Index: /trunk/src/proj_field.m =================================================================== --- /trunk/src/proj_field.m (revision 911) +++ /trunk/src/proj_field.m (revision 912) @@ -1010,4 +1010,10 @@ end +%% interpolation range +thresh2=[]; +if isfield(ObjectData,'RangeInterp') + thresh2=ObjectData.RangeInterp*ObjectData.RangeInterp;%square of interpolation range (do not interpolate beyond this range) +end + %% initiate Matlab structure for physical field [ProjData,errormsg]=proj_heading(FieldData,ObjectData); @@ -1303,8 +1309,9 @@ Disty=G(XI,YI)-YI;% diff of y coordinates with the nearest measurement point Dist=Distx.*Distx+Disty.*Disty; - for ivar=1:numel(VarVal) - VarVal{ivar}(Dist>16*ProjData.CoordMesh)=NaN;% % put to NaN interpolated positions further than 4 meshes from initial data - end - + if ~isempty(thresh2) + for ivar=1:numel(VarVal) + VarVal{ivar}(Dist>thresh2)=NaN;% % put to NaN interpolated positions further than 4 meshes from initial data + end + end if isfield(CellInfo{icell},'CheckSub') && CellInfo{icell}.CheckSub && ~isempty(vector_x_proj) ProjData.(FieldData.ListVarName{vector_x_proj})=ProjData.(FieldData.ListVarName{vector_x_proj})-VarVal{1}; @@ -1358,7 +1365,9 @@ for ilist=1:numel(ListVarName)% reshape data, excluding coordinates (ilist=1-2), TODO: rationalise VarName=ListVarName{ilist}; + VarDimName{ilist}={'coord_y','coord_x'}; ProjData.(VarName)=DataOut.(VarName); - ProjData.(VarName)(Dist>16*ProjData.CoordMesh)=NaN;% put to NaN interpolated positions further than 4 meshes from initial data - VarDimName{ilist}={'coord_y','coord_x'}; + if ~isempty(thresh2) + ProjData.(VarName)(Dist>thresh2)=NaN;% put to NaN interpolated positions further than RangeInterp from initial data + end end end Index: /trunk/src/series.m =================================================================== --- /trunk/src/series.m (revision 911) +++ /trunk/src/series.m (revision 912) @@ -1929,5 +1929,5 @@ end end - filename_joblist=fullfile(DirOAR,'0_job_list.txt');%create name of the global executable file + filename_joblist=fullfile(DirOAR,'job_list.txt');%create name of the global executable file filename_log=fullfile(DirLog,'job_list.stdout');%file for output messages of the master oar process filename_errors=fullfile(DirLog,'job_list.stderr');%file for error messages of the master oar process @@ -1947,8 +1947,8 @@ % shorter than the wall time: in the time interval 'checkpoint' (WallTimeOneJob) before the end of the allowed duration, % the oar job restarts when an individual job ends. - JobTime=CPUTime*BlockLength*nbfield_j% estimated time for one individual job (in minutes) + JobTime=CPUTime*BlockLength*nbfield_j;% estimated time for one individual job (in minutes) % wall time (in hours ) for each oar job, allowing 10 individual jobs, but limited to 23 h: WallTimeTotal=min(23,4*JobTime/60); - disp(['WallTimeTotal: ' num2str(WallTimeTotal) ' hours']) + %disp(['WallTimeTotal: ' num2str(WallTimeTotal) ' hours']) % estimated time of an individual job (in min), with a margin of error WallTimeOneJob=min(4*JobTime+10,WallTimeTotal*60/2);% estimated max time of an individual job for checkpoint @@ -3396,5 +3396,5 @@ elseif isequal(Civ,4) || isequal(Civ,5) imax=3; - elseif isequal(Civ,6) %patch2 + else%if isequal(Civ,6) %patch2 imax=4; end Index: /trunk/src/series/check_data_files.m =================================================================== --- /trunk/src/series/check_data_files.m (revision 911) +++ /trunk/src/series/check_data_files.m (revision 912) @@ -154,6 +154,10 @@ if strcmp(FileType{iview},'civx')||strcmp(FileType{iview},'civdata') if isfield(FileInfo,'CivStage') - liststage={'civ1','fix1','patch1','civ2','fix2','patch2'}; - lastfield=liststage{FileInfo.CivStage}; + liststage={'civ','fix','patch'}; + stagechoice=1+mod(FileInfo.CivStage-1,3); + iter=1+floor((FileInfo.CivStage-1)/3); + lastfield=[liststage{stagechoice} num2str(iter)]; + %liststage={'civ1','fix1','patch1','civ2','fix2','patch2'}; + %lastfield=liststage{FileInfo.CivStage}; end end Index: /trunk/src/series/civ_series.m =================================================================== --- /trunk/src/series/civ_series.m (revision 911) +++ /trunk/src/series/civ_series.m (revision 912) @@ -356,6 +356,28 @@ end end - if ~CheckOverwrite && exist(ncfile,'file') - continue% skip iteration if the mode overwrite is desactivated and the result file already exists + ncfile_out=ncfile;% by default + if isfield (Param.ActionInput,'Civ2') + i1_civ2=i1_series_Civ2(ifield); + i2_civ2=i1_civ2; + if ~isempty(i2_series_Civ2) + i2_civ2=i2_series_Civ2(ifield); + end + j1_civ2=1; + if ~isempty(j1_series_Civ2) + j1_civ2=j1_series_Civ2(ifield); + end + j2_civ2=i1_civ2; + if ~isempty(j2_series_Civ2) + j2_civ2=j2_series_Civ2(ifield); + end + if strcmp(Param.ActionInput.ListCompareMode,'PIV') + ncfile_out=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i1_civ2,i2_civ2,j1_civ2,j2_civ2); + else % displacement + ncfile_out=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i2_civ2,[],j2_civ2); + end + end + if ~CheckOverwrite && exist(ncfile_out,'file') + disp(['existing output file ' ncfile_out ' already exists, skip to next field']) + continue% skip iteration if the mode overwrite is desactivated and the result file already exists end end @@ -582,18 +604,18 @@ par_civ2.ImageA=[]; par_civ2.ImageB=[]; - i1=i1_series_Civ2(ifield); - i2=i1; - if ~isempty(i2_series_Civ2) - i2=i2_series_Civ2(ifield); - end - j1=1; - if ~isempty(j1_series_Civ2) - j1=j1_series_Civ2(ifield); - end - j2=j1; - if ~isempty(j2_series_Civ2) - j2=j2_series_Civ2(ifield); - end - ImageName_A_Civ2=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1,[],j1); +% i1_civ2=i1_series_Civ2(ifield); +% i2_civ2=i1_civ2; +% if ~isempty(i2_series_Civ2) +% i2_civ2=i2_series_Civ2(ifield); +% end +% j1_civ2=1; +% if ~isempty(j1_series_Civ2) +% j1_civ2=j1_series_Civ2(ifield); +% end +% j2_civ2=i1_civ2; +% if ~isempty(j2_series_Civ2) +% j2_civ2=j2_series_Civ2(ifield); +% end + ImageName_A_Civ2=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_civ2,[],j1_civ2); if strcmp(ImageName_A_Civ2,ImageName_A) && isequal(FrameIndex_A_Civ1(ifield),FrameIndex_A_Civ2(ifield)) @@ -602,5 +624,5 @@ [par_civ2.ImageA,VideoObject_A] = read_image(ImageName_A_Civ2,FileType_A,VideoObject_A,FrameIndex_A_Civ2(ifield)); end - ImageName_B_Civ2=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2,[],j2); + ImageName_B_Civ2=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_civ2,[],j2_civ2); if strcmp(ImageName_B_Civ2,ImageName_B) && isequal(FrameIndex_B_Civ1(ifield),FrameIndex_B_Civ2) par_civ2.ImageB=par_civ1.ImageB; @@ -608,9 +630,9 @@ [par_civ2.ImageB,VideoObject_B] = read_image(ImageName_B_Civ2,FileType_B,VideoObject_B,FrameIndex_B_Civ2(ifield)); end - if strcmp(Param.ActionInput.ListCompareMode,'PIV') - ncfile=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i1,i2,j1,j2); - else % displacement - ncfile=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i2,[],j2); - end +% if strcmp(Param.ActionInput.ListCompareMode,'PIV') +% ncfile_out=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i1,i2,j1,j2); +% else % displacement +% ncfile_out=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i2,[],j2); +% end par_civ2.ImageWidth=FileInfo_A.Width; par_civ2.ImageHeight=FileInfo_A.Height; @@ -712,5 +734,5 @@ Civ2_Dt=1; else - Civ2_Dt=time(i2+1,j2+1)-time(i1+1,j1+1); + Civ2_Dt=time(i2_civ2+1,j2_civ2+1)-time(i1_civ2+1,j1_civ2+1); end end @@ -737,8 +759,8 @@ Data.Civ2_ImageB=ImageName_B; if strcmp(Param.ActionInput.ListCompareMode,'displacement') - Data.Civ2_Time=time(i2+1,j2+1);% the time is the time of the secodn image + Data.Civ2_Time=time(i2_civ2+1,j2_civ2+1);% the time is the time of the secodn image Data.Civ2_Dt=1;% time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading else - Data.Civ2_Time=(time(i2+1,j2+1)+time(i1+1,j1+1))/2; + Data.Civ2_Time=(time(i2_civ2+1,j2_civ2+1)+time(i1_civ2+1,j1_civ2+1))/2; Data.Civ2_Dt=Civ2_Dt; end @@ -863,7 +885,7 @@ %% write result in a netcdf file if requested if CheckOutputFile - errormsg=struct2nc(ncfile,Data); + errormsg=struct2nc(ncfile_out,Data); if isempty(errormsg) - disp([ncfile ' written']) + disp([ncfile_out ' written']) else disp(errormsg) Index: /trunk/src/set_object.m =================================================================== --- /trunk/src/set_object.m (revision 911) +++ /trunk/src/set_object.m (revision 912) @@ -38,5 +38,5 @@ function varargout = set_object(varargin) -% Last Modified by GUIDE v2.5 15-Jun-2015 19:51:15 +% Last Modified by GUIDE v2.5 16-Jun-2015 00:33:59 % Begin initialization code - DO NOT REFRESH @@ -307,4 +307,5 @@ set(handles.num_DY,'Visible','off') set(handles.num_DZ,'Visible','off') +set(handles.num_RangeInterp,'Visible','off') switch ObjectStyle @@ -322,4 +323,5 @@ set(handles.num_DX,'Visible','on') set(handles.num_DX,'TooltipString','num_DX: mesh for the interpolated field along the line') + set(handles.num_RangeInterp,'Visible','on') end case {'rectangle','ellipse'} @@ -341,11 +343,12 @@ set(handles.num_DX,'Visible','on') set(handles.num_DY,'Visible','on') + set(handles.num_RangeInterp,'Visible','on') else set(handles.num_DX,'Visible','off') set(handles.num_DY,'Visible','off') end - if isequal(ProjMode,'interp_lin') - set(handles.num_DZ,'Visible','on') - end +% if isequal(ProjMode,'interp_lin') +% set(handles.num_DZ,'Visible','on') +% end case {'volume'} set(handles.num_RangeX_1,'Visible','on') @@ -372,8 +375,8 @@ % set default values read in the plot of uvmat to initiate the mesh if isequal(ProjMode,'interp_lin')|| isequal(ProjMode,'interp_tps') + huvmat=findobj('Tag','uvmat');%find the current uvmat interface handle + UvData=get(huvmat,'UserData');%Data associated to the current uvmat interface if isempty(str2num(get(handles.num_DX,'String')))||isempty(str2num(get(handles.num_DY,'String'))); - huvmat=findobj('Tag','uvmat');%find the current uvmat interface handle - UvData=get(huvmat,'UserData');%Data associated to the current uvmat interface - Field=UvData.Field; +% Field=UvData.Field; if isfield(UvData.Field,'CoordMesh')&&~isempty(UvData.Field.CoordMesh) set(handles.num_DX,'String',num2str(UvData.Field.CoordMesh)) @@ -387,4 +390,7 @@ set(handles.CoordUnit,'String',Field.CoordUnit) end + end + if isempty(str2num(get(handles.num_RangeInterp,'String'))) + set(handles.num_RangeInterp,'String',num2str(3*UvData.Field.CoordMesh))% default interpolationlength= 3 meshes end end @@ -416,5 +422,5 @@ huvmat=findobj('Tag','uvmat');%find the current uvmat interface handle UvData=get(huvmat,'UserData');%Data associated to the current uvmat interface -if isfield(UvData,'X') & isfield(UvData,'Y') & isfield(UvData,'Z') +if isfield(UvData,'X') && isfield(UvData,'Y') && isfield(UvData,'Z') Z=norm_plane(1)*(UvData.X)+norm_plane(2)*(UvData.Y)+norm_plane(3)*(UvData.Z); set(handles.z_slider,'Min',min(Z)) @@ -691,6 +697,10 @@ t=struct2xml(Object); t=set(t,1,'name','ProjObject'); - save(t,FullName) - msgbox_uvmat('CONFIRMATION',[FullName ' saved']) + try + save(t,FullName) + msgbox_uvmat('CONFIRMATION',[FullName ' saved']) + catch ME + msgbox_uvmat('ERROR',ME.message) + end end end @@ -801,21 +811,2 @@ function num_RangeInterp_Callback(hObject, eventdata, handles) -% hObject handle to num_RangeInterp (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles structure with handles and user data (see GUIDATA) - -% Hints: get(hObject,'String') returns contents of num_RangeInterp as text -% str2double(get(hObject,'String')) returns contents of num_RangeInterp as a double - - -% --- Executes during object creation, after setting all properties. -function num_RangeInterp_CreateFcn(hObject, eventdata, handles) -% hObject handle to num_RangeInterp (see GCBO) -% eventdata reserved - to be defined in a future version of MATLAB -% handles empty - handles not created until after all CreateFcns called - -% Hint: edit controls usually have a white background on Windows. -% See ISPC and COMPUTER. -if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) - set(hObject,'BackgroundColor','white'); -end