Changeset 847

Timestamp:

Jan 15, 2015, 6:05:57 PM (10 years ago)

Author:

sommeria

Message:

various

Location:

trunk/src

Files:

• geometry_calib.fig (modified) (previous)
• geometry_calib.m (modified) (2 diffs)
• msgbox_uvmat.m (modified) (1 diff)
• phys_ima.m (deleted)
• proj_field.m (modified) (3 diffs)
• series/civ_input.fig (modified) (previous)
• uvmat.m (modified) (5 diffs)

trunk/src/geometry_calib.m

@@ -170 +170 @@
 %------------------------------------------------------------------------
 %% look for the GUI uvmat and check for an image as input
-set(handles.APPLY,'BackgroundColor',[1 1 0])
-huvmat=findobj(allchild(0),'Name','uvmat');
+set(handles.APPLY,'BackgroundColor',[1 1 0])% paint APPLY button in yellow to show activation
+huvmat=findobj(allchild(0),'Name','uvmat');% look for the GUI uvmat
 hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat
 
 RootPath='';
 if ~isempty(hhuvmat.RootPath)&& ~isempty(hhuvmat.RootFile)
-    RootPath=get(hhuvmat.RootPath,'String');
+    RootPath=get(hhuvmat.RootPath,'String');% path to the currently displayed image
     SubDirBase=regexprep(get(hhuvmat.SubDir,'String'),'\..+$','');
     outputfile=[fullfile(RootPath,SubDirBase) '.xml'];%xml file associated with the currently displayed image
@@ -326 +326 @@
 
 %% store the calibration data, by default in the xml file of the currently displayed image
-UvData=get(hhuvmat.uvmat,'UserData');
-% NbSlice_j=1;%default
-% ZStart=Z_plane;
-% ZEnd=Z_plane;
-% volume_scan='n';
-% if isfield(UvData,'XmlData')
-%     if isfield(UvData.XmlData,'TranslationMotor')
-%         NbSlice_j=UvData.XmlData.TranslationMotor.Nbslice;
-%         ZStart=UvData.XmlData.TranslationMotor.ZStart/10;
-%         ZEnd=UvData.XmlData.TranslationMotor.ZEnd/10;
-%         volume_scan='y';
-%     end
-% end
-
 answer=msgbox_uvmat('INPUT_Y-N',{'store calibration data';...
     ['Error rms (along x,y)=' num2str(GeometryCalib.ErrorRms) ' pixels'];...
     ['Error max (along x,y)=' num2str(GeometryCalib.ErrorMax) ' pixels']});
-
-%% get plane position(s)
-if ~strcmp(answer,'Yes')
+if strcmp(answer,'Yes') %store the calibration data
+    if strcmp(calib_cell{val}(1:2),'3D')%set the plane position for 3D (projection) calibration
+        msgbox_uvmat('CONFIRMATION',{['The current image series is assumed by default in the plane of the calib points z=' num2str(Z_plane) ] ; 'can be modified by MenuSetSlice in the upper bar menu of uvmat'})
+        GeometryCalib.SliceCoord=Z_plane'*[0 0 1];
+    end
+else
     GeometryCalib=[];
     index=1;
-    return
-end
-if strcmp(calib_cell{val}(1:2),'3D')%set the plane position for 3D (projection) calibration
-    msgbox_uvmat('CONFIRMATION',{['The current image series is assumed by default in the plane of the calib points z=' num2str(Z_plane) ] ; 'can be modified by MenuSetSlice in the upper bar menu of uvmat'})
-%     input_key={'Z (first position)','Z (last position)','Z (water surface)', 'refractive index','NbSlice','volume scan (y/n)','tilt angle y axis','tilt angle x axis'};
-%     input_val=[{num2str(ZEnd)} {num2str(ZStart)} {num2str(ZStart)} {'1.333'} num2str(NbSlice_j) {volume_scan} {'0'} {'0'}];
-%     answer=inputdlg(input_key,'slice position(s)',ones(1,8), input_val,'on');
-%     GeometryCalib.NbSlice=str2double(answer{5});
-%     GeometryCalib.VolumeScan=answer{6};
-%     if isempty(answer)
-%         Z_plane=0; %default
-%     else
-%         Z_plane=linspace(str2double(answer{1}),str2double(answer{2}),GeometryCalib.NbSlice);
-%     end
-     GeometryCalib.SliceCoord=Z_plane'*[0 0 1];
-%     GeometryCalib.SliceAngle(:,3)=0;
-%     GeometryCalib.SliceAngle(:,2)=str2double(answer{7})*ones(GeometryCalib.NbSlice,1);%rotation around y axis (to generalise)
-%     GeometryCalib.SliceAngle(:,1)=str2double(answer{8})*ones(GeometryCalib.NbSlice,1);%rotation around x axis (to generalise)
-%     GeometryCalib.InterfaceCoord=[0 0 str2double(answer{3})];
-%     GeometryCalib.RefractionIndex=str2double(answer{4});
 end
 

trunk/src/msgbox_uvmat.m

@@ -106 +106 @@
         case 'INPUT_Y-N'
             icontype='quest';
-            testCancel=1; %no cancel button
+            testCancel=0; %no cancel button
             testNo=1; % button No activated
         case 'RULER'

trunk/src/proj_field.m

@@ -1329 +1329 @@
                         XIndexMin=1;
                     end
-%                         YIndexMin=(Coord{NbDim-1}(1)-YMax)/DY+1;
-% %                         YIndexMax=(Coord{NbDim-1}(1)-YMin)/DY+1;
-%                         Ybound(2)=Coord{NbDim-1}(1)-DY*(YIndexMax-1);
-%                         Ybound(1)=Coord{NbDim-1}(1)-DY*(YIndexMin-1);
-%                     end
-%                     if testXMin%test_direct(NbDim)==1
-%                         XIndexMin=(XMin-Coord{NbDim}(1))/DX+1;% matrix index corresponding to the min x value for the new field
-%                         XIndexMax=(XMax-Coord{NbDim}(1))/DX+1;% matrix index corresponding to the max x value for the new field
-%                         Xbound(1)=Coord{NbDim}(1)+DX*(XIndexMin-1);%  x value corresponding to XIndexMin
-%                         Xbound(2)=Coord{NbDim}(1)+DX*(XIndexMax-1);%  x value corresponding to XIndexMax
-%                     else
-%                         XIndexMin=(Coord{NbDim}(1)-XMax)/DX+1;
-%                         XIndexMax=(Coord{NbDim}(1)-XMin)/DX+1;
-%                         Xbound(2)=Coord{NbDim}(1)+DX*(XIndexMax-1);
-%                         Xbound(1)=Coord{NbDim}(1)+DX*(XIndexMin-1);
-%                     end
                     YIndexRange(1)=ceil(min(YIndexMin,YIndexMax));%first y index to select from the previous field
                     YIndexRange(1)=max(YIndexRange(1),1);% avoid bound lower than the first index
@@ -1461 +1445 @@
                         VarName=FieldData.ListVarName{ivar};
                         if size(FieldData.(VarName),3)==1
-                            ProjData.(VarName)=interp2(X,Y,double(FieldData.(VarName)),XI,YI,'*linear');
+                            ProjData.(VarName)=interp2(X,Y,double(FieldData.(VarName)),XI,YI,'*linear');%interpolation fct
                         else
                             ProjData.(VarName)=interp2(X,Y,double(FieldData.(VarName)(:,:,1)),XI,YI,'*linear');
                             for icolor=2:size(FieldData.(VarName),3)% project 'color' components
-                                ProjData.(VarName)=cat(3,ProjData.(VarName),interp2(X,Y,double(FieldData.(VarName)(:,:,icolor)),XI,YI,'*linear')); %TO TEST
+                                ProjData.(VarName)=cat(3,ProjData.(VarName),interp2(X,Y,double(FieldData.(VarName)(:,:,icolor)),XI,YI,'*linear')); 
                             end
+                        end
+                        if isa(FieldData.(VarName),'uint8')
+                            ProjData.(VarName)=uint8(ProjData.(VarName));%put result to integer 8 bits if the initial field is integer (image)
+                        elseif isa(FieldData.(VarName),'uint16')
+                            ProjData.(VarName)=uint16(ProjData.(VarName));%put result to integer 16 bits if the initial field is integer (image)
                         end
                         ListVarName=[ListVarName VarName];
@@ -1540 +1529 @@
                     eval(['ProjData.' WName '=NormVec_X*ProjData.' UName '+ NormVec_Y*ProjData.' VName '+ NormVec_Z* ProjData.' WName ';']);
                 end
-                %                 if ~isequal(Psi,0)
-                %                     eval(['ProjData.' UName '=cos(Psi)* ProjData.' UName '- sin(Psi)*ProjData.' VName ';']);
-                %                     eval(['ProjData.' VName '=sin(Psi)* ProjData.' UName '+ cos(Psi)*ProjData.' VName ';']);
-                %                 end
             end
         end

trunk/src/uvmat.m

@@ -4120 +4120 @@
 % --- read the data displayed for the input rootfile windows (new): TODO use read_GUI
 %------------------------------------------------------------------------
-function [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles)
+function [RootPath,SubDir,RootFile,FileIndices,FileExt,NomType]=read_file_boxes(handles)
 
 InputFile=read_GUI(handles.InputFile);
@@ -4128 +4128 @@
 FileIndices=InputFile.FileIndex;
 FileExt=InputFile.FileExt;
-
+NomType=InputFile.NomType;
 
 %------------------------------------------------------------------------
@@ -4321 +4321 @@
 
 %----------------------------------------------------------------
-% --- Executes on menu selection FieldName
+% --- Executes on menu selection FieldName_1
 function FieldName_1_Callback(hObject, eventdata, handles)
 %-------------------------------------------------
@@ -4468 +4468 @@
     case 'image'
         %% look for image corresponding to civ data
-        imagename='';
         if  isfield(UvData.Field,'Civ2_ImageA')%get the corresponding input image in the netcdf file
             imagename=UvData.Field.Civ2_ImageA;
@@ -4474 +4473 @@
             imagename=UvData.Field.Civ1_ImageA;
         else
+            [RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
             SubDirBase=regexprep(SubDir,'\..*','');%take the root part of SubDir, before the first dot '.'
-            imagename=fullfile_uvmat(RootPath,SubDirBase,RootFile,'.png',NomType,i1,[],j1,[]);
+            imagename=fullfile_uvmat(RootPath,SubDirBase,RootFile,'.png','_1',i1,[],j1,[]);
         end
         if ~exist(imagename,'file')