Changeset 569

Timestamp:

Feb 19, 2013, 7:19:07 PM (12 years ago)

Author:

sommeria

Message:

many corrections; introduction of browse_data to scan the whole set of data, used also to replicate data in calibration mode

Location:

trunk/src

Files:

• ListDir.m (modified) (1 diff)
• browse_data.fig (added)
• browse_data.m (added)
• fill_GUI.m (modified) (1 diff)
• find_field_cells.m (modified) (2 diffs)
• geometry_calib.m (modified) (5 diffs)
• plot_field.m (modified) (17 diffs)
• proj_field.m (modified) (8 diffs)
• set_object.m (modified) (1 diff)
• update_project.fig (modified) (previous)
• update_project.m (modified) (6 diffs)
• uvmat.fig (modified) (previous)
• uvmat.m (modified) (6 diffs)
• view_field.m (modified) (2 diffs)

trunk/src/ListDir.m

@@ -1 @@
-%'ListDir': scan the structure of the directory tree (for dataview.m)
+%'ListDir': scan the structure of the directory tree (for browse_data.m)
 %------------------------------------------------------------------------
 % function [ListDevices,ListRecords,ListXml,List]=ListDir(CurrentPath,ListExperiments,ListDevices_in,ListRecords_in)

trunk/src/fill_GUI.m

@@ -31 +31 @@
         hh=[];
         input_data=Param.(fields{ifield});
-%                     display(fields{ifield})
-%                     display(input_data)
         check_done=0;
         if isfield(handles,fields{ifield})

trunk/src/find_field_cells.m

@@ -232 +232 @@
     if CoordSize(ilist)==2% case of uniform grid coordinate defined by lower and upper bounds only
         ListDimName{ilist}=ListCoordName{ilist};% replace the dimension name by the coordinate variable name 
-%         if check_var
-%             check_index= strcmp(ListCoordName{ilist},Data.ListDimName);
-%             CoordSize(ilist)=Data.DimValue(check_index);
-%         else
-%             CoordSize(ilist)=numel(Data.(ListCoordName{ilist}));
-% %         end
-%     else
-%         CoordSize(ilist)=DimValue;
     end
 end
@@ -288 +280 @@
 NbDim=[NbDim NewNbDim];
 CellInfo=[CellInfo NewCellInfo];
-
-%% suppress empty cells
-check_empty=cellfun(@isempty,CellInfo);
-%check_empty=cellfun(@isempty,CellVarIndex);
-CellInfo(check_empty)=[];
-
-% CellVarIndex(check_empty)=[];
-NbDim(check_empty)=[];
-% CoordType(check_empty)=[];
-% VarRole(check_empty)=[];
+% 
+% %% suppress empty cells
+% check_empty=cellfun(@isempty,CellInfo);
+% CellInfo(check_empty)=[];
+% NbDim(check_empty)=[];
+
+%% suppress empty cells or cells with a single coordinate variable 
+check_remove=false(size(CellInfo));
+for icell=1:numel(check_remove)
+    if isempty(CellInfo{icell})||(numel(CellInfo{icell}.VarIndex)==1 && check_coord(icell))
+        check_remove(icell)=1;
+    end
+end
+CellInfo(check_remove)=[];
+NbDim(check_remove)=[];
 
 %% document roles of non-coordinate variables

trunk/src/geometry_calib.m

@@ -150 +150 @@
 
 %------------------------------------------------------------------------
-% --- Executes on button press in calibrate_lin.
+% --- Executes on button press APPLY (used to launch the calibration).
 function APPLY_Callback(hObject, eventdata, handles)
 %------------------------------------------------------------------------
@@ -156 +156 @@
 huvmat=findobj(allchild(0),'Name','uvmat');
 hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat
-FileExt=get(hhuvmat.FileExt,'String');
-% check_input=0;
-% if ~isempty(FileExt)
-%     if ~isempty(imformats(FileExt(2:end))) ||strcmpi(FileExt,'.avi')
-%         check_input=1;
-%     end
-% end
-% % if ~check_input
-%     msgbox_uvmat('ERROR','open an image with uvmat to perform calibration')
-%     return
-% end
-
+
+RootPath='';
+if ~isempty(hhuvmat.RootPath)&& ~isempty(hhuvmat.RootFile)
+    RootPath=get(hhuvmat.RootPath,'String');
+    SubDirBase=regexprep(get(hhuvmat.SubDir,'String'),'\..+$','');
+    outputfile=[fullfile(RootPath,SubDirBase) '.xml'];%xml file associated with the currently displayed image
+else
+    question={'save the calibration data and point coordinates in'};
+    def={fullfile(RootPath,'ObjectCalib.xml')};
+    options.Resize='on';
+    answer=inputdlg(question,'',1,def,options);
+    outputfile=answer{1};
+end
+[GeometryCalib,index]=calibrate(handles,hhuvmat);% apply calibration
+
+%% copy the xml file from the old location if appropriate, then update with the calibration parameters
+if ~exist(outputfile,'file') && ~isempty(SubDirBase)
+    oldxml=[fullfile(RootPath,SubDirBase,get(hhuvmat.RootFile,'String')) '.xml'];
+    if exist(oldxml,'file')
+        [success,message]=copyfile(oldxml,outputfile);%copy the old xml file to a new one with the new convention
+    end
+end
+errormsg=update_imadoc(GeometryCalib,outputfile);% introduce the calibration data in the xml file
+if ~strcmp(errormsg,'')
+    msgbox_uvmat('ERROR',errormsg);
+end
+
+%% display image with new calibration in the currently opened uvmat interface
+hhh=findobj(hhuvmat.PlotAxes,'Tag','calib_marker');% delete calib points and markers
+if ~isempty(hhh)
+    delete(hhh);
+end
+hhh=findobj(hhuvmat.PlotAxes,'Tag','calib_points');
+if ~isempty(hhh)
+    delete(hhh);
+end
+set(hhuvmat.CheckFixLimits,'Value',0)% put FixedLimits option to 'off'
+set(hhuvmat.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
+UserData=get(handles.geometry_calib,'UserData');
+UserData.XmlInputFile=outputfile;%save the current xml file name
+set(handles.geometry_calib,'UserData',UserData)
+uvmat('RootPath_Callback',hObject,eventdata,hhuvmat); %file input with xml reading  in uvmat, show the image in phys coordinates
+MenuPlot_Callback(hObject, eventdata, handles)
+set(handles.ListCoord,'Value',index)% indicate in the list the point with max deviation (possible mistake)
+ListCoord_Callback(hObject, eventdata, handles)
+figure(handles.geometry_calib)
+
+%------------------------------------------------------------------------
+% --- Executes on button press in REPLICATE
+function REPLICATE_Callback(hObject, eventdata, handles)
+%------------------------------------------------------------------------
+
+%% look for the GUI uvmat and check for an image as input
+huvmat=findobj(allchild(0),'Name','uvmat');
+hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat
+GeometryCalib=calibrate(handles,hhuvmat);% apply calibration
+
+%% open the GUI browse_data
+CalibData=get(handles.geometry_calib,'UserData');%read the calibration image source on the interface userdata
+if isfield(CalibData,'XmlInputFile')
+    InputDir=fileparts(fileparts(CalibData.XmlInputFile));
+end
+answer=msgbox_uvmat('INPUT_TXT','Campaign to calibrate?',InputDir); 
+if strcmp(answer,'Cancel')
+    return
+end
+OutPut=browse_data(answer);
+nbcalib=0;
+for ilist=1:numel(OutPut.Experiment)
+    SubDirBase=regexprep(OutPut.Device{1},'\..+$','');
+    XmlName=fullfile(OutPut.Campaign,OutPut.Experiment{ilist},[SubDirBase '.xml']);
+    % copy the xml file from the old location if appropriate, then update with the calibration parameters
+    if ~exist(XmlName,'file') && ~isempty(SubDirBase)
+        oldxml=fullfile(OutPut.Campaign,OutPut.Experiment{ilist},SubDirBase,[get(hhuvmat.RootFile,'String') '.xml']);
+        if exist(oldxml,'file')
+            [success,message]=copyfile(oldxml,XmlName);%copy the old xml file to a new one with the new convention
+        end
+    end
+    errormsg=update_imadoc(GeometryCalib,XmlName);% introduce the calibration data in the xml file
+    if ~strcmp(errormsg,'')
+        msgbox_uvmat('ERROR',errormsg);
+    else
+        display([XmlName ' updated with calibration parameters'])
+        nbcalib=nbcalib+1;
+    end
+end
+msgbox_uvmat('CONFIMATION',[SubDirBase ' calibrated for ' num2str(nbcalib) ' experiments']);
+
+%------------------------------------------------------------------------
+% --- activate calibration and store parameters in ouputfile .
+function [GeometryCalib,index]=calibrate(handles,hhuvmat)
+%------------------------------------------------------------------------
 %% read the current calibration points
 Coord_cell=get(handles.ListCoord,'String');
@@ -220 +300 @@
 
 %% store the calibration data, by default in the xml file of the currently displayed image
-UvData=get(huvmat,'UserData');
+UvData=get(hhuvmat.uvmat,'UserData');
 NbSlice_j=1;%default
 ZStart=Z_plane;
@@ -233 +313 @@
     end
 end
-RootPath='';
-% RootFile='';
-if ~isempty(hhuvmat.RootPath)&& ~isempty(hhuvmat.RootFile)
-    RootPath=get(hhuvmat.RootPath,'String');
-    SubDirBase=regexprep(get(hhuvmat.SubDir,'String'),'\..+$','');
-    outputfile=[fullfile(RootPath,SubDirBase) '.xml'];%xml file associated with the currently displayed image
-else
-    SubDirBase='';
-    question={'save the calibration data and point coordinates in'};
-    def={fullfile(RootPath,'ObjectCalib.xml')};
-    options.Resize='on';
-    answer=inputdlg(question,'save average in a new file',1,def,options);
-    outputfile=answer{1};
-end
-answer=msgbox_uvmat('INPUT_Y-N',{[outputfile ' updated with calibration data'];...
+
+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']});
 
-%% record the calibration parameters and display the current image of uvmat in the new phys coordinates
-if strcmp(answer,'Yes')
-    if strcmp(calib_cell{val}(1:2),'3D')%set the plane position for 3D (projection) calibration
-       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');
-        %answer_1=msgbox_uvmat('INPUT_TXT',' Z= ',num2str(Z_plane)); 
-        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
-    UserData=get(handles.geometry_calib,'UserData');
-    
-    % get the timing from the xml file using the old convention if appropriate
-    if ~exist(outputfile,'file') && ~isempty(SubDirBase)     
-        oldxml=[fullfile(RootPath,SubDirBase,get(hhuvmat.RootFile,'String')) '.xml'];
-        if exist(oldxml,'file')
-        [success,message]=copyfile(oldxml,outputfile);%copy the old xml file to a new one with the new convention
-        end
-    end   
-    errormsg=update_imadoc(GeometryCalib,outputfile);% introduce the calibration data in the xml file
-    if ~strcmp(errormsg,'')
-        msgbox_uvmat('ERROR',errormsg);
-    end
-    
-    %display image with new calibration in the currently opened uvmat interface
-    hhh=findobj(hhuvmat.PlotAxes,'Tag','calib_marker');% delete calib points and markers
-    if ~isempty(hhh)
-        delete(hhh);      
-    end
-    hhh=findobj(hhuvmat.PlotAxes,'Tag','calib_points');
-    if ~isempty(hhh)
-        delete(hhh);
-    end
-    set(hhuvmat.CheckFixLimits,'Value',0)% put FixedLimits option to 'off'
-    set(hhuvmat.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
-    
-    UserData.XmlInputFile=outputfile;%save the current xml file name
-    set(handles.geometry_calib,'UserData',UserData)
-    uvmat('RootPath_Callback',hObject,eventdata,hhuvmat); %file input with xml reading  in uvmat, show the image in phys coordinates
-    MenuPlot_Callback(hObject, eventdata, handles)
-    set(handles.ListCoord,'Value',index)% indicate in the list the point with max deviation (possible mistake)
-    ListCoord_Callback(hObject, eventdata, handles)
-    figure(handles.geometry_calib)
-end
-
-%------------------------------------------------------------------
-% --- Executes on button press in calibrate_lin.
-
-function REPLICATE_Callback(hObject, eventdata, handles)
-%------------------------------------------------------------------------
-
-%% Apply calibration
-calib_cell=get(handles.calib_type,'String'); %#ok<NASGU>
-val=get(handles.calib_type,'Value'); %#ok<NASGU>
-
-%read the current calibration points
-Coord_cell=get(handles.ListCoord,'String');
-Object=read_geometry_calib(Coord_cell);
-Coord=Object.Coord;
-
-% apply the calibration, whose type is selected in  handles.calib_type
-if ~isempty(Coord)
-    calib_cell=get(handles.calib_type,'String');
-    val=get(handles.calib_type,'Value');
-    GeometryCalib=feval(['calib_' calib_cell{val}],Coord,handles);
-else
-    msgbox_uvmat('ERROR','No calibration points, abort')
+%% get plane position(s)
+if ~strcmp(answer,'Yes')
     return
-end 
-
-if ~isempty(Coord)
-    %check error
-    X=Coord(:,1);
-    Y=Coord(:,2);
-    Z=Coord(:,3);
-    x_ima=Coord(:,4);
-    y_ima=Coord(:,5);
-    [Xpoints,Ypoints]=px_XYZ(GeometryCalib,X,Y,Z);
-    GeometryCalib.ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(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)]=max(abs(Ypoints-y_ima));
-%     [EM,ind_dim]=max(GeometryCalib.ErrorMax);
-    %set the Z position of the reference plane used for calibration
-    Z_plane=[];
-    if isequal(max(Z),min(Z))
-        Z_plane=Z(1);
-    end
-    answer_1=msgbox_uvmat('INPUT_TXT',' Z= ',num2str(Z_plane)); 
-    Z_plane=str2double(answer_1);
-    GeometryCalib.NbSlice=1;
-    GeometryCalib.SliceCoord=[0 0 Z_plane];
-    %set the coordinate unit
-    unitlist=get(handles.CoordUnit,'String');
-    unit=unitlist{get(handles.CoordUnit,'value')};
-    GeometryCalib.CoordUnit=unit;
-    %record the points
-    GeometryCalib.SourceCalib.PointCoord=Coord;
-end
-
-%% display calibration paprameters
-display_intrinsic(GeometryCalib,handles)%display calibration intrinsic parameters
-
-% Display extrinsinc parameters (rotation and translation of camera with  respect to the phys coordiantes)
-set(handles.Tx,'String',num2str(GeometryCalib.Tx_Ty_Tz(1),4))
-set(handles.Ty,'String',num2str(GeometryCalib.Tx_Ty_Tz(2),4))
-set(handles.Tz,'String',num2str(GeometryCalib.Tx_Ty_Tz(3),4))
-set(handles.Phi,'String',num2str(GeometryCalib.omc(1),4))
-set(handles.Theta,'String',num2str(GeometryCalib.omc(2),4))
-set(handles.Psi,'String',num2str(GeometryCalib.omc(3),4))
-
-%% open the GUI dataview 
-h_dataview=findobj(allchild(0),'name','dataview');
-if ~isempty(h_dataview)
-    delete(h_dataview)
-end
-CalibData=get(handles.geometry_calib,'UserData');%read the calibration image source on the interface userdata
-% InputFile='';
-if isfield(CalibData,'XmlInputFile')
-    InputDir=fileparts(CalibData.XmlInputFile);
-    [InputDir,DirName]=fileparts(InputDir);
-end
-SubCampaignTest='n'; %default
-testup=0;
-if isfield(CalibData,'SubCampaign')
-    SubCampaignTest='y';
-    dir_ref=CalibData.SubCampaign;
-    testup=1;
-elseif isfield(CalibData,'Campaign')
-    dir_ref=CalibData.Campaign;
-    testup=1;
-end
-while testup
-    [InputDir,DirName]=fileparts(InputDir);
-    if strcmp(DirName,dir_ref)
-        break
-    end
-end
-InputDir=fullfile(InputDir,DirName);
-answer=msgbox_uvmat('INPUT_TXT','Campaign ?',InputDir); 
-if strcmp(answer,'Cancel')
-    return
-end
-
-dataview(answer,SubCampaignTest,GeometryCalib);
+end
+if strcmp(calib_cell{val}(1:2),'3D')%set the plane position for 3D (projection) calibration
+    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
+
+
 
 %------------------------------------------------------------------------
@@ -456 +391 @@
 GeometryCalib.R=[R [0;0;-epsilon]];
 GeometryCalib.omc=(180/pi)*[acos(GeometryCalib.R(1,1)) 0 0];
+
 %------------------------------------------------------------------------
 % determine the tsai parameters for a view normal to the grid plane

trunk/src/plot_field.m

@@ -102 +102 @@
 if ~exist('PlotParam','var'),PlotParam=[];end;
 PlotType='text'; %default
-PlotParamOut=PlotParam;%default
 if ~isfield(PlotParam,'Coordinates')
     PlotParam.Coordinates=[];
 end
+PlotParamOut=PlotParam;%default
 
 %% check input structure
@@ -152 +152 @@
     haxes=axes;
     set(haxes,'position',[0.13,0.2,0.775,0.73])
-    PlotParam.NextPlot='add'; %parameter for plot_profile and plot_his
+    PlotParamOut.NextPlot='add'; %parameter for plot_profile 
 else
     hfig=get(haxes,'parent');
@@ -160 +160 @@
 
 %% set axes properties
-if isfield(PlotParam.Coordinates,'CheckFixLimits') && isequal(PlotParam.Coordinates.CheckFixLimits,1)  %adjust the graph limits
+if isfield(PlotParamOut.Coordinates,'CheckFixLimits') && isequal(PlotParamOut.Coordinates.CheckFixLimits,1)  %adjust the graph limits
     set(haxes,'XLimMode', 'manual')
     set(haxes,'YLimMode', 'manual')
@@ -171 +171 @@
 % end
 errormsg='';
-PlotParamOut.Coordinates=[]; %default output 
+%PlotParamOut.Coordinates=[]; %default output 
 AxeData=get(haxes,'UserData');
 
@@ -179 +179 @@
 else  %plot 2D field
     if ~exist('PosColorbar','var'),PosColorbar=[];end;
-    [tild,PlotParamOut,PlotType,errormsg]=plot_plane(Data,CellInfo(index_2D),haxes,PlotParam,PosColorbar);
+    [tild,PlotParamOut,PlotType,errormsg]=plot_plane(Data,CellInfo(index_2D),haxes,PlotParamOut,PosColorbar);
     AxeData.NbDim=2;
     if testzoomaxes && isempty(errormsg)
-        [zoomaxes,PlotParamOut,tild,errormsg]=plot_plane(Data,CellInfo(index_2D),zoomaxes,PlotParam,PosColorbar);
+        [zoomaxes,PlotParamOut,tild,errormsg]=plot_plane(Data,CellInfo(index_2D),zoomaxes,PlotParamOut,PosColorbar);
         AxeData.ZoomAxes=zoomaxes;
     end
@@ -193 +193 @@
     end
 else %plot 1D field (usual graph y vs x)
-    Coordinates=plot_profile(Data,CellInfo(index_1D),haxes,PlotParam.Coordinates);%
+    PlotParamOut.Coordinates=plot_profile(Data,CellInfo(index_1D),haxes,PlotParamOut.Coordinates);%
     if testzoomaxes
-        [zoomaxes,Coordinates]=plot_profile(Data,CellInfo(index_1D),zoomaxes,PlotParam.Coordinates);
+        [zoomaxes,PlotParamOut.Coordinates]=plot_profile(Data,CellInfo(index_1D),zoomaxes,PlotParamOut.Coordinates);
         AxeData.ZoomAxes=zoomaxes;
     end
-    if ~isempty(Coordinates)
-        PlotParamOut.Coordinates=Coordinates;
-    end
+%     if ~isempty(Coordinates)
+%         PlotParamOut.Coordinates=Coordinates;
+%     end
     PlotType='line';
 end
@@ -231 +231 @@
 %     AxeData=[];
     if isfield(PlotParamOut,'MinX')
-        AxeData.RangeX=[PlotParamOut.MinX PlotParamOut.MaxX];%'[PlotParamOut.MinX PlotParamOut.MaxX];
-        AxeData.RangeY=[PlotParamOut.MinY PlotParamOut.MaxY];%[PlotParamOut.MinY PlotParamOut.MaxY]
+        AxeData.RangeX=[PlotParamOut.MinX PlotParamOut.MaxX];
+        AxeData.RangeY=[PlotParamOut.MinY PlotParamOut.MaxY];
     end
     set(haxes,'UserData',AxeData)
@@ -359 +359 @@
 ytitle='';
 test_newplot=1;
-
+MinX=[];
+MaxX=[];
+MinY_cell=[];
+MaxY_cell=[];
 %loop on input  fields
 for icell=1:numel(CellInfo)
@@ -367 +370 @@
     coord_x_name{icell}=data.ListVarName{coord_x_index};
     coord_x{icell}=data.(data.ListVarName{coord_x_index});%coordinate variable set as coord_x
-    if isempty(find(strcmp(coord_x_name{icell},coord_x_name(1:end-1)))) %xtitle not already selected
+    if isempty(find(strcmp(coord_x_name{icell},coord_x_name(1:end-1)), 1)) %xtitle not already selected
         xtitle=[xtitle coord_x_name{icell}];
         if isfield(data,'VarAttribute')&& numel(data.VarAttribute)>=coord_x_index && isfield(data.VarAttribute{coord_x_index},'units')
@@ -375 +378 @@
         end
     end
-    XMin(icell)=min(coord_x{icell});
-    XMax(icell)=max(coord_x{icell});
+    MinX(icell)=min(coord_x{icell});
+    MaxX(icell)=max(coord_x{icell});
     testplot(coord_x_index)=0;
     if isfield(CellInfo{icell},'VarIndex_ancillary')
@@ -399 +402 @@
         charplot_0='''-''';
     end
-    YMin=0;
-    YMax=1;%default
+    MinY=[];
+    MaxY=[];%default
+    
+    nbplot=0;
     for ivar=1:length(VarIndex)
         if testplot(VarIndex(ivar))
             VarName=data.ListVarName{VarIndex(ivar)};
+            nbplot=nbplot+1;
             ytitle=[ytitle VarName];
             if isfield(data,'VarAttribute')&& numel(data.VarAttribute)>=VarIndex(ivar) && isfield(data.VarAttribute{VarIndex(ivar)},'units')
@@ -412 +418 @@
             eval(['data.' VarName '=squeeze(data.' VarName ');'])
             %eval(['min(data.' VarName ')'])
-            YMin(ivar)=min(min(data.(VarName)));
-            YMax(ivar)=max(max(data.(VarName)));
+            MinY(ivar)=min(min(data.(VarName)));
+            MaxY(ivar)=max(max(data.(VarName)));
             plotstr=[plotstr 'coord_x{' num2str(icell) '},data.' VarName ',' charplot_0 ','];
             eval(['nbcomponent2=size(data.' VarName ',2);']);
@@ -429 +435 @@
         end
     end
-    YMin_cell(icell)=min(YMin);
-    YMax_cell(icell)=max(YMax);
+    if ~isempty(MinY)
+    MinY_cell(icell)=min(MinY);
+    MaxY_cell(icell)=max(MaxY);
+    end
 end
 
@@ -478 +486 @@
     end
     htitle=title(title_str);
-%     txt=ver('MATLAB');
-%     Release=txt.Release;
-%     relnumb=str2double(Release(3:4));
-%     if relnumb >= 14
     set(htitle,'Interpreter','none')% desable tex interpreter
-%     end
 end
 
 %% determine axes bounds
-%CoordinatesOut.RangeX=[min(XMin) max(XMax)];
-%CoordinatesOut.RangeY=[min(YMin_cell) max(YMax_cell)];
 fix_lim=isfield(Coordinates,'CheckFixLimits') && Coordinates.CheckFixLimits;
+check_lim=isfield(Coordinates,'MinX')&&isfield(Coordinates,'MaxX')&&isfield(Coordinates,'MinY')&&isfield(Coordinates,'MaxY');
 if fix_lim
-    if ~isfield(Coordinates,'MinX')||~isfield(Coordinates,'MaxX')||~isfield(Coordinates,'MinY')||~isfield(Coordinates,'MaxY')
-        fix_lim=0; %free limits if lits are not set,
+    if ~check_lim
+        fix_lim=0; %free limits if limits are not set,
     end 
 end
@@ -498 +500 @@
     set(haxes,'XLim',[Coordinates.MinX Coordinates.MaxX])
     set(haxes,'YLim',[Coordinates.MinY Coordinates.MaxY])
-else    
-    CoordinatesOut.MinX=min(XMin);
-    CoordinatesOut.MaxX=max(XMax);
-    CoordinatesOut.MinY=min(YMin_cell);
-    CoordinatesOut.MaxY=max(YMax_cell);
+else
+    if ~isempty(MinX)
+        if check_lim
+            CoordinatesOut.MinX=min(min(MinX),CoordinatesOut.MinX);
+            CoordinatesOut.MaxX=max(max(MaxX),CoordinatesOut.MaxX);
+        else
+            CoordinatesOut.MinX=min(MinX);
+            CoordinatesOut.MaxX=max(MaxX);
+        end
+    end
+    if ~isempty(MinY_cell)
+        if check_lim
+            CoordinatesOut.MinY=min(min(MinY_cell),CoordinatesOut.MinY);
+            CoordinatesOut.MaxY=max(max(MaxY_cell),CoordinatesOut.MaxY);
+        else
+            CoordinatesOut.MinY=min(MinY_cell);
+            CoordinatesOut.MaxY=max(MaxY_cell);
+        end
+    end
 end
 
@@ -791 +807 @@
         PlotParamOut.Scalar.MinA=MinA;
         PlotParamOut.Scalar.MaxA=MaxA;
+        PlotParamOut.Scalar.Npx=size(A,2);
+        PlotParamOut.Scalar.Npy=size(A,1);
         % case of contour plot
         if CheckContour
@@ -1089 +1107 @@
 %store the coordinate extrema occupied by the field
 if ~isempty(Data)
-    XMin=[];
-    XMax=[];
-    YMin=[];
-    YMax=[];
+    MinX=[];
+    MaxX=[];
+    MinY=[];
+    MaxY=[];
     fix_lim=isfield(PlotParam.Coordinates,'CheckFixLimits') && PlotParam.Coordinates.CheckFixLimits;
     if fix_lim
         if isfield(PlotParam.Coordinates,'MinX')&&isfield(PlotParam.Coordinates,'MaxX')&&isfield(PlotParam.Coordinates,'MinY')&&isfield(PlotParam.Coordinates,'MaxY')
-            XMin=PlotParam.Coordinates.MinX;
-            XMax=PlotParam.Coordinates.MaxX;
-            YMin=PlotParam.Coordinates.MinY;
-            YMax=PlotParam.Coordinates.MaxY;
-        end  %else PlotParamOut.XMin =PlotParam.XMin...
+            MinX=PlotParam.Coordinates.MinX;
+            MaxX=PlotParam.Coordinates.MaxX;
+            MinY=PlotParam.Coordinates.MinY;
+            MaxY=PlotParam.Coordinates.MaxY;
+        end  %else PlotParamOut.MinX =PlotParam.MinX...
     else
         if test_ima %both background image and vectors coexist, take the wider bound
-            XMin=min(AX);
-            XMax=max(AX);
-            YMin=min(AY);
-            YMax=max(AY);
+            MinX=min(AX);
+            MaxX=max(AX);
+            MinY=min(AY);
+            MaxY=max(AY);
             if test_vec
-                XMin=min(XMin,min(vec_X));
-                XMax=max(XMax,max(vec_X));
-                YMin=min(YMin,min(vec_Y));
-                YMax=max(YMax,max(vec_Y));
+                MinX=min(MinX,min(vec_X));
+                MaxX=max(MaxX,max(vec_X));
+                MinY=min(MinY,min(vec_Y));
+                MaxY=max(MaxY,max(vec_Y));
             end
         elseif test_vec
-            XMin=min(vec_X);
-            XMax=max(vec_X);
-            YMin=min(vec_Y);
-            YMax=max(vec_Y);
-        end
-    end
-    PlotParamOut.Coordinates.MinX=XMin;
-    PlotParamOut.Coordinates.MaxX=XMax;
-    PlotParamOut.Coordinates.MinY=YMin;
-    PlotParamOut.Coordinates.MaxY=YMax;
-    if XMax>XMin
-        set(haxes,'XLim',[XMin XMax]);% set x limits of frame in axes coordinates
-    end
-    if YMax>YMin
-        set(haxes,'YLim',[YMin YMax]);% set x limits of frame in axes coordinates
+            MinX=min(vec_X);
+            MaxX=max(vec_X);
+            MinY=min(vec_Y);
+            MaxY=max(vec_Y);
+        end
+    end
+    PlotParamOut.Coordinates.MinX=MinX;
+    PlotParamOut.Coordinates.MaxX=MaxX;
+    PlotParamOut.Coordinates.MinY=MinY;
+    PlotParamOut.Coordinates.MaxY=MaxY;
+    if MaxX>MinX
+        set(haxes,'XLim',[MinX MaxX]);% set x limits of frame in axes coordinates
+    end
+    if MaxY>MinY
+        set(haxes,'YLim',[MinY MaxY]);% set x limits of frame in axes coordinates
     end
     set(haxes,'YDir','normal')

trunk/src/proj_field.m

@@ -887 +887 @@
 
 %% mesh sizes DX and DY
+DX=[];
+DY=[];%default
 if isfield(ObjectData,'DX') && ~isempty(ObjectData.DX)
      DX=abs(ObjectData.DX);%mesh of interpolation points 
-else
-    DX=FieldData.Mesh;
+% else
+%     DX=FieldData.Mesh;
 end
 if isfield(ObjectData,'DY') && ~isempty(ObjectData.DY)
      DY=abs(ObjectData.DY);%mesh of interpolation points 
-else
-    DY=FieldData.Mesh;
-end
-if  ~strcmp(ObjectData.ProjMode,'projection') && (DX==0||DY==0)
-        errormsg='DX or DY missing';
-        display(errormsg)
+% else
+%     DY=FieldData.Mesh;
+end
+if  ~strcmp(ObjectData.ProjMode,'projection') && (isempty(DX)||isempty(DY))
+        errormsg='DX or DY not defined';
         return
 end
@@ -913 +914 @@
         XMax=max(ObjectData.RangeX);
         testXMin=XMax>XMin;
-        testXMax=1;
+        testXMax=1;% range restriction along X
 else
     XMin=FieldData.XMin;%default
@@ -960 +961 @@
 ProjData.VarDimName={};
 ProjData.VarAttribute={};
-if ~isequal(DX,0)&& ~isequal(DY,0)
+if ~isempty(DX) && ~isempty(DY)
     ProjData.Mesh=sqrt(DX*DY);%define typical data mesh, useful for mouse selection in plots
 elseif isfield(FieldData,'Mesh')
@@ -1234 +1235 @@
             
             %% case of input fields defined on a structured  grid
-        case 'grid'
-            
+        case 'grid'         
             VarName=FieldData.ListVarName{VarIndex(1)};%get the first variable of the cell to get the input matrix dimensions
             DimValue=size(FieldData.(VarName));%input matrix dimensions
@@ -1275 +1275 @@
             Coord_z=[];
             Coord_y=[];
-            Coord_x=[];
-            
+            Coord_x=[];      
             for idim=1:NbDim %loop on space dimensions
                 test_interp(idim)=0;%test for coordiate interpolation (non regular grid), =0 by default
@@ -1302 +1301 @@
                 end
             end
-            if DY==0
+            if isempty(DY)
                 DY=abs(DCoord_min(NbDim-1));
             end
             npY=1+round(abs(Coord{NbDim-1}(end)-Coord{NbDim-1}(1))/DY);%nbre of points after interpol
-            if DX==0
+            if isempty(DX)
                 DX=abs(DCoord_min(NbDim));
             end
@@ -1369 +1368 @@
                 coord_x_proj=linspace(XMax,XMin,npX);%abscissa of the new pixels along the line
             end
-            % case with no  interpolation
+            % case with no interpolation
             if isequal(ProjMode{icell},'projection') && (~testangle || test90y || test90x)
-                if  NbDim==2 && ~testXMin && ~testXMax && ~testYMin && ~testYMax
+                if  NbDim==2 && ~testXMin && ~testXMax && ~testYMin && ~testYMax% no range restriction
                     ProjData.ListVarName=[ProjData.ListVarName FieldData.ListVarName(VarIndex)];
                     ProjData.VarDimName=[ProjData.VarDimName FieldData.VarDimName(VarIndex)];  
@@ -1408 +1407 @@
                     end
                     min_indy=max(min_indy,1);% deals with margin (bound lower than the first index)
-                    min_indx=max(min_indx,1);
-                    
+                    min_indx=max(min_indx,1);                  
                     if test90y
                         ind_new=[3 2 1];
                         DimCell={AYProjName,AXProjName};
-                        %                     DimValue=DimValue(ind_new);
                         iz=ceil((ObjectData.Coord(1,1)-Coord{3}(1))/DX)+1;
                         for ivar=VarIndex

trunk/src/set_object.m

@@ -504 +504 @@
             hhview_field=guidata(hview_field);
             [PlotType,PlotParam]=plot_field(ProjData,hhview_field.PlotAxes,read_GUI(hview_field));%update an existing  plot in view_field
-            write_plot_param(hhview_field,PlotParam); %update the display of plotting parameters for the current object
+            errormsg=fill_GUI(PlotParam,hhview_field);
+            if ~isempty(errormsg)
+                msgbox_uvmat('ERROR',errormsg)
+                return
+            end
+       %     write_plot_param(hhview_field,PlotParam); %update the display of plotting parameters for the current object
         end
         haxes=findobj(hview_field,'tag','axes3');

trunk/src/update_project.m

@@ -22 +22 @@
 function varargout = update_project(varargin)
 
-% Last Modified by GUIDE v2.5 01-Jul-2012 15:47:48
+% Last Modified by GUIDE v2.5 15-Feb-2013 19:22:23
 
 % Begin initialization code - DO NOT EDIT
@@ -45 +45 @@
 %------------------------------------------------------------------------
 % --- Executes just before update_project is made visible.
-function update_project_OpeningFcn(hObject, eventdata, handles, RootDir, SubCampaignTst,GeometryCalib)
+function update_project_OpeningFcn(hObject, eventdata, handles, RootXml, SubCampaignTst,GeometryCalib)
 %------------------------------------------------------------------------
 % Choose default command line output for update_project
@@ -94 +94 @@
    set(handles.SubCampaignTest,'Value',1);
 end
-if exist('RootDir','var') 
-   set(handles.SourceDir,'String',RootDir);
-   set(handles.clean_civ_cmx,'Visible','off')
+if exist('RootXml','var') 
+    RootDir=fileparts(RootXml);
+    [s,Heading]=xml2struct(RootXml);%read the xml file
+    if isfield(s,'SourceDir')
+        set(handles.SourceDir,'String',s.SourceDir);%display the source dir if a mirror has been opened
+        set(handles.MirrorDir,'String',RootDir);%display the opened mirror dir
+        set(handles.CreateMirror,'String','update_mirror')
+    else %a source dir has been opened
+        set(handles.SourceDir,'String',RootDir);
+        set(handles.CreateMirror,'String','create_mirror')
+    end
+    SourceDir_Callback([],[], handles)
+ %  set(handles.clean_civ_cmx,'Visible','off')
    set(handles.edit_xml,'Visible','off')
    set(handles.HELP,'Visible','off')
@@ -104 +114 @@
    set(hObject,'Visible','on')
    drawnow
-   RootDirectory_Callback(hObject, eventdata, handles)
+%    RootDirectory_Callback(hObject, eventdata, handles)
    % UIWAIT makes translate_points wait for user response (see UIRESUME)
    uiwait(handles.figure);
@@ -198 +208 @@
                 idir=idir+1;
                 ExpName{idir}=hdir(ilist).name;
-                mirror=fullfile(MirrorDir,ExpName{idir})
+                mirror=fullfile(MirrorDir,ExpName{idir});
                 if ~exist(mirror,'dir')
                    mkdir(mirror)
@@ -818 +828 @@
     uiresume(handles.figure);
 end 
-
-
-

trunk/src/uvmat.m

@@ -334 +334 @@
 function MenuBrowse_Callback(hObject, eventdata, handles)
 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
-%oldfile=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
 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
@@ -352 +351 @@
 %% display the selected field and related information
 display_file_name( handles,fileinput)
+
+% -----------------------------------------------------------------------
+% --- Executes on the menu Open/Browse campaign...
+% search the file inside a campaign, using the GUI view_data
+function MenuBrowseCampaign_Callback(hObject, eventdata, handles)
+% -----------------------------------------------------------------------
+CampaignPath=fileparts(fileparts(get(handles.RootPath,'String')));
+DirFull = uigetdir(CampaignPath,'Select a Campaign dir, then press OK');
+if ~ischar(DirFull)|| ~exist(DirFull,'dir')
+    return
+end
+OutPut=browse_data(DirFull);% open the GUI browse_data to get select a campaign dir, experiment and device
+if ~isfield(OutPut,'Campaign')
+    return
+end
+DirName=fullfile(OutPut.Campaign,OutPut.Experiment{1},OutPut.Device{1});
+hdir=dir(DirName); %list files and dirs
+for ilist=1:numel(hdir)
+    if ~isequal(hdir(ilist).isdir,1)%look for files, not dir
+        FileName=hdir(ilist).name;
+        FileType=get_file_type(fullfile(DirName,FileName));
+        switch FileType
+            case {'image','multimage','civx','civdata','netcdf'}
+            break
+        end
+    end
+end
+
+%% display the selected field and related information
+display_file_name( handles,fullfile(DirName,FileName))
 
 % -----------------------------------------------------------------------
@@ -432 +461 @@
     end
 end
+
+% --------------------------------------------------------------------
+function MenuBrowseCampaign_1_Callback(hObject, eventdata, handles)
+% -----------------------------------------------------------------------
+CampaignPath=fileparts(fileparts(get(handles.RootPath,'String')));
+DirFull = uigetdir(CampaignPath,'Select a Campaign dir, then press OK');
+if ~ischar(DirFull)|| ~exist(DirFull,'dir')
+    return
+end
+OutPut=browse_data(DirFull);% open the GUI browse_data to get select a campaign dir, experiment and device
+if ~isfield(OutPut,'Campaign')
+    return
+end
+DirName=fullfile(OutPut.Campaign,OutPut.Experiment{1},OutPut.Device{1});
+hdir=dir(DirName); %list files and dirs
+for ilist=1:numel(hdir)
+    if ~isequal(hdir(ilist).isdir,1)%look for files, not dir
+        FileName=hdir(ilist).name;
+        FileType=get_file_type(fullfile(DirName,FileName));
+        switch FileType
+            case {'image','multimage','civx','civdata','netcdf'}
+            break
+        end
+    end
+end
+
+%% display the selected field and related information
+set(handles.SubField,'Value',1)
+display_file_name( handles,fullfile(DirName,FileName),2)
 
 % -----------------------------------------------------------------------
@@ -2623 +2681 @@
             ObjectData.A=flag_mask.*double(ObjectData.A);
             ObjectData.A=feval(AClass,ObjectData.A);
-%             ind_off=[];
-%             if isfield(ObjectData,'ListVarName')
-%                 for ilist=1:length(ObjectData.ListVarName)
-%                     if isequal(ObjectData.ListVarName{ilist},'Mask')||isequal(ObjectData.ListVarName{ilist},'MaskX')||isequal(ObjectData.ListVarName{ilist},'MaskY')
-%                         ind_off=[ind_off ilist];
-%                     end
-%                 end
-%                 ObjectData.ListVarName(ind_off)=[];
-%                 VarDimIndex(ind_off)=[];
-%                 ind_off=[];
-%              
-%             end
         end
         if ~isempty(ObjectData)
-            PlotType='none'; %default
+            %PlotType='none'; %default
             if imap==2 && isempty(view_field_handle)
                 view_field(ObjectData)
@@ -4947 +4993 @@
 end
 
-
-% --------------------------------------------------------------------
-function MenuSetProject_Callback(hObject, eventdata, handles)
-RootPath=get(handles.RootPath,'String');
-ProjectDir = uigetdir(fileparts(fileparts(RootPath)), 'select the project source directory');
-datatree_browser(ProjectDir)
-
-
-% --------------------------------------------------------------------
-function MenuBrowseProject_Callback(hObject, eventdata, handles)
-RootPath=get(handles.RootPath,'String');
-ProjectDir = uigetdir(fileparts(fileparts(RootPath)), 'select the project directory');
-datatree_browser(ProjectDir)
-
-
 % --- Executes on selection change in Coord_y.
 function Coord_y_Callback(hObject, eventdata, handles)
@@ -4971 +5002 @@
 % --- Executes on button press in CheckColorBar.
 function CheckColorBar_Callback(hObject, eventdata, handles)
-% hObject    handle to CheckColorBar (see GCBO)
-% eventdata  reserved - to be defined in a future version of MATLAB
-% handles    structure with handles and user data (see GUIDATA)
-
-% Hint: get(hObject,'Value') returns toggle state of CheckColorBar
-

trunk/src/view_field.m

@@ -83 +83 @@
         set(handles.Vectors,'Visible','on')
     end
-    write_plot_param(handles,PlotParamOut);% update the display of the plotting parameters
+    errormsg=fill_GUI(PlotParamOut,handles);
+    if ~isempty(errormsg)
+        msgbox_uvmat('ERROR',errormsg)
+        return
+    end
+    %write_plot_param(handles,PlotParamOut);% update the display of the plotting parameters
 end
 
@@ -775 +780 @@
 PlotParam=read_GUI(handles.view_field);
 [PP,PlotParamOut]= plot_field(AxeData,handles.PlotAxes,PlotParam);
-write_plot_param(handles,PlotParamOut); %update the auto plot parameters
+errormsg=fill_GUI(PlotParamOut,handles);
+    if ~isempty(errormsg)
+        msgbox_uvmat('ERROR',errormsg)
+        return
+    end
+%write_plot_param(handles,PlotParamOut); %update the auto plot parameters
 
 %------------------------------------------------------------------------