Changeset 993 for trunk/src/series

Timestamp:

Feb 6, 2017, 11:29:01 AM (8 years ago)

Author:

sommeria

Message:

various updates

Location:

trunk/src/series

Files:

• civ2vel_3C.m (modified) (1 diff)
• civ_series.m (modified) (7 diffs)
• extract_multitif_parallel.m (modified) (4 diffs)

trunk/src/series/civ2vel_3C.m

@@ -358 +358 @@
         end
     end
-    %remove wrong vector
-    temp=find(Data{1}.FF==0);
-    X1=Data{1}.X(temp);
-    Y1=Data{1}.Y(temp);
-    U1=Data{1}.U(temp);
-    V1=Data{1}.V(temp);
-    
+    %remove wrong vector  
+    if isfield(Data{1},'FF')
+        temp=find(Data{1}.FF==0);
+        X1=Data{1}.X(temp);
+        Y1=Data{1}.Y(temp);
+        U1=Data{1}.U(temp);
+        V1=Data{1}.V(temp);
+    else
+        X1=Data{1}.X;
+        Y1=Data{1}.Y;
+        U1=Data{1}.U;
+        V1=Data{1}.V;
+    end
     Ua=griddata(X1,Y1,U1,Xa,Ya);
     Va=griddata(X1,Y1,V1,Xa,Ya);
-    
-    [Ua,Va,Xa,Ya]=Ud2U(XmlData{1}.GeometryCalib,Xa,Ya,Ua,Va); % convert Xd data to X 
+    [Ua,Va,Xa,Ya]=Ud2U(XmlData{1}.GeometryCalib,Xa,Ya,Ua,Va); % convert Xd data to X
     [A]=get_coeff(XmlData{1}.GeometryCalib,Xa,Ya,XI,YI,ZI); %get coef A~
     
-    %remove wrong vector
-    temp=find(Data{2}.FF==0);
-    X2=Data{2}.X(temp);
-    Y2=Data{2}.Y(temp);
-    U2=Data{2}.U(temp);
-    V2=Data{2}.V(temp);
+    %remove wrong vector  
+    if isfield(Data{1},'FF')
+        temp=find(Data{2}.FF==0);
+        X2=Data{2}.X(temp);
+        Y2=Data{2}.Y(temp);
+        U2=Data{2}.U(temp);
+        V2=Data{2}.V(temp);
+    else
+        X2=Data{2}.X;
+        Y2=Data{2}.Y;
+        U2=Data{2}.U;
+        V2=Data{2}.V;
+    end
     Ub=griddata(X2,Y2,U2,Xb,Yb);
     Vb=griddata(X2,Y2,V2,Xb,Yb);
-
-    [Ub,Vb,Xb,Yb]=Ud2U(XmlData{2}.GeometryCalib,Xb,Yb,Ub,Vb); % convert Xd data to X 
+    [Ub,Vb,Xb,Yb]=Ud2U(XmlData{2}.GeometryCalib,Xb,Yb,Ub,Vb); % convert Xd data to X
+    
     [B]=get_coeff(XmlData{2}.GeometryCalib,Xb,Yb,XI,YI,ZI); %get coef B~
-   
+    
     
     % System to solve

trunk/src/series/civ_series.m

@@ -60 +60 @@
     Data.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
     Data.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
-    if isfield(Data,'ActionInput') && isfield(Data.ActionInput,'PairIndices')&& strcmp(Data.ActionInput.PairIndices.ListPairMode,'pair j1-j2')
-        Data.Desable_j_index='on';% hide the j index in series (set by the pair choice in civ_input)
-    end
+    %     if isfield(Data,'ActionInput') && isfield(Data.ActionInput,'PairIndices')&& strcmp(Data.ActionInput.PairIndices.ListPairMode,'pair j1-j2')
+    %         Data.Desable_j_index='on';% hide the j index in series (set by the pair choice in civ_input)
+    %     end
     Data.NbSlice='off'; %nbre of slices ('off' by default)
     Data.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
@@ -73 +73 @@
     Data.OutputFileMode='NbInput_i';% one output file expected per value of i index (used for waitbar)
     Data.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1)
+    if isequal(Data.ActionInput.PairIndices.ListPairMode,'pair j1-j2')
+        if isfield(Data.ActionInput.PairIndices,'ListPairCiv2')
+            str_civ=Data.ActionInput.PairIndices.ListPairCiv2;
+        else
+            str_civ=Data.ActionInput.PairIndices.ListPairCiv1;
+        end
+        r=regexp(str_civ,'^j= (?<num1>[a-z])-(?<num2>[a-z])','names');
+        if isempty(r)
+            r=regexp(str_civ,'^j= (?<num1>[A-Z])-(?<num2>[A-Z])','names');
+            if isempty(r)
+                r=regexp(str_civ,'^j= (?<num1>\d+)-(?<num2>\d+)','names');
+            end
+        end
+        if ~isempty(r)
+            Data.j_index_1=stra2num(r.num1);
+            Data.j_index_2=stra2num(r.num2);
+        end
+    end
     return
 end
@@ -200 +218 @@
         end
         if isempty(i1_series_Civ1)||(~isempty(PairCiv2) && isempty(i1_series_Civ2))
-            disp_uvmat('ERROR','no image pair fo civ in the input file index range',checkrun)
+            disp_uvmat('ERROR','no image pair for civ in the input file index range',checkrun)
             return
         end
@@ -208 +226 @@
     try
         if Param.ActionInput.CheckCiv1% Civ1 is performed
+            first_ima=1;
             ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(1),[],j1_series_Civ1(1));
-            if ~exist(ImageName_A,'file')
+            if checkrun 
+                if ~exist(ImageName_A,'file')
                 disp_uvmat('ERROR',['first input image ' ImageName_A ' does not exist'],checkrun)
                 return
+                end
+            else
+%                 for ifile=1:numel(i1_series_Civ1)
+%                     if 
             end
             [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A);
@@ -412 +436 @@
                 if ~isempty(ME.message)
                     disp_uvmat('ERROR', ['error reading input image: ' ME.message],checkrun)
-                    return
+                    continue
                 end
             end
@@ -1155 +1179 @@
 [npy,npx]=size(result_conv);
 result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1  (=0 by discretisation, to avoid divergence in the log)
-%the following 8 lines are copyright (c) 1998, Uri Shavit, Roi Gurka, Alex Liberzon, Technion ￜ Israel Institute of Technology
+%the following 8 lines are copyright (c) 1998, Uri Shavit, Roi Gurka, Alex Liberzon, Technion ??? Israel Institute of Technology
 %http://urapiv.wordpress.com
 peaky = y;
@@ -1192 +1216 @@
         for j=-1:1
             %following 15 lines based on
-            %H. Nobach ￜ M. Honkanen (2005)
+            %H. Nobach ??? M. Honkanen (2005)
             %Two-dimensional Gaussian regression for sub-pixel displacement
             %estimation in particle image velocimetry or particle position
             %estimation in particle tracking velocimetry
-            %Experiments in Fluids (2005) 38: 511ￜ515
+            %Experiments in Fluids (2005) 38: 511???515
             c10(j+2,i+2)=i*log(result_conv(y+j, x+i));
             c01(j+2,i+2)=j*log(result_conv(y+j, x+i));

trunk/src/series/extract_multitif_parallel.m

@@ -95 +95 @@
         return
     end
-    xmlinput=uigetfile_uvmat('pick xml file for timing',fileparts(fileparts(FirstFileName)),'.xml');
-    [tild,ParamOut.ActionInput.XmlFile]=fileparts(xmlinput);
-    ParamOut.ActionInput.XmlFile
-    
+    ParamOut.ActionInput.XmlFile=uigetfile_uvmat('pick xml file for timing',fileparts(fileparts(FirstFileName)),'.xml');  
     return
 end
@@ -140 +137 @@
 
 %% Timing
-XmlInputFile=fullfile(Param.InputTable{1,1},[Param.ActionInput.XmlFile '.xml'])
-XmlInput=imadoc2struct(XmlInputFile,'Camera');
-
-%% create the xml file of PCO camera
+XmlInputFile=Param.ActionInput.XmlFile;
+[XmlInput,errormsg]=imadoc2struct(XmlInputFile,'Camera');
+if ~isempty(errormsg)
+    disp(['bad xml input file: ' errormsg])
+    return
+end
+ImagesPerLevel=size(XmlInput.Time,2)-1;%100;%use the xmlinformation to get the nbre of j indices
+
+%% create the xml file of PCO camera if it does not exist
+Newxml=fullfile(Param.InputTable{1,1},[Param.InputTable{1,2} '.xml']);
+if ~exist(Newxml,'file')
 XmlInput.Camera.CameraName='PCO';
-t=struct2xml(XmlInput.Camera);
+XmlInput=rmfield(XmlInput,'Time');
+XmlInput=rmfield(XmlInput,'TimeUnit');
+t=struct2xml(XmlInput);
 t=set(t,1,'name','ImaDoc');
-save(t,fullfile(Param.InputTable{1,1},[Param.InputTable{1,2} '.xml']))
+save(t,Newxml);
+end
 
 %% Main loop
 
-ImagesPerLevel=size(XmlInput.Time,2)-1;%100;
+
 % count=0;
 %count=316;%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%CORRECTION EXP08: 4684 images -> start at 316 start 67->_11_1
 %count=1934%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%CORRECTION EXP07: 3066 images
 %% loop on the files
-%for ifile=1:numel(ListFile)
-%     update_waitbar(WaitbarHandle,ifile/numel(ListFile))
-%     if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue')
-%         disp('program stopped by user')
-%         break
-%     end
-%    ImageName=fullfile(DirImages,ListFile{ifile});
-%   NbFrames=numel(imfinfo(ImageName));
-% loop on the frames within the tiff file
+% include the first tiff file with no index in the first iteration
 if Param.IndexRange.first_i==1% first slice of processing
     firstindex=0;
    count=0;
-%     count=3;
 else
     firstindex=Param.IndexRange.first_i;
@@ -174 +172 @@
     NbFrames=numel(imfinfo(ImageName));
    count=Param.IndexRange.first_i*NbFrames;
- %   count=Param.IndexRange.first_i*NbFrames+3;
 end
 for ifile=firstindex:Param.IndexRange.last_i
     if firstindex==0 && ifile==0% first slice of processing
-            ImageName=fullfile(Param.InputTable{1,1},Param.InputTable{1,2},'im.tif')
+        ImageName=fullfile(Param.InputTable{1,1},Param.InputTable{1,2},'im.tif')
     else
         ImageName=fullfile(Param.InputTable{1,1},Param.InputTable{1,2},['im@' num2str(ifile,'%04d') '.tif'])
@@ -202 +199 @@
     end
 end
-    %end
-
-% for ifile=1:numel(ListFile)
-%     update_waitbar(WaitbarHandle,ifile/numel(ListFile))
-%     if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue')
-%         disp('program stopped by user')
-%         break
-%     end
-%     ImageName=fullfile(DirImages,ListFile{ifile});
-%     NbFrames=numel(imfinfo(ImageName));
-%     % loop on the frames within the tiff file
-%     for iframe=1:NbFrames      
-%         A=imread(ImageName,iframe);
-% 
-%         if isequal(ImagesPerLevel,1)% mode series 
-%             i_index=count+1;
-%             OutputFile=fullfile(OutputDir,['img_' num2str(count+1) '.png']);
-%         else % indices i and j 
-%             i_index=fix(count/ImagesPerLevel)+1;
-%             j_index=mod(count,ImagesPerLevel)+1;
-%             OutputFile=fullfile(OutputDir,['img_' num2str(i_index) '_' num2str(j_index) '.png']);
-%         end
-%         imwrite(A,OutputFile,'BitDepth',16)
-%         count=count+1;
-%     end
-% end
-
-%% create the xml file of PCO camera
-% XmlInput.Camera.CameraName='PCO';
-% t=struct2xml(XmlInput.Camera);
-% t=set(t,1,'name','ImaDoc');
-% save(t,fullfile(Param.InputTable{1,1},'PCO.xml'))
-
-%% remove initial files if transfer OK
-%     if i_index== (size(XmlInput.Time,1)-1)
-% 
-%         [SUCCESS,MESSAGE]=rmdir(DirImages,'s')
-%        
-%     end
+
+
+