Changeset 999 for trunk

Timestamp:

Feb 17, 2017, 12:17:59 PM (8 years ago)

Author:

g7moreau

Message:

• Remove tab and end of line space

Location:

trunk/src

Files:

• civ_3D.m (modified) (110 diffs)
• toolbox_calib/init_intrinsic_param.m (modified) (4 diffs)
• toolbox_calib/normalize_pixel.m (modified) (1 diff)

trunk/src/civ_3D.m

@@ -1 @@
-%'civ_3D': function associated with the interface 'civ_3D.fig' for PIV in volume   
+%'civ_3D': function associated with the interface 'civ_3D.fig' for PIV in volume
 %------------------------------------------------------------------------
 %  provides an interface for the software CIVx
@@ -55 +55 @@
 % varargin   command line arguments to civ_3D (see VARARGIN)
 global test_batch patch_new_exe%=1 if patch processing available
-%filebase: root name 
+%filebase: root name
 %nom_type: nomencalture used ('png_old','_i_j'...)
 %list of field numbers to process
-%subdir: subdirectory of the opened netcdf file 
+%subdir: subdirectory of the opened netcdf file
 %ind_opening: operation number advised for beginning (1=civ1,2=fix1,3=patch1,4=civ2,5=fix2,6=patch2),
 %ind_a_opening ind_b_opening chosen pair from the opened netcdf file
@@ -70 +70 @@
 nom_type=[]; % nomenclature type
 ext=[];
-testall=0; 
+testall=0;
 browse=[];
 
-%load the initial parameters if the interface is started from uvmat 
+%load the initial parameters if the interface is started from uvmat
 if ~isempty(varargin)% the interface is opened from uvmat
     varcell=varargin{1};
@@ -95 +95 @@
     ind_opening=1; % proposed operation number (1=civ1,2=fix1,3=patch1,4=civ2,5=fix2,6=patch2)
     ind_a_opening=1; % proposed index in the menu of fields a
-    ind_b_opening=2; % proposed index in the menu of fields b   
+    ind_b_opening=2; % proposed index in the menu of fields b
 end
 
 if exist('ext','var') & length(ext)>1 & (~isempty(imformats(ext([2:end])))|...
                        isequal(ext,'.avi')|isequal(ext,'.AVI'));%if an image file has been opened by uvmat
-        browse.ext_ima=ext; 
+        browse.ext_ima=ext;
         if exist('nom_type_read','var')
             browse.nom_type_ima=nom_type_read; % the image nomenclature is stored
@@ -116 +116 @@
 
 % set(handles.ImaDoc,'String',ext)
-  
+
 %read names of the .exe file to adjust the interface according to
 %available prog
@@ -139 +139 @@
     end
 end
-   
+
 patch_new_exe='';
 todo_patch='';
@@ -152 +152 @@
 if isfield(sparam,'SGE')
     sge=str2num(sparam.SGE);
-end   
+end
 name_todo=fullfile(todo_path,'TODO.txt')
 test_batch=1;
@@ -160 +160 @@
     test_batch=0;
 end
-if exist(name_todo,'file')~=2 
+if exist(name_todo,'file')~=2
     msgbox_uvmat('ERROR',['no batch distributed processing available, queue file ' name_todo ' absent']);
   %  test_batch=0;  % Problems to detect file on linux/nfs filesystems
@@ -233 +233 @@
 else
     num_ref_j=floor((num_a+num_b)/2);
-    browse.incr_pair(2)=num_b-num_a; 
+    browse.incr_pair(2)=num_b-num_a;
 end
 set(handles.first_i,'String',num2str(num_ref_i));
@@ -240 +240 @@
 set(handles.browse_root,'UserData',browse);
 if ~isempty(varargin)% the interface is opened from uvmat
-    displ_filebase_Callback(hObject, eventdata, handles); 
+    displ_filebase_Callback(hObject, eventdata, handles);
 end
 
@@ -275 +275 @@
          end
          if isfield(h,'RootPath')&ischar(h.RootPath)
-%                 oldfile=h.filebase{1} 
+%                 oldfile=h.filebase{1}
                  oldfile=h.RootPath;
          end
@@ -291 +291 @@
 
 [FileName, PathName, filtindex] = uigetfile( menu, 'Pick a file',oldfile);
-fileinput=[PathName FileName];%complete file name 
+fileinput=[PathName FileName];%complete file name
 sizf=size(fileinput);
 if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
@@ -327 +327 @@
 if length(ext)>1 & (~isempty(imformats(ext([2:end])))||...
                        isequal(lower(ext),'.avi')||isequal(ext,'.vol'));%if an image file has been opened by uvmat
-    browse.ext_ima=ext; 
+    browse.ext_ima=ext;
     browse.nom_type_ima=nom_type;
     browse.field_count=str2num(field_count);
@@ -335 +335 @@
 if isequal(ext,'.nc')
     browse.nom_type_nc=nom_type;
-    ind_opening=2;% propose 'fix' as the default option    
+    ind_opening=2;% propose 'fix' as the default option
     Data=nc2struct(fileinput,[]);
     if isfield(Data,'fix') & isequal(Data.fix,1)
@@ -379 +379 @@
     set(handles.first_i,'String',num2str(ref_i));
     set(handles.last_i,'String',num2str(ref_i));
-    set(handles.ref_i,'String',num2str(ref_i)); 
+    set(handles.ref_i,'String',num2str(ref_i));
 end
 if isequal(ind_opening,1)
@@ -427 +427 @@
 field_count=1;%default
 nom_type_nc=[];
-npx=[];%default 
+npx=[];%default
 npy=[];
 TimeUnit='s'; %default
@@ -437 +437 @@
 ext=get(handles.ImaDoc,'String');
 browse=get(handles.browse_root,'UserData');%default
-if ~isempty(browse) 
+if ~isempty(browse)
     if isfield(browse,'ext_ima')
         ext_ima=browse.ext_ima;
@@ -468 +468 @@
 if isfield(browse,'pxcmx') & isfield(browse,'pxcmy')
     pxcmx=num2str(browse.pxcmx);
-    pxcmy=num2str(browse.pxcmy); 
+    pxcmy=num2str(browse.pxcmy);
 else
     pxcmx=1;%default
-    pxcmy=1; 
+    pxcmy=1;
 end
  %look for an image documentation file
@@ -481 +481 @@
          ext='.civ_3D';
          set(handles.ImaDoc,'String','.civ_3D')
-    elseif exist([filebase '.avi'],'file') 
+    elseif exist([filebase '.avi'],'file')
          ext='.avi';
          set(handles.ImaDoc,'String','.avi')
@@ -511 +511 @@
         if isfield(XmlData,'GeometryCalib')
             tsai=XmlData.GeometryCalib;
-            if isfield(tsai,'f') & isfield(tsai,'Tz') & isfield(tsai,'dpx') & isfield(tsai,'dpy')& isfield(tsai,'R') 
+            if isfield(tsai,'f') & isfield(tsai,'Tz') & isfield(tsai,'dpx') & isfield(tsai,'dpy')& isfield(tsai,'R')
                  rot2D=tsai.R([1:2],[1,2]);
                  pxcmx_search=tsai.f * sqrt(det(rot2D))/(tsai.Tz*tsai.dpx);
-                 pxcmy_search=tsai.f * sqrt(det(rot2D))/(tsai.Tz*tsai.dpy);           
+                 pxcmy_search=tsai.f * sqrt(det(rot2D))/(tsai.Tz*tsai.dpy);
             end
-            if isfield(tsai,'CoordUnit') 
+            if isfield(tsai,'CoordUnit')
                  CoordUnit=tsai.CoordUnit;
             end
-        end               
+        end
         if isempty(ext_ima_read)
               ext_ima='.png';%default
@@ -531 +531 @@
                 nom_type_ima=nom_type_read;
         end
-        
-elseif isequal(ext,'.avi')|isequal(ext,'.AVI') 
+
+elseif isequal(ext,'.avi')|isequal(ext,'.AVI')
         nom_type_ima='avi';
         ext_ima=ext;
@@ -542 +542 @@
             nbfield=info.NumFrames;%number of frames
         end
-        time=(dt*[0:nbfield-1])';%list of image times   
+        time=(dt*[0:nbfield-1])';%list of image times
         set(handles.dt,'String',num2str(dt*1000));%store the time interval between successive images
-        
-     % no image documentation file found: look for a series of existing images or .nc files 
-elseif ~isequal(ext,'.nc') 
+
+     % no image documentation file found: look for a series of existing images or .nc files
+elseif ~isequal(ext,'.nc')
         subdir=get(handles.subdir_civ1,'String');
         incr_pair=[0 0];%default
@@ -572 +572 @@
         field_i=field_count;%look for the minimum file number in the series
         idetect=1;
-        while idetect==1 
+        while idetect==1
                     field_i=field_i-1;
                     imagename=name_generator(filebase,field_i,1,ext_ima,nom_type_ima);
@@ -592 +592 @@
 end
 if isequal(nom_type_ima,'none')% no file numbering used
-  first_i=1; 
+  first_i=1;
   last_i=1;
    first_j=1;
@@ -653 +653 @@
     end
 end
-mode_Callback(hObject, eventdata, handles)  
+mode_Callback(hObject, eventdata, handles)
 
 %%%%%% initialize waitbars and RUN button
@@ -666 +666 @@
     set(handles.BATCH,'BackgroundColor',[1 0 0])
 end
-    
+
 %%%%% store the root input filename for future opening
 dir_perso=prefdir;
@@ -678 +678 @@
     relnumb=str2num(Release(3:4));
     if relnumb >= 14
-        save (profil_perso,'RootPath','-V6'); %store the root name for future opening of uvmat 
+        save (profil_perso,'RootPath','-V6'); %store the root name for future opening of uvmat
     else
         save (profil_perso,'RootPath'); %store the root name for future opening of uvmat
@@ -742 +742 @@
          displ_num(3,index)=0;
          displ_num(4,index)=0;
-     end       
+     end
      set(handles.jtext,'Visible','On')
      set(handles.first_j,'Visible','On')
@@ -764 +764 @@
         set(handles.ref_i,'Visible','Off')
     end
-elseif isequal(mode,'series(Di)') | isequal(mode,'st_series(Di)') 
+elseif isequal(mode,'series(Di)') | isequal(mode,'st_series(Di)')
      for index=1:min(nbfield-1,200)
          displ_num(1,index)=0;
@@ -778 +778 @@
      set(handles.ref_i,'Visible','On')
 elseif isequal(mode,'displacement')%the pairs have the same indices
-     displ_num(1,1)=0; 
+     displ_num(1,1)=0;
      displ_num(2,1)=0;
      displ_num(3,1)=0;
@@ -812 +812 @@
         set(handles.ref_j,'Visible','Off')
     end
-end  
+end
 set(handles.list_pair_civ1,'UserData',displ_num);
 find_netcpair_civ1(hObject, eventdata, handles)
@@ -855 +855 @@
     else
         nom_type_nc='_i_j1-j2';
-    end    
+    end
 end
 browse.nom_type_nc=nom_type_nc;
@@ -874 +874 @@
 if isempty(time)
     time=[0 1];
-end 
+end
 displ_num=get(handles.list_pair_civ1,'UserData');
 
-%eliminate the first pairs inconsistent with the position 
+%eliminate the first pairs inconsistent with the position
 if isempty(displ_num)
     nbpair=0;
@@ -890 +890 @@
 nbpair=min(200,nbpair);%limit the number of displayed pairs to 200
 
-%look for existing processed pairs involving the field at the middle of the series if civ1 will not 
+%look for existing processed pairs involving the field at the middle of the series if civ1 will not
 % be performed, while the result is needed for next steps.
 displ_pair={''};
@@ -897 +897 @@
 if get(handles.CIV1,'Value')==0 %
     dirname=fullfile(filepath,subdir_civ1,ext_dir);
-    if ~exist(fullfile(filepath,subdir_civ1,ext_dir),'dir') 
+    if ~exist(fullfile(filepath,subdir_civ1,ext_dir),'dir')
          msgbox_uvmat('ERROR',['no civ1 file available: subdirectory ' subdir_civ1 ' does not exist']);
          set(handles.list_pair_civ1,'String',{});
          return
     end
-    for ipair=1:nbpair   
+    for ipair=1:nbpair
         filename=name_generator(filebase,ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair),'.nc',nom_type_nc,1,...
         ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair),subdir_civ1);
@@ -908 +908 @@
     end
     if ~exist('select','var') | isequal(select,zeros(size(1:nbpair)))
-        if isfield(browse,'incr_pair') 
+        if isfield(browse,'incr_pair')
             num_i1=ref_i-floor(browse.incr_pair(1)/2);
             num_i2=ref_i+ceil(browse.incr_pair(1)/2);
@@ -917 +917 @@
             testpair=1;
         else
-            if  isequal(mode,'series(Dj)') | isequal(mode,'st_series(Dj)') 
+            if  isequal(mode,'series(Dj)') | isequal(mode,'st_series(Dj)')
                 msgbox_uvmat('ERROR',['no civ1 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ1]);
             else
@@ -928 +928 @@
     end
 end
-if isequal(mode,'series(Di)') 
+if isequal(mode,'series(Di)')
     if testpair
-              displ_pair{1}=['Di= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];        
-    else 
+              displ_pair{1}=['Di= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];
+    else
        for ipair=1:nbpair
-          if select(ipair)          
+          if select(ipair)
               dt=time(ref_i+displ_num(4,ipair),1)-time(ref_i+displ_num(3,ipair),1);%time interval dt
               displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)];
-          else 
+          else
              displ_pair{ipair}='...'; %pair not displayed in the menu
           end
@@ -947 +947 @@
            displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ...
                         ' :dt= ' num2str(dt*1000)];
-       else 
+       else
           displ_pair{ipair}='...'; %pair not displayed in the menu
-        end   
+        end
    end
 elseif isequal(mode,'displacement')
-    displ_pair={'Di=Dj=0'};  
-end   
+    displ_pair={'Di=Dj=0'};
+end
 set(handles.list_pair_civ1,'String',displ_pair');
 ichoice=min(find(select));
@@ -968 +968 @@
 set(gcf,'Pointer','arrow')
 %--------------------------------------------------------------
-% determine the menu for civ2 pairs depending on the existing netcdf file at the 
-%middle of the series set by first_i, incr, last_i 
+% determine the menu for civ2 pairs depending on the existing netcdf file at the
+%middle of the series set by first_i, incr, last_i
 %--------------------------------------------------------------
 function find_netcpair_civ2(hObject, eventdata, handles)
@@ -1002 +1002 @@
     else
         nom_type_nc='_i_j1-j2';
-    end    
+    end
 end
 browse.nom_type_nc=nom_type_nc;
@@ -1032 +1032 @@
 
 
-%eliminate the first pairs inconsistent with the position 
+%eliminate the first pairs inconsistent with the position
 if isempty(displ_num)
     nbpair=0;
 else
     nbpair=length(displ_num(1,:));%nbre of displayed pairs
-    if  isequal(mode,'series(Di)') | isequal(mode,'st_series(Di)') 
+    if  isequal(mode,'series(Di)') | isequal(mode,'st_series(Di)')
         nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index
-    elseif  isequal(mode,'series(Dj)') | isequal(mode,'st_series(Dj)') 
+    elseif  isequal(mode,'series(Dj)') | isequal(mode,'st_series(Dj)')
         nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index
     end
@@ -1045 +1045 @@
 nbpair=min(200,nbpair);%limit the number of displayed pairs to 200
 
-%look for existing processed pairs involving the field at the middle of the series if civ1 will not 
+%look for existing processed pairs involving the field at the middle of the series if civ1 will not
 % be performed, while the result is needed for next steps.
 displ_pair={''}; %default
 select=ones(size(1:nbpair));%default =1 for nubers of displayed pairs
 if get(handles.CIV2,'Value')==0 & get(handles.CIV1,'Value')==0 & get(handles.FIX1,'Value')==0 & get(handles.PATCH1,'Value')==0%&...
-    if ~exist(fullfile(filepath,subdir_civ2,ext_dir),'dir') 
+    if ~exist(fullfile(filepath,subdir_civ2,ext_dir),'dir')
          errordlg(['no civ2 file available: subdirectory ' subdir_civ2 ' does not exist'])
          set(handles.list_pair_civ2,'String',{});
          return
     end
-    for ipair=1:nbpair       
+    for ipair=1:nbpair
         [filename]=name_generator(filebase,ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair),'.nc',nom_type_nc,1,...
         ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair),subdir_civ1);
@@ -1061 +1061 @@
     end
     if  isequal(select,zeros(size(1:nbpair)))
-        if isfield(browse,'incr_pair') 
+        if isfield(browse,'incr_pair')
             num_i1=ref_i-floor(browse.incr_pair(1)/2);
             num_i2=ref_i+floor((browse.incr_pair(1)+1)/2);
@@ -1069 +1069 @@
             select(1)=exist(filename,'file');
         else
-            if  isequal(mode,'series(Dj)') | isequal(mode,'st_series(Dj)') 
+            if  isequal(mode,'series(Dj)') | isequal(mode,'st_series(Dj)')
                 msgbox_uvmat('ERROR',['no civ2 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ2])
             else
@@ -1079 +1079 @@
     end
 end
-if isequal(mode,'series(Di)')  | isequal(mode,'st_series(Di)') 
+if isequal(mode,'series(Di)')  | isequal(mode,'st_series(Di)')
     if  ~isequal(get(handles.ext_txt,'String'),'dt(ms)=')
        for ipair=1:nbpair
@@ -1085 +1085 @@
               dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt
               displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)];
-          else 
+          else
              displ_pair{ipair}='...'; %pair not displayed in the menu
           end
@@ -1093 +1093 @@
          if select(ipair)
             displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt_unit*ipair)];
-         else 
+         else
             displ_pair{ipair}='...'; %pair not displayed in the menu
          end
@@ -1103 +1103 @@
               dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt
               displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)];
-          else 
+          else
              displ_pair{ipair}='...'; %pair not displayed in the menu
           end
@@ -1113 +1113 @@
            displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ...
                         ' :dt= ' num2str(dt*1000)];
-       else 
+       else
           displ_pair{ipair}='...'; %pair not displayed in the menu
-       end   
+       end
    end
 elseif isequal(mode,'displacement')
-    displ_pair={'Di=Dj=0'};  
-end   
+    displ_pair={'Di=Dj=0'};
+end
 set(handles.list_pair_civ2,'String',displ_pair');
 ichoice=min(find(select));
@@ -1128 +1128 @@
 set(gcf,'Pointer','arrow')
 %----------------------------------------------------
-%  determine the list of index pairs of processing file 
+%  determine the list of index pairs of processing file
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 function [num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=...
@@ -1150 +1150 @@
     set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
 num1=[first_i:incr:last_i];
-if isequal (mode,'series(Di)') 
+if isequal (mode,'series(Di)')
      %recognize the pair civ1 from the display
-        indsel=find((double(str_civ1)<48)|(double(str_civ1)>57));% character indices of non numerical characters
+    indsel=find((double(str_civ1)<48)|(double(str_civ1)>57));% character indices of non numerical characters
     str_raw=str_civ1(indsel);
     indsepar=find(str_raw=='|'); %character index of the separator
@@ -1160 +1160 @@
     else
         d2=str2num(str_civ1([indsel(indsepar)+1:indsel(indsepar+1)-1]));
-    end   
+    end
     %recognize the pair civ2 from the display
     num1_civ1=num1-d1;% set of first image numbers
@@ -1251 +1251 @@
 set(handles.list_pair_civ2,'Value',index_pair);
 
-%update first_i and last_i according to the chosen image pairs 
+%update first_i and last_i according to the chosen image pairs
 mode_list=get(handles.mode,'String');
 mode_value=get(handles.mode,'Value');
@@ -1281 +1281 @@
     set(handles.first_j,'String',num2str(num1(1)));
     set(handles.last_j,'String',num2str(num1(end)));
-end 
+end
 
 %------------------------------------------------------------------
@@ -1287 +1287 @@
 function list_pair_civ2_Callback(hObject, eventdata, handles)
 
-index_pair=get(handles.list_pair_civ2,'Value');%get the selected position index in the menu 
-
-%update first_i and last_i according to the chosen image pairs 
+index_pair=get(handles.list_pair_civ2,'Value');%get the selected position index in the menu
+
+%update first_i and last_i according to the chosen image pairs
 mode_list=get(handles.mode,'String');
 mode_value=get(handles.mode,'Value');
@@ -1319 +1319 @@
     set(handles.first_j,'String',num2str(num1(1)));
     set(handles.last_j,'String',num2str(num1(end)));
-end 
+end
 
 
@@ -1392 +1392 @@
     return
 end
- 
+
 %choice of batch priority
 ind_answer=2;
@@ -1404 +1404 @@
                 'SelectionMode','single',...
                 'ListString',str,'ListSize',[200 200],'Name','job priority','InitialValue',3);
-        if isequal(v,0) % to handle Cancel button and figure close,  
+        if isequal(v,0) % to handle Cancel button and figure close,
            return % a better way should be create
         end
@@ -1426 +1426 @@
     cur_dir=pwd;
     if ~isequal(cur_dir(2:3),':\')
-        cd(matlabroot); %move to the Matlab root directory if the current Matlab dir does not allow the dos command or is M: 
+        cd(matlabroot); %move to the Matlab root directory if the current Matlab dir does not allow the dos command or is M:
     end
     [ss,ww]=dos(['net use ' filebase(1:2)]);
@@ -1457 +1457 @@
 
 [num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=...
-find_pair_indices(handles,mode); %determine the pairs of processing file 
+find_pair_indices(handles,mode); %determine the pairs of processing file
 
 %check dir
@@ -1491 +1491 @@
 nbfield=length(num1_civ1);
 nbslice=length(num_a_civ1);
-   
+
 %check the existence of the netcdf and image files involved
 % if box_test(1)==1;%CIV1 activated
-detect=1; 
+detect=1;
 while detect==1 %name a new subdir if one of the netcdf files already exists
       for ifile=1:nbfield
@@ -1529 +1529 @@
             cd(currentdir)
             return
-     end     
+     end
      if ~exist(filecell_ima2_civ1{ifile},'file')
             msgbox_uvmat('ERROR',[filecell_ima2_civ1{ifile} ' not found'])
@@ -1539 +1539 @@
 end
 
-cd(currentdir);%come back to the initial working directory 
+cd(currentdir);%come back to the initial working directory
 % if ~isequal(m2,'')
 %      msgbox(m2);%error message for directory creation
@@ -1549 +1549 @@
 
 for ifile=1:nbfield
-    i_cmd=0; 
+    i_cmd=0;
        cmd='#!/bin/bash';
        cmd=char({cmd;'#$ -cwd'});
@@ -1556 +1556 @@
     filename_cmx([end-1:end])='cm';%name of cmx file
     filename_cmx=[filename_cmx 'x'];
-    
+
 %CIV1
     if box_test(1)==1
@@ -1575 +1575 @@
         civAllxml=set(civAllxml,1,'name','civ3d3c');
     %    save(civAllxml)
-        par_civ1_3d_xml=fullfile(par_civ1.path,[resu_file '.xml']);%[par_civ1.path '/test_to_change.xml'];
-         pvalue=num2str((1-ind_answer)*500)
-        save(civAllxml,par_civ1_3d_xml);
+        par_civ1_3d_xml=fullfile(par_civ1.path,[resu_file '.xml']);%[par_civ1.path '/test_to_change.xml'];
+      pvalue=num2str((1-ind_answer)*500)
+        save(civAllxml,par_civ1_3d_xml);
      nb_processor='8';
-         ['echo /CIVX/bin/MPI/lam-7.1.3_g95/bin/mpirun C  ' Civ3D3CBin ' -p ' par_civ1_3d_xml '|qsub -p ' pvalue ' -q lam.q -pe lam_loose ' nb_processor ' -e ' par_civ1_3d_xml '.errors -o ' par_civ1_3d_xml '.log' ]
-         eval ( ['!echo /CIVX/bin/MPI/lam-7.1.3_g95/bin/mpirun C  ' Civ3D3CBin ' -p ' par_civ1_3d_xml '|qsub -p ' pvalue ' -q lam.q -pe lam_loose ' nb_processor ' -e ' par_civ1_3d_xml '.errors -o ' par_civ1_3d_xml '.log' ])
-
-    end           
+     ['echo /CIVX/bin/MPI/lam-7.1.3_g95/bin/mpirun C  ' Civ3D3CBin ' -p ' par_civ1_3d_xml '|qsub -p ' pvalue ' -q lam.q -pe lam_loose ' nb_processor ' -e ' par_civ1_3d_xml '.errors -o ' par_civ1_3d_xml '.log' ]
+     eval ( ['!echo /CIVX/bin/MPI/lam-7.1.3_g95/bin/mpirun C  ' Civ3D3CBin ' -p ' par_civ1_3d_xml '|qsub -p ' pvalue ' -q lam.q -pe lam_loose ' nb_processor ' -e ' par_civ1_3d_xml '.errors -o ' par_civ1_3d_xml '.log' ])
+
+    end
 end
 
@@ -1591 +1591 @@
 [Path,Name]=fileparts(filebase);
 namefig=fullfile(Path,subdir_civ2,Name);
-detect=1; 
+detect=1;
 while detect==1
     namefigfull=[namefig '.fig'];
@@ -1619 +1619 @@
         end
 
-  
+
 %----------------------------------------------------
 function first_j_Callback(hObject, eventdata, handles)
@@ -1714 +1714 @@
     num_a=1;
     num_b=1;
-elseif isequal (mode, 'series(Dj)') 
+elseif isequal (mode, 'series(Dj)')
     num1=1;
     num2=1;
@@ -1752 +1752 @@
 subdir=get(handles.subdir_civ1,'String');
 set(handles.subdir_civ2,'String',subdir);
-if get(handles.CIV1,'Value')==0 
+if get(handles.CIV1,'Value')==0
     find_netcpair_civ1(hObject, eventdata, handles); %update the list of available pairs from netcdf files in the new directory
 end
@@ -1828 +1828 @@
     set(handles.get_mask_civ2,'Value',1)
     set(handles.get_mask_fix2,'Value',1)
-end 
+end
 set(handles.mask_fix1,'String',mask_displ)
 set(handles.mask_civ2,'String',mask_displ)
@@ -1858 +1858 @@
 else
     set(handles.get_mask_fix2,'Value',1)
-end 
+end
 set(handles.mask_civ2,'String',mask_displ)
 set(handles.mask_fix2,'String',mask_displ)
@@ -1884 +1884 @@
 if isequal(mask_displ,'no mask')
     set(handles.get_mask_fix2,'Value',0)
-end 
+end
 set(handles.mask_fix2,'String',mask_displ)
 end
@@ -1890 +1890 @@
 %---------------------------------------
 function [nbslice, flag_mask]=get_mask(filebase,handles)
-%detect mask files, images with appropriate file base 
+%detect mask files, images with appropriate file base
 %[filebase '_' xx 'mask'], xx=nbslice
 %flag_mask=1 indicates detection
@@ -1930 +1930 @@
           nbslice=1;
     end
-end    
+end
 %------------------------------
 
@@ -2013 +2013 @@
 value=get(handles.browse_gridciv1,'Value');
 if value
-        filebase=get(handles.displ_filebase,'String');
-        [FileName, PathName, filterindex] = uigetfile( ...
+    filebase=get(handles.displ_filebase,'String');
+    [FileName, PathName, filterindex] = uigetfile( ...
            {'*.grid', ' (*.grid)';
             '*.grid',  '.grid files '; ...
             '*.*', 'All Files (*.*)'}, ...
             'Pick a file',filebase);
-        filegrid=fullfile(PathName,FileName);
+    filegrid=fullfile(PathName,FileName);
     if isempty(FileName)|isempty(PathName)|isequal(FileName,0)|~exist(filegrid,'file')
         set(handles.browse_gridciv1,'Value',0);
         set(handles.grid_civ1,'string','');
-            set(handles.dx_civ1,'Visible','on');
-            set(handles.dy_civ1,'Visible','on');
-            set(handles.grid_civ2,'string','');
+        set(handles.dx_civ1,'Visible','on');
+        set(handles.dy_civ1,'Visible','on');
+        set(handles.grid_civ2,'string','');
         if get(handles.CIV2,'Value')
-                set(handles.dx_civ2,'Visible','on');
-                set(handles.dy_civ2,'Visible','on');
+            set(handles.dx_civ2,'Visible','on');
+            set(handles.dy_civ2,'Visible','on');
         end
     else
-                set(handles.grid_civ1,'string',filegrid);
-                set(handles.dx_civ1,'Visible','off');
-                set(handles.dy_civ1,'Visible','off');
-                set(handles.grid_civ2,'string',filegrid);
-                set(handles.dx_civ2,'Visible','off');
-                set(handles.dy_civ2,'Visible','off');
+        set(handles.grid_civ1,'string',filegrid);
+        set(handles.dx_civ1,'Visible','off');
+        set(handles.dy_civ1,'Visible','off');
+        set(handles.grid_civ2,'string',filegrid);
+        set(handles.dx_civ2,'Visible','off');
+        set(handles.dy_civ2,'Visible','off');
 % set(handles.grid_patch1,'string',filegrid);
 % set(handles.grid_patch2,'string',filegrid);
@@ -2042 +2042 @@
 else
     set(handles.grid_civ1,'string','');
-        set(handles.dx_civ1,'Visible','on');
-        set(handles.dy_civ1,'Visible','on');
-        set(handles.grid_civ2,'string','');
+    set(handles.dx_civ1,'Visible','on');
+    set(handles.dy_civ1,'Visible','on');
+    set(handles.grid_civ2,'string','');
     if get(handles.CIV2,'Value')
-            set(handles.dx_civ2,'Visible','on');
-            set(handles.dy_civ2,'Visible','on');
+        set(handles.dx_civ2,'Visible','on');
+        set(handles.dy_civ2,'Visible','on');
     end
 end
@@ -2286 +2286 @@
     set(handles.MaxIma2,'Visible','off')
     set(handles.ImaThreshold2,'Value',0)
-    if isequal(get(handles.FIX2,'Value'),0) & isequal(get(handles.PATCH2,'Value'),0) 
+    if isequal(get(handles.FIX2,'Value'),0) & isequal(get(handles.PATCH2,'Value'),0)
         set(handles.list_pair_civ2,'Visible','off')
         set(handles.subdir_civ2,'Visible','off')
@@ -2323 +2323 @@
 % set(handles.rho_civ2_title,'Visible','off')
 % set(handles.frame_subdirciv2,'BackgroundColor',[0.831 0.816 0.784])
-% if isequal(get(handles.FIX2,'Value'),0) & isequal(get(handles.PATCH2,'Value'),0) 
+% if isequal(get(handles.FIX2,'Value'),0) & isequal(get(handles.PATCH2,'Value'),0)
 %     set(handles.list_pair_civ2,'Visible','off')
 %     set(handles.subdir_civ2,'Visible','off')
@@ -2367 +2367 @@
 set(handles.inf_sup2,'Visible','off')
 set(handles.field_ref2,'Visible','off')
-if isequal(get(handles.CIV2,'Value'),0) & isequal(get(handles.PATCH2,'Value'),0) 
+if isequal(get(handles.CIV2,'Value'),0) & isequal(get(handles.PATCH2,'Value'),0)
     set(handles.list_pair_civ2,'Visible','off')
     set(handles.subdir_civ2,'Visible','off')
@@ -2407 +2407 @@
 set(handles.get_gridpatch2,'Visible','off')
 set(handles.grid_patch2,'Visible','off')
-if isequal(get(handles.CIV2,'Value'),0) & isequal(get(handles.FIX2,'Value'),0) 
+if isequal(get(handles.CIV2,'Value'),0) & isequal(get(handles.FIX2,'Value'),0)
     set(handles.list_pair_civ2,'Visible','off')
     set(handles.subdir_civ2,'Visible','off')
@@ -2459 +2459 @@
 par.ratioHoverZ=1;
 
-%      
+%
 % %----------------------------------------------------------------
 % function par=read_param_civ2(handles,file_ima)
@@ -2469 +2469 @@
 %     par.dx=get(handles.dx_civ2,'String');
 %     par.dy=get(handles.dy_civ2,'String');
-%     if isequal(str2num(par.dx),[]) 
+%     if isequal(str2num(par.dx),[])
 %          if isempty(get(handles.grid_civ2,'String'));
 %              par.dx='0'; %just read by civ_3D program, not used
@@ -2487 +2487 @@
 %     par.pxcmx=get(handles.pxcmx,'String');
 %     par.pxcmy=get(handles.pxcmy,'String');
-%     if isempty(str2num(par.pxcmx)) |isempty(str2num(par.pxcmy)) 
+%     if isempty(str2num(par.pxcmx)) |isempty(str2num(par.pxcmy))
 %         par.pxcmx='1';
 %          par.pxcmy='1';
@@ -2515 +2515 @@
 %changes : filename_cmx -> filename ( no extension )
 
-            if isequal(par.Dt,'0')
-                par.Dt='1' ;%case of 'displacement' mode
-            end         
- 
+    if isequal(par.Dt,'0')
+        par.Dt='1' ;%case of 'displacement' mode
+    end
+
     textcmx={'##############   CMX file';...
     ['FirstImage ' par.filename_ima_a];...
@@ -2555 +2555 @@
     %             timeL2=clock;
     %     timciv1=etime(timeL2,timeL1)
-          if sge  
+          if sge
           cmd_CIV1=[civ1_exe ' -f ' filename '.cmx' ]; % redirect standard output to the log file
           else
@@ -2561 +2561 @@
           end
     if(isunix)
-        [Rootbat,Filebat,extbat]=fileparts(namelog);
-        ncName=fullfile(Rootbat,[ Filebat '.nc']);
-            cmd_CIV1=char({cmd_CIV1 ; ['mv ' namelog  ' ' namelog '.civ1.log'];['chmod g+w ' ncName]});
+        [Rootbat,Filebat,extbat]=fileparts(namelog);
+        ncName=fullfile(Rootbat,[ Filebat '.nc']);
+        cmd_CIV1=char({cmd_CIV1 ; ['mv ' namelog  ' ' namelog '.civ1.log'];['chmod g+w ' ncName]});
     else
         cmd_CIV1=char({cmd_CIV1 ; ['copy /Y ' namelog ' ' namelog '.civ1.log']});
@@ -2577 +2577 @@
     civ1.image1=par.filename_ima_a;
     civ1.image2=par.filename_ima_b;
-    civ1.imageSize_X=par.npx; 
+    civ1.imageSize_X=par.npx;
     civ1.imageSize_Y=par.npy;
     civ1.outputFileName=[filename '.nc'];
@@ -2602 +2602 @@
     civ1.pixcmy=par.pxcmy;
     civ1.convectFlow='n';
-  
+
     xml_civ1_parameters=civ1;
-   
+
 %---------------------------------------------------------
 %CIV2  CIV2  CIV2 CIV2
@@ -2613 +2613 @@
    if isequal(par.Dt,'0')
                 par.Dt='1' ;%case of 'displacement' mode
-  end 
+  end
 textcmx={'##############   CMX file';...
 ['FirstImage ' par.filename_ima_a];...
@@ -2620 +2620 @@
 ['Mask ' par.maskflag];...
 ['MaskName ' par.maskname];...
-['ImageSize ' par.npx ' ' par.npy];...   
+['ImageSize ' par.npx ' ' par.npy];...
 ['CorrelationBoxesSize ' par.ibx ' ' par.iby];...
 ['SearchBoxeSize ' par.ibx ' ' par.iby];...
@@ -2660 +2660 @@
 if isempty(dir(helpfile)), errordlg('Please put the help file uvmat_doc.html in the directory UVMAT/UVMAT_DOC')
 else
-web([helpfile '#civ_3D'])    
+web([helpfile '#civ_3D'])
 end
 
@@ -2675 +2675 @@
     A=uint16(A);
 elseif isequal(nom_type,'raw_SMD')
-    [fid,message]=fopen(filename,'r');    
+    [fid,message]=fopen(filename,'r');
     B=fread(fid,Inf,'int16',0,'ieee-le');%read 16 bit binary file
     A=(reshape(B,npx,npy))'; %remplissage ligne par ligne avec une matrice colonne ? transposer(uB) pour avoir une matrice ligne
@@ -2688 +2688 @@
     A=uint16(A);
 end
-        
+
 %----------------------------------------------------------------
 %Executes on carriage return on the time interval dt
@@ -2718 +2718 @@
 mode_value=get(handles.mode,'Value');
 mode=mode_list{mode_value};
-if isequal(get(handles.CIV1,'Value'),0)| isequal(mode,'series(Di)') 
+if isequal(get(handles.CIV1,'Value'),0)| isequal(mode,'series(Di)')
     find_netcpair_civ1(hObject, eventdata, handles);% update the menu of pairs depending on the available netcdf files
 end
@@ -2731 +2731 @@
 mode_value=get(handles.mode,'Value');
 mode=mode_list{mode_value};
-if isequal(get(handles.CIV1,'Value'),0)| isequal(mode,'series(Dj)') 
+if isequal(get(handles.CIV1,'Value'),0)| isequal(mode,'series(Dj)')
     find_netcpair_civ1(hObject, eventdata, handles);% update the menu of pairs depending on the available netcdf files
 end
@@ -2747 +2747 @@
     browse.nom_type_ima1=browse.nom_type_ima;
     set(handles.browse_root,'UserData',browse);
-    set(handles.displ_filebase2,'Visible','On');%mkes the second file input window visible 
+    set(handles.displ_filebase2,'Visible','On');%mkes the second file input window visible
     set(handles.displ_filebase2,'String',filebase);
     mode_store=get(handles.mode,'String');%get the present 'mode'
@@ -2772 +2772 @@
         '*.*', 'All Files (*.*)'}, ...
         'Pick a file',filebase);
-    
+
 fileinput=[PathName FileName];
 sizf=size(fileinput);
@@ -2820 +2820 @@
 set(handles.thresh_vel,'String','1');%default threshold
 set(handles.ref_fix1,'Enable','on')
- 
+
 %---------------------------------------------------------------
 % --- Executes on button press in get_ref_fix2.
@@ -2850 +2850 @@
 %     [path,name]=fileparts(ref.filebase);
     set(handles.ref_fix2,'String',[fullfile(ref.subdir,File) '....nc']);
-    set(handles.ref_fix2,'UserData',ref)    
+    set(handles.ref_fix2,'UserData',ref)
     menu_field{1}='civ1';
 %     [cte_detect,vdt,cte_read]=read_netcdf(fileinput,{'patch','civ2','patch2'});
@@ -2893 +2893 @@
     set(handles.ref_fix1,'String','');
     set(handles.thresh_vel1,'String','0');
- 
+
 
 %------------------------------------------------------
@@ -3092 +3092 @@
 
 
-%'name2display': extracts the root name and field numbers from an input filename 
+%'name2display': extracts the root name and field numbers from an input filename
 %--------------------------------------------------------------------
 %[RootPath,RootFile,field_count,str2,str_a,str_b,ext,nom_type,subdir]=name2display(fileinput)
@@ -3161 +3161 @@
 last=double(last_str);%corresponding ascii code
 penult=double(RootFile(indcur-1));%ascii code of the penultimate character
-testsub=0; %default 
+testsub=0; %default
 % % case of an indexed series in a single file
 % if strcmpi(ext,'.avi')
@@ -3168 +3168 @@
 % %the penultimate character is a number and the last one a letter (lower case: last >= 97 && last <= 122
 % %                                                                 capital
-% %                                                                 letter:  last >= 65 && last <= 90)  
+% %                                                                 letter:  last >= 65 && last <= 90)
 if  penult >= 48 && penult <= 57 && ((last >= 65 && last <= 90)||(last >= 97 && last <= 122))
     str_a=last_str; %extract appendix a,b,c... or A,B,C... as output.
@@ -3185 +3185 @@
     else
         nom_type=[nom_type 'a'];
-    end   
+    end
 elseif strcmp(filelit(end-2:end),'-_-_')%new  nomenclature appendix num1-num2_num_a-num_b
     field_count=num0;
@@ -3201 +3201 @@
     testsub=1;
     indcur=separ1-1;
-elseif strcmp(filelit(end-2:end),'__-')%new  nomenclature appendix num1_num2-num2 
+elseif strcmp(filelit(end-2:end),'__-')%new  nomenclature appendix num1_num2-num2
     indcur=separ1-1;
     field_count=num1;
@@ -3231 +3231 @@
 elseif RootFile(indcur-2)=='_'% search appendix a,b,c,d
     lasts=RootFile(indcur-1:indcur);
-%     if isequal(length(last),2) 
+%     if isequal(length(last),2)
         str_a=lasts(1);%put appendix a,b,c, ou d
         str_b=lasts(2);%put appendix a,b,c, ou d
@@ -3237 +3237 @@
         field_count=RootFile(separ0+1:separ1-1);
         indcur=separ0;
-        if double(lasts) >= 97 & double(lasts)<= 122 
+        if double(lasts) >= 97 & double(lasts)<= 122
             nom_type='_ab';
             testsub=1;
-        elseif double(lasts) >= 65 & double(lasts) <= 90 
+        elseif double(lasts) >= 65 & double(lasts) <= 90
             nom_type='_AB';
             testsub=1;
@@ -3249 +3249 @@
 %search for other names with counter
 else
-    if length(ext)>1     
+    if length(ext)>1
             num=1;count=0; % extract the numerical appendix
             while num==1;
                 filascii=double(RootFile(indcur));
                 if (48>filascii)||(filascii>57); % select the non-numerical characters
-                    num=0; 
+                    num=0;
                 else
                     indcur=indcur-1; count=count+1;
                 end
             end
-            if count~=0   
+            if count~=0
                 field_count=RootFile(indcur+1:indcur+count);% set the selected field number'%03d'
                 charstring=['%0' num2str(length(field_count)) 'd'];

trunk/src/toolbox_calib/init_intrinsic_param.m

@@ -9 +9 @@
 %OUTPUT: fc: Camera focal length
 %        cc: Principal point coordinates
-%             kc: Distortion coefficients
+%        kc: Distortion coefficients
 %        alpha_c: skew coefficient
 %        KK: The camera matrix (containing fc, cc and alpha_c)
@@ -89 +89 @@
 
 for kk=1:n_ima,
-    
+
     if active_images(kk),
-        
+
         eval(['Hkk = H_' num2str(kk) ';']);
-        
-        Hkk = Sub_cc * Hkk;   
-        
+
+        Hkk = Sub_cc * Hkk;
+
         % Extract vanishing points (direct and diagonals):
-        
+
         V_hori_pix = Hkk(:,1);
         V_vert_pix = Hkk(:,2);
         V_diag1_pix = (Hkk(:,1)+Hkk(:,2))/2;
         V_diag2_pix = (Hkk(:,1)-Hkk(:,2))/2;
-        
+
         V_hori_pix = V_hori_pix/norm(V_hori_pix);
         V_vert_pix = V_vert_pix/norm(V_vert_pix);
         V_diag1_pix = V_diag1_pix/norm(V_diag1_pix);
         V_diag2_pix = V_diag2_pix/norm(V_diag2_pix);
-        
+
         a1 = V_hori_pix(1);
         b1 = V_hori_pix(2);
         c1 = V_hori_pix(3);
-        
+
         a2 = V_vert_pix(1);
         b2 = V_vert_pix(2);
         c2 = V_vert_pix(3);
-        
+
         a3 = V_diag1_pix(1);
         b3 = V_diag1_pix(2);
         c3 = V_diag1_pix(3);
-        
+
         a4 = V_diag2_pix(1);
         b4 = V_diag2_pix(2);
         c4 = V_diag2_pix(3);
-        
+
         A_kk = [a1*a2  b1*b2;
             a3*a4  b3*b4];
-        
+
         b_kk = -[c1*c2;c3*c4];
-        
-        
+
+
         A = [A;A_kk];
         b = [b;b_kk];
-        
+
     end;
-    
+
 end;
 
@@ -148 +148 @@
 end;
 
-    
+
 
 if two_focals_init
@@ -185 +185 @@
 fprintf(1,'Principal point:       cc = [ %3.5f   %3.5f ]\n',cc);
 fprintf(1,'Skew:             alpha_c = [ %3.5f ]   => angle of pixel = %3.5f degrees\n',alpha_c,90 - atan(alpha_c)*180/pi);
-fprintf(1,'Distortion:            kc = [ %3.5f   %3.5f   %3.5f   %3.5f   %5.5f ]\n',kc);   
+fprintf(1,'Distortion:            kc = [ %3.5f   %3.5f   %3.5f   %3.5f   %5.5f ]\n',kc);

trunk/src/toolbox_calib/normalize_pixel.m

@@ -41 +41 @@
 
 if norm(kc) ~= 0,
-        % Third: Compensate for lens distortion:
-        xn = comp_distortion_oulu(x_distort,kc);
+    % Third: Compensate for lens distortion:
+    xn = comp_distortion_oulu(x_distort,kc);
 else
    xn = x_distort;