Changeset 341

Timestamp:

Dec 19, 2011, 5:00:54 PM (13 years ago)

Author:

sommeria

Message:

various bugs corrected

Location:

trunk/src

Files:

• geometry_calib.m (modified) (12 diffs)
• series.m (modified) (3 diffs)
• set_object.m (modified) (1 diff)
• uvmat.m (modified) (2 diffs)

trunk/src/geometry_calib.m

@@ -99 +99 @@
 %set menu of calibration options
 set(handles.calib_type,'String',{'rescale';'linear';'3D_linear';'3D_quadr';'3D_extrinsic'})
-inputxml='';
+% inputxml='';
 if exist('inputfile','var')&& ~isempty(inputfile)
     struct.XmlInputFile=inputfile;
-    [Pathsub,RootFile,field_count,str2,str_a,str_b,ext]=name2display(inputfile);
-    if ~strcmp(ext,'.xml')
-        inputfile=[fullfile(Pathsub,RootFile) '.xml'];%xml file corresponding to the input file
+%     [Pathsub,RootFile,field_count,str2,str_a,str_b,ext]=name2display(inputfile);
+    [RootPath,~,RootFile,~,~,~,~,FileExt]=fileparts_uvmat(inputfile);
+    if ~strcmp(FileExt,'.xml')
+        inputfile=[fullfile(RootPath,RootFile) '.xml'];%xml file corresponding to the input file
     end
     set(handles.ListCoord,'String',{'......'})
@@ -134 +135 @@
 if ~isempty(huvmat)
     handles=guidata(huvmat);
-%     set(handles.MenuMask,'enable','on')
-%     set(handles.MenuGrid,'enable','on')
-%     set(handles.MenuObject,'enable','on')
-%     set(handles.MenuEdit,'enable','on')
-%     set(handles.edit,'enable','on')
     hobject=findobj(handles.axes3,'tag','calib_points');
     if ~isempty(hobject)
@@ -179 +175 @@
     GeometryCalib.ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima)));
     [GeometryCalib.ErrorMax(2),index(2)]=max(abs(Ypoints-y_ima));
-    [EM,ind_dim]=max(GeometryCalib.ErrorMax);
+    [~,ind_dim]=max(GeometryCalib.ErrorMax);
     index=index(ind_dim);
     %set the Z position of the reference plane used for calibration
@@ -222 +218 @@
 hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat
 RootPath='';
-RootFile='';
+% RootFile='';
 if ~isempty(hhuvmat.RootPath)&& ~isempty(hhuvmat.RootFile)
-    testhandle=1;
+%     testhandle=1;
     RootPath=get(hhuvmat.RootPath,'String');
     RootFile=get(hhuvmat.RootFile,'String');
@@ -321 +317 @@
     [Xpoints,Ypoints]=px_XYZ(GeometryCalib,X,Y,Z);
     GeometryCalib.ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima)));
-    [GeometryCalib.ErrorMax(1),index(1)]=max(abs(Xpoints-x_ima));
+    [GeometryCalib.ErrorMax(1)]=max(abs(Xpoints-x_ima));
     GeometryCalib.ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima)));
-    [GeometryCalib.ErrorMax(2),index(2)]=max(abs(Ypoints-y_ima));
-    [EM,ind_dim]=max(GeometryCalib.ErrorMax);
-%     index=index(ind_dim);
+    [GeometryCalib.ErrorMax(2)]=max(abs(Ypoints-y_ima));
+%     [EM,ind_dim]=max(GeometryCalib.ErrorMax);
     %set the Z position of the reference plane used for calibration
     Z_plane=[];
@@ -360 +355 @@
 end
 CalibData=get(handles.geometry_calib,'UserData');%read the calibration image source on the interface userdata
-InputFile='';
+% InputFile='';
 if isfield(CalibData,'XmlInputFile')
     InputDir=fileparts(CalibData.XmlInputFile);
@@ -388 +383 @@
 
 dataview(answer,SubCampaignTest,GeometryCalib);
-        
-%     if isfield(Heading,'Device') && isequal([filename ext],Heading.Device)
-%         [XmlInput,filename,ext]=fileparts(XmlInput);
-%         Device=Heading.Device;
-%     end
-%     if isfield(Heading,'Experiment') && isequal([filename ext],Heading.Experiment)
-%         [PP,filename,ext]=fileparts(XmlInput);
-%     end
-%     testinput=0;
-%     if isfield(Heading,'SubCampaign') && isequal([filename ext],Heading.SubCampaign)
-%         SubCampaignTest='y';
-%         testinput=1;
-%     elseif isfield(Heading,'Campaign') && isequal([filename ext],Heading.Campaign)
-%         testinput=1;
-% %     end 
-% end
-% if ~testinput
-%     filename='PROJETS';%default
-%     if isfield(CalibData,'XmlInputFile')
-%          [pp,filename]=fileparts(CalibData.XmlInputFile);
-%     end
-%     while ~isequal(filename,'PROJETS') && numel(filename)>1
-%         filename_1=filename;
-%         pp_1=pp;
-%         [pp,filename]=fileparts(pp);
-%     end
-%     XmlInput=fullfile(pp_1,filename_1);
-%     testinput=1;
-% end
-% if testinput
-%     outcome=dataview(XmlInput,SubCampaignTest,GeometryCalib);
-% end
 
 %------------------------------------------------------------------------
@@ -429 +392 @@
 x_ima=Coord(:,4);
 y_ima=Coord(:,5);
-[px,sx]=polyfit(X,x_ima,1);
-[py,sy]=polyfit(Y,y_ima,1);
-T_x=px(2);
-T_y=py(2);
+[px]=polyfit(X,x_ima,1);
+[py]=polyfit(Y,y_ima,1);
+% T_x=px(2);
+% T_y=py(2);
 GeometryCalib.CalibrationType='rescale';
 GeometryCalib.fx_fy=[px(1) py(1)];%.fx_fy corresponds to pxcm along x and y
 GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
 GeometryCalib.Tx_Ty_Tz=[px(2)/px(1) py(2)/py(1) 1];
-%GeometryCalib.R=[1,0,0;0,1,0;0,0,0];
 GeometryCalib.omc=[0 0 0];
 
@@ -452 +414 @@
 XY_mat=[ones(size(X)) X Y];
 a_X1=XY_mat\x_ima; %transformation matrix for X
-% x1=XY_mat*a_X1;%reconstruction
-% err_X1=max(abs(x1-x_ima));%error
 a_Y1=XY_mat\y_ima;%transformation matrix for X
-% y1=XY_mat*a_Y1;
-% err_Y1=max(abs(y1-y_ima));%error
-% R=[a_X1(2),a_X1(3),0;a_Y1(2),a_Y1(3),0;0,0,1];
 R=[a_X1(2),a_X1(3);a_Y1(2),a_Y1(3)];
 epsilon=sign(det(R));
@@ -469 +426 @@
 GeometryCalib.fx_fy(2)=(a_Y1(3)/a_X1(2))*GeometryCalib.fx_fy(1);
 GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
-%GeometryCalib.Tx_Ty_Tz=[a_X1(1) a_Y1(1) 1]; 
 GeometryCalib.Tx_Ty_Tz=[a_X1(1)/GeometryCalib.fx_fy(1) a_Y1(1)/GeometryCalib.fx_fy(2) 1];
 R(1,:)=R(1,:)/GeometryCalib.fx_fy(1);
@@ -740 +696 @@
 
 
-%--------------------------------------------------------------------------
-function GeometryCalib=calib_tsai(Coord,handles)% OBSOLETE: old version using gauthier's bianry ccal_fo
-% NOT USED
-%------------------------------------------------------------------------
-%TSAI
-path_uvmat=which('uvmat');% check the path detected for source file uvmat
-path_UVMAT=fileparts(path_uvmat); %path to UVMAT
-xmlfile=fullfile(path_UVMAT,'PARAM.xml');%name of the file containing names of binary executables
-if exist(xmlfile,'file')
-    t=xmltree(xmlfile);% read the (xml) file containing names of binary executables
-    sparam=convert(t);% convert to matlab structure
-end
-if ~isfield(sparam,'GeometryCalibBin')
-    msgbox_uvmat('ERROR',['calibration program <GeometryCalibBin> undefined in parameter file ' xmlfile])
-    return
-end
-Tsai_exe=sparam.GeometryCalibBin;
-if ~exist(Tsai_exe,'file')%the binary is defined in /bin, default setting
-     Tsai_exe=fullfile(path_UVMAT,Tsai_exe);
-end
-if ~exist(Tsai_exe,'file')
-    msgbox_uvmat('ERROR',['calibration program ' sparam.GeometryCalibBin ' defined in PARAM.xml does not exist'])
-    return
-end
-
-textcoord=num2str(Coord,4);
-dlmwrite('t.txt',textcoord,'');  
-% ['!' Tsai_exe ' -fx 0 -fy t.txt']
-eval(['!' Tsai_exe ' -f t.txt > tsaicalib.log']);
-if ~exist('calib.dat','file')
-    msgbox_uvmat('ERROR','no output from calibration program Tsai_exe: possibly too few points')
-end
-calibdat=dlmread('calib.dat');
-delete('calib.dat')
-%delete('t.txt')
-GeometryCalib.CalibrationType='tsai';
-GeometryCalib.focal=calibdat(10);
-GeometryCalib.dpx_dpy=[calibdat(5) calibdat(6)];
-GeometryCalib.Cx_Cy=[calibdat(7) calibdat(8)];
-GeometryCalib.sx=calibdat(9);
-GeometryCalib.kappa1=calibdat(11);
-GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
-GeometryCalib.Tx_Ty_Tz=[calibdat(12) calibdat(13) calibdat(14)];
-Rx_Ry_Rz=calibdat(15:17);
-sa = sin(Rx_Ry_Rz(1)) ; 
-ca=cos(Rx_Ry_Rz(1));
-sb=sin(Rx_Ry_Rz(2));
-cb =cos(Rx_Ry_Rz(2));
-sg =sin(Rx_Ry_Rz(3));
-cg =cos(Rx_Ry_Rz(3)); 
-r1 = cb * cg;
-r2 = cg * sa * sb - ca * sg;
-r3 = sa * sg + ca * cg * sb;
-r4 = cb * sg;
-r5 = sa * sb * sg + ca * cg;
-r6 = ca * sb * sg - cg * sa;
-r7 = -sb;
-r8 = cb * sa;
-r9 = ca * cb;
-%EN DEDUIRE MATRICE R ??
-GeometryCalib.R=[r1,r2,r3;r4,r5,r6;r7,r8,r9];
-
 %------------------------------------------------------------------------
 % --- determine the rms of calibration error
@@ -855 +749 @@
 % RootFile='';
 if ~isempty(hhuvmat.RootPath)&& ~isempty(hhuvmat.RootFile)
-    testhandle=1;
+%     testhandle=1;
     RootPath=get(hhuvmat.RootPath,'String');
     RootFile=get(hhuvmat.RootFile,'String');

trunk/src/series.m

@@ -480 +480 @@
 set(handles.waitbar_frame,'Units','pixels')
 pos=get(handles.waitbar_frame,'Position');
-xima=0.5:pos(3)-0.5;
+xima=0.5:pos(3)-0.5;% pixel positions on the image representing the existing file indices
 yima=0.5:pos(4)-0.5;
 [XIma,YIma]=meshgrid(xima,yima);
@@ -491 +491 @@
 file_ima=double((i1_series(:,:,1)>0)');
 if size(file_ima,1)==1
-    file_ima=ones(pos(4),1)*file_ima;
-end
-CData(:,:,2)=interp2(Ind_i,Ind_j,file_ima,XIma,YIma,'nearest');
+    CLine=interp1(ind_i,file_ima,xima,'nearest');
+    CData(:,:,2)=ones(size(yima'))*CLine;
+%     file_ima=ones(pos(4),1)*file_ima;
+%     Ind_i=
+else
+    CData(:,:,2)=interp2(Ind_i,Ind_j,file_ima,XIma,YIma,'nearest');
+end
 set(handles.waitbar_frame,'CData',CData)
 set(handles.waitbar_frame,'Units','normalized')
@@ -1489 +1493 @@
 % set(handles.waitbar,'Position',waitbarpos)
 
-
+if isfield(Series.IndexRange,'NbSlice')
 Series.NbSlice=Series.IndexRange.NbSlice;
+end
 if last_i < first_i | last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),...
     set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;

trunk/src/set_object.m

@@ -673 +673 @@
 ListObject=get(hhuvmat.ListObject,'String');%position in the objet list
 IndexObj=get(hhuvmat.ListObject,'Value')
-% name of the object
+
+%% read the object on the GUI set_object
 ObjectName=get(handles.TITLE,'String');%name of the current object defiend in set_object
 ObjectData=read_set_object(handles);%read the input parameters defining the object in the GUI set_object

trunk/src/uvmat.m

@@ -555 +555 @@
 fileinput=read_file_boxes(handles);
 % detect the file type, get the movie object if relevant, and look for the corresponding file series:
-[i1_series,i2_series,j1_series,j2_series,~,FileType,MovieObject]=find_file_series(fileinput);
+[RootPath,RootFile,i1_series,i2_series,j1_series,j2_series,~,FileType,MovieObject]=find_file_series(fileinput);
 % initiate the input file series and refresh the current field view: 
 update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject);
@@ -1040 +1040 @@
 
 %[path,name,ext]=fileparts(fileinput_1);
-[RootPath_1,SubDir_1,RootFile_1,i1,i2,j1,j2,FileExt_1]=fileparts_uvmat(fileinput_1);
-[i1_series,i2_series,j1_series,j2_series,NomType,FileType,MovieObject]=find_file_series(fileinput_1);
+[~,SubDir_1,~,i1,i2,j1,j2,FileExt_1]=fileparts_uvmat(fileinput_1);
+[RootPath_1,RootFile_1,i1_series,i2_series,j1_series,j2_series,NomType,FileType,MovieObject]=find_file_series(fileinput_1);
 % [RootPath_1,RootFile_1,field_count,str2,str_a,str_b,FileExt_1,NomType_1,SubDir_1]=name2display(fileinput_1);
 switch FileType