Changeset 476 for trunk/src

Timestamp:

Jun 25, 2012, 10:50:51 AM (12 years ago)

Author:

sommeria

Message:

bugs corrected +
* filter parameter multiplied by 1000 in filter_tps*

Location:

trunk/src

Files:

• check_files.m (modified) (3 diffs)
• civ.m (modified) (9 diffs)
• fill_GUI.m (modified) (2 diffs)
• filter_tps.m (modified) (4 diffs)
• series.m (modified) (2 diffs)
• uvmat.m (modified) (4 diffs)

trunk/src/check_files.m

@@ -54 +54 @@
     'fileparts_uvmat';...% extracts the root name,field indexes and nomenclature type from an input filename
     'fill_GUI';...% fill a GUI with handles 'handles' from input data Param 
+    'filter_tps';...% find the thin plate spline coefficients for interpolation-smoothing
     'find_field_indices';...% group the variables of a nc-formated Matlab structure into 'fields' with common dimensions
     'find_file_series';...%check the content of an input file and find the corresponding file series
@@ -128 +129 @@
 
 %% loop on the list of functions in the uvmat package
-
 icount=0;
 datnum=zeros(1,length(list_fct));
@@ -160 +160 @@
         [tild,result]=system(['svn status'  dir_fct]);
         svn_info.status=result;
+        errormsg =[errormsg {['SVN revision : ' num2str(svn_info.cur_rev)]}];
         if svn_info.rep_rev>svn_info.cur_rev
-            errormsg {length(errormsg)+1}=['Repository now at revision ' num2str(svn_info.rep_rev) '. Please type svn update in uvmat folder'];
+            errormsg =[errormsg ...
+                {['Repository now at revision ' num2str(svn_info.rep_rev) '. Please type svn update in uvmat folder']}];
         end
         modifications=regexp(svn_info.status,'M\s[^(\n|\>)]+','match');
         if ~isempty(modifications)
-            for k=1:length(modifications)
-                errormsg {length(errormsg)+1}=modifications{k};
-            end
+            errormsg=[errormsg modifications];
         end
+    else
+        errormsg=[errormsg {'SVN not available'}];
     end
 catch ME
-    errormsg=ME.message;
+    errormsg=[errormsg {'SVN not available'}];
 end
 errormsg=errormsg';

trunk/src/civ.m

@@ -356 +356 @@
     elseif ~isempty(Data.absolut_time_T0')% case of  civx data,
         set(handles.Program,'Value',1) %select Cix by default
-        ListProgram_Callback([],[], handles)
+        Program_Callback([],[], handles)
         if ~isempty(Data.fix2)
             ind_opening=5;
@@ -423 +423 @@
 set(handles.RootFile,'String',RootFile)
 if strcmp(ExtInput,'.nc')
-    SubDirCiv=regexprep(SubDir,[SuddirImages '^'],'');%suppress the root  SuddirImages;
+    SubDirCiv=regexprep(SubDir,[SubdirImages '^'],'');%suppress the root  SuddirImages;
 else
     SubDirCiv= '.civ';
@@ -449 +449 @@
 
 %% look for an image documentation file
-XmlFileName=find_imadoc(RootPath,SubDir,RootFile,FileExt);
+XmlFileName=find_imadoc(RootPath,SubDir,RootFile,ImaExt);
 % SubDirBase=regexprep(SubDir,'\..*','');%take the root part of SubDir, before the first dot '.'
 % filexml=fullfile(RootPath,[SubDirBase '.xml']);% new convention: xml above the image dir
@@ -482 +482 @@
     [XmlData,warntext]=imadoc2struct(XmlFileName);
     nom_type_read=[];
-    if isfield(XmlData,'Heading')&&isfield(XmlData.Heading','ImageName')&&ischar(XmlData.Heading.ImageName)% get image nom type and extension from the xml file
-        [~,tild,tild,tild,tild,tild,tild,tild,nom_type_read]=fileparts_uvmat(XmlData.Heading.ImageName);
-        fullname=fullfile(fileparts(RootName),XmlData.Heading.ImageName); %full name (including path) of the first image defined by the xmle file,
-        if ~exist(fullname,'file')
-            msgbox_uvmat('WARNING',['FirstImage ' fullname ' defined in the xml file does not exist'])
-        end
-    end
+%     if isfield(XmlData,'Heading')&&isfield(XmlData.Heading','ImageName')&&ischar(XmlData.Heading.ImageName)% get image nom type and extension from the xml file
+%         [~,tild,tild,tild,tild,tild,tild,tild,nom_type_read]=fileparts_uvmat(XmlData.Heading.ImageName);
+%         fullname=fullfile(fileparts(RootName),XmlData.Heading.ImageName); %full name (including path) of the first image defined by the xmle file,
+%         if ~exist(fullname,'file')
+%             msgbox_uvmat('WARNING',['FirstImage ' fullname ' defined in the xml file does not exist'])
+%         end
+%     end
     if isfield(XmlData,'Time') && ~isempty(XmlData.Time)
         time=XmlData.Time;
@@ -1183 +1183 @@
     end
     if Param.CheckCiv2
-        [Param.Civ2.FileTypeA,FileInfoA_civ2,Param.Civ2.ImageA]=get_file_type(filecell.ima1.civ2{1});
-        [Param.Civ2.FileTypeB,FileInfoB_civ2,Param.Civ2.ImageB]=get_file_type(filecell.ima2.civ2{1});
+        [Param.Civ2.FileTypeA,ImageInfoA_civ2,Param.Civ2.ImageA]=get_file_type(filecell.ima1.civ2{1});
+        [Param.Civ2.FileTypeB,ImageInfoB_civ2,Param.Civ2.ImageB]=get_file_type(filecell.ima2.civ2{1});
     end
 % end
@@ -1206 +1206 @@
 
         if Param.CheckCiv1
-            % read image-dependent parameters
-            
+            % read image-dependent parameters          
             if ~checkframe% && size(time,1)>=i2_civ1(ifile) && size(time,2)>=j2_civ1(j)
                 Param.Civ1.Dt=(time(i2_civ1(ifile)+1,j2_civ1(j)+1)-time(i1_civ1(ifile)+1,j1_civ1(j)+1));
@@ -1220 +1219 @@
             Param.Civ1.ImageA=filecell.ima1.civ1{ifile,j};
             Param.Civ1.ImageB=filecell.ima2.civ1{ifile,j};
-            Param.Civ1.ImageBitDepth=FileInfoA_civ1.BitDepth;
-            Param.Civ1.ImageWidth=FileInfoA_civ1.Width;
-            Param.Civ1.ImageHeight=FileInfoA_civ1.Height;
+            Param.Civ1.ImageBitDepth=ImageInfoA_civ1.BitDepth;
+            Param.Civ1.ImageWidth=ImageInfoA_civ1.Width;
+            Param.Civ1.ImageHeight=ImageInfoA_civ1.Height;
             Param.Civ1.FrameIndexA=i1_civ1(ifile);
             Param.Civ1.FrameIndexB=i2_civ1(ifile);
@@ -1294 +1293 @@
             end
 
-            Param.Civ2.ImageBitDepth=FileInfoA_civ2.BitDepth;
-            Param.Civ2.ImageWidth=FileInfoA_civ2.Width;
-            Param.Civ2.ImageHeight=FileInfoA_civ2.Height;
+            Param.Civ2.ImageBitDepth=ImageInfoA_civ2.BitDepth;
+            Param.Civ2.ImageWidth=ImageInfoA_civ2.Width;
+            Param.Civ2.ImageHeight=ImageInfoA_civ2.Height;
             Param.Civ2.FrameIndexA=i1_civ2(ifile);
             Param.Civ2.FrameIndexB=i2_civ2(ifile);           
@@ -1499 +1498 @@
             else
                 for p=1:length(batch_file_list)
-                    fid=fopen( batch_file_list{p});
+%                     civ_matlab([batch_file_list{p} '.xml'], [batch_file_list{p} '.nc'])
+                    fid=fopen(batch_file_list{p});
                     eval(fscanf(fid,'%s'));
                     fclose(fid);

trunk/src/fill_GUI.m

@@ -47 +47 @@
                     set(hh,'String',input_data)
                 case{'listbox','popupmenu'}
-                    input_data
                     if isnumeric(input_data)
                         input_data=num2str(input_data);
@@ -59 +58 @@
                         iline=find(strcmp(input_data{idata},menu));
                         if isempty(iline)
-                            values(idata)=numel(menu)+1;
-                            menu=[menu;input_data(idata)];
+                            values(idata)=1;
+                            menu=[input_data(idata);menu];
                         else
-                            values(idata)=iline;
+                            values(idata)=iline(1);
                         end
                     end
-                    set(hh,'String',[menu;input_data(idata)])
+                    set(hh,'String',menu)
                     set(hh,'Value',values)
             end

trunk/src/filter_tps.m

@@ +1 @@
+%'filter_tps': find the thin plate spline coefficients for interpolation-smoothing
 %------------------------------------------------------------------------
-% patch function
+% [SubRange,NbSites,Coord_tps,U_tps,V_tps,W_tps,U_smooth,V_smooth,W_smooth,FF] =filter_tps(Coord,U,V,W,SubDomain,Rho,Threshold)
+%
 % OUTPUT:
 % SubRange(NbCoord,NbSubdomain,2): range (min, max) of the coordiantes x and y respectively, for each subdomain
@@ -10 +12 @@
 %
 % INPUT:
-% X, Y: set of coordinates of the initial data
+% coord=[X Y]: matrix whose first column is the x coordinates of the initial data, the second column the y coordiantes
 % U,V: set of velocity components of the initial data
 % Rho: smoothing parameter
@@ -16 +18 @@
 % Subdomain: estimated number of data points in each subdomain
 
-%function [SubRangx,SubRangy,nbpoints,FF,U_smooth,V_smooth,X_tps,Y_tps,U_tps,V_tps,Indices_tps] =filter_tps(Coord,U,V,W,SubDomain,Rho,Threshold)
 function [SubRange,NbSites,Coord_tps,U_tps,V_tps,W_tps,U_smooth,V_smooth,W_smooth,FF] =filter_tps(Coord,U,V,W,SubDomain,Rho,Threshold)
 %subdomain decomposition
 warning off
-% U=reshape(U,[],1);
-% V=reshape(V,[],1);
-% X=reshape(X,[],1);
-% Y=reshape(Y,[],1);
 nbvec=size(Coord,1);
 W_tps=[];%default
@@ -43 +40 @@
 CentreY=reshape(CentreY,1,[]);% Y positions of subdomain centres
 CentreX=reshape(CentreX,1,[]);% X positions of subdomain centres
-rho=Siz(1)*Siz(2)*Rho/1000000;%optimum rho increase as the area of the subdomain (division by 10^6 to reach good values with the default GUI input)
+rho=Siz(1)*Siz(2)*Rho/1000;%optimum rho increase as the area of the subdomain (division by 10^6 to reach good values with the default GUI input)
 U_tps_sub=zeros(nbvec,NbSubDomain);%default spline
 V_tps_sub=zeros(nbvec,NbSubDomain);%default spline

trunk/src/series.m

@@ -101 +101 @@
 end
 if isfield(param,'FileName')
+    InputTable={'','','','',''};
+    set(handles.InputTable,'Data',InputTable)
     if isfield(param,'FileName_1')
         display_file_name(handles,param.FileName_1,0)
@@ -107 +109 @@
         display_file_name(handles,param.FileName,0)
     end
-    InputTable={'','','','',''};
-    set(handles.InputTable,'Data',InputTable)
 end  
 

trunk/src/uvmat.m

@@ -207 +207 @@
 guidata(hObject, handles);
 
-%% check the path and date of modification of all functions in uvmat
-path_to_uvmat=which ('uvmat');% check the path detected for source file uvmat
-[errormsg,date_str,svn_info]=check_files;%check the path of the functions called by uvmat.m
-date_str=['last modification: ' date_str];
-
-
 %% set the position of colorbar and ancillary GUIs:
 set(hObject,'Units','Normalized')
@@ -330 +324 @@
     end
 else
-   if ishandle(handles.UVMAT_title)
-       set(handles.UVMAT_title,'String',...
-           [{'Copyright  LEGI UMR 5519 /CNRS-UJF-Grenoble INP, 2010'};...
-           {'GNU General Public License'};...
-           {path_to_uvmat};...
-           {date_str};...
-           {['SVN revision : ' num2str(svn_info.cur_rev)]};...
-           errormsg]);
-   end
+    %% check the path and date of modification of all functions in uvmat
+    path_to_uvmat=which ('uvmat');% check the path detected for source file uvmat
+    [infomsg,date_str,svn_info]=check_files;%check the path of the functions called by uvmat.m   
+    date_str=['last modification: ' date_str];
+    if ishandle(handles.UVMAT_title)
+        set(handles.UVMAT_title,'String',...
+            [{'Copyright  LEGI UMR 5519 /CNRS-UJF-Grenoble INP, 2010'};...
+            {'GNU General Public License'};...
+            {path_to_uvmat};...
+            {date_str};...
+            infomsg]);
+    end
 end
 set(handles.uvmat,'UserData',UvData)
@@ -4127 +4124 @@
     set(handles.ViewObject,'value',1)
     ViewObject_Callback(hObject, eventdata, handles)
-%     if isempty(hset_object)% open the GUI set_object with data of the currently selected object
-%         ViewObject_Callback(hObject, eventdata, handles)
-%         %         hset_object=findobj(allchild(0),'Tag','set_object');
-%     else
-%         hhset_object=guidata(hset_object);
-%         set(hhset_object.PLOT,'enable','on');
-%         set(get(hset_object,'children'),'enable','on')
-%     end
 else % desctivate object edit mode
     set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])  
@@ -4586 +4575 @@
 set(handles.edit_object,'Value',1)
 edit_Callback(hObject, eventdata, handles)
-
-% %------------------------------------------------------------------------
-% function enable_transform(handles,state)
-% %------------------------------------------------------------------------
-% set(handles.transform_fct,'Visible',state)
-% set(handles.TRANSFORM_txt,'Visible',state)    
-% set(handles.transform_fct,'Visible',state)  
-% set(handles.path_transform,'Visible',state)
-% set(handles.pxcmx_txt,'Visible',state)
-% set(handles.pxcmy_txt,'Visible',state)
-% set(handles.pxcm,'Visible',state)
-% set(handles.pycm,'Visible',state)
 
 %------------------------------------------------------------------------