Changeset 93

Timestamp:

May 27, 2010, 7:25:58 PM (14 years ago)

Author:

sommeria

Message:

FFT: improved to deal with NaN data
merge_proj: corrected to reproduce dt if unique
uvmat.fig: tooltip corrected
plot_field: bug for isocontour corrected,
im_filter: cleaning
phys_polar: spatial derivative included (still to check)
set_obeject.fig: minor correction
struct2nc: comments improved
uvmat: button NB implemented
read_civxdata: error message improved

Location:

trunk/src

Files:

• get_field/FFT.m (modified) (2 diffs)
• plot_field.m (modified) (10 diffs)
• read_civxdata.m (modified) (5 diffs)
• series/merge_proj.m (modified) (6 diffs)
• set_object.fig (modified) (previous)
• struct2nc.m (modified) (1 diff)
• transform_field/im_filter.m (modified) (1 diff)
• transform_field/phys_polar.m (modified) (4 diffs)
• uvmat.fig (modified) (previous)
• uvmat.m (modified) (1 diff)

trunk/src/get_field/FFT.m

@@ -6 +6 @@
     return %exit the function 
 end
-
+GUI_input=[];
 %initiation
 hhget_field=guidata(hget_field);
@@ -29 +29 @@
 % get variable
 eval(['Var= Field.' ordinate_name ';']);
-np=size(Var);
+np=size(Var)
 np_freq=floor(np(1)/2);
 dx=1;%default
 dfreq=1/np(1);%default frequency interval (abscissa= array index)
+sum_data=sum(Var,2);
 if ~isequal(abscissa_name,'')
     eval(['Coord_x= Field.' abscissa_name ';']);
-    ind_select=find(~isinf(Coord_x));%detect infinite values
+    ind_select=find(~isinf(Coord_x)&~isnan(sum_data));%detect infinite values
     Coord_x=Coord_x(ind_select);
     Var=Var(ind_select,:);

trunk/src/plot_field.m

@@ -172 +172 @@
 % check the cells of fields :
 % testnbdim=1;
-[CellVarIndex,NbDim,VarType,errormsg]=find_field_indices(Data);
+[CellVarIndex,NbDim,VarType,errormsg]=find_field_indices(Data)
 
 if ~isempty(errormsg)
@@ -324 +324 @@
 coord_x_index=[];
 test_newplot=1;
-hh=findobj(haxes,'tag','plot_line');
+% hh=findobj(haxes,'tag','plot_line');
 % num_curve=numel(hh);
-icurve=0;
+% icurve=0;
 for icell=1:length(CellVarIndex)
     testfalse=0;
@@ -362 +362 @@
     end
     eval(['coord_x{icell}=data.' data.ListVarName{coord_x_index} ';']);%coordinate variable set as coord_x
-    testcoordvar=1;
+%     testcoordvar=1;
     testplot(coord_x_index)=0;
     if ~isempty(VarType{icell}.ancillary')
@@ -425 +425 @@
                 eval(['varmean=mean(double(data.' VarName '));']);%mean value
                 textmean=[textmean; {[VarName 'mean= ' num2str(varmean,4)]}];
-                if nbcomponent1==1| nbcomponent2==1
+                if nbcomponent1==1|| nbcomponent2==1
                     legend_str=[legend_str {VarName}]; %variable with one component
                 else  %variable with severals  components
@@ -553 +553 @@
         VarType.coord=VarType.coord(ind_coord);
     end
-    idim_Y=[];  
+%     idim_Y=[];  
     test_grid=0;
     if ~isempty(ivar_U) && ~isempty(ivar_V)% vector components detected
@@ -563 +563 @@
             eval(['vec_U=Data.' Data.ListVarName{ivar_U} ';']) 
             eval(['vec_V=Data.' Data.ListVarName{ivar_V} ';']) 
-            'TESTplot'
-            VarType.coord
             if ~isempty(ivar_X) && ~isempty(ivar_Y)% 2D field (with unstructured coordinates or structured ones (then ivar_X and ivar_Y empty)     
                 eval(['vec_X=Data.' Data.ListVarName{ivar_X} ';']) 
@@ -748 +746 @@
             end
             if ~isfield(PlotParam.Scalar,'IncrA')
-                PlotParam.Scalar.IncrA=[];
-            end
-            if isempty(PlotParam.Scalar.IncrA)% | PlotParam.Scalar.AutoScal==0
+                PlotParam.Scalar.IncrA=NaN;
+            end
+            if isnan(PlotParam.Scalar.IncrA)% | PlotParam.Scalar.AutoScal==0
                 cont=colbartick(MinA,MaxA);
                 intercont=cont(2)-cont(1);%default
@@ -767 +765 @@
             sizpx=(AX(end)-AX(1))/(np(2)-1);
             sizpy=(AY(1)-AY(end))/(np(1)-1);
-            x_cont=[AX(1):sizpx:AX(end)]; % pixel x coordinates for image display 
+            x_cont=AX(1):sizpx:AX(end); % pixel x coordinates for image display 
             y_cont=AY(1):-sizpy:AY(end); % pixel x coordinates for image display
             txt=ver;%version of Matlab
@@ -857 +855 @@
     %display the colorbar code for B/W images if Poscolorbar not empty
     if siz==2 && exist('PosColorbar','var')&& ~isempty(PosColorbar)
-        if isempty(hcol)|~ishandle(hcol)
+        if isempty(hcol)||~ishandle(hcol)
              hcol=colorbar;%create new colorbar
         end
@@ -981 +979 @@
         end
         nb_sel=length(ind_sel);
-        ind_sel=ind_sel([1:2:nb_sel]);% take half the points on a line
+        ind_sel=ind_sel(1:2:nb_sel);% take half the points on a line
         vec_X=vec_X(ind_sel);
         vec_Y=vec_Y(ind_sel);

trunk/src/read_civxdata.m

@@ -1 +1 @@
 %'read_civxdata': reads civx data from netcdf files
-%------------------------------------------------------------------
-% COMBINE ET REMPLACE read_ncfield, read_vel et read_scalar_new
 %------------------------------------------------------------------
 % OUTPUT:
@@ -20 +18 @@
 %            .CoordType: expresses the type of coordinate ('px' for image, 'sig' for instruments, or 'phys')
 %            .dt: time interval for the corresponding image pair
-%            .CivStage: =0, ??? A UTILISER POUR REMPLACER civ
-        %           =1, civ1 has been performed only
-        %           =2, fix1 has been performed
-        %           =3, pacth1 has been performed
-        %           =4, civ2 has been performed 
-        %           =5, fix2 has been performed
-        %           =6, pacth2 has been performed
+%            .CivStage: =0, 
+%                   =1, civ1 has been performed only
+%                   =2, fix1 has been performed
+%                   =3, pacth1 has been performed
+%                   =4, civ2 has been performed 
+%                   =5, fix2 has been performed
+%                   =6, pacth2 has been performed
 %            .X, .Y, .Z: set of vector coordinates 
 %            .U,.V,.W: corresponding set of vector components
@@ -37 +35 @@
 %            .A, .AX, .AY: additional scalar
 % dt:time interval of the image pair red from a single file, or vector with
- 
 % pixcmx,pixcmy: scaling factors (from the first file)
 % vel_type_out: string representing the selected velocity type (civ1,civ2,filter1...)
@@ -68 +65 @@
     FieldNames=[]; %default
 end
-
 VelTypeOut=VelType;%default
 [var,role,units,vel_type_out_cell]=varcivx_generator(FieldNames,VelType);%determine the names of constants and variables to read
@@ -76 +72 @@
 end
 if isequal(vardetect,0)
-     Field.Txt=[FieldNames ' not accessible in ' filename '/' VelType];
+     Field.Txt=[reshape(FieldNames,1,numel(FieldNames)) ' not accessible in ' filename '/' VelType];
      return
 end

trunk/src/series/merge_proj.m

@@ -267 +267 @@
                     Field{iview}.VarAttribute=SubField.VarAttribute;
                 end
+                if isfield(Field{iview},'Txt')
+                    msgbox_uvmat('ERROR',Field{iview}.Txt)
+                    return
+                end
                 if isfield(Field{iview},'Time')
                     timeread(iview)=Field{iview}.Time;
@@ -280 +284 @@
                 Field{iview}=transform_fct(Field{iview},XmlData{iview});%transform to phys if requested
             end
-            min(Field{iview}.X)
             if testcivx
                     Field{iview}=calc_field(FieldName,Field{iview});
             end
-            min(Field{iview}.X)
 
             %projection on object (gridded plane)
@@ -350 +352 @@
             MergeData.nb_coord=2;
             MergeData.nb_dim=2;
-            MergeData.dt=1;
+            dt=[];
+            if isfield(Field{1},'dt')&& isnumeric(Field{1}.dt)
+                dt=Field{1}.dt;
+            end
+            for iview =2:numel(Field)
+                if ~(isfield(Field{iview},'dt')&& isequal(Field{iview}.dt,dt))
+                    dt=[];%dt not the same for all fields
+                end
+            end
+            if isempty(dt)
+                MergeData.ListGlobalAttribute(6)=[];
+            else
+               MergeData.dt=dt;
+            end
+            %MergeData.dt=1;
             MergeData.Time=time_i;
             error=struct2nc(mergename,MergeData); %save result file
@@ -387 +403 @@
     return
 end
+
+
+
 
 %group the variables (fields of 'FieldData') in cells of variables with the same dimensions
@@ -412 +431 @@
         test_grid=0;
     end
-%    DimIndices=Data{1}.VarDimIndex{VarIndex(1)};%indices of the dimensions of the first variable (common to all variables in the cell)
     %case of input fields with unstructured coordinates
     if ~test_grid
@@ -423 +441 @@
     %case of fields defined on a structured  grid 
     else  
-%        DimValue=MergeData.DimValue(DimIndices);%set of dimension values
         testFF=0;
         for iview=2:nbview
-%             if ~isequal(DimValue,Data{iview}.DimValue(DimIndices))
-%                 MergeData.Txt='ERROR: attempt at merging structured fields with different sizes';
-%                 return
-%             end
             for ivar=VarIndex
                 VarName=MergeData.ListVarName{ivar};

trunk/src/struct2nc.m

@@ -1 @@
-%'struct2nc': create a netcdf file from a Matlab structure
+% 'struct2nc': create a netcdf file from a Matlab structure
 %---------------------------------------------------------------------
 % errormsg=struct2nc(flname,Data)
 %
-%OUPUT:
-%errormsg=error message, =[]: default, no error
+% OUPUT:
+% errormsg=error message, =[]: default, no error
 %
-%INPUT:
-%flname: name of the netcdf file to create (must end with the extension '.nc')
+% INPUT:
+% flname: name of the netcdf file to create (must end with the extension '.nc')
 %  Data: structure containing all the information of the netcdf file (or netcdf object)
 %           with fields:
-%         (optional) .ListGlobalAttribute: cell listing the names of the global attributes
-%                    .Att_1,Att_2... : values of the global attributes
-%         (requested)  .ListVarName: list of variable names to select (cell array of  char strings {'VarName1', 'VarName2',...} ) 
-%         (requested)  .VarDimName: list of dimension names for each element of .ListVarName (cell array of string cells)                         
-%         (requested) .Var1, .Var2....: variables (Matlab arrays) with names listed in .ListVarName
-%
+%       (optional) .ListGlobalAttribute: list (cell array of character strings) of the names of the global attributes Att_1, Att_2...
+%                  .Att_1,Att_2...: values of the global attributes
+%      (requested) .ListVarName: list of the variable names Var_1, Var_2....(cell array of character strings). 
+%      (requested) .VarDimName: list of dimension names for each element of .ListVarName (cell array of string cells)
+%       (optional) .VarAttribute: cell array of structures of the form .VarAttribute{ivar}.key=value, defining an attribute key name and value for the variable #ivar
+%      (requested) .Var1, .Var2....: variables (Matlab arrays) with names listed in .ListVarName
+
 %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
 %  Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org.

trunk/src/transform_field/im_filter.m

@@ -11 +11 @@
 
 DataOut=DataIn; %default
-
 Atype=class(DataIn.A)% detect integer 8 or 16 bits
-DataOut.A=filter2(Mfiltre,DataIn.A); 
-DataOut.A=feval(Atype,DataOut.A);
+if numel(size(DataIn.A))==3
+    DataOut.A=filter2(Mfiltre,sum(DataIn.A,3));%filter the input image, after summation on the color component (for color images)
+    DataOut.A=uint16(DataOut.A); %transform to 16 bit images
+else
+    DataOut.A=filter2(Mfiltre,DataIn.A)
+    DataOut.A=feval(Atype,DataOut.A);%transform to the initial image format
+end
  

trunk/src/transform_field/phys_polar.m

@@ -28 +28 @@
 end
 test_1=0;
-if nargin==4
+if nargin==4% case of two input fields
     test_1=1;
     Data_1=varargin{3};
@@ -65 +65 @@
 
 iscalar=0;
+%transform first field to cartesian phys coordiantes
 if  ~isempty(Calib{1})
     DataOut=phys_1(Data,Calib{1},origin_xy,radius_offset,angle_offset,angle_scale);
@@ -80 +81 @@
     end
 end
-
+%transform second field (if exists) to cartesian phys coordiantes
 if test_1
     DataOut_1=phys_1(Data_1,Calib{2},origin_xy,radius_offset,angle_offset,angle_scale);
@@ -153 +154 @@
             DataOut.V=(-UX.*sin(theta)+VY.*cos(theta));%./(DataOut.X)%+radius_ref);%angular velocity calculated 
             %shift and renormalize the angular velocity
+            end
+        end
+        %transform of spatial derivatives
+        if isfield(Data,'X') && ~isempty(Data.X) && isfield(Data,'DjUi') && ~isempty(Data.DjUi)...
+                && isfield(Data,'dt')
+            if ~isempty(Data.dt)
+                % estimate the Jacobian matrix DXpx/DXphys
+                for ip=1:length(Data.X)
+                    [Xp1,Yp1]=phys_XYZ(Calib,Data.X(ip)+0.5,Data.Y(ip),Z);
+                    [Xm1,Ym1]=phys_XYZ(Calib,Data.X(ip)-0.5,Data.Y(ip),Z);
+                    [Xp2,Yp2]=phys_XYZ(Calib,Data.X(ip),Data.Y(ip)+0.5,Z);
+                    [Xm2,Ym2]=phys_XYZ(Calib,Data.X(ip),Data.Y(ip)-0.5,Z);
+                    %Jacobian matrix DXpphys/DXpx
+                    DjXi(1,1)=(Xp1-Xm1);
+                    DjXi(2,1)=(Yp1-Ym1);
+                    DjXi(1,2)=(Xp2-Xm2);
+                    DjXi(2,2)=(Yp2-Ym2);
+                    DjUi(:,:)=Data.DjUi(ip,:,:);
+                    DjUi=(DjXi*DjUi')/DjXi;% =J-1*M*J , curvature effects (derivatives of J) neglected
+                    DataOut.DjUi(ip,:,:)=DjUi';
+                end
+                DataOut.DjUi =  DataOut.DjUi/Data.dt;   %     min(Data.DjUi(:,1,1))=DUDX
             end
         end

trunk/src/uvmat.m

@@ -1167 +1167 @@
 UvData.NewSeries=1; %flag for run0: begin a new series
 
-[FileName,RootPath,FileBase,FileIndices,FileExt]=read_file_boxes_1(handles);
+[FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes_1(handles);
 if ~exist(FileName,'file')
     msgbox_uvmat('ERROR',['input file ' FileName ' not found']);