Index: trunk/src/get_field.m =================================================================== --- trunk/src/get_field.m (revision 1196) +++ trunk/src/get_field.m (revision 1197) @@ -627,14 +627,6 @@ var_component=find(test_component);% list of variable indices elligible as unstructured coordinates var_coord=find(test_coord);% % list of variable indices elligible as gridded coordinates -% index_coord=[]; -% index_component=[]; -% for iscalar=1:numel(scalar_index) -% index_component=[index_component find(var_component==scalar_index(iscalar),1)]; -% index_coord=[index_coord find(var_coord==scalar_index(iscalar),1)]; -% end -% var_component(index_component)=[]; -% var_coord(index_coord)=[]; ListCoord=Field.Display.ListVarName([var_coord var_component]); -%coord_val=zeros(size(ListCoord)); + %% set default selection for grid coordinates @@ -903,11 +895,12 @@ function Coord_x_Callback(hObject, DimCell, handles) -index=get(handles.Coord_x,'Value'); string=get(handles.Coord_x,'String'); -VarName=string{index}; +VarName=string{get(handles.Coord_x,'Value')}; if ~ischar(DimCell)% no dimension as input update_field(handles,VarName)% update the display of the variable 'VarName' and its dimensions in the general list of variables end -if isequal(get(handles.FieldOption,'Value'),1) +MenuFieldOption=get(handles.FieldOption,'String'); +FieldOption=MenuFieldOption{get(handles.FieldOption,'Value')}; +if strcmp(FieldOption,'1D_plot') set_coord_y_options(handles,VarName) end Index: trunk/src/read_field.m =================================================================== --- trunk/src/read_field.m (revision 1196) +++ trunk/src/read_field.m (revision 1197) @@ -16,9 +16,10 @@ % FileType: type of file, as determined by the function get_file_info.m % ParamIn: movie object or Matlab structure of input parameters -% .FieldName: name (char string) of the input field (for Civx data) -% .VelType: char string giving the type of velocity data ('civ1', 'filter1', 'civ2'...) -% .ColorVar: variable used for vector color +% .VelType: (for civdata) char string giving the type of velocity data ('civ1', 'filter1', 'civ2'...) +% .FieldName:(for general netcdf files) name (char string) or list of names (cell of char strings) of fields to read +% .ColorVar:(for general netcdf files) variable possibly 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 'frame_index' +% .TimeVarName: name of the variable considered as 'time' % frame_index: frame number for movies or multidimensional netcdf files with dim >2 % Index: trunk/src/series.m =================================================================== --- trunk/src/series.m (revision 1196) +++ trunk/src/series.m (revision 1197) @@ -3067,8 +3067,9 @@ TimeTable{LineIndex,5}=get_time(Param.IndexRange.MaxIndex_i(LineIndex),MaxIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName); % Max time 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')])% A VERIFIER !!!!!! - set(handles.FileIndex,'String','') + TimeName=['var:' GetFieldData.Time.TimeName]; + % set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName]) +% set(handles.NomType,'String','*') +% set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!! +% set(handles.FileIndex,'String','') ParamIn.TimeVarName=GetFieldData.Time.TimeName; case 'matrix_index' @@ -3361,7 +3362,8 @@ %------------------------------------------------------------------------ function CheckMask_Callback(hObject, eventdata, handles) - +% SeriesData=get(handles.series,'UserData'); if get(handles.CheckMask,'Value') + set(handles.DeleteMask,'Visible','on') Param=read_GUI_series(handles); % displayed parameters @@ -3379,16 +3381,21 @@ %checkmask=zeros(NbView,1); for iview=1:NbView - checkmask=0; + checkmask=false; FirstFileName=fullfile_uvmat(Param.InputTable{iview,1},Param.InputTable{iview,2},Param.InputTable{iview,3},... Param.InputTable{iview,5},Param.InputTable{iview,4},i1,i2,j1,j2); - % [FileInfo,VideoObject]=get_file_info(FirstFileName); + [FileInfo,VideoObject]=get_file_info(FirstFileName); -% Data=nc2struct(FirstFileName); - if isfield(Data,'Civ2_Mask') - if exist(Data.Civ2_Mask,'file') - MaskTable{iview,1}=Data.Civ2_Mask; - checkmask=1; + % Data=nc2struct(FirstFileName); + if isfield(FileInfo,'MaskFile') && isfield(FileInfo,'MaskExt') + if isfield(FileInfo,'MaskNbSlice')&& exist([FileInfo.MaskFile '_1' FileInfo.MaskExt],'file') + MaskTable{iview,1}=[FileInfo.MaskFile '_1' FileInfo.MaskExt]; + MaskTable{iview,2}=num2str(FileInfo.MaskNbSlice); + checkmask=true; + elseif exist([FileInfo.MaskFile FileInfo.MaskExt],'file') + MaskTable{iview,1}=[FileInfo.MaskFile FileInfo.MaskExt]; + MaskTable{iview,2}=''; + checkmask=true; end end @@ -3410,6 +3417,6 @@ end set(handles.MaskTable,'Data',MaskTable) - set(handles.CheckMask,'Value',0) -end +end + % % if ~isempty(NewMask) Index: trunk/src/series/civ_series.m =================================================================== --- trunk/src/series/civ_series.m (revision 1196) +++ trunk/src/series/civ_series.m (revision 1197) @@ -276,5 +276,4 @@ time_patch2=0; if ~isempty(RUNHandle)% update the waitbar in interactive mode with GUI series (checkrun=1) - update_waitbar(WaitbarHandle,ifield/NbField) if checkrun && ~strcmp(get(RUNHandle,'BusyAction'),'queue') disp('program stopped by user') Index: trunk/src/series/merge_proj.m =================================================================== --- trunk/src/series/merge_proj.m (revision 1196) +++ trunk/src/series/merge_proj.m (revision 1197) @@ -354,4 +354,8 @@ end [MaskData,~,errormsg] = read_field(maskname,'image'); + if ~isempty(errormsg) + disp(['error reading ' maskname ' :' errormsg]) + return + end if ~isempty(NbSlice_calib) MaskData.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform Index: trunk/src/series/turb_correlation_x.m =================================================================== --- trunk/src/series/turb_correlation_x.m (revision 1196) +++ trunk/src/series/turb_correlation_x.m (revision 1197) @@ -94,9 +94,9 @@ %% root input file(s) name, type and index series -RootPath=Param.InputTable(:,1); -RootFile=Param.InputTable(:,3); -SubDir=Param.InputTable(:,2); -NomType=Param.InputTable(:,4); -FileExt=Param.InputTable(:,5); +RootPath=Param.InputTable{:,1}; +RootFile=Param.InputTable{:,3}; +%SubDir=Param.InputTable(:,2); +NomType=Param.InputTable{1,4}; +%FileExt=Param.InputTable(:,5); [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); %%%%%%%%%%%% @@ -108,62 +108,23 @@ % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices %%%%%%%%%%%% NbView=1 : a single input series -NbView=numel(i1_series);%number of input file series (lines in InputTable) +%NbView=numel(i1_series);%number of input file series (lines in InputTable) NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) NbField_i=size(i1_series{1},2); %nb of fields for the i index NbField=NbField_j*NbField_i; %total number of fields -%% determine the file type on each line from the first input file -ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; -NcTypeOptions={'netcdf','civx','civdata'}; -for iview=1:NbView - if ~exist(filecell{iview,1}','file') - msgbox_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist']) - return - end - [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1}); - FileType{iview}=FileInfo{iview}.FileType; - CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images - CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files - if ~isempty(j1_series{iview}) - frame_index{iview}=j1_series{iview}; - else - frame_index{iview}=i1_series{iview}; - end -end - -%% calibration data and timing: read the ImaDoc files -XmlData=[]; -[XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series); -if size(time,1)>1 - diff_time=max(max(diff(time))); - if diff_time>0 - msgbox_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)]) - end -end - -%% coordinate transform or other user defined transform -transform_fct='';%default -if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName) - addpath(Param.FieldTransform.TransformPath) - transform_fct=str2func(Param.FieldTransform.TransformName); - rmpath(Param.FieldTransform.TransformPath) -end - -%%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% - % EDIT FROM HERE - -%% check the validity of input file types -if CheckImage{1} - FileExtOut='.png'; % write result as .png images for image inputs -elseif CheckNc{1} - FileExtOut='.nc';% write result as .nc files for netcdf inputs +%% determine the file type on each line from the first input file + +[FileInfo,MovieObject]=get_file_info(filecell{1,1}); +FileType=FileInfo.FileType; + +if ~isempty(j1_series{1}) + frame_index=j1_series{1}; else - msgbox_uvmat('ERROR',['invalid file type input ' FileType{1}]) - return -end - + frame_index=i1_series{1}; +end %% settings for the output file -NomTypeOut=nomtype2pair(NomType{1});% determine the index nomenclature type for the output file +FileExtOut='.nc';% write result as .nc files for netcdf inputs +NomTypeOut=nomtype2pair(NomType);% determine the index nomenclature type for the output file first_i=i1_series{1}(1); last_i=i1_series{1}(end); @@ -177,8 +138,13 @@ %% Set field names and velocity types InputFields{1}=[];%default (case of images) -if isfield(Param,'InputFields') - InputFields{1}=Param.InputFields; -end - +%%%%%%%%%%%%%%%%%%%%% +if isfield(Param.IndexRange,'TimeSource') && find(regexp(Param.IndexRange.TimeSource,'^var:'))==1 + Param.InputFields.TimeVarName=regexprep(Param.IndexRange.TimeSource,'^var:',''); +end +%%%%%%%%%%%%%%%%%%%% +% if isfield(Param,'InputFields') +% InputFields{1}=Param.InputFields; +% end +Param.InputFields.FieldName={'Uprime','Vprime'}; nbfiles=0; nbmissing=0; @@ -197,10 +163,14 @@ disp('loop for mean started') for index=1:NbField - update_waitbar(WaitbarHandle,index/NbField) - if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue') - disp('program stopped by user') - break - end - [Field,tild,errormsg] = read_field(filecell{1,index},FileType{iview},InputFields{iview},frame_index{iview}(index)); + % if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue') + % disp('program stopped by user') + % break + % end + [Field,~,errormsg] = read_field(filecell{1,index},FileType,Param.InputFields,frame_index(index)); + + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + Field.U=Field.Uprime; + Field.V=Field.Vprime; + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% if index==1 %first field if ~isfield(Field,'U')||~isfield(Field,'V') @@ -208,9 +178,10 @@ return end + [npy,npx]=size(Field.U); UMean=zeros(npy,npx); VMean=zeros(npy,npx); Counter=zeros(npy,npx); - % transcripts the global attributes + % transcripts the global attributes if isfield(Field,'ListGlobalAttribute') DataOut.ListGlobalAttribute= Field.ListGlobalAttribute; @@ -236,11 +207,11 @@ disp('loop for correlation started') for index=1:NbField - update_waitbar(WaitbarHandle,index/NbField) if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue') disp('program stopped by user') break end - [Field,tild,errormsg] = read_field(filecell{1,index},FileType{iview},InputFields{iview},frame_index{iview}(index)); - + [Field,~,errormsg] = read_field(filecell{1,index},FileType,Param.InputFields,frame_index(index)); + Field.U=Field.Uprime; + Field.V=Field.Vprime; %%%%%%%%%%%% MAIN RUNNING OPERATIONS %%%%%%%%%%%% if index==1 %first field @@ -281,5 +252,5 @@ VVCorr(ishift+npcorr+1,:,:)=Field.V.*V_shift; UVCorr(ishift+npcorr+1,:,:)=Field.U.*V_shift; - FFCorr(ishift+npcorr+1,:,:)=FF | FF_shift; + FFCorr(ishift+npcorr+1,:,:)=FF | FF_shift; end DataOut.UUCorr=DataOut.UUCorr+UUCorr; @@ -322,5 +293,5 @@ %% writing the result file as netcdf file -OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j,last_j); +OutputFile=fullfile_uvmat(RootPath,OutputDir,RootFile,FileExtOut,NomTypeOut,first_i,last_i,first_j,last_j); %case of netcdf input file , determine global attributes errormsg=struct2nc(OutputFile,DataOut); %save result file @@ -331,7 +302,2 @@ end - -%% open the result file with uvmat (in RUN mode) -if checkrun - uvmat(OutputFile)% open the last result file with uvmat -end