Changeset 576 for trunk/src

Timestamp:

Mar 4, 2013, 8:13:53 AM (12 years ago)

Author:

sommeria

Message:

grid improved for civ: computation done closer to the edge. set_grid improved.

Location:

trunk/src

Files:

• browse_data.fig (modified) (previous)
• browse_data.m (modified) (1 diff)
• civ.m (modified) (7 diffs)
• civ_matlab.m (modified) (12 diffs)
• find_field_cells.m (modified) (4 diffs)
• proj_field.m (modified) (3 diffs)
• read_civdata.m (modified) (1 diff)
• read_field.m (modified) (1 diff)
• set_grid.fig (modified) (previous)
• set_grid.m (modified) (13 diffs)
• uvmat.m (modified) (16 diffs)

trunk/src/browse_data.m

@@ -93 +93 @@
     end
     scan_campaign(handles,Campaign)
-%     SourceDir_Callback([],[], handles)
-   set(handles.edit_xml,'Visible','off')
-   set(handles.HELP,'Visible','off')
    set(handles.OK,'Visible','on')
    set(handles.Cancel,'Visible','on')

trunk/src/civ.m

@@ -3326 +3326 @@
 %------------------------------------------------------------------------
 % --- function called to look for grid files
-function [nbslice, flag_mask]=get_grid(filebase,handles)
-%------------------------------------------------------------------------
-flag_mask=0;%default
+function [nbslice, flag_grid]=get_grid(filebase,handles)
+%------------------------------------------------------------------------
+flag_grid=0;%default
 nbslice=1;
 [Path,Name]=fileparts(filebase);
 currentdir=pwd;
 cd(Path);%move in the dir of the root name filebase
-maskfiles=dir([Name '_*grid_*.grid']);%look for mask files
+gridfiles=dir([Name '_*grid_*.grid']);%look for grid files
 cd(currentdir);%come back to the current working directory
-if ~isempty(maskfiles)
-    flag_mask=1;
-    maskname=maskfiles(1).name;% take the first mask file in the list
-    [Path2,Name,ext]=fileparts(maskname);
+if ~isempty(gridfiles)
+    flag_grid=1;
+    gridname=gridfiles(1).name;% take the first grid file in the list
+    [Path2,Name,ext]=fileparts(gridname);
     Namedouble=double(Name);
     val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
-    ind_mask=findstr('grid',Name);
-    i=ind_mask-1;
+    ind_grid=findstr('grid',Name);
+    i=ind_grid-1;
     while val(i)==0 && i>0
         i=i-1;
     end
-    nbslice=str2double(Name(i+1:ind_mask-1));
+    nbslice=str2double(Name(i+1:ind_grid-1));
     if ~isnan(nbslice) && Name(i)=='_'
-        flag_mask=1;
+        flag_grid=1;
     else
         msgbox_uvmat('ERROR',['bad grid file ' Name ext ' found in ' Path2])
@@ -3415 +3415 @@
 %------------------------------------------------------------------------
 value=get(hObject,'Value');
-hparent=get(hObject,'parent');
+hparent=get(hObject,'parent');%handles of the parent panel
 hchildren=get(hparent,'children');
-handle_txtbox=findobj(hchildren,'tag','txt_Grid');
+handle_txtbox=findobj(hchildren,'tag','Grid');% look for the grid name box in the same panel
 handle_dx=findobj(hchildren,'tag','num_Dx');
 handle_dy=findobj(hchildren,'tag','num_Dy');
@@ -3435 +3435 @@
             filebase=filegrid;
         end
-        [FileName, PathName, filterindex] = uigetfile( ...
+        [FileName, PathName] = uigetfile( ...
             {'*.grid', ' (*.grid)';
             '*.grid',  '.grid files '; ...
@@ -3468 +3468 @@
     hchildren=get(handles.Civ2,'children');
     handle_checkbox=findobj(hchildren,'tag','CheckGrid');
-    handle_txtbox=findobj(hchildren,'tag','txt_Grid');
+    handle_txtbox=findobj(hchildren,'tag','Grid');
     handle_dx=findobj(hchildren,'tag','num_Dx');
     handle_dy=findobj(hchildren,'tag','num_Dy');
@@ -3482 +3482 @@
         set(handle_txtbox,'Visible','on')
         set(handle_txtbox,'String',filegrid)
-%     else
-%         set(handle_checkbox,'Value',0);
-%         set(handles.CheckGrid,'Value',0);
-%         set(handle_dx,'Visible','on');
-%         set(handle_dy,'Visible','on');
-%          set(handle_title_dx,'Visible','on');
-%         set(handle_title_dy,'Visible','on');
-%         set(handle_txtbox,'Visible','off')
     end 
 end
@@ -3532 +3524 @@
     set(handles.CheckMask,'Value',1)
     end
-%     switch parent_tag
-% %         case 'Fix1'
-% %             stage=2;
-%         case 'Civ2'
-%              stage=3;
-% %         case 'Fix2'
-% %             stage=4;
-%     end
-%     set(handles.Mask(stage:end),'Visible','on')
-%     set(handles.Mask(stage:end),'String',filemask)
-%     set(handles.CheckMask(stage:end),'Value',1)
 else
     set(hObject,'Value',0);
@@ -3548 +3529 @@
 end
 
-
+%------------------------------------------------------------------------
 % --- Executes on button press in get_gridpatch1.
 function get_gridpatch1_Callback(hObject, eventdata, handles)
+%------------------------------------------------------------------------
 filebase=get(handles.RootPath,'String');
 [FileName, PathName, filterindex] = uigetfile( ...

trunk/src/civ_matlab.m

@@ -51 +51 @@
 check_civ1=0;%default
 check_patch1=0;%default
-%         ImageFileA=Param.Civ1.ImageA;
-%         ImageFileB=Param.Civ1.ImageB;
-%         if isfield(Param,'Civ2')
-%             ImageFileA_civ2=Param.Civ2.ImageA;
-%              ImageFileB_civ2=Param.Civ2.ImageB;
-%         end
+
 % case of input Param set by an xml file (batch mode)
 if ischar(Param)
     Param=xml2struct(Param); %if Param is the name of an xml file, read this file as a Matlab structure
-%     if isfield(Param,'Civ1')
-%         if strcmp(Param.Civ1.FileTypeA,'video')
-%             Param.Civ1.ImageA=VideoReader(regexprep(Param.Civ1.ImageA,'''','\'));% remove spurious ' appearing in Windows;
-%         elseif strcmp(Param.Civ1.FileTypeA,'mmreader')
-%             Param.Civ1.ImageA=mmreader(regexprep(Param.Civ1.ImageA,'''','\'));% remove spurious ' appearing in Windows
-%         end
-%         if strcmp(Param.Civ1.FileTypeB,'video')
-%             Param.Civ1.ImageB=VideoReader(regexprep(Param.Civ1.ImageB,'''','\'));% remove spurious ' appearing in Windows
-%         elseif strcmp(Param.Civ1.FileTypeB,'mmreader')
-%             Param.Civ1.ImageB=mmreader(regexprep(Param.Civ1.ImageB,'''','\'));% remove spurious ' appearing in Windows
-%         end
-%     end
-%     if isfield(Param,'Civ2')
-%         if strcmp(Param.Civ2.FileTypeA,'video')
-%             Param.Civ2.ImageA=VideoReader(regexprep(Param.Civ2.ImageA,'''','\'));% remove spurious ' appearing in Windows;
-%         elseif strcmp(Param.Civ2.FileTypeA,'mmreader')
-%             Param.Civ2.ImageA=mmreader(regexprep(Param.Civ2.ImageA,'''','\'));% remove spurious ' appearing in Windows
-%             if strcmp(Param.Civ2.FileTypeB,'video')
-%                 Param.Civ2.ImageB=VideoReader(regexprep(Param.Civ2.ImageB,'''','\'));% remove spurious ' appearing in Windows
-%             elseif strcmp(Param.Civ2.FileTypeB,'mmreader')
-%                 Param.Civ2.ImageB=mmreader(regexprep(Param.Civ2.ImageB,'''','\'));% remove spurious ' appearing in Windows
-%             end;
-%         end
-%     end
 end
 
@@ -116 +87 @@
     % caluclate velocity data (y and v in indices, reverse to y component)
     [xtable ytable utable vtable ctable F result_conv errormsg] = civ (par_civ1);
-    
-    % to try the reverse_pair method, uncomment below
-    %     [xtable1 ytable1 utable1 vtable1 ctable1 F1 result_conv1 errormsg1] = civ (Param.Civ1);
-    %     Param.Civ1.reverse_pair=1;
-    %     [xtable2 ytable2 utable2 vtable2 ctable2 F2 result_conv2 errormsg2] = civ (Param.Civ1);
-    %     xtable=[xtable1; xtable2];
-    %     ytable=[ytable1; ytable2];
-    %     utable=[utable1; -utable2];
-    %     vtable=[vtable1; -vtable2];
-    %     ctable=[ctable1; ctable2];
-    %     F=[F1; F2];
-    %     result_conv=[result_conv1; result_conv2];
-    %     errormsg=[errormsg1; errormsg2];
     if ~isempty(errormsg)
         return
@@ -271 +229 @@
         end
     end
-    ibx2=ceil(par_civ2.CorrBoxSize(1)/2);
-    iby2=ceil(par_civ2.CorrBoxSize(2)/2);
-    isx2=ibx2+4;% search ara +-4 pixels around the guess
-    isy2=iby2+4;
-    % shift from par_civ2.filename_nc1
-    % shiftx=velocity interpolated at position
-    miniy=max(1+isy2,1+iby2);
-    minix=max(1+isx2,1+ibx2);
-    maxiy=min(size(par_civ2.ImageA,1)-isy2,size(par_civ2.ImageA,1)-iby2);
-    maxix=min(size(par_civ2.ImageA,2)-isx2,size(par_civ2.ImageA,2)-ibx2);
-    [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy);
-    GridX=reshape(GridX,[],1);
-    GridY=reshape(GridY,[],1);
-    Shiftx=zeros(size(GridX));% shift expected from civ1 data
-    Shifty=zeros(size(GridX));
-    nbval=zeros(size(GridX));
+    %     ibx2=ceil(par_civ2.CorrBoxSize(1)/2);
+    %     iby2=ceil(par_civ2.CorrBoxSize(2)/2);
+    %     isx2=ibx2+4;% search ara +-4 pixels around the guess
+    %     isy2=iby2+4;
+    %     % shift from par_civ2.filename_nc1
+    %     % shiftx=velocity interpolated at position
+    %     miniy=max(1+isy2,1+iby2);
+    %     minix=max(1+isx2,1+ibx2);
+    %     maxiy=min(size(par_civ2.ImageA,1)-isy2,size(par_civ2.ImageA,1)-iby2);
+    %     maxix=min(size(par_civ2.ImageA,2)-isx2,size(par_civ2.ImageA,2)-ibx2);
+    %     [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy);
+    %     GridX=reshape(GridX,[],1);
+    %     GridY=reshape(GridY,[],1);
+    if isfield(par_civ2,'Grid')% grid points set as input file
+        if ischar(par_civ2.Grid)%read the grid file if the input is a file name
+            par_civ2.Grid=dlmread(par_civ2.Grid);
+            par_civ2.Grid(1,:)=[];%the first line must be removed (heading in the grid file)
+        end
+    else% automatic grid
+        minix=floor(par_civ2.Dx/2)-0.5;
+        maxix=minix+par_civ2.Dx*floor((par_civ2.ImageWidth-1)/par_civ2.Dx);
+        miniy=floor(par_civ2.Dy/2)-0.5;
+        maxiy=minix+par_civ2.Dy*floor((par_civ2.ImageHeight-1)/par_civ2.Dy);
+        [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy);
+        par_civ2.Grid(:,1)=reshape(GridX,[],1);
+        par_civ2.Grid(:,2)=reshape(GridY,[],1);
+    end
+    Shiftx=zeros(size(par_civ2.Grid,1));% shift expected from civ1 data
+    Shifty=zeros(size(par_civ2.Grid,1));
+    nbval=zeros(size(par_civ2.Grid,1));
     if par_civ2.CheckDeformation
-        DUDX=zeros(size(GridX));
-        DUDY=zeros(size(GridX));
-        DVDX=zeros(size(GridX));
-        DVDY=zeros(size(GridX));
+        DUDX=zeros(size(par_civ2.Grid,1));
+        DUDY=zeros(size(par_civ2.Grid,1));
+        DVDX=zeros(size(par_civ2.Grid,1));
+        DVDY=zeros(size(par_civ2.Grid,1));
     end
     NbSubDomain=size(Data.Civ1_SubRange,3);
@@ -316 +288 @@
         mask=imread(par_civ2.Mask);
     end
-    par_civ2.SearchBoxSize(1)=2*isx2+1;
-    par_civ2.SearchBoxSize(2)=2*isy2+1;
+    ibx2=ceil(par_civ2.CorrBoxSize(1)/2);
+    iby2=ceil(par_civ2.CorrBoxSize(2)/2);
+    %     isx2=ibx2+4;% search ara +-4 pixels around the guess
+    %     isy2=iby2+4;
+    par_civ2.SearchBoxSize(1)=2*ibx2+9;% search ara +-4 pixels around the guess
+    par_civ2.SearchBoxSize(2)=2*iby2+9;
+    %par_civ2.SearchBoxSize(1)=2*isx2+1;
+    %par_civ2.SearchBoxSize(2)=2*isy2+1;
     par_civ2.SearchBoxShift=[Shiftx(nbval>=1)./nbval(nbval>=1) Shifty(nbval>=1)./nbval(nbval>=1)];
-%     par_civ2.SearchBoxShift(2)=Shifty(nbval>=1)./nbval(nbval>=1);
     par_civ2.Grid=[GridX(nbval>=1)-par_civ2.SearchBoxShift(:,1)/2 GridY(nbval>=1)-par_civ2.SearchBoxShift(:,2)/2];% grid taken at the extrapolated origin of the displacement vectors
     if par_civ2.CheckDeformation
@@ -329 +306 @@
     % caluclate velocity data (y and v in indices, reverse to y component)
     [xtable ytable utable vtable ctable F] = civ (par_civ2);
-    %     diff_squared=(utable-par_civ2.Shiftx).*(utable-par_civ2.Shiftx)+(vtable+par_civ2.Shifty).*(vtable+par_civ2.Shifty);
-    %     F(diff_squared>=4)=4; %flag vectors whose distance to the guess exceeds 2 pixels
     list_param=(fieldnames(Param.Civ2))';
     list_remove={'pxcmx','pxcmy','npx','npy','gridflag','maskflag','term_a','term_b','T0'};
@@ -350 +325 @@
     end
     Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param {'Civ2_Time','Civ2_Dt'}];
-    %     Data.Civ2_Time=par_civ2.Time;
-    %     Data.Civ2_Dt=par_civ2.Dt;
     nbvar=numel(Data.ListVarName);
     Data.ListVarName=[Data.ListVarName {'Civ2_X','Civ2_Y','Civ2_U','Civ2_V','Civ2_F','Civ2_C'}];%  cell array containing the names of the fields to record
@@ -475 +448 @@
 %methods perform better and will maybe be implemented in the future.
 
-%% prepare grid
+%% prepare measurement grid
+if isfield(par_civ,'Grid')% grid points set as input 
+    if ischar(par_civ.Grid)%read the drid file if the input is a file name
+        par_civ.Grid=dlmread(par_civ.Grid);
+        par_civ.Grid(1,:)=[];%the first line must be removed (heading in the grid file)
+    end
+else% automatic grid
+    minix=floor(par_civ.Dx/2)-0.5;
+    maxix=minix+par_civ.Dx*floor((par_civ.ImageWidth-1)/par_civ.Dx);
+    miniy=floor(par_civ.Dy/2)-0.5;
+    maxiy=minix+par_civ.Dy*floor((par_civ.ImageHeight-1)/par_civ.Dy);
+    [GridX,GridY]=meshgrid(minix:par_civ.Dx:maxix,miniy:par_civ.Dy:maxiy);
+    par_civ.Grid(:,1)=reshape(GridX,[],1);
+    par_civ.Grid(:,2)=reshape(GridY,[],1);
+end
+nbvec=size(par_civ.Grid,1);
+
+%% prepare correlation and search boxes 
 ibx2=ceil(par_civ.CorrBoxSize(1)/2);
 iby2=ceil(par_civ.CorrBoxSize(2)/2);
@@ -482 +472 @@
 shiftx=round(par_civ.SearchBoxShift(:,1));
 shifty=-round(par_civ.SearchBoxShift(:,2));% sign minus because image j index increases when y decreases
-if isfield(par_civ,'Grid')
-    if ischar(par_civ.Grid)%read the drid file if the input is a file name
-        par_civ.Grid=dlmread(par_civ.Grid);
-        par_civ.Grid(1,:)=[];%the first line must be removed (heading in the grid file)
-    end
-else% automatic measurement grid
-%     ibx2=ceil(par_civ.Bx/2);
-%     iby2=ceil(par_civ.By/2);
-%     isx2=ceil(par_civ.Searchx/2);
-%     isy2=ceil(par_civ.Searchy/2);
-    miniy=max(1+isy2+shifty,1+iby2);
-    minix=max(1+isx2-shiftx,1+ibx2);
-    maxiy=min(par_civ.ImageHeight-isy2+shifty,par_civ.ImageHeight-iby2);
-    maxix=min(par_civ.ImageWidth-isx2-shiftx,par_civ.ImageWidth-ibx2);
-    [GridX,GridY]=meshgrid(minix:par_civ.Dx:maxix,miniy:par_civ.Dy:maxiy);
-    par_civ.Grid(:,1)=reshape(GridX,[],1);
-    par_civ.Grid(:,2)=reshape(GridY,[],1);
-end
-nbvec=size(par_civ.Grid,1);
-if numel(shiftx)==1
+if numel(shiftx)==1% case of a unique shift for the whole field( civ1)
     shiftx=shiftx*ones(nbvec,1);
     shifty=shifty*ones(nbvec,1);
 end
+
 %% Default output
 xtable=par_civ.Grid(:,1);
@@ -561 +533 @@
     %  20>=mask: velocity=0
 checkmask=0;
+MinA=min(min(par_civ.ImageA));
+MinB=min(min(par_civ.ImageB));
 if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask)
    checkmask=1;
@@ -569 +543 @@
   %  check_noflux=(par_civ.Mask<100) ;%TODO: to implement
     check_undefined=(par_civ.Mask<200 & par_civ.Mask>=20 );
-    par_civ.ImageA(check_undefined)=min(min(par_civ.ImageA));% put image A to zero (i.e. the min image value) in the undefined  area
-    par_civ.ImageB(check_undefined)=min(min(par_civ.ImageB));% put image B to zero (i.e. the min image value) in the undefined  area
+    par_civ.ImageA(check_undefined)=MinA;% put image A to zero (i.e. the min image value) in the undefined  area
+    par_civ.ImageB(check_undefined)=MinB;% put image B to zero (i.e. the min image value) in the undefined  area
 end
 
@@ -587 +561 @@
     jref=round(par_civ.ImageHeight-par_civ.Grid(ivec,2)+0.5);% yindex on the image B for the middle of the correlation box
     if ~(checkmask && par_civ.Mask(jref,iref)<=20) %velocity not set to zero by the black mask
-        if jref-iby2<1 || jref+iby2>par_civ.ImageHeight|| iref-ibx2<1 || iref+ibx2>par_civ.ImageWidth||...
-              jref+shifty(ivec)-isy2<1||jref+shifty(ivec)+isy2>par_civ.ImageHeight|| iref+shiftx(ivec)-isx2<1 || iref+shiftx(ivec)+isx2>par_civ.ImageWidth  % we are outside the image
-            F(ivec)=3;
-        else
-            image1_crop=par_civ.ImageA(jref-iby2:jref+iby2,iref-ibx2:iref+ibx2);%extract a subimage (correlation box) from image A
-            image2_crop=par_civ.ImageB(jref+shifty(ivec)-isy2:jref+shifty(ivec)+isy2,iref+shiftx(ivec)-isx2:iref+shiftx(ivec)+isx2);%extract a larger subimage (search box) from image B
+%         if jref-iby2<1 || jref+iby2>par_civ.ImageHeight|| iref-ibx2<1 || iref+ibx2>par_civ.ImageWidth||...
+%               jref+shifty(ivec)-isy2<1||jref+shifty(ivec)+isy2>par_civ.ImageHeight|| iref+shiftx(ivec)-isx2<1 || iref+shiftx(ivec)+isx2>par_civ.ImageWidth  % we are outside the image
+%             F(ivec)=3;
+%         else
+            F(ivec)=0;
+            subrange1_x=iref-ibx2:iref+ibx2;% x indices defining the first subimage
+            subrange1_y=jref-iby2:jref+iby2;% y indices defining the first subimage
+            subrange2_x=iref+shiftx(ivec)-isx2:iref+shiftx(ivec)+isx2;%x indices defining the second subimage
+            subrange2_y=jref+shifty(ivec)-isy2:jref+shifty(ivec)+isy2;%y indices defining the second subimage
+            image1_crop=MinA*ones(numel(subrange1_y),numel(subrange1_x));% default value=min of image A
+            image2_crop=MinA*ones(numel(subrange2_y),numel(subrange2_x));% default value=min of image A
+            check1_x=subrange1_x>=1 & subrange1_x<=par_civ.ImageWidth;% check which points in the subimage 1 are contained in the initial image 1
+            check1_y=subrange1_y>=1 & subrange1_y<=par_civ.ImageHeight;
+            check2_x=subrange2_x>=1 & subrange2_x<=par_civ.ImageWidth;% check which points in the subimage 2 are contained in the initial image 2
+            check2_y=subrange2_y>=1 & subrange2_y<=par_civ.ImageHeight;
+            image1_crop(check1_y,check1_x)=par_civ.ImageA(subrange1_y(check1_y),subrange1_x(check1_x));%extract a subimage (correlation box) from image A
+            image2_crop(check2_y,check2_x)=par_civ.ImageB(subrange2_y(check2_y),subrange2_x(check2_x));%extract a larger subimage (search box) from image B
             image1_mean=mean(mean(image1_crop));
             image2_mean=mean(mean(image2_crop));
@@ -603 +588 @@
                 F(ivec)=3;
             end
-        end      
+%         end      
         if F(ivec)~=3
             image1_crop=image1_crop-image1_mean;%substract the mean

trunk/src/find_field_cells.m

@@ -20 +20 @@
 %              _warnflag: index of warnflag    
 %      .FieldRequest= 'interp_lin', 'interp_tps' indicate whether lin interpolation  or derivatives (tps) is needed to calculate the requested field
-%      .Operation = operation to be performed to finalise the field cell after projection
+%      .FieldName = operation to be performed to finalise the field cell after projection
 %      .SubCheck=0 /1 indicate that the field must be substracted (second  entry in uvmat)
 % NbDim: array with the length of CellVarIndex, giving the space dimension of each field cell
@@ -87 +87 @@
 Role=num2cell(blanks(nbvar));%initialize a cell array of nbvar blanks
 FieldRequest=regexprep(Role,' ',''); % fieldRequest set to '' by default
-Operation=cell(size(Role)); % fieldRequest set to {} by default
+FieldName=cell(size(Role)); % fieldRequest set to {} by default
 CheckSub=zeros(size(Role));% =1 for fields to substract
 Role=regexprep(Role,' ','scalar'); % Role set to 'scalar' by default
@@ -98 +98 @@
             FieldRequest{ivar}=Data.VarAttribute{ivar}.FieldRequest;
         end
-        if isfield(Data.VarAttribute{ivar},'Operation')
-            Operation{ivar}=Data.VarAttribute{ivar}.Operation;
+        if isfield(Data.VarAttribute{ivar},'FieldName')
+            FieldName{ivar}=Data.VarAttribute{ivar}.FieldName;
         end
         if isfield(Data.VarAttribute{ivar},'CheckSub')
@@ -318 +318 @@
             CellInfo{icell}.FieldRequest=FieldRequest{ivar};
         end
-        if ~isempty(Operation{ivar})
-            CellInfo{icell}.Operation=Operation{ivar};
+        if ~isempty(FieldName{ivar})
+            CellInfo{icell}.FieldName=FieldName{ivar};
         end
         if CheckSub(ivar)==1

trunk/src/proj_field.m

@@ -861 +861 @@
 %project on a plane 
 % AJOUTER flux,circul,error
- function  [ProjData,errormsg] = proj_plane(FieldData, ObjectData)
+function  [ProjData,errormsg] = proj_plane(FieldData, ObjectData)
 %-----------------------------------------------------------------
 
@@ -1185 +1185 @@
                         FieldData=rmfield(FieldData,FieldData.ListVarName{CellInfo{icell}.VarIndex_warnflag});
                     end
-                    [VarVal,ListFieldProj,VarAttribute,errormsg]=calc_field_interp([coord_X coord_Y],FieldData,CellInfo{icell}.Operation,XI,YI);
+                    [VarVal,ListFieldProj,VarAttribute,errormsg]=calc_field_interp([coord_X coord_Y],FieldData,CellInfo{icell}.FieldName,XI,YI);
                     if isfield(CellInfo{icell},'CheckSub') && CellInfo{icell}.CheckSub && ~isempty(vector_x_proj)
                         ProjData.(ProjData.ListVarName{vector_x_proj})=ProjData.(ProjData.ListVarName{vector_x_proj})-VarVal{1};
@@ -1221 +1221 @@
                 XI=XI+ObjectData.Coord(1,1);
                 YI=YI+ObjectData.Coord(1,2);
-                [DataOut,VarAttribute,errormsg]=calc_field_tps(Coord,NbSites,SubRange,FieldVar,CellInfo{icell}.Operation,cat(3,XI,YI));   
+                [DataOut,VarAttribute,errormsg]=calc_field_tps(Coord,NbSites,SubRange,FieldVar,CellInfo{icell}.FieldName,cat(3,XI,YI));   
                 ListFieldProj=(fieldnames(DataOut))';
                 VarDimName=cell(size(ListFieldProj));

trunk/src/read_civdata.m

@@ -116 +116 @@
     Field.VarAttribute{ivar}.FieldRequest=FieldRequest;
     if strcmp(role{var_ind(ivar)},'vector_x')
-        Field.VarAttribute{ivar}.Operation=FieldNames;
+        Field.VarAttribute{ivar}.FieldName=FieldNames;
         ivar_U=ivar;
     end
     if strcmp(role{var_ind(ivar)},'vector_x_tps')
-        Field.VarAttribute{ivar}.Operation=FieldNames;
+        Field.VarAttribute{ivar}.FieldName=FieldNames;
         ivar_U_tps=ivar;
     end

trunk/src/read_field.m

@@ -41 +41 @@
     if isfield(ParamIn,'FieldName')
         if ischar(ParamIn.FieldName)
-            ParamIn.FieldName={ParamIn.FieldName};
+            InputField={ParamIn.FieldName};
         else
             InputField= ParamIn.FieldName;

trunk/src/set_grid.m

@@ -22 +22 @@
 function varargout = set_grid(varargin)
 
-% Last Modified by GUIDE v2.5 23-Apr-2010 15:44:47
+% Last Modified by GUIDE v2.5 01-Mar-2013 22:41:43
 
 % Begin initialization code - DO NOT PLOT
@@ -32 +32 @@
                    'gui_LayoutFcn',  [] , ...
                    'gui_Callback',   []);
-% if nargin & isstr(varargin{1})
-%     gui_State.gui_Callback = str2func(varargin{1});
-% end
+               
 if nargin && ischar(varargin{1})
     gui_State.gui_Callback = str2func(varargin{1});
@@ -43 +41 @@
     gui_mainfcn(gui_State, varargin{:});
 end
-% End initialization code - DO NOT PLOT
 
 %-------------------------------------------------------------------
@@ -54 +51 @@
 %'data': read from an existing object selected in the interface
 %      .TITLE : class of object ('POINTS','LINE',....)
-%      .DX,DY,DZ; meshes for regular grids
+%      .num_DX,num_DY,DZ; meshes for regular grids
 %      .Coord: object position coordinates
 %      .ParentButton: handle of the uicontrol object calling the interface
@@ -60 +57 @@
 %  if =[] or absent, no plot (mask mode in uvmat)
 % parameters on the uvmat interface (obtained by 'get_plot_handle.m')
-function set_grid_OpeningFcn(hObject, eventdata, handles,inputfile,CoordType)
+function set_grid_OpeningFcn(hObject, eventdata, handles,InputFile,InputField)
 
 % Choose default command line output for set_grid
@@ -68 +65 @@
 guidata(hObject, handles);
 
-%default
-% set(hObject,'Unit','Normalized')% set the unit normalized to the screen size
-% set(hObject,'Position',[0.7 0.1 0.25 0.5])%set the position of the set_grid interface 
+%default 
 set(hObject,'DeleteFcn',@closefcn)
-% set(handles.TITLE,'Value',1)
-%set(handles.ObjectStyle,'Value',1)
-%set(handles.ProjMode,'Value',1)
-set(handles.MenuCoord,'ListboxTop',1)
-set(handles.MenuCoord,'Value',1);
-set(handles.MenuCoord,'String',{'phys';'px'});
-if exist('inputfile','var')& ~isempty(inputfile)
-   set(handles.image_1,'String',inputfile)
-   set(handles.image_2,'String',inputfile)
-end
-if exist('CoordType','var')
-    if strcmp(CoordType,'px')
-        set(handles.MenuCoord,'Value',2)
-    end
+set(hObject,'WindowButtonDownFcn',{'mouse_down'})%set mouse click action function
+set(handles.CoordType,'ListboxTop',1)
+set(handles.CoordType,'Value',1);
+set(handles.CoordType,'String',{'phys';'px'});
+if exist('InputFile','var')
+   set(handles.ImageA,'String',InputFile)
+end
+
+%% use InputField input from uvmat
+check_pixel=0;
+if exist('InputField','var')
+    if strcmp(InputField.CoordUnit,'pixel')
+        set(handles.CoordType,'Value',2)
+        set(handles.TxtWarning,'Visible','on')
+        Mesh=20;%default mesh in pixel
+        check_pixel=1;
+    else
+        set(handles.CoordType,'Value',1)
+        InputField.CoordMesh=20*InputField.CoordMesh; % about 20 pixels
+        % adjust the mesh to a value 1, 2 , 5 *10^n
+        ord=10^(floor(log10(InputField.CoordMesh)));%order of magnitude
+        if InputField.CoordMesh/ord>=5
+            Mesh=5*ord;
+        elseif InputField.CoordMesh/ord>=2
+            Mesh=2*ord;
+        else
+            Mesh=ord;
+        end
+    end
+    Input.DX=Mesh;
+    Input.DY=Mesh;
+    Input.XMin=(Mesh/2)*ceil(InputField.XMin/(Mesh/2))-0.5*check_pixel;
+    Input.XMax=Input.XMin+Mesh*floor((InputField.XMax-Input.XMin)/Mesh)-0.5*check_pixel;
+    Input.YMin=(Mesh/2)*ceil(InputField.YMin/(Mesh/2))-0.5*check_pixel;
+    Input.YMax=Input.YMin+Mesh*floor((InputField.YMax-Input.YMin)/Mesh)-0.5*check_pixel;
+    errormsg=fill_GUI(Input,handles);
 end
 
@@ -93 +110 @@
 varargout{1} = handles.output;
 varargout{2}=handles;
-
-
-%-----------------------------------------------------
-% --- Executes on button press in import.
-function import_Callback(hObject, eventdata, handles)
-%get the object file 
-oldfile='';
-huvmat=findobj('Tag','uvmat');
-if isempty(huvmat)
-    huvmat=findobj(allchild(0),'Name','series');
-end
-hchild=get(huvmat,'Children');
-hrootpath=findobj(hchild,'Tag','RootPath');
-oldfile=get(hrootpath,'String');
-if iscell(oldfile)
-    oldfile=oldfile{1};
-end
-%[FileName,PathName] = uigetfile('*.civ','Select a .civ file',oldfile)
-[FileName, PathName, filterindex] = uigetfile( ...
-       {'*.xml;*.mat', ' (*.xml,*.mat)';
-       '*.xml',  '.xml files '; ...
-        '*.mat',  '.mat matlab files '}, ...
-        'Pick a file',oldfile);
-fileinput=[PathName FileName];%complete file name 
-testblank=findstr(fileinput,' ');%look for blanks
-if ~isempty(testblank)
-    errordlg('forbidden input file name: contain blanks')
-    return
-end
-sizf=size(fileinput);
-if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end
-
-%read the file
- t=xmltree(fileinput);
- s=convert(t);
-testmode=0;
-if isfield(s,'ProjMode')
-        menu=get(handles.ProjMode,'String');
-        for iline=1:length(menu)
-            if isequal(menu{iline},s.ProjMode)
-                set(handles.ProjMode,'Value',iline)
-                testmode=1;
-                break
-            end
-        end
-end
-
-ProjMode_Callback(hObject, eventdata, handles);%visualize the appropriate edit boxes
-if isfield(s,'CoordType')
-    if isequal(s.CoordType,'phys')
-        set(handles.MenuCoord,'Value',1)
-    elseif isequal(s.CoordType,'px')
-        set(handles.MenuCoord,'Value',2)
-    else
-        warndlg('unknown CoordType (px or phys) in set_grid.m')
-    end
-end
-if isfield(s,'XMax')
-    set(handles.XMax,'String',s.XMax)
-end
-if isfield(s,'XMin')
-    set(handles.XMin,'String',s.XMin)
-end
-if isfield(s,'YMax')
-    set(handles.YMax,'String',s.YMax)
-end
-if isfield(s,'YMin')
-    set(handles.YMin,'String',s.YMin)
-end
-if isfield(s,'DX')
-    set(handles.DX,'String',s.DX)
-end
-if isfield(s,'DY')
-    set(handles.DY,'String',s.DY)
-end
-if ~isfield(s,'Coord')
-    XObject='0';%default
-    YObject='0';
-elseif ischar(s.Coord)
-    line=str2num(s.Coord);
-    XObject=num2str(line(1));
-    YObject=num2str(line(2));
-else
-    for i=1:length(s.Coord)
-        line=str2num(s.Coord{i});
-        XObject{i}=num2str(line(1));
-        YObject{i}=num2str(line(2));
-    end
-end
-set(handles.XObject,'String',XObject)
-set(handles.YObject,'String',YObject)
-%METTRA A JOUR ASPECT DE L'INTERFACE (COMME set_grid_Opening
 
 %----------------------------------------------------
@@ -196 +121 @@
     if isequal(tag,'edit')
         set(parent_button,'BackgroundColor',[0.7 0.7 0.7]);
-    else 
+    else
         set(parent_button,'BackgroundColor',[0 1 0]);
     end
@@ -204 +129 @@
 % --- Executes on button press in plot: PLOT the defined object and its projected field
 function plot_Callback(hObject, eventdata, handles)
-grid_pix_A=get_grid(handles);
-huvmat=uvmat(get(handles.image_1,'String'));
+[grid_pix_A,grid_pix_B,grid_phys]=get_grid(read_GUI(handles.set_grid));
+huvmat=findobj(allchild(0),'tag','uvmat');
 hhuvmat=guidata(huvmat);
-set(hhuvmat.transform_fct,'Value',1)
-uvmat('run0_Callback',hObject,eventdata,hhuvmat); %file input with xml reading  in uvmat
-axes(hhuvmat.axes3);
+axes(hhuvmat.PlotAxes);
 hold on
-plot(grid_pix_A(:,1),grid_pix_A(:,2),'.')
-
-% --- Executes on button press in plot_2.
-function plot_2_Callback(hObject, eventdata, handles)
-[grid_pix_A,grid_pix_B]=get_grid(handles);
-huvmat=uvmat(get(handles.image_2,'String'));
-hhuvmat=guidata(huvmat);
-set(hhuvmat.transform_fct,'Value',1)
-uvmat('run0_Callback',hObject,eventdata,hhuvmat); %file input with xml reading  in uvmat
-axes(hhuvmat.axes3);
-hold on
-plot(grid_pix_B(:,1),grid_pix_B(:,2),'.')
-
-
-
-% --- Executes on button press in MenuCoord.
-function MenuCoord_Callback(hObject, eventdata, handles)
-
+UvData=get(huvmat,'UserData');
+if isfield(UvData.Field, 'CoordUnit')&& strcmp(UvData.Field.CoordUnit,'pixel')
+    plot(grid_pix_A(:,1),grid_pix_A(:,2),'.')
+else
+    plot(grid_phys(:,1),grid_phys(:,2),'.')
+end
+
+%% display grid in second image defiend
+if ~isempty(grid_pix_B)
+    hviewfield=view_field(get(handles.imageB,'String'));
+    hhviewfield=guidata(hviewfield);
+    axes(hhviewfield.PlotAxes);
+    hold on
+    if isfield(UvData.Field, 'CoordUnit')&& strcmp(UvData.Field.CoordUnit,'pixel')
+        plot(grid_pix_B(:,1),grid_pix_B(:,2),'.')
+    else
+        plot(grid_phys(:,1),grid_phys(:,2),'.')
+    end
+end
+
+%------------------------------------------------------------------------
+% --- Executes on button press in CoordType.
+function CoordType_Callback(hObject, eventdata, handles)
+%------------------------------------------------------------------------
+set(handles.num_XMin,'String','')
+set(handles.num_XMax,'String','')
+set(handles.num_DX,'String','')
+set(handles.num_YMin,'String','')
+set(handles.num_YMax,'String','')
+set(handles.num_DY,'String','')
+set(handles.num_Z,'String','')
+if isequal(get(handles.CoordType,'Value'),2)
+    set(handles.TxtWarning,'visible','on')
+else
+    set(handles.TxtWarning,'visible','on')
+end
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -247 +188 @@
 
 % ------------------------------------------------------
-function save_Callback(hObject, eventdata, handles)
+function Save_Callback(hObject, eventdata, handles)
 % ------------------------------------------------------
-[grid_pix_A,grid_pix_B]=get_grid(handles);
+[grid_pix_A,grid_pix_B]=get_grid(read_GUI(handles.set_grid));
+
 
  %ECRIRE FICHIERS
 nbpointsA=size(grid_pix_A);
-XA=grid_pix_A(:,1);
+XA=grid_pix_A(:,1);%index=position+0.5 rounded at the nearest integer value
 YA=grid_pix_A(:,2);
 unitcolumn=32*ones(size(XA));
@@ -263 +205 @@
 textgrid={tete;txt};
 textout=char(textgrid);
-imageA=get(handles.image_1,'String');
+imageA=get(handles.ImageA,'String');
 RootPath=fileparts_uvmat(imageA);
-%[Pathsub]=name2display(imageA);
 Answer = msgbox_uvmat('INPUT_TXT','grid file name (*.grid)',fullfile(RootPath,'gridA.grid'));
-% Answer = inputdlg('grid file name (*.grid)',' ',1,{fullfile(Pathsub,'gridA.grid')},'on');
 dlmwrite(Answer,textout,'');
 msgbox_uvmat('CONFIRMATION',[Answer ' written as ASCII text file']);
 if ~isempty(grid_pix_B)
     nbpointsB=size(grid_pix_B);
-    XB=grid_pix_B(:,1);
-    YB=grid_pix_B(:,2);
+    XB=round(grid_pix_B(:,1)+0.5);%index=position+0.5 rounded at the nearest integer value
+    YB=round(grid_pix_B(:,2)+0.5);
     unitcolumn=32*ones(size(XB));
     Xchar=num2str(XB);
@@ -287 +227 @@
 end
 
-%-------------------------
-function [grid_pix_A,grid_pix_B]=get_grid(handles)
-%Object=read_set_object(handles);%read the set_grid interface;
+
+%------------------------------------------------------------------------
+function [grid_pix_A,grid_pix_B,grid_phys]=get_grid(GUI)
+%------------------------------------------------------------------------
 grid_pix_B=[];%default
-DX=str2num(get(handles.DX,'String'));
-DY=str2num(get(handles.DY,'String'));
-XMin=str2num(get(handles.XMin,'String'));
-XMax=str2num(get(handles.XMax,'String'));
-YMin=str2num(get(handles.YMin,'String'));
-YMax=str2num(get(handles.YMax,'String'));
-array_realx=XMin:DX:XMax;
-array_realy=YMin:DY:YMax;
-nx_patch=length(array_realx);
-ny_patch=length(array_realy);
-[grid_realx,grid_realy]=meshgrid(array_realx,array_realy);
-grid_real(:,1)=reshape(grid_realx,nx_patch*ny_patch,1);
-grid_real(:,2)=reshape(grid_realy,nx_patch*ny_patch,1);
-grid_real(:,3)=zeros(nx_patch*ny_patch,1);
- 
-imageA=get(handles.image_1,'String');
-imageB=get(handles.image_2,'String');
-testB=1;
-if isempty(imageA) || isequal(imageA,'')
-    if isempty(imageB) || isequal(imageB,'')
-        msgbox_uvmat('ERROR','at least one image file name must be introduced')
-    else
-        imageA=imageB;
-        testB=0;
-    end
-end
-if isempty(imageB) || isequal(imageB,'') || isequal(imageA,imageB)
-    testB=0;
-end
-
-testexist=exist(imageA,'file');
-if isequal(testexist,0)
+array_x=GUI.XMin:GUI.DX:GUI.XMax;% array of x values
+array_y=GUI.YMin:GUI.DY:GUI.YMax;% array of y values
+[grid_x,grid_y]=meshgrid(array_x,array_y);% matrices of x and y values
+grid_x=reshape(grid_x,[],1); %matrix of x  values reshaped in line
+grid_y=reshape(grid_y,[],1);%matrix of y values reshaped in line
+% grid_z=zeros(nx_patch*ny_patch,1);% plane coordinates (TODO: 3D grids)
+
+%% check the input image A
+if ~exist(GUI.ImageA,'file')
     msgbox_uvmat('ERROR',['input image file' imageA 'does not exist'])
     return
 end
-%[Pathsub,RootFile,field_count,str2,str_a,str_b,FileExt,NomType,SubDir]=name2display(imageA);
-[RootPath,~,RootFile,~,~,~,~,FileExt]=fileparts_uvmat(imageA);
-form=imformats(FileExt(2:end));
-if isempty(form)% if the extension corresponds to an image format recognized by Matlab
-     msgbox_uvmat('ERROR',['error: ' imageA ' is not an image name recognized by Matlab '])
-     return
-end
-fileAxml=[fullfile(RootPath,RootFile) '.xml'];
-[XmlDataA,error]=imadoc2struct(fileAxml); 
-if isfield(XmlDataA,'GeometryCalib')
-     tsaiA=XmlDataA.GeometryCalib;
- else
-     msgbox_uvmat('WARNING','no geometric calibration available for image A')
-     tsaiA=[];
-end
-MenuCoord=get(handles.MenuCoord,'String');
-val=get(handles.MenuCoord,'Value');
-if isempty(tsaiA)||strcmp(MenuCoord{val},'px')
-    grid_imaA(:,1)=grid_real(:,1);
-    grid_imaA(:,2)=grid_real(:,2);
-else
-    [grid_imaA(:,1),grid_imaA(:,2)]=px_XYZ(tsaiA,grid_real(:,1),grid_real(:,2),0);
-end
-    A=imread(imageA);
-   siz=size(A);
-   npxA=siz(2);
-   npyA=siz(1);
-
-flagA=grid_imaA(:,1)>0 & grid_imaA(:,1)<npxA & grid_imaA(:,2)>0 & grid_imaA(:,2)<npyA; 
-
-if testB
-    testexist=exist(imageB,'file');
-    if isequal(testexist,0)
-        msgbox_uvmat('ERROR',['input image file' imageB 'does not exist'])
+[FileType,tild,VideoObject]=get_file_type(GUI.ImageA);
+switch FileType
+    case {'image','multimage','video','mmreader'}% case of input image or movie OK
+    otherwise
+        msgbox_uvmat('ERROR',['error: ' GUI.ImageA ' is not an image type recognized by Matlab '])
         return
-    end
-    %[RootPath,RootFile,field_count,str2,str_a,str_b,FileExt,NomType,SubDir]=name2display(imageB);
-    [RootPath,~,RootFile,~,~,~,~,FileExt]=fileparts_uvmat(imageB);
-    form=imformats(FileExt(2:end));
-    if isempty(form)% if the extension corresponds to an image format recognized by Matlab
-        msgbox_uvmat('ERROR',['error: ' imageB ' is not an image name recognized by Matlab '])
+end
+[RootPath,SubDir,RootFile,tild,tild,tild,tild,FileExt]=fileparts_uvmat(GUI.ImageA);
+
+%% transform to pixels if the grid is defined in phys coordinates
+grid_x_imaA=grid_x;%default grid in image A coordinates
+grid_y_imaA=grid_y;
+% MenuCoord=get(handles.CoordType,'String');% type of coordinates for grid definition, phys or pixel
+if strcmp(GUI.CoordType,'phys')
+    fileAxml=fullfile(RootPath,[SubDir '.xml']);% new convention for xml name
+    if ~exist(fileAxml,'file')
+        fileAxml=[fullfile(RootPath,RootFile) '.xml'];% old convention for xml name
+    end
+    tsaiA=[];%default
+    if exist(fileAxml,'file')
+        [XmlDataA,errormsg]=imadoc2struct(fileAxml);
+        if ~isempty(errormsg)
+            msgbox_uvmat('ERROR',['error in ' fileAxml ': ' errormsg])
+            return
+        end
+        if isfield(XmlDataA,'GeometryCalib')
+            tsaiA=XmlDataA.GeometryCalib;
+        end
+    end
+    if isempty(tsaiA)
+        msgbox_uvmat('WARNING','no geometric calibration available for image A, phys =pixel')
+    else
+        [grid_x_imaA,grid_y_imaA]=px_XYZ(tsaiA,grid_x,grid_y,GUI.Z);
+    end
+end
+
+%% detect the grid points which are inside image A
+A=read_image(GUI.ImageA,FileType,VideoObject,1);
+npxA=size(A,2);
+npyA=size(A,1);
+flag=grid_x_imaA>=1 & grid_x_imaA<=npxA & grid_y_imaA>=1 & grid_y_imaA<=npyA;% ='true' inside the image
+
+%% detect the grid points which are inside image B if relevant (use for stereo PIV)
+if isfield(GUI,'ImageB')
+    if ~exist(imageB,'file')
+        msgbox_uvmat('ERROR',['input image file' GUI.ImageB 'does not exist'])
         return
     end
-    fileBxml=[fullfile(RootPath,RootFile) '.xml'];
-    [XmlDataB,error]=imadoc2struct(fileBxml);
-    if isfield(XmlDataB,'GeometryCalib')
-        tsaiB=XmlDataB.GeometryCalib;
-    else
-        msgbox_uvmat('WARNING','no geometric calibration available for image B')
-        tsaiB=[];
-    end
-    %[error,Heading,NomType_read,ext_ima_read,time,TimeUnit,mode,NbSlice,...
-    %     npxB,npyB,tsaiB]=read_imadoc(fileBxml,0);
-    [grid_imaB(:,1),grid_imaB(:,2)]=px_XYZ(tsaiB,grid_real(:,1),grid_real(:,2),0);
-    %     if isempty(npxB)|isempty(npyB)
-    B=imread(imageB);
-    siz=size(B);
-    npxB=siz(2);
-    npyB=siz(1);
-    %     end
-    flagB=grid_imaB(:,1)>0 & grid_imaB(:,1)<npxB & grid_imaB(:,2)>0 & grid_imaB(:,2)<npyB;
-end
-if testB
-    ind_good=find(flagA==1&flagB==1);
-    XimaB=grid_imaB(ind_good,1);
-    YimaB=grid_imaB(ind_good,2);
-else
-    ind_good=find(flagA==1);
-end
-XimaA=grid_imaA(ind_good,1);
-YimaA=grid_imaA(ind_good,2);
-
-grid_real_x=grid_real(ind_good,1);
-grid_real_y=grid_real(ind_good,2);
-nx_patch_new=length(grid_real_x); 
-grid_real2(:,1)=grid_real_x;
-grid_real2(:,2)=grid_real_y;
-grid_real2(:,3)=zeros(nx_patch_new,1);
-if isempty(tsaiA)||strcmp(MenuCoord{val},'px')
-    grid_pix_A(:,1)=grid_real2(:,1);
-   grid_pix_A(:,2)= grid_real2(:,2);
-else
-    [grid_pix_A(:,1),grid_pix_A(:,2)]=px_XYZ(tsaiA,grid_real2(:,1),grid_real2(:,2));
-end
-if testB
-    [grid_pix_B(:,1),grid_pix_B(:,2)]=px_XYZ(tsaiB,grid_real2(:,1),grid_real2(:,2));
-end
-
+    [RootPathB,SubDirB,RootFileB,tild,tild,tild,tild,FileExt]=fileparts_uvmat(GUI.ImageB);
+    fileBxml=fullfile(RootPathB,[SubDirB '.xml']);% new convention for xml name
+    if ~exist(fileBxml,'file')
+        fileBxml=[fullfile(RootPathB,RootFileB) '.xml'];% old convention for xml name
+    end
+    tsaiB=[];%default
+    if exist(fileBxml,'file')
+        [XmlDataB,errormsg]=imadoc2struct(fileBxml);
+        if ~isempty(errormsg)
+            msgbox_uvmat('ERROR',['error in ' fileAxml ': ' errormsg])
+            return
+        end
+        if isfield(XmlDataB,'GeometryCalib')
+            tsaiB=XmlDataB.GeometryCalib;
+        end
+    end
+    if isempty(tsaiB)
+        msgbox_uvmat('WARNING','no geometric calibration available for image B, phys =pixel')
+        grid_x_imaB=grid_x;
+        grid_y_imaB=grid_y;
+    else
+        [grid_x_imaB,grid_y_imaB]=px_XYZ(tsaiB,grid_x,grid_y,GUI.Z);
+    end
+    B=imread(GUI.ImageB);
+    npxB=size(B,2);
+    npyB=size(B,1);
+    flagB=grid_x_imaB>=1 & grid_x_imaB<=npxB & grid_y_imaB>=1 & grid_y_imaB<=npyB;
+    flag=flagA & flagB;
+    grid_pix_B(:,1)=round(grid_x_imaB(flag));
+    grid_pix_B(:,2)=round(grid_y_imaB(flag));
+end
+
+grid_x_imaA=grid_x_imaA(flag);
+grid_y_imaA=grid_y_imaA(flag);
+grid_pix_A=[grid_x_imaA grid_y_imaA];
+grid_x=grid_x(flag);
+grid_y=grid_y(flag);
+grid_phys=[grid_x grid_y];
+
+
+function GetImageB_Callback(hObject, eventdata, handles)
+if isequal(get(handles.GetImageB,'Value'),1)
+    set(handles.ImageB,'Visible','on')
+    [FileName, PathName, filterindex] = uigetfile( ...
+            {'*.*', 'All Files (*.*)'}, ...
+            'Pick the second image file',fileparts(fileparts(get(handles.ImageA,'String'))));
+        ImageB=fullfile(PathName,FileName);
+        [FileType,tild,VideoObject]=get_file_type(ImageB);
+    switch FileType
+        case {'image','multimage','video','mmreader'}% case of input image or movie OK
+            set(handles.ImageB,'String',ImageB)
+        otherwise
+            msgbox_uvmat('ERROR',['error: ' imageB ' is not an image type recognized by Matlab '])
+            return
+    end
+else
+    set(handles.ImageB,'Visible','off')
+end
 
 
@@ -430 +366 @@
 
 
+function ImageA_Callback(hObject, eventdata, handles)
+% hObject    handle to ImageA (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hints: get(hObject,'String') returns contents of ImageA as text
+%        str2double(get(hObject,'String')) returns contents of ImageA as a double

trunk/src/uvmat.m

@@ -216 +216 @@
 
 %% load the list of previously browsed files in menus Open, Open_1 and transform_fct
- dir_perso=prefdir; % path to the directory .matlab for personal data
- profil_perso=fullfile(dir_perso,'uvmat_perso.mat');% personal data file uvmauvmat_perso.mat' in .matlab
+ dir_perso=prefdir; % path to the directory .matlab containing the personal data of the current user
+ profil_perso=fullfile(dir_perso,'uvmat_perso.mat');% personal data file uvmat_perso.mat' in .matlab
  if exist(profil_perso,'file')
      h=load (profil_perso);
      if isfield(h,'MenuFile')% load the menu of previously opened files
          for ifile=1:min(length(h.MenuFile),5)
-             eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',h.MenuFile{ifile});'])
-             eval(['set(handles.MenuFile_' num2str(ifile) '_1,''Label'',h.MenuFile{ifile});'])
+             set(handles.(['MenuFile_' num2str(ifile)]),'Label',h.MenuFile{ifile});
+             set(handles.(['MenuFile_' num2str(ifile) '_1']),'Label',h.MenuFile{ifile});
          end
+     end
+     if isfield(h,'RootPath')
+         set(handles.RootPath,'UserData',h.RootPath); %store the previous campaign in the UserData of RootPath
      end
      if isfield(h,'transform_fct') && iscell(h.transform_fct) % load the menu of transform fct set by user
@@ -335 +338 @@
 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
 oldfile=fullfile(RootPath,SubDir);
-if isempty(oldfile)||isequal(oldfile,'') %loads the previously stored file name and set it as default in the file_input box
-         dir_perso=prefdir;
-         profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
-         if exist(profil_perso,'file')
-              h=load (profil_perso);
-             if isfield(h,'MenuFile_1')
-                  oldfile=h.MenuFile_1;
-             end
-         end
+if isempty(oldfile) %loads the previously stored file name and set it as default in the file_input box
+    oldfile=get(handles.RootPath,'UserData');
 end
 [FileName, PathName] = uigetfile({'*.*','All Files(*.*)'},'Pick a file',oldfile);
@@ -357 +353 @@
 function MenuBrowseCampaign_Callback(hObject, eventdata, handles)
 % -----------------------------------------------------------------------
-CampaignPath=fileparts(fileparts(get(handles.RootPath,'String')));
+RootPath=get(handles.RootPath,'String');
+if isempty(RootPath)
+    RootPath=get(handles.RootPath,'UserData');%use Rootpath recored from the personal file at uvmat opening
+end
+CampaignPath=fileparts(fileparts(RootPath));
 DirFull = uigetdir(CampaignPath,'Select a Campaign dir, then press OK');
 if ~ischar(DirFull)|| ~exist(DirFull,'dir')
@@ -447 +447 @@
 set(handles.MenuFile_4_1,'Label',MenuFile_4)
 set(handles.MenuFile_5_1,'Label',MenuFile_5)
-dir_perso=prefdir;
-profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
-if exist(profil_perso,'file')
-    save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
-else
-    txt=ver('MATLAB');
-    Release=txt.Release;
-    relnumb=str2double(Release(3:4));
-    if relnumb >= 14
-        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
-    else
-        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
-    end
-end
+% dir_perso=prefdir;
+% profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
+% if exist(profil_perso,'file')
+%     save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
+% else
+%     txt=ver('MATLAB');
+%     Release=txt.Release;
+%     relnumb=str2double(Release(3:4));
+%     if relnumb >= 14
+%         save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
+%     else
+%         save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
+%     end
+% end
 
 % --------------------------------------------------------------------
@@ -787 +787 @@
 end
 for ifile=1:min(length(MenuFile),5)
-    eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
-    eval(['set(handles.MenuFile_' num2str(ifile) '_1,''Label'',MenuFile{ifile});'])
+    set(handles.(['MenuFile_' num2str(ifile)]),'Label',MenuFile{ifile});
+    set(handles.(['MenuFile_' num2str(ifile) '_1']),'Label',MenuFile{ifile});
 end
 dir_perso=prefdir;
 profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
 if exist(profil_perso,'file')
-    save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
+    save (profil_perso,'MenuFile','RootPath','-append'); %store the file names for future opening of uvmat
 else
-    save (profil_perso,'MenuFile','-V6'); %store the file names for future opening of uvmat
+    save (profil_perso,'MenuFile','RootPath','-V6'); %store the file names for future opening of uvmat
 end
 
@@ -1411 +1411 @@
         choice_value=get(handles.transform_fct,'Value');
         transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
-%         transform_list=get(handles.transform_fct,'UserData');
-%         transform=transform_list{choice_value};
         transform=get(handles.path_transform,'UserData');
         if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
@@ -1441 +1439 @@
             axes(handles.PlotAxes)
             hold on    
-            size(flagmask)
-           % MaskData.maskhandle=image(Mask.AX,Mask.AY,imflag,'Tag','mask','HitTest','off','AlphaData',0.6*flagmask);
             MaskData.maskhandle=image(Mask.AX,Mask.AY,imflag,'Tag','mask','HitTest','off','AlphaData',0.6*ones(size(flagmask)));
-%             set(MaskData.maskhandle,'AlphaData',0.6*flagmask)
             set(handles.CheckMask,'UserData',MaskData)
         end
@@ -1932 +1927 @@
 
 %px to phys or other transform on field
-% menu_transform=get(handles.transform_fct,'String');
-% choice_value=get(handles.transform_fct,'Value');
-% transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
-% transform_list=get(handles.transform_fct,'UserData');
 transform=get(handles.path_transform,'UserData');
 if  ~isempty(transform)
@@ -2067 +2058 @@
         list_fields=get(handles.FieldName,'String');% list menu fields
         FieldName= list_fields{get(handles.FieldName,'Value')}; % selected field
+        % if get_field... is selected, the GUI get_field will be used to enter fields 
         if ~strcmp(FieldName,'get_field...')
             if get(handles.FixVelType,'Value')
@@ -2073 +2065 @@
             end
         end
+        % case of input vector field, get the scalar used for vector color
         if ~isempty(regexp(FieldName,'^vec('))
             list_code=get(handles.ColorCode,'String');% list menu fields
@@ -2132 +2125 @@
 end
 Field{1}.ZIndex=z_index; %used for multiplane 3D calibration
-% end
+
 
 %% choose and read a second field FileName_1 if defined
@@ -2461 +2454 @@
 end
 
+%UvData.Field=get_bounds(UvData.Field);
 
 %% get bounds and mesh (needed  to propose default options for projection objects)
@@ -3391 +3385 @@
 %-------------------------------------------------------
 % 
-% UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface 
 if isequal(get(handles.edit_vect,'Value'),1)
     test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
@@ -3403 +3396 @@
     set(handles.CheckZoom,'Value',0)
     set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
-%     set(handles.create,'Value',0)
-%     set(handles.create,'BackgroundColor',[0 1 0])
     set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
     set(gcf,'Pointer','arrow')
-%     UvData.MouseAction='edit_vect';
 else
     set(handles.record,'Visible','off')
@@ -4143 +4133 @@
 function edit_object_Callback(hObject, eventdata, handles)
 %-------------------------------------------------------------------
-UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface 
 hset_object=findobj(allchild(0),'Tag','set_object');
 if get(handles.edit_object,'Value')
@@ -4903 +4892 @@
 [RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
 FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];
-CoordList=get(handles.transform_fct,'String');
-val=get(handles.transform_fct,'Value');
-set_grid(FileName,CoordList{val});% call the set_object interface
+UvData=get(handles.uvmat,'UserData');
+% CoordList=get(handles.transform_fct,'String');
+% val=get(handles.transform_fct,'Value');
+set_grid(FileName,UvData.Field);% call the set_object interface