Changeset 985

Timestamp:

Jan 20, 2017, 5:17:25 PM (8 years ago)

Author:

sommeria

Message:

image with vectors fixed

Location:

trunk/src

Files:

• series/civ2vel_3C.m (modified) (23 diffs)
• series/stereo_civ.m (modified) (8 diffs)
• series/stereo_input.m (modified) (1 diff)
• sub_field.m (modified) (1 diff)

trunk/src/series/civ2vel_3C.m

@@ -1 @@
-%'civ2vel_3C': combine velocity fields from two cameras to get the three velocity components 
-% used with the GUI 'series':
-%           first input line =raw PIV camera 1 (image coordinates)
-%           second input line=raw PIV camera 2 (image coordinates)
-% Three modes:
-%   1) no additional input: measurements assumed in the reference plane (laser sheet)
-%   2) measurement surface obtained by stereoscopic comparison of the images of the two cameras.
-%           third input line =surface z(x,y) given by correlation between camera 1 and 2 (expressed in phys apparent coordinates)
-%   3)  surface z(x,y) given by adding the displacements of each camera with a third intermediate camera (#3) used to reduce the 
-% to reduce the angle for stereoscopic view.
-%           third input line =correlation between camera 1 and 3 (expressed in phys apparent coordinates)
-%           fourth input line =corelation between camera 2 and 3 (expressed in phys apparent coordinates)
-%                
+%'civ2vel_3C': combine velocity fields from two cameras to get three velocity components
 %------------------------------------------------------------------------
 % function ParamOut=civ2vel_3C(Param)
@@ -19 +7 @@
 %
 %INPUT:
-% 
 % In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series.
 % In batch mode, Param is the name of the corresponding xml file containing the same information
@@ -28 +15 @@
 % see the current structure Param)
 %    .InputTable: cell of input file names, (several lines for multiple input)
-%                      each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}.
-%                3 or 4 lines used as described above
+%                      each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
 %    .OutputSubDir: name of the subdirectory for data outputs
 %    .OutputDirExt: directory extension for data outputs
@@ -36 +22 @@
 %             .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled   Matlab fct
 %             .RUN =0 for GUI input, =1 for function activation
-%             .RunMode='local','background', 'cluster': type of function  use          
+%             .RunMode='local','background', 'cluster': type of function  use
+%             
 %    .IndexRange: set the file or frame indices on which the action must be performed
 %    .InputFields: sub structure describing the input fields withfields
@@ -47 +34 @@
 
 %=======================================================================
-% Copyright 2008-2017, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
+% Copyright 2008-2015, LEGI UMR 5519 / CNRS UJF G-INP, Grenoble, France
 %   http://www.legi.grenoble-inp.fr
 %   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
@@ -65 +52 @@
 
 function ParamOut=civ2vel_3C(Param)
-
+disp('test')
 %% set the input elements needed on the GUI series when the function is selected in the menu ActionName or InputTable refreshed
 if isstruct(Param) && isequal(Param.Action.RUN,0)
@@ -137 +124 @@
 %% define the directory for result file (with path=RootPath{1})
 OutputDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
+%
+% if ~isfield(Param,'InputFields')
+%     Param.InputFields.FieldName='';
+% end
 
 %% calibration data and timing: read the ImaDoc files
@@ -169 +160 @@
     return
 end
-ObjectData=Param.ProjObject;% Object attached to the GUI series
+ObjectData=Param.ProjObject;
 xI=ObjectData.RangeX(1):ObjectData.DX:ObjectData.RangeX(2);
 yI=ObjectData.RangeY(1):ObjectData.DY:ObjectData.RangeY(2);
@@ -177 +168 @@
 W=zeros(size(XI,1),size(XI,2));
 
-%%%% MAIN LOOP ON FIELDS %%%%%
+%% MAIN LOOP ON FIELDS
 warning off
 
@@ -184 +175 @@
     CheckOverwrite=Param.CheckOverwrite;
 end
-for field_index=1:NbField
-    
-    update_waitbar(WaitbarHandle,field_index/NbField)% waitbar to visualise progress (in RUN mode)
-    
-    %% generating the name of the output file for the merged field
-    i1=i1_series{1}(field_index);
+for index=1:NbField
+    
+    update_waitbar(WaitbarHandle,index/NbField)
+    
+    
+    
+    
+      %% generating the name of the merged field
+    i1=i1_series{1}(index);
     if ~isempty(i2_series{end})
-        i2=i2_series{end}(field_index);
+        i2=i2_series{end}(index);
     else
         i2=i1;
@@ -198 +192 @@
     j2=1;
     if ~isempty(j1_series{1})
-        j1=j1_series{1}(field_index);
+        j1=j1_series{1}(index);
         if ~isempty(j2_series{end})
-            j2=j2_series{end}(field_index);
+            j2=j2_series{end}(index);
         else
             j2=j1;
@@ -207 +201 @@
     OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},'.nc','_1-2',i1,i2,j1,j2);
     
-    %% program stop if requested on the GUI
+    %%
+    
+   
     if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue')
         disp('program stopped by user')
@@ -213 +209 @@
     end
     
-    %% check existence of the output file
-    if (~CheckOverwrite && exist(OutputFile,'file'))
-        disp('existing output file already exists, skip to next field')
-        continue% skip iteration if the mode overwrite is desactivated and the result file already exists
-    end
-    
+     if (~CheckOverwrite && exist(OutputFile,'file'))  
+            disp('existing output file already exists, skip to next field')
+            continue% skip iteration if the mode overwrite is desactivated and the result file already exists
+     end   
+     
     %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%%
     Data=cell(1,NbView);%initiate the set Data
+    timeread=zeros(1,NbView);
     
     %get Xphys,Yphys,Zphys from 1 or 2 stereo folders. Positions are taken
     %at the middle between to time step
-    ZItemp=zeros(size(XI,1),size(XI,2),2);
-    if field_index==1
+   clear ZItemp
+   ZItemp=zeros(size(XI,1),size(XI,2),2);
+   
+   if index==1
         first_img=i1_series{1,1}(1,1); %id of the first image of the series
-    end
-    
-    idtemp=0;
-    % get the surface shape corresponding to the PIV measurements
-    for indextemp=field_index:field_index+1;%TODO: generalise to field index intervals>1 for PIV
-        idtemp=idtemp+1;        
-        if NbView==3 % if there is only 1 stereo folder (2 cameras only), extract directly Xphys,Yphys and Zphys  
-            InputFile_3=fullfile(Param.InputTable{3,1},Param.InputTable{3,2},[Param.InputTable{3,3} '_' int2str(first_img+indextemp-1) '.nc']);
-            % Data{1}: =raw PIV camera 1 only
-            % Data{2}: =raw PIV camera 2 only
-            % Data{3}: =correlation between camera 1 and 2 
-            [Data{3},tild,errormsg] = nc2struct(InputFile_3);%read input file       
-            if  exist('Data{3}.Civ3_FF','var') % FF is present, remove wrong vector
-                temp=find(Data{3}.Civ3_FF==0);
-                Zphys=Data{3}.Zphys(temp);
-                Yphys=Data{3}.Yphys(temp);
-                Xphys=Data{3}.Xphys(temp);
-            else
-                Zphys=Data{3}.Zphys;
-                Yphys=Data{3}.Yphys;
-                Xphys=Data{3}.Xphys;
+   end
+     
+     idtemp=0;
+ for indextemp=index:index+1; 
+     idtemp=idtemp+1;
+    if NbView==3 % if there is only 1 stereo folder, extract directly Xphys,Yphys and Zphys
+      
+        
+        
+        [Data{3},tild,errormsg] = nc2struct([Param.InputTable{3,1},'/',Param.InputTable{3,2},'/',Param.InputTable{3,3},'_',int2str(first_img+indextemp-1),'.nc']); 
+       
+        if  exist('Data{3}.Civ3_FF','var') % FF is present, remove wrong vector
+            temp=find(Data{3}.Civ3_FF==0);
+            Zphys=Data{3}.Zphys(temp);
+            Yphys=Data{3}.Yphys(temp);
+            Xphys=Data{3}.Xphys(temp);
+        else 
+            Zphys=Data{3}.Zphys;
+            Yphys=Data{3}.Yphys;
+            Xphys=Data{3}.Xphys;
+        end
+        
+        
+        
+    elseif NbView==4 % is there is 2 stereo folders, get global U and V and compute Zphys
+        
+        
+        %test if the seconde camera is the same for both folder
+        for i=3:4
+        indpt(i)=strfind(Param.InputTable{i,2},'.'); % indice of the "." is the folder name 1
+        indline(i)=strfind(Param.InputTable{i,2},'-'); % indice of the "-" is the folder name1
+        camname{i}=Param.InputTable{i,2}(indline(i)+1:indpt(i)-1);% extract the second camera name 
+        end
+        
+        if strcmp(camname{3},camname{4})==0 
+            disp_uvmat('ERROR','The 2 stereo folders should have the same camera for the second position',checkrun)
+            return
+        end
+        
+   
+        
+        [Data{3},tild,errormsg] = nc2struct([Param.InputTable{3,1},'/',Param.InputTable{3,2},'/',Param.InputTable{3,3},'_',int2str(first_img+indextemp-1),'.nc']); 
+    
+        if exist('Data{3}.Civ3_FF','var') % if FF is present, remove wrong vector
+            temp=find(Data{3}.Civ3_FF==0);
+            Xmid3=Data{3}.Xmid(temp);
+            Ymid3=Data{3}.Ymid(temp);
+            U3=Data{3}.Uphys(temp);
+            V3=Data{3}.Vphys(temp);
+        else 
+            Xmid3=Data{3}.Xmid;
+            Ymid3=Data{3}.Ymid;
+            U3=Data{3}.Uphys;
+            V3=Data{3}.Vphys;
+        end
+        %temporary gridd of merging the 2 stereos datas
+        [xq,yq] = meshgrid(min(Xmid3+(U3)/2):(max(Xmid3+(U3)/2)-min(Xmid3+(U3)/2))/128:max(Xmid3+(U3)/2),min(Ymid3+(V3)/2):(max(Ymid3+(V3)/2)-min(Ymid3+(V3)/2))/128:max(Ymid3+(V3)/2));
+        
+        %1st folder : interpolate the first camera (Dalsa1) points on the second (common) camera
+        %(Dalsa 3)
+        x3Q=griddata(Xmid3+(U3)/2,Ymid3+(V3)/2,Xmid3-(U3)/2,xq,yq);
+        y3Q=griddata(Xmid3+(U3)/2,Ymid3+(V3)/2,Ymid3-(V3)/2,xq,yq);
+        
+        
+
+         [Data{4},tild,errormsg] = nc2struct([Param.InputTable{4,1},'/',Param.InputTable{4,2},'/',Param.InputTable{4,3},'_',int2str(first_img+indextemp-1),'.nc']); 
+        if exist('Data{4}.Civ3_FF','var') % if FF is present, remove wrong vector
+            temp=find(Data{4}.Civ3_FF==0);
+            Xmid4=Data{4}.Xmid(temp);
+            Ymid4=Data{4}.Ymid(temp);
+            U4=Data{4}.Uphys(temp);
+            V4=Data{4}.Vphys(temp);
+        else 
+            Xmid4=Data{4}.Xmid;
+            Ymid4=Data{4}.Ymid;
+            U4=Data{4}.Uphys;
+            V4=Data{4}.Vphys;
+        end
+        
+        %2nd folder :interpolate the first camera (Dalsa2) points on the second (common) camera
+        %(Dalsa 3)
+        x4Q=griddata(Xmid4+(U4)/2,Ymid4+(V4)/2,Xmid4-(U4)/2,xq,yq);
+        y4Q=griddata(Xmid4+(U4)/2,Ymid4+(V4)/2,Ymid4-(V4)/2,xq,yq);
+        
+        xmid=reshape((x4Q+x3Q)/2,length(xq(:,1)).*length(xq(1,:)),1);
+        ymid=reshape((y4Q+y3Q)/2,length(yq(:,1)).*length(yq(1,:)),1);
+        u=reshape(x4Q-x3Q,length(xq(:,1)).*length(xq(1,:)),1);
+        v=reshape(y4Q-y3Q,length(yq(:,1)).*length(yq(1,:)),1);
+        
+        
+        [Zphys,Xphys,Yphys,error]=shift2z(xmid, ymid, u, v,XmlData); %get Xphy,Yphy and Zphys
+        %remove NaN 
+        tempNaN=isnan(Zphys);tempind=find(tempNaN==1);
+        Zphys(tempind)=[];
+        Xphys(tempind)=[];
+        Yphys(tempind)=[];
+        error(tempind)=[];
+         
+    end
+    
+            if NbView>2   
+       ZItemp(:,:,idtemp)=griddata(Xphys,Yphys,Zphys,XI,YI); %interpolation on the choosen gridd
             end
-            
-        elseif NbView==4 % is there is 2 stereo folders, get global U and V and compute Zphys 
-            % Data{1}: =raw PIV camera 1 only (left)
-            % Data{2}: =raw PIV camera 2 only (right) (no PIV done with middle camera)
-            % Data{3}: =corelation between camera 1 and 3 (left and middle)
-            % Data{4}: =corelation between camera 2 and 3 (right and middle)
-            % test if the second camera (3) is the same for both folders 
-            for i=3:4
-                indpt(i)=strfind(Param.InputTable{i,2},'.'); % indice of the "." is the folder name 1
-                indline(i)=strfind(Param.InputTable{i,2},'-'); % indice of the "-" is the folder name1
-                camname{i}=Param.InputTable{i,2}(indline(i)+1:indpt(i)-1);% extract the second camera name
-            end        
-            if strcmp(camname{3},camname{4})==0
-                disp_uvmat('ERROR','The 2 stereo folders should have the same camera for the second position',checkrun)
-                return
-            end      
-            [Data{3},tild,errormsg] = nc2struct(InputFile_3);       
-            if exist('Data{3}.Civ3_FF','var') % if FF is present, remove wrong vector
-                temp=find(Data{3}.Civ3_FF==0);
-                Xmid3=Data{3}.Xmid(temp);
-                Ymid3=Data{3}.Ymid(temp);
-                U3=Data{3}.Uphys(temp);
-                V3=Data{3}.Vphys(temp);
-            else
-                Xmid3=Data{3}.Xmid;
-                Ymid3=Data{3}.Ymid;
-                U3=Data{3}.Uphys;
-                V3=Data{3}.Vphys;
-            end
-            %temporary grid of merging the 2 stereos data
-            [xq,yq] = meshgrid(min(Xmid3+(U3)/2):(max(Xmid3+(U3)/2)-min(Xmid3+(U3)/2))/128:max(Xmid3+(U3)/2),min(Ymid3+(V3)/2):(max(Ymid3+(V3)/2)-min(Ymid3+(V3)/2))/128:max(Ymid3+(V3)/2));
-            
-            %1st folder : interpolate the first camera points on the second (common) camera
-            %(Dalsa 3)
-            x3Q=griddata(Xmid3+(U3)/2,Ymid3+(V3)/2,Xmid3-(U3)/2,xq,yq);
-            y3Q=griddata(Xmid3+(U3)/2,Ymid3+(V3)/2,Ymid3-(V3)/2,xq,yq);
-            
-            InputFile_4=fullfile(Param.InputTable{4,1},Param.InputTable{4,2},[Param.InputTable{4,3} '_' int2str(first_img+indextemp-1) '.nc']);
-            [Data{4},tild,errormsg] = nc2struct(InputFile_4);
-            if exist('Data{4}.Civ3_FF','var') % if FF is present, remove wrong vector
-                temp=find(Data{4}.Civ3_FF==0);
-                Xmid4=Data{4}.Xmid(temp);
-                Ymid4=Data{4}.Ymid(temp);
-                U4=Data{4}.Uphys(temp);
-                V4=Data{4}.Vphys(temp);
-            else
-                Xmid4=Data{4}.Xmid;
-                Ymid4=Data{4}.Ymid;
-                U4=Data{4}.Uphys;
-                V4=Data{4}.Vphys;
-            end
-            %2nd folder :interpolate the first camera (Dalsa2) points on the second (common) camera
-            %(Dalsa 3)
-            x4Q=griddata(Xmid4+(U4)/2,Ymid4+(V4)/2,Xmid4-(U4)/2,xq,yq);
-            y4Q=griddata(Xmid4+(U4)/2,Ymid4+(V4)/2,Ymid4-(V4)/2,xq,yq);
-            
-            %add the displacements of the two camera pairs
-            xmid=reshape((x4Q+x3Q)/2,length(xq(:,1)).*length(xq(1,:)),1);
-            ymid=reshape((y4Q+y3Q)/2,length(yq(:,1)).*length(yq(1,:)),1);
-            u=reshape(x4Q-x3Q,length(xq(:,1)).*length(xq(1,:)),1);
-            v=reshape(y4Q-y3Q,length(yq(:,1)).*length(yq(1,:)),1);
-            
-            % get the surface z(x,y) from the combined displacement
-            [Zphys,Xphys,Yphys,error]=shift2z(xmid, ymid, u, v,XmlData); %get Xphy,Yphy and Zphys
-            %remove NaN
-            tempNaN=isnan(Zphys);tempind=find(tempNaN==1);
-            Zphys(tempind)=[];
-            Xphys(tempind)=[];
-            Yphys(tempind)=[];
-            error(tempind)=[];
-            
-        end
-        if NbView>2
-        ZItemp(:,:,idtemp)=griddata(Xphys,Yphys,Zphys,XI,YI); %interpolation on the choosen grid
-        end
-        
-    end
-    ZI=mean(ZItemp,3); %mean between two the two times used for surface measurement
+    
+end
+    ZI=mean(ZItemp,3); %mean between two the two time step
     Vtest=ZItemp(:,:,2)-ZItemp(:,:,1);
     
@@ -332 +336 @@
     [Xb,Yb]=px_XYZ(XmlData{2}.GeometryCalib,XI,YI,ZI);% set of image coordinates on view b
     
-    
+   
     for iview=1:2
-        %% reading PIV input file(s)
-        [Data{iview},tild,errormsg]=read_civdata(filecell{iview,field_index},{'vec(U,V)'},Param.InputFields.VelType);
+        %% reading input file(s)
+        [Data{iview},tild,errormsg]=read_civdata(filecell{iview,index},{'vec(U,V)'},'*');
         if ~isempty(errormsg)
             disp_uvmat('ERROR',['ERROR in civ2vel_3C/read_field/' errormsg],checkrun)
@@ -354 +358 @@
         end
     end
-    %remove false vectors
+    %remove wrong vector
     temp=find(Data{1}.FF==0);
     X1=Data{1}.X(temp);
@@ -364 +368 @@
     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 false vectors
+    %remove wrong vector
     temp=find(Data{2}.FF==0);
     X2=Data{2}.X(temp);
@@ -375 +379 @@
     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
     S=ones(size(XI,1),size(XI,2),3);
     D=ones(size(XI,1),size(XI,2),3,3);
-    
+
     S(:,:,1)=A(:,:,1,1).*Ua+A(:,:,2,1).*Va+B(:,:,1,1).*Ub+B(:,:,2,1).*Vb;
     S(:,:,2)=A(:,:,1,2).*Ua+A(:,:,2,2).*Va+B(:,:,1,2).*Ub+B(:,:,2,2).*Vb;
@@ -403 +407 @@
             W(indj,indi)=dxyz(3);
         end
-    end
+    end   
     Error=zeros(size(XI,1),size(XI,2),4);
     Error(:,:,1)=A(:,:,1,1).*U+A(:,:,1,2).*V+A(:,:,1,3).*W-Ua;
@@ -410 +414 @@
     Error(:,:,4)=B(:,:,2,1).*U+B(:,:,2,2).*V+B(:,:,2,3).*W-Vb;
     
+    
+
+    
+  
+    
     %% recording the merged field
-    if field_index==1% initiate the structure at first index
+    if index==1% initiate the structure at first index
         MergeData.ListGlobalAttribute={'Conventions','Time','Dt'};
         MergeData.Conventions='uvmat';
@@ -418 +427 @@
         MergeData.ListVarName={'coord_x','coord_y','Z','U','V','W','Error'};
         MergeData.VarDimName={'coord_x','coord_y',{'coord_y','coord_x'},{'coord_y','coord_x'}...
-            {'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'}};
+                {'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'}};
         MergeData.coord_x=xI;
         MergeData.coord_y=yI;
@@ -427 +436 @@
     MergeData.Z=ZI;
     
-    %     mfx=(XmlData{1}.GeometryCalib.fx_fy(1)+XmlData{2}.GeometryCalib.fx_fy(1))/2;
-    %     mfy=(XmlData{1}.GeometryCalib.fx_fy(2)+XmlData{2}.GeometryCalib.fx_fy(2))/2;
+%     mfx=(XmlData{1}.GeometryCalib.fx_fy(1)+XmlData{2}.GeometryCalib.fx_fy(1))/2;
+%     mfy=(XmlData{1}.GeometryCalib.fx_fy(2)+XmlData{2}.GeometryCalib.fx_fy(2))/2;
     MergeData.Error=0.5*sqrt(sum(Error.^2,3));
     errormsg=struct2nc(OutputFile,MergeData);%save result file
@@ -451 +460 @@
 A(:,:,2,3)=(R(6)-R(9)*Y)./T;
 
-function [U,V,X,Y]=Ud2U(Calib,Xd,Yd,Ud,Vd) 
-% convert image coordinates to view angles, after removal of  quadratic distorsion
-% input in pixel, output in radians
+function [U,V,X,Y]=Ud2U(Calib,Xd,Yd,Ud,Vd) % convert Xd to X  and Ud to U
+
 X1d=Xd-Ud/2;
 X2d=Xd+Ud/2;
@@ -474 +482 @@
 z=0;
 error=0;
+
 
 %% first image

trunk/src/series/stereo_civ.m

@@ -92 +92 @@
 end
 [tild,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
+time=[];
 for iview=1:size(Param.InputTable,1)
     XmlFileName=find_imadoc(Param.InputTable{iview,1},Param.InputTable{iview,2},Param.InputTable{iview,3},Param.InputTable{iview,5});
@@ -135 +136 @@
 i2_series_Civ1=i1_series{2};i2_series_Civ2=i1_series{2};
 if isempty(j1_series{1})
+        FrameIndex_A_Civ1=i1_series_Civ1;
+    FrameIndex_B_Civ1=i2_series_Civ1;
     j1_series_Civ1=ones(size(i1_series{1}));
     j2_series_Civ1=ones(size(i1_series{2}));
@@ -140 +143 @@
     j1_series_Civ1=j1_series{1};
     j2_series_Civ1=j1_series{2};
+     FrameIndex_A_Civ1=j1_series_Civ1;
+    FrameIndex_B_Civ1=j2_series_Civ1;
 end
 j1_series_Civ2=j1_series_Civ1;
 j2_series_Civ2=j2_series_Civ1;
-NomTypeNc=NomType_A;
-if isempty(j1_series_Civ1)
-    FrameIndex_A_Civ1=i1_series_Civ1;
-    FrameIndex_B_Civ1=i2_series_Civ1;
-    j1_series_Civ1=ones(size(i1_series_Civ1));
-    j2_series_Civ1=ones(size(i1_series_Civ1));
-else
-    FrameIndex_A_Civ1=j1_series_Civ1;
-    FrameIndex_B_Civ1=j2_series_Civ1;
-end
+
+% if isempty(j1_series_Civ1)
+%     FrameIndex_A_Civ1=i1_series_Civ1;
+%     FrameIndex_B_Civ1=i2_series_Civ1;
+%     j1_series_Civ1=ones(size(i1_series_Civ1));
+%     j2_series_Civ1=ones(size(i1_series_Civ1));
+% else
+%     FrameIndex_A_Civ1=j1_series_Civ1;
+%     FrameIndex_B_Civ1=j2_series_Civ1;
+% end
 if isempty(PairCiv2)
     FrameIndex_A_Civ2=FrameIndex_A_Civ1;
@@ -231 +236 @@
     end
 end
-
+if ismember(FileType_A,{'mmreader','video','cine_phantom'})
+    NomTypeNc='_1';
+else
+    NomTypeNc=NomType_A;
+end
 
 %% Output directory
@@ -244 +253 @@
 
 %% get timing from input video
-if isempty(time) && ~isempty(find(strcmp(FileType_A,{'mmreader','video','cine_phantom'})))% case of video input
+if isempty(time) && ismember(FileType_A,{'mmreader','video','cine_phantom'})% case of video input
     time=zeros(FileInfo_A.NumberOfFrames+1,2);
     time(:,2)=(0:1/FileInfo_A.FrameRate:(FileInfo_A.NumberOfFrames)/FileInfo_A.FrameRate)';
@@ -281 +290 @@
     Civ1Dir=OutputDir;
 
-        ncfile=fullfile_uvmat(RootPath_A,Civ1Dir,[RootFile_A,'_All'],'.nc',NomTypeNc,i2_series_Civ1(ifield),[],...
-            j1_series_Civ1(ifield),j2_series_Civ1(ifield));
-        
-        
-        ncfile2=fullfile_uvmat(RootPath_A,Civ1Dir,[RootFile_A,'_Light'],'.nc',NomTypeNc,i2_series_Civ1(ifield),[],...
+%         ncfile=fullfile_uvmat(RootPath_A,Civ1Dir,[RootFile_A,'_All'],'.nc',NomTypeNc,i2_series_Civ1(ifield),[],...
+%             j1_series_Civ1(ifield),j2_series_Civ1(ifield));
+        
+        
+        ncfile2=fullfile_uvmat(RootPath_A,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i2_series_Civ1(ifield),[],...
             j1_series_Civ1(ifield),j2_series_Civ1(ifield));
         
@@ -824 +833 @@
     
     %% write result in a netcdf file if requested
-    if LSM ~= 1 % store all data
-        if exist('ncfile','var')
-            errormsg=struct2nc(ncfile,Data);
-            if isempty(errormsg)
-                disp([ncfile ' written'])
-            else
-                disp(errormsg)
-            end
-        end
-    else
+%     if LSM ~= 1 % store all data
+%         if exist('ncfile','var')
+%             errormsg=struct2nc(ncfile,Data);
+%             if isempty(errormsg)
+%                 disp([ncfile ' written'])
+%             else
+%                 disp(errormsg)
+%             end
+%         end
+%     else
        % store only phys data
         Data_light.ListVarName={'Xphys','Yphys','Zphys','Civ3_C','Xmid','Ymid','Uphys','Vphys','Error'};
@@ -856 +865 @@
        end
        
-    end
+%     end
 end
 disp(['ellapsed time for the loop ' num2str(toc) ' s'])

trunk/src/series/stereo_input.m

@@ -2338 +2338 @@
     check_input=0;
     if isfield(Param,'ActionInput')
-        if isfield(Param.ActionInput,'Program')&& strcmp(Param.ActionInput.Program,'civ_series')
+        if isfield(Param.ActionInput,'Program')&& strcmp(Param.ActionInput.Program,'stereo_civ')
             fill_GUI(Param.ActionInput,handles.civ_input)% fill the elements of the GUI series with the input parameters
             set(handles.ConfigSource,'String',filexml)

trunk/src/sub_field.m

@@ -165 +165 @@
 check_rename=zeros(size(ListVarNameSub));
 check_remove=zeros(size(ListVarNameSub));
-VarDimNameSub={};
+VarDimNameSub=Field_1.VarDimName;
 VarAttributeSub={};
 if isfield(Field_1,'VarAttribute')&&~isempty(Field_1.VarAttribute)