Changeset 693 for trunk

Timestamp:

Oct 29, 2013, 12:28:57 PM (11 years ago)

Author:

sommeria

Message:

bug repaired geometry_calib/Detect grid, + corrections in get_field

Location:

trunk/src

Files:

• geometry_calib.fig (modified) (previous)
• geometry_calib.m (modified) (10 diffs)
• get_field.fig (modified) (previous)
• get_field.m (modified) (11 diffs)
• mouse_motion.m (modified) (1 diff)
• nc2struct.m (modified) (5 diffs)
• read_field.m (modified) (1 diff)
• uvmat.m (modified) (2 diffs)

trunk/src/geometry_calib.m

@@ -50 +50 @@
 % Edit the above text to modify the response to help geometry_calib
 
-% Last Modified by GUIDE v2.5 02-Sep-2013 16:47:27
+% Last Modified by GUIDE v2.5 29-Oct-2013 06:46:10
 
 % Begin initialization code - DO NOT edit
@@ -114 +114 @@
 set(handles.Copy,'Position',[151 Height-394 120 30])%  rank 6
 set(handles.CLEAR_PTS,'Position',[297 Height-394 120 30])%  rank 6
+set(handles.ClearLine,'Position',[297 Height-364 120 30])%  rank 6
 set(handles.phys_title,'Position',[38 Height-426 125 20])%  rank 7
 set(handles.CoordUnit,'Position',[151 Height-426 120 30])%  rank 7
@@ -230 +231 @@
     Data=get(handles.ListCoord,'Data');
     Data(:,6)=zeros(size(Data,1),1);
-    Data(index,6)=1;% indicate in the list the point with max deviation (possible mistake)
+    Data(index,6)=-1;% indicate in the list the point with max deviation (possible mistake)
     set(handles.ListCoord,'Data',Data)% indicate in the list the point with max deviation (possible mistake)
     figure(handles.geometry_calib)
@@ -881 +882 @@
 huvmat=findobj(allchild(0),'Name','uvmat');
 UvData=get(huvmat,'UserData');
-A=UvData.Field.A;
+A=UvData.Field.A;%currently displayed image
 npxy=size(A);
 X=[CalibData.grid.x_0 CalibData.grid.x_1 CalibData.grid.x_0 CalibData.grid.x_1]';%corner absissa in the phys coordinates (cm)
 Y=[CalibData.grid.y_0 CalibData.grid.y_0 CalibData.grid.y_1 CalibData.grid.y_1]';%corner ordinates in the phys coordinates (cm)
 
-%calculate transform matrices for plane projection
+%calculate transform matrices for plane projection: rectangle assumed to be viewed in perspective
 % reference: http://alumni.media.mit.edu/~cwren/interpolator/ by Christopher R. Wren
 B = [ X Y ones(size(X)) zeros(4,3)        -X.*corners_X -Y.*corners_X ...
@@ -898 +899 @@
 
 % transform grid image into 'phys' coordinates 
-GeometryCalib.CalibrationType='linear';
+GeometryCalib.CalibrationType='3D_linear';
 GeometryCalib.fx_fy=[1 1];
 GeometryCalib.Tx_Ty_Tz=[Amat(1,3) Amat(2,3) 1];
@@ -918 +919 @@
 DataOut=phys(Data,Calib);
 rmpath(fullfile(path_UVMAT,'transform_field'))
-Amod=DataOut.A;
+Amod=DataOut.A;% current imgage expressed in 'phys' coord
 Rangx=DataOut.AX;
 Rangy=DataOut.AY;
@@ -936 +937 @@
 ind_range_y=ceil(abs(GeometryCalib.R(2,2)*CalibData.grid.Dy/3));% range of search of image ma around each point obtained by linear interpolation from the marked points
 nbpoints=size(T,1);
+%lokk for image maxima around each expected pgrid point
 for ipoint=1:nbpoints
     i0=1+round((T(ipoint,1)-Rangx(1))/Dx);%round(Xpx(ipoint));
@@ -962 +964 @@
     Delta(ipoint,2)=(y_shift+ind_y_max+j0min-j0-1)*Dy;
 end
-Tmod=T(:,(1:2))+Delta;
-[Xpx,Ypx]=px_XYZ(GeometryCalib,Tmod(:,1),Tmod(:,2));
-% for ipoint=1:nbpoints
-%      Coord{ipoint,1}=num2str(T(ipoint,1),4);%display coordiantes with 4 digits
-%      Coord{ipoint,2}=num2str(T(ipoint,2),4);%display coordiantes with 4 digits
-%      Coord{ipoint,3}=num2str(T(ipoint,3),4);%display coordiantes with 4 digits;
-%      Coord{ipoint,4}=num2str(Xpx(ipoint),4);%display coordiantes with 4 digits
-%      Coord{ipoint,5}=num2str(Ypx(ipoint),4);%display coordiantes with 4 digits
-% end
+Tmod=T(:,(1:2))+Delta;% 'phys' coordinates of the detected points 
+Tmod(:,2)=flipdim(Tmod(:,2),1);% inverse the order of y coordinates
+[Xpx,Ypx]=px_XYZ(GeometryCalib,Tmod(:,1),Tmod(:,2));% image coordinates of the detected points
 Coord=[T Xpx Ypx zeros(size(T,1),1)];
 set(handles.ListCoord,'Data',Coord)
@@ -1250 +1246 @@
     Data=get(handles.ListCoord,'Data');
     Data(:,6)=zeros(size(Data,1),1);
-    Data(iline,6)=1;% mark the selected line
+    Data(iline,6)=-1;% mark the selected line
     set(handles.ListCoord,'Data',Data)
     update_calib_marker(Data(iline,:))
@@ -1340 +1336 @@
     set(hhh,'Position',[XCoord-ind_range/2 YCoord-ind_range/2 ind_range ind_range])
 end
+
+%------------------------------------------------------------------------
+% --- Executes on button press in ClearLine: remove the selected line in the table Coord
+%------------------------------------------------------------------------
+function ClearLine_Callback(hObject, eventdata, handles)
+
+Coord=get(handles.ListCoord,'Data');
+ind=find(Coord(:,6));%find the marker '-' for line selection
+if isempty(ind)
+    msgbox_uvmat('WARNING','no line suppressed, select a line in the table')
+else
+    answer=msgbox_uvmat('INPUT_Y-N',['suppress line ' num2str(ind) '?']);
+    if isequal(answer,'Yes')
+Coord(:,6)=zeros(size(Coord,1),1);% desactivate the current line mark
+Coord(ind,:)=[];
+PLOT_Callback(hObject,eventdata,handles)
+set(handles.APPLY,'BackgroundColor',[1 0 1])
+set(handles.ListCoord,'Data',Coord);
+    end
+end

trunk/src/get_field.m

@@ -34 +34 @@
 function varargout = get_field(varargin)
 
-% Last Modified by GUIDE v2.5 09-Jun-2013 11:15:54
+% Last Modified by GUIDE v2.5 23-Oct-2013 23:44:17
 
 % Begin initialization code - DO NOT EDIT
@@ -97 +97 @@
         check_singleton(idim)=isequal(Field.DimValue(dim_index),1);%check_singleton=1 for singleton
     end
-    Field.Check0D(ilist)=(isequal(check_singleton,ones(1,NbDim)));% =1 if the variable reduces to a single value
+    Field.Check0D(ilist)=(isequal(check_singleton,ones(1,NbDim)))||(~isequal(Field.VarType(ilist),4)&&~isequal(Field.VarType(ilist),5));% =1 if the variable reduces to a single value
     if ~Field.Check0D(ilist)
     Field.Display.VarDimName{ilist}=Field.VarDimName{ilist}(~check_singleton);% eliminate singletons in the list of variable dimensions
@@ -137 +137 @@
 end
 if Field.MaxDim>=2
-    ListSwitchVarIndexTime=[ListSwitchVarIndexTime;{'variable'};{'dim index'}];% the time can be chosen as a dim index
+    ListSwitchVarIndexTime=[ListSwitchVarIndexTime;{'variable'};{'matrix index'}];% the time can be chosen as a dim index
 end
 
@@ -144 +144 @@
     time_index=find(strcmp(ParamIn.TimeAttrName,Field.Display.ListGlobalAttribute),1);
 else
-    time_index=find(~cellfun('isempty',regexp(Field.Display.ListGlobalAttribute,'Time')),1);
+    time_index=find(~cellfun('isempty',regexp(Field.Display.ListGlobalAttribute,'Time')),1);% look for global attribute containing name 'Time'
 end
 if ~isempty(time_index)
@@ -517 +517 @@
 %% set default coord selection
 if numel(find(test_coord))>3
+     SwitchVarIndexTime=get(handles.SwitchVarIndexTime,'String');
+    if numel(SwitchVarIndexTime)<3
+        SwitchVarIndexTime=[SwitchVarIndexTime;'matrix_index'];
+        set(handles.SwitchVarIndexTime,'String',SwitchVarIndexTime)
+    end
     set(handles.SwitchVarIndexTime,'Value',3)% the last dim must be considered as time
+    SwitchVarIndexTime_Callback([], [], handles)
 end
 if numel(var_component)<2
@@ -554 +560 @@
         set(handles.TimeName,'Value',1)
         set(handles.TimeName,'String',ListTime)
-    case 'dim index'
+    case 'matrix index'
         if numel(find(test_coord))<3
             ListTime={''};
@@ -579 +585 @@
 test_coord=zeros(size(Field.Display.VarDimName)); %=1 when variable #ilist is eligible as structured coordiante
 dim_var=Field.Display.VarDimName{scalar_index};%list of dimensions of the selected variable
-for ilist=1:numel(Field.Display.VarDimName)
-    dimnames=Field.Display.VarDimName{ilist}; %list of dimensions for variable #ilist
-    if isequal(dimnames,dim_var)
-        test_component(ilist)=1;
-    elseif numel(dimnames)==1 && ~isempty(find(strcmp(dimnames{1},dim_var)))%variable ilist is a 1D array which can be coordinate variable
-        test_coord(ilist)=1;
+CheckDimensionX=get(handles.CheckDimensionX,'Value');
+CheckDimensionY=get(handles.CheckDimensionY,'Value');
+if ~CheckDimensionX  || ~CheckDimensionY
+    %look for coordinate variables among the other variables
+    for ilist=1:numel(Field.Display.VarDimName)
+        dimnames=Field.Display.VarDimName{ilist}; %list of dimensions for variable #ilist
+        if isequal(dimnames,dim_var)
+            test_component(ilist)=1;% the listed variable has the same dimension as the selected scalar-> possibly chosen as unstructured coordinate
+        elseif numel(dimnames)==1 && ~isempty(find(strcmp(dimnames{1},dim_var), 1))%variable ilist is a 1D array which can be coordinate variable
+            test_coord(ilist)=1;
+        end
     end
 end
@@ -593 +604 @@
 %% set default coord selection
 if numel(find(test_coord))>3
+    SwitchVarIndexTime=get(handles.SwitchVarIndexTime,'String');
+    if numel(SwitchVarIndexTime)<3
+        SwitchVarIndexTime=[SwitchVarIndexTime;'matrix_index'];
+        set(handles.SwitchVarIndexTime,'String',SwitchVarIndexTime)
+    end
     set(handles.SwitchVarIndexTime,'Value',3)% the last dim must be considered as time
+    SwitchVarIndexTime_Callback([], [], handles)
 end
 % if numel(var_component)<2
@@ -623 +640 @@
     end
 end
-set(handles.Coord_x,'Value',coord_val(1))
-set(handles.Coord_y,'Value',coord_val(2))
-set(handles.Coord_y,'String',ListCoord)
-set(handles.Coord_x,'String',ListCoord)
-
+if  CheckDimensionX
+    set(handles.Coord_x,'Value',2)
+    set(handles.Coord_x,'String',dim_var')
+else
+    set(handles.Coord_x,'Value',coord_val(1))
+    set(handles.Coord_x,'String',ListCoord)
+end
+if  CheckDimensionY
+    set(handles.Coord_y,'Value',1)
+    set(handles.Coord_y,'String',dim_var')
+else
+    set(handles.Coord_y,'Value',coord_val(2))
+    set(handles.Coord_y,'String',ListCoord)
+end
 
 %% set list of time coordinates
@@ -871 +897 @@
         end
         set(handles.TimeName, 'String',TimeVarName)
-    case 'dim index'% TimeName menu represents the available dimensions
-        set(handles.TimeName, 'Visible','on')
-        TimeVarName=Field.Display.SingleDimName;
-        List=get(handles.TimeName,'String');
-        option=List{get(handles.TimeName,'Value')};
-        ind=find(strcmp(option,TimeVarName));
-        if isempty(ind)
-            set(handles.TimeName, 'Value',1);
-        else
-            set(handles.TimeName, 'Value',ind);
-        end
-        set(handles.TimeName, 'String',TimeVarName)
+    case 'matrix_index'% TimeName menu represents the available dimensions
+        set(handles.TimeName, 'Visible','on')     
+        set(handles.TimeName, 'Value',1);
+        set(handles.TimeName, 'String',Field.Display.ListDimName)
 end
 
@@ -920 +938 @@
     end
 end
+
+% --- Executes on button press in CheckDimensionY.
+function CheckDimensionX_Callback(hObject, eventdata, handles)
+FieldList=get(handles.FieldOption,'String');
+FieldOption=FieldList{get(handles.FieldOption,'Value')};
+switch FieldOption
+    case '1D plot'
+        
+    case 'scalar'
+       scalar_Callback(hObject, eventdata, handles)
+    case 'vectors'
+end
+
+% --- Executes on button press in CheckDimensionY.
+function CheckDimensionY_Callback(hObject, eventdata, handles)
+FieldList=get(handles.FieldOption,'String');
+FieldOption=FieldList{get(handles.FieldOption,'Value')};
+switch FieldOption
+    case '1D plot'
+        
+    case 'scalar'
+       scalar_Callback(hObject, eventdata, handles)
+    case 'vectors'
+end
+% hObject    handle to CheckDimensionY (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 CheckDimensionY

trunk/src/mouse_motion.m

@@ -418 +418 @@
                     Data=get(h_ListCoord,'Data');
                     Data(:,6)=zeros(size(Data,1),1);
-                    Data(index_point,6)=1;%mrk the point on the GUI geometry_calib
+                    Data(index_point,6)=-1;%mrk the point on the GUI geometry_calib
                     set(h_ListCoord,'Data',Data);
                     hhh=findobj('Tag','calib_marker');%look for handle of point marker (circle)

trunk/src/nc2struct.m

@@ -13 +13 @@
 %                    .VarDimName: list of dimension names for each element of .ListVarName (cell array of string cells)                         
 %                    .Var1, .Var2....: variables (Matlab arrays) with names listed in .ListVarName
-%                  ListDimName=list of dimension (added information, not requested for field description)
-%                  DimValue= vlalues of dimensions (added information, not requested for field description)
+%                  .ListDimName=list of dimension (added information, not requested for field description)
+%                  .DimValue= vlalues of dimensions (added information, not requested for field description)
+%                  .VarType= integers giving the type of variable as coded by netcdf= 2 for char, =4 for single,=( for double
 %         .Txt: error message
 %  var_detect: vector with same length as the cell array ListVarName, = 1 for each detected variable and 0 else.
@@ -166 +167 @@
     for ncvar=1:nvars %loop on the variables of the netcdf file
         %get name, type, dimensions and attribute numbers of each variable 
-        [ListVarNameNetcdf{ncvar},xtype,dimids{ncvar},nbatt(ncvar)] = netcdf.inqVar(nc,ncvar-1);
+        [ListVarNameNetcdf{ncvar},xtype(ncvar),dimids{ncvar},nbatt(ncvar)] = netcdf.inqVar(nc,ncvar-1);
     end  
     testmulti=0;
@@ -221 +222 @@
             end
             try
-            if ischar(valuestr)
-               % valuestr=regexprep(valuestr,{'\\','\/','\.','\-',' '},{'_','_','_','_','_'});%remove  '\','.' or '-' if exists
-                eval(['Data.VarAttribute{ivar}.' attname '=''' valuestr ''';'])
-            elseif isempty(valuestr)
-                eval(['Data.VarAttribute{ivar}.' attname '=[];'])
-            elseif isnumeric(valuestr)
-                eval(['Data.VarAttribute{ivar}.' attname '=valuestr;'])
+             if isempty(valuestr)
+                Data.VarAttribute{ivar}.(attname)=valuestr;
             end
             catch ME
@@ -233 +229 @@
                 display(valuestr)
                 display(ME.message)         
-                eval(['Data.VarAttribute{ivar}.atrr_' num2str(iatt) '=''not read'';'])
+                Data.VarAttribute{ivar}.(['atrr_' num2str(iatt)])='not read';
             end
         end
@@ -255 +251 @@
                 if var_dim{ivar}(end)==TimeDimIndex% if the last dim of the variable is the time
                     slice_length=prod(var_dim{ivar}(1:end-1));
-                    Data.(VarName)=double(netcdf.getVar(nc,var_index(ivar)-1),TimeIndex*slice_length,slice_length); %read the variable data
+                    Data.(VarName)=double(netcdf.getVar(nc,var_index(ivar)-1,TimeIndex*slice_length,slice_length)); %read the variable data
                     CheckSub=1;
                 end
             end
             if ~CheckSub
-                Data.(VarName)=double(netcdf.getVar(nc,var_index(ivar)-1)); %read the whole variable data
-            end
-        end
-    end
+                Data.(VarName)=netcdf.getVar(nc,var_index(ivar)-1); %read the whole variable data
+                if xtype(var_index(ivar))==5
+                Data.(VarName)=double(Data.(VarName)); %transform to double for single pecision
+                end
+            end
+        end
+    end
+    Data.VarType=xtype(var_index);
     
     %%  -------- close fle-----------

trunk/src/read_field.m

@@ -20 +20 @@
 %     .ColorVar: variable used for vector color
 %     .Npx, .Npy: nbre of pixels along x and y (used for .vol input files)
+%     .TimeDimName: name of the dimension considered as 'time', selected index value then set by input 'num'   
 % num: frame number for movies
 %

trunk/src/uvmat.m

@@ -2352 +2352 @@
     if strcmp(TimeName,'civdata')||strcmp(TimeName,'civx')
         abstime=Field{1}.Time;
-    elseif ~isempty(regexp(TimeName,'^att:'))||~isempty(regexp(TimeName,'^dim:'))||~isempty(regexp(TimeName,'^var:'))
+    elseif ~isempty(regexp(TimeName,'^att:'))||~isempty(regexp(TimeName,'^var:'))
         abstime=Field{1}.(TimeName(5:end));%the time is an attribute or variale selected by get_file
+    elseif ~isempty(regexp(TimeName,'^dim:'))
+        abstime=str2num(get(handles.i1,'String'));
     end
     if isfield(Field{1},'Dt')
@@ -3127 +3129 @@
             XName=GetFieldData.Coordinates.Coord_x;
             TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
-            if strcmp(TimeNameStr,'file index')
-                set(handles.TimeName,'String','');
-            else
-                set(handles.TimeName,'String',[TimeNameStr(1:3) ':' GetFieldData.Time.TimeName]);
-            end
-            if strcmp(TimeNameStr,'variable')||strcmp(TimeNameStr,'dim index')% we scan a variable index, not a file index
-                set(handles.NomType,'String','*')
-                set(handles.RootFile,FileName)
-            end
-            %     set(handles.TimeValue,'String' SwitchVarIndexTime
+            switch TimeNameStr
+                case 'file index'
+                    set(handles.TimeName,'String','');
+                case 'attribute'
+                    set(handles.TimeName,'String',['att:' GetFieldData.Time.TimeName]);
+                case 'variable'
+                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
+                    set(handles.NomType,'String','*')
+                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
+                    set(handles.FileIndex,'String','')
+                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
+                case 'matrix_index'
+                    set(handles.TimeName,'String',['dim:' GetFieldData.Time.TimeName]);
+                    set(handles.NomType,'String','*')
+                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
+                    set(handles.FileIndex,'String','')
+                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
+            end
             set(handles.Coord_x,'String',XName)
             if ischar(YName)