*SeqData.height,classname),SeqData.width,SeqData.height);%read the current image
-    A=A';
-    BinSize(NbBinFile)=BinSize(NbBinFile)+SeqData.width*SeqData.height*SeqData.bytesperpixel*8; %record bits read
-    j1=[];
-    if ~isequal(nbfield2,1)
-        j1=mod(ii-1,nbfield2)+1;
-    end
-    i1=floor((ii-1)/nbfield2)+1;
-    OutputFile=fullfile_uvmat(PathDir,SeqData.sequencename,'img','.png',NomTypeNew,i1,[],j1);% TODO: set NomTypeNew from SeqData.mode 
-    try
-        imwrite(A,OutputFile,'BitDepth',BitDepth) % case of 16 bit images
-        disp([OutputFile ' written']);
-        [s,errormsg] = fileattrib(OutputFile,'-w','a'); %set images to read only '-w' for all users ('a')
-        if ~s
-%             disp_uvmat('ERROR',errormsg,checkrun);
+        fname_prev=fname;
+        A=reshape(fread(fid,SeqData.width*SeqData.height,classname),SeqData.width,SeqData.height);%read the current image
+        A=A';
+        BinSize(NbBinFile)=BinSize(NbBinFile)+SeqData.width*SeqData.height*SeqData.bytesperpixel*8; %record bits read
+        j1=[];
+        if ~isequal(nbfield2,1)
+            j1=mod(ii-1,nbfield2)+1;
+        end
+        i1=floor((ii-1)/nbfield2)+1;
+        
+        try
+            imwrite(A,OutputFile,'BitDepth',BitDepth) % case of 16 bit images
+            disp([OutputFile ' written']);
+            % [s,errormsg] = fileattrib(OutputFile,'-w','a'); %set images to read only '-w' for all users ('a')
+            %         if ~s
+            % %             disp_uvmat('ERROR',errormsg,checkrun);
+            %             return
+            %         end
+        catch ME
+            errormsg=ME.message;
             return
         end
-    catch ME
-        errormsg=ME.message;
-        return
     end
 end
 fclose(fid)
-toc
+