Index: trunk/src/find_file_series.m =================================================================== --- trunk/src/find_file_series.m (revision 1195) +++ trunk/src/find_file_series.m (revision 1196) @@ -50,5 +50,5 @@ %% get input root name and info on the input file if isempty(regexp(FilePath,'^http://','once'))% case of usual file input -fullfileinput=fullfile(FilePath,fileinput);% input file name with path + fullfileinput=fullfile(FilePath,fileinput);% input file name with path else fullfileinput=[FilePath '/' fileinput]; % case of web input @@ -216,10 +216,10 @@ if ~isempty(ind_select) - [tild,ifile_min]=min(ref_ij(ind_select)); - [tild,tild,tild,tild,tild,tild,tild,tild,NomType]=fileparts_uvmat(ListFiles{ind_select(ifile_min)});% update the representation of indices (number of 0 before the number) + [~,ifile_min]=min(ref_ij(ind_select)); + [~,~,~,~,~,~,~,~,NomType]=fileparts_uvmat(ListFiles{ind_select(ifile_min)});% update the representation of indices (number of 0 before the number) NomType=regexprep(NomType,['^' NomTypePref],''); %% update the file type if the input file does not exist (pb of 0001) if isempty(FileInfo.FileName) - [FileInfo,MovieObject]=get_file_info(fullfile(FilePath,ListFiles{ifile_min})); + [FileInfo,MovieObject]=get_file_info(fullfile(FilePath,ListFiles{ind_select(ifile_min)})); end end @@ -293,5 +293,5 @@ if size(i2_series,3)>1 %pairs i1 -i2 diff_index=abs(i2_series-i1_series); - [tild,ind_pair]=sort(diff_index,3,'descend'); + [~,ind_pair]=sort(diff_index,3,'descend'); for ref_i=1:size(i1_series,1) for ref_j=1:size(j1_series,2) @@ -305,5 +305,5 @@ elseif size(j2_series,3)>1 %pairs j1 -j2 diff_index=abs(j2_series-j1_series); - [tild,ind_pair]=sort(diff_index,3,'descend'); + [~,ind_pair]=sort(diff_index,3,'descend'); for ref_i=1:size(i1_series,1) for ref_j=1:size(j1_series,2) Index: trunk/src/get_field.m =================================================================== --- trunk/src/get_field.m (revision 1195) +++ trunk/src/get_field.m (revision 1196) @@ -115,5 +115,5 @@ check_singleton(idim)=isequal(Field.DimValue(dim_index),1);%check_singleton=1 for singleton end - Field.Check0D(ilist)=(isequal(check_singleton,ones(1,NbDim)))||(~isequal(Field.VarType(ilist),4)&&~isequal(Field.VarType(ilist),5)&&~isequal(Field.VarType(ilist),6));% =1 if the variable reduces to a single value + Field.Check0D(ilist)=isequal(check_singleton,ones(1,NbDim));% =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 @@ -123,5 +123,5 @@ Field.VarAttribute={}; end -if numel(Field.VarAttribute)=ilist && isfield(Field.Display.VarAttribute{ilist},'Role') Role=Field.Display.VarAttribute{ilist}.Role; if strcmp(Role,'coord_x')||strcmp(Role,'coord_y') - test_coord(ilist)=1; + test_coord(ilist)=true; end end dimnames=Field.Display.VarDimName{ilist}; %list of dimensions for variable #ilist if numel(dimnames)==1 && strcmp(dimnames{1},Field.Display.ListVarName{ilist})%dimension variable - test_coord(ilist)=1; + test_coord(ilist)=true; end end @@ -529,5 +529,5 @@ set(handles.Coord_y,'String',ListCoord) val_y=1; -if strcmp(VarName,ListCoord{1})&& numel(ListCoord)>=2 +if ~isempty(ListCoord) && strcmp(VarName,ListCoord{1})&& numel(ListCoord)>=2 val_y=2; end Index: trunk/src/get_file_info.m =================================================================== --- trunk/src/get_file_info.m (revision 1195) +++ trunk/src/get_file_info.m (revision 1196) @@ -207,6 +207,10 @@ [Data,tild,tild,errormsg]=nc2struct(fileinput,[]); if isempty(errormsg) - if isfield(Data,'Conventions') && ~isempty(find(strcmp(Data.Conventions,{'uvmat/civdata','uvmat/civdata/compress'}), 1)) + if isfield(Data,'Conventions') && ismember(Data.Conventions,{'uvmat/civdata','uvmat/civdata/compress'}) + if strcmp(Data.Conventions,'uvmat/civdata') FileInfo.FileType='civdata'; % test for civ velocity fields + else + FileInfo.FileType='civdata_compress'; % test for civ velocity fields + end FileInfo.CivStage=Data.CivStage; MaskFile=''; @@ -285,9 +289,9 @@ case {'image','multimage','video','mmreader','rdvision','image_DaVis','cine_phantom','telopsIR'} FileInfo.FieldType='image'; - case {'civdata','pivdata_fluidimage'} + case {'civdata','civdata_compress','pivdata_fluidimage'} FileInfo.FieldType='civdata'; end -if strcmp(FileInfo.FieldType,'image') || ismember (FileInfo.FileType,{'mat','netcdf','civdata'}) +if strcmp(FileInfo.FieldType,'image') || ismember (FileInfo.FileType,{'mat','netcdf','civdata','civdata_compress'}) FileInfo.FileIndexing='on'; % allow to detect file index for scanning series else Index: trunk/src/nc2struct.m =================================================================== --- trunk/src/nc2struct.m (revision 1195) +++ trunk/src/nc2struct.m (revision 1196) @@ -282,11 +282,14 @@ Data.(VarName)=squeeze(Data.(VarName));%remove singeton dimension else - disp(VarName) - xtype(var_index(ivar)) +% disp(VarName) +% xtype(var_index(ivar)) Data.(VarName)=netcdf.getVar(nc,var_index(ivar)-1); %read the whole variable data - end - Data.(VarName)=double(Data.(VarName)); %transform all variables to double pecision + end + if xtype(var_index(ivar))==5 %single precision + Data.(VarName)=double(Data.(VarName)); %transform all variables to double pecision + end + % Data.(VarName)=double(Data.(VarName)); %transform all variables to double pecision if isfield(Data,'VarAttribute') && numel(Data.VarAttribute)>=ivar && isfield(Data.VarAttribute{ivar},'scale_factor') - Data.(VarName)=Data.VarAttribute{ivar}.scale_factor *Data.(VarName); + Data.(VarName)=Data.VarAttribute{ivar}.scale_factor *double(Data.(VarName)); end end Index: trunk/src/read_civdata.m =================================================================== --- trunk/src/read_civdata.m (revision 1195) +++ trunk/src/read_civdata.m (revision 1196) @@ -121,6 +121,6 @@ end if strcmp(Data.Conventions,'uvmat/civdata/compress') - Field.X=Field.X-0.5+Field.U/2;% shift to the convected position - Field.Y=Field.Y-0.5+Field.V/2; + Field.X=double(Field.X)-0.5+Field.U/2;% shift to the convected position + Field.Y=double(Field.Y)-0.5+Field.V/2; end switch VelTypeOut Index: trunk/src/read_field.m =================================================================== --- trunk/src/read_field.m (revision 1195) +++ trunk/src/read_field.m (revision 1196) @@ -81,5 +81,5 @@ %% distingush different input file types switch FileType - case {'civdata','civdata_3D'}% format for civ results + case {'civdata','civdata_compress','civdata_3D'}% format for civ results [Field,ParamOut.VelType,errormsg]=read_civdata(FileName,InputField,ParamIn.VelType,frame_index); if ~isempty(errormsg),errormsg=['read_civdata / ' errormsg];return,end Index: trunk/src/series.m =================================================================== --- trunk/src/series.m (revision 1195) +++ trunk/src/series.m (revision 1196) @@ -609,7 +609,7 @@ else [XmlFileName,Rank]=find_imadoc(InputTable{iview,1},InputTable{iview,2}); - if ~isempty(XmlFileName) && Rank==0 + if ~isempty(XmlFileName) XmlData=read_imadoc(XmlFileName); - if ~isempty(XmlData.FileSeries) + if Rank==0 && ~isempty(XmlData.FileSeries) set(handles.Relabel,'Visible','on') answer='Yes'; @@ -637,9 +637,9 @@ end [Param.FileInfo,VideoObject]=get_file_info(FirstFile); + else + set(handles.Relabel,'Value',0) end end Param.XmlData=XmlData; - else - set(handles.Relabel,'Value',0) end end @@ -1086,10 +1086,15 @@ nbfield=nbfield-1; %remove the possible index 0 nbfield_j=nbfield_j-1; %remove the possible index 0 - MaxIndex_i=get(handles.MaxIndex_i,'Data'); - MaxIndex_j=get(handles.MaxIndex_j,'Data'); - MaxIndex_i(1,:)=nbfield; - MaxIndex_j(1,:)=nbfield_j; - MinIndex_i(1,:)=1; - MinIndex_j(1,:)=1; +% MaxIndex_i=get(handles.MaxIndex_i,'Data'); +% MaxIndex_j=get(handles.MaxIndex_j,'Data'); +% MaxIndex_i(1,:)=nbfield; +% MaxIndex_j(1,:)=nbfield_j; +% MinIndex_i(1,:)=1; +% MinIndex_j(1,:)=1; + MaxIndex_i=nbfield; + MaxIndex_j=nbfield_j; + MinIndex_i=1; + MinIndex_j=1; + first_i=str2double(get(handles.num_first_i,'String')); @@ -2601,9 +2606,9 @@ iview_netcdf=[]; for iview=1:numel(SeriesData.FileInfo) - if strcmp(SeriesData.FileInfo{iview}.FileType,'civx')||strcmp(SeriesData.FileInfo{iview}.FileType,'civdata') - iview_civ=[iview_civ iview]; - iview_netcdf=[iview_netcdf iview];% all nc files, icluding civ - elseif strcmp(SeriesData.FileInfo{iview}.FileType,'netcdf') - iview_netcdf=[iview_netcdf iview]; + if ismember(SeriesData.FileInfo{iview}.FileType,{'civx','civdata','civdata_compress','netcdf'}) + iview_netcdf=[iview_netcdf iview]; + if ismember(SeriesData.FileInfo{iview}.FileType,{'civx','civdata','civdata_compress'}) + iview_civ=[iview_civ iview]; + end end end @@ -2612,5 +2617,5 @@ if ~iscell(FieldList),FieldList={FieldList};end FieldList_1=get(handles.FieldName_1,'String'); % previous list as default -if ~iscell(FieldList_1),FieldList_1={FieldList_1};end +% if ~iscell(FieldList_1),FieldList_1={FieldList_1};end CheckPivData_1=0; % indicate whether FieldName_1 has been updated with civ data, 0 by default handles_coord=[handles.Coord_x handles.Coord_y handles.Coord_z handles.Coord_x_title handles.Coord_y_title handles.Coord_z_title]; @@ -2977,5 +2982,5 @@ field_index=get(handles.FieldName,'Value'); field=FieldListInit{field_index(1)}; -if isequal(field,'add_field...') +if strcmp(field,'add_field...') FieldListInit(field_index(1))=[]; SeriesData=get(handles.series,'UserData'); @@ -2984,5 +2989,5 @@ end % input line for which the field choice is relevant - iview=find(ismember(FileType,{'netcdf','civx','civdata'})); % all nc files, icluding civ + iview=find(ismember(FileType,{'netcdf','civx','civdata','civdata_compress'})); % all nc files, icluding civ hget_field=findobj(allchild(0),'name','get_field'); if ~isempty(hget_field) @@ -3861,38 +3866,42 @@ %------------------------------------------------------------------------ % --- set the visibility of relevant velocity type menus: -function menu=set_veltype_display(Civ,FileType) +function menu=set_veltype_display(CivStage,FileType) %------------------------------------------------------------------------ if ~exist('FileType','var') FileType='civx'; end +imin=1; switch FileType case 'civx' menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'}; - if isequal(Civ,0) + if isequal(CivStage,0) imax=0; - elseif isequal(Civ,1) || isequal(Civ,2) + elseif isequal(CivStage,1) || isequal(CivStage,2) imax=1; - elseif isequal(Civ,3) + elseif isequal(CivStage,3) imax=3; - elseif isequal(Civ,4) || isequal(Civ,5) + elseif isequal(CivStage,4) || isequal(CivStage,5) imax=4; - elseif isequal(Civ,6) %patch2 + elseif isequal(CivStage,6) %patch2 imax=6; end - case 'civdata' + case {'civdata','civdata_compress'} menu={'civ1';'filter1';'civ2';'filter2'}; - if isequal(Civ,0) + if isequal(CivStage,0) imax=0; - elseif isequal(Civ,1) || isequal(Civ,2) + elseif isequal(CivStage,1) || isequal(CivStage,2) imax=1; - elseif isequal(Civ,3) + elseif isequal(CivStage,3) imax=2; - elseif isequal(Civ,4) || isequal(Civ,5) + elseif isequal(CivStage,4) || isequal(CivStage,5) imax=3; - else%if isequal(Civ,6) %patch2 + else%if isequal(CivStage,6) %patch2 imax=4; end -end -menu=menu(1:imax); + if strcmp(FileType,'civdata_compress') && CivStage>=4 + imin=CivStage-3; + end +end +menu=menu(imin:imax); Index: trunk/src/series/civ_input.m =================================================================== --- trunk/src/series/civ_input.m (revision 1195) +++ trunk/src/series/civ_input.m (revision 1196) @@ -186,5 +186,5 @@ % CoordUnit='';%default % pxcm_search=1; -if isfield(SeriesData,'Time') &&numel(SeriesData.Time')>=1 && ~isempty(SeriesData.Time{1}) +if isfield(SeriesData,'Time') && numel(SeriesData.Time')>=1 && ~isempty(SeriesData.Time{1}) time=SeriesData.Time{1}; end @@ -192,13 +192,4 @@ TimeUnit=Param.IndexRange.TimeUnit; end -% if isfield(SeriesData,'GeometryCalib') -% tsai=SeriesData.GeometryCalib; -% if isfield(tsai,'fx_fy') -% pxcm_search=max(tsai.fx_fy(1),tsai.fx_fy(2));%pixels:cm estimated for the search range -% end -% if isfield(tsai,'CoordUnit') -% CoordUnit=tsai.CoordUnit; -% end -% end %% timing display @@ -249,4 +240,9 @@ set(handles.(ListOptions{index}),'value',0) fill_civ_input(Data,handles); %fill civ_input with the parameters retrieved from an input Civ file + if index<=3 + set(handles.(ListOptions{index}),'Visible','off') + PanelTag=regexprep(ListOptions{index},'Check','') + set(handles.(PanelTag),'Visible','off') + end end if isempty(FileInfo) @@ -259,10 +255,7 @@ set(handles.(ListOptions{index}),'String',regexprep(ListOptions{index},'Check','redo ')) end -% for index = ind_opening+1:6 -% set(handles.(ListOptions{index}),'value',1) -% end set(handles.CheckCiv3,'Visible','off')% make visible the switch 'iterate/repet' for Civ2. - set(handles.CheckCiv3,'Value',0)% select'iterate/repet' by default - else + %set(handles.CheckCiv3,'Value',0)% select'iterate/repet' by default + else %civ3 proposed for index = 1:3 set(handles.(ListOptions{index}),'value',0) @@ -273,4 +266,5 @@ set(handles.CheckCiv3,'Visible','on')% make visible the switch 'iterate/repet' for Civ2. set(handles.CheckCiv3,'Value',1)% select'iterate/repet' by default + set(handles.CheckCiv3,'String',{'civ3'})% select'iterate/repet' by default end checkrefresh=1; @@ -631,9 +625,6 @@ for ilist=1:length(options) if checkbox(ilist) -% set(handles.(options{ilist}),'Visible','on') set(handles.(options{ilist}),'Enable','on') -% set(handles.(['Check' options{ilist}]),'Strin else -% set(handles.(options{ilist}),'Visible','off') set(handles.(options{ilist}),'Enable','off') end Index: trunk/src/series/civ_series.m =================================================================== --- trunk/src/series/civ_series.m (revision 1195) +++ trunk/src/series/civ_series.m (revision 1196) @@ -974,5 +974,5 @@ Data.VarAttribute{4}.scale_factor=1/inv_scale_factor; Data.VarAttribute{5}.Role='ancillary'; - Data.VarAttribute{5}.scale_factor=1/inv_scale_factor; + Data.VarAttribute{5}.scale_factor=1/100;%scla factor for correlation Data.VarAttribute{6}.Role='errorflag'; Data.X=uint16(Civ_X); @@ -980,11 +980,9 @@ Data.U=int16(inv_scale_factor*Civ_U); Data.V=int16(inv_scale_factor*Civ_V); - Data.C=uint8(inv_scale_factor*Civ_C); + Data.C=uint8(100*Civ_C); Data.FF=uint8(Civ_FF); + % add smoothed field if ptch is done if (Param.ActionInput.CheckPatch1 && ~Param.ActionInput.CheckCiv2) ||Param.ActionInput.CheckPatch2 nbvar=6; - % Data.ListVarName=[Data.ListVarName {'U_smooth','V_smooth','SubRange','NbCentres','Coord_tps','U_tps','V_tps'}]; - % Data.VarDimName=[Data.VarDimName {'nb_vec','nb_vec',{'nb_coord','nb_bounds','nb_subdomain'},{'nb_subdomain'},... - % {'nb_tps','nb_coord','nb_subdomain'},{'nb_tps','nb_subdomain'},{'nb_tps','nb_subdomain'}}]; Data.ListVarName=[Data.ListVarName {'U_smooth','V_smooth'}]; Data.VarDimName=[Data.VarDimName {'nb_vec','nb_vec'}]; @@ -995,19 +993,5 @@ Data.U_smooth=int16(inv_scale_factor*Civ_U_smooth); Data.V_smooth=int16(inv_scale_factor*Civ_V_smooth); - % Data.VarAttribute{nbvar+5}.Role='coord_tps'; - % Data.VarAttribute{nbvar+6}.Role='vector_x'; - % Data.VarAttribute{nbvar+7}.Role='vector_y'; - % Data.U_smooth=int16(inv_scale_factor*U_smooth); - % Data.V_smooth=int16(inv_scale_factor*V_smooth); - % Data.SubRange=SubRange; - % Data.NbCentres=NbCentres; - % Data.Coord_tps=Coord_tps; - % Data.U_tps=U_tps; - % Data.V_tps=V_tps; - end - % - % if ~isempty(inv_scale_factor) - % Data=compress_data(Data,inv_scale_factor);% compress the data using integers instead of (single precision)floating reals - % end + end errormsg=struct2nc(ncfile_out,Data); if isempty(errormsg) Index: trunk/src/series/merge_proj.m =================================================================== --- trunk/src/series/merge_proj.m (revision 1195) +++ trunk/src/series/merge_proj.m (revision 1196) @@ -92,4 +92,25 @@ msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist']) end + VelocityRange=[];%default + VelGradientRange=[];%default + if isfield(Param,'ActionInput') + if isfield(Param.ActionInput,'VelocityRange') + VelocityRange= Param.ActionInput.VelocityRange; + end + if isfield(Param.ActionInput,'VelGradientRange') + VelGradientRange= Param.ActionInput.VelGradientRange; + end + end + prompt = {'velocity range (max modulus) for 16 bit integer records (32 bit reals if empty)';... + 'range (max modulus) for vel derivatives (curl, div...) for 16 bit integer records (32 bit reals if empty)'}; + dlg_title = 'set scale_factor for result writing as 16 bit integer (instead of 32 bit reals by default)'; + num_lines= 2; + def = { num2str(VelocityRange),num2str(VelGradientRange)}; + answer = inputdlg(prompt,dlg_title,num_lines,def); + if isempty(answer) + return + end + ParamOut.ActionInput.VelocityRange=str2num(answer{1}); + ParamOut.ActionInput.VelGradientRange=str2num(answer{2}); return end @@ -109,4 +130,12 @@ WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series end +scale_factor_inv_uv=[]; +if isfield(Param.ActionInput,'VelocityRange') && ~isempty(Param.ActionInput.VelocityRange) + scale_factor_inv_uv=floor(32767/Param.ActionInput.VelocityRange); +end +scale_factor_inv_dudv=[]; +if isfield(Param.ActionInput,'VelGradientRange') && ~isempty(Param.ActionInput.VelGradientRange) + scale_factor_inv_dudv=floor(32767/Param.ActionInput.VelGradientRange); +end %% define the directory for result file (with path=RootPath{1}) @@ -139,5 +168,7 @@ %% determine the file type on each line from the first input file -NcTypeOptions={'netcdf','civx','civdata','pivdata_fluidimage'}; +NcTypeOptions={'netcdf','civx','civdata','civdata_compress','pivdata_fluidimage'}; +frame_index=cell(NbView,1);FileInfo=cell(NbView,1);MovieObject=cell(NbView,1);ParamIn=cell(NbView,1); +FileType=cell(NbView,1);CheckImage=zeros(NbView,1);CheckNc=zeros(NbView,1); for iview=1:NbView if ~exist(filecell{iview,1}','file') @@ -150,11 +181,11 @@ FileType{iview}='netcdf'; end - CheckImage{iview}=strcmp(FileInfo{iview}.FieldType,'image');% =1 for images - if CheckImage{iview} + CheckImage(iview)=strcmp(FileInfo{iview}.FieldType,'image');% =1 for images + if CheckImage(iview) ParamIn{iview}=MovieObject{iview}; else ParamIn{iview}=Param.InputFields; end - CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files + CheckNc(iview)=ismember(FileType{iview},NcTypeOptions);% =1 for netcdf files if ~isempty(j1_series{iview}) frame_index{iview}=j1_series{iview}; @@ -163,5 +194,5 @@ end end -if NbView >1 && max(cell2mat(CheckImage))>0 && ~isfield(Param,'ProjObject') +if NbView >1 && max(CheckImage)>0 && ~isfield(Param,'ProjObject') disp_uvmat('ERROR','projection on a common grid is needed to concatene images: use a Projection Object of type ''plane'' with ProjMode=''interp_lin''',checkrun) return @@ -201,22 +232,18 @@ end end -%%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% - % EDIT FROM HERE %% check the validity of input file types -for iview=1:NbView - if ~isequal(CheckImage{iview},1)&&~isequal(CheckNc{iview},1) - disp_uvmat('ERROR','input set of input series: need either netcdf either image series',checkrun) +if ~(CheckImage | CheckNc) + disp_uvmat('ERROR',' netcdf or image series needed as input',checkrun) return - end end %% output file type -if min(cell2mat(CheckImage))==1 && (~Param.CheckObject || strcmp(Param.ProjObject.Type,'plane')) +if min(CheckImage)==1 && (~Param.CheckObject || strcmp(Param.ProjObject.Type,'plane')) FileExtOut='.png'; %image output (input and proj result = image) else FileExtOut='.nc'; %netcdf output end -if isempty(j1_series{1}) +if isempty(j1_series{1})||max(j1_series{1})==1 NomTypeOut='_1'; else @@ -232,9 +259,5 @@ -%% Set field names and velocity types -%use Param.InputFields for all views - %% MAIN LOOP ON FIELDS -%%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% @@ -261,5 +284,4 @@ end j1=1; - j2=1; if ~isempty(j1_series{1}) j1=j1_series{1}(index); @@ -277,5 +299,5 @@ for iview=1:NbView %% reading input file(s) - [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},ParamIn{iview},frame_index{iview}(index)); + [Data{iview},~,errormsg] = read_field(filecell{iview,index},FileType{iview},ParamIn{iview},frame_index{iview}(index)); if isempty(errormsg) disp([filecell{iview,index} ' read OK']) @@ -307,9 +329,8 @@ %% calculate tps coefficients if needed - - check_proj_tps= strcmp(FileType{iview},'civdata') && isfield(Param,'ProjObject')&&~isempty(Param.ProjObject)... + check_proj_tps= ismember(FileType{iview},{'civdata','civdata_compress'}) && isfield(Param,'ProjObject')&&~isempty(Param.ProjObject)... && strcmp(Param.ProjObject.ProjMode,'interp_tps')&&~isfield(Data{iview},'Coord_tps'); if check_proj_tps - Data{iview}=tps_coeff_field(Data{iview},check_proj_tps); + Data{iview}=tps_coeff_field(Data{iview},check_proj_tps); end @@ -326,5 +347,5 @@ if Param.CheckMask % introduce multilevel mask like for civ NbSlice=Param.MaskTable{iview,2}; - [RootPath_mask,SubDir_mask,RootFile_mask,i1_mask,i2_mask,j1_mask,j2_mask,Ext_mask]=fileparts_uvmat(Param.MaskTable{iview,1}); + [RootPath_mask,SubDir_mask,RootFile_mask,~,~,~,~,Ext_mask]=fileparts_uvmat(Param.MaskTable{iview,1}); i1_mask=mod(i1-1,NbSlice)+1; maskname=fullfile_uvmat(RootPath_mask,SubDir_mask,RootFile_mask,Ext_mask,'_1',i1_mask); @@ -334,6 +355,6 @@ [MaskData,~,errormsg] = read_field(maskname,'image'); if ~isempty(NbSlice_calib) - MaskData.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform - end + MaskData.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform + end if ~isempty(transform_fct) && nargin(transform_fct)>=2 MaskData=transform_fct(MaskData,XmlData{iview}); @@ -351,6 +372,4 @@ else MergeData=transform_fct(Data{1},XmlData{1},Data{2}); %combine the two input file series - % else - % MergeData=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2});%combine the two input file series with calibration parameters end if ~isempty(errormsg) @@ -362,5 +381,5 @@ if ~isempty(time) timeread=time(index); - elseif ~isempty(find(timeread))% time defined from ImaDoc + elseif ~isempty(find(timeread, 1))% time defined from ImaDoc timeread=mean(timeread(timeread~=0));% take average over times form the files (when defined) else @@ -372,8 +391,8 @@ if strcmp(FileExtOut,'.png') %output as image if index==1 - if strcmp(class(MergeData.A),'uint8') - BitDepth=8; + if isa(MergeData.A,'uint8') + BitDepth=8; else - BitDepth=16; + BitDepth=16; end %write xml calibration file, using the first file @@ -429,5 +448,5 @@ MergeData.Time=timeread; end - % position of projection plane + % position of projection plane if isfield(Data{1},'ProjObjectCoord')&& isfield(Data{1},'ProjObjectAngle') ProjObjectCoord=Data{1}.ProjObjectCoord; @@ -471,4 +490,28 @@ end end + if ~isempty(scale_factor_inv_uv) + index_U=find(strcmp(MergeData.ListVarName,'U')); + if ~isempty(index_U) + MergeData.VarAttribute{index_U}.scale_factor=1/scale_factor_inv_uv; + MergeData.U=int16(scale_factor_inv_uv*MergeData.U); + end + index_V=find(strcmp(MergeData.ListVarName,'V')); + if ~isempty(index_V) + MergeData.VarAttribute{index_V}.scale_factor=1/scale_factor_inv_uv; + MergeData.V=int16(scale_factor_inv_uv*MergeData.V); + end + end + if ~isempty(scale_factor_inv_dudv) + index_var=find(strcmp(MergeData.ListVarName,'curl')); + if ~isempty(index_var) + MergeData.VarAttribute{index_var}.scale_factor=1/scale_factor_inv_dudv; + MergeData.curl=int16(scale_factor_inv_uv*MergeData.curl); + end + index_var=find(strcmp(MergeData.ListVarName,'div')); + if ~isempty(index_var) + MergeData.VarAttribute{index_var}.scale_factor=1/scale_factor_inv_dudv; + MergeData.div=int16(scale_factor_inv_dudv*MergeData.div); + end + end error=struct2nc(OutputFile,MergeData);%save result file if isempty(error) @@ -495,5 +538,5 @@ NbView=length(Data); if NbView==1% if there is only one field, just reproduce it in MergeData - return + return end Index: trunk/src/uvmat.m =================================================================== --- trunk/src/uvmat.m (revision 1195) +++ trunk/src/uvmat.m (revision 1196) @@ -298,5 +298,5 @@ UvData.Field.coord_x=[0.5 size(input,2)-0.5]; UvData.Field.coord_y=[size(input,1)-0.5 0.5]; - testinputfield=1; + %testinputfield=1; end else @@ -4439,4 +4439,5 @@ end + %% extract the fields to use % eliminate false data if relevant (false flag FF exists) @@ -4488,12 +4489,13 @@ end end - %unit - units=[]; %default - for ivar=1:numel(Field.ListVarName) - if strcmp(Field.ListVarName{ivar},FieldName) - if isfield(Field,'VarAttribute') && numel(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'units') - units=Field.VarAttribute{ivar}.units; - break - end + units=''; scale_factor=NaN; %default + %determine the bin size for histogram + FieldIndex=find(strcmp(FieldName,Field.ListVarName)); + if isfield(Field,'VarAttribute') && numel(Field.VarAttribute)>=FieldIndex + if isfield(Field.VarAttribute{FieldIndex},'units') + units=Field.VarAttribute{FieldIndex}.units; + end + if isfield(UvData.Field.VarAttribute{FieldIndex},'scale_factor') + scale_factor=UvData.Field.VarAttribute{FieldIndex}.scale_factor; end end @@ -4503,15 +4505,22 @@ Histo.VarAttribute{1}.units=units; end - VarMesh=(Amax-Amin)/100; - ord=10^(floor(log10(VarMesh)));%order of magnitude - if VarMesh/ord >=5 - VarMesh=5*ord; - elseif VarMesh/ord >=2 - VarMesh=2*ord; + %determine the bin size for histogram + if isa(FieldHisto,'integer') + VarMesh=max(1,(Amax-Amin)/100); + elseif (Amax-Amin)/scale_factor<100 + VarMesh=scale_factor;% take the integer mesh used to store the field else - VarMesh=ord; - end - Amin=VarMesh*(ceil(Amin/VarMesh)); - Amax=VarMesh*(floor(Amax/VarMesh)); + VarMesh=(Amax-Amin)/100; + ord=10^(floor(log10(VarMesh)));%order of magnitude + if VarMesh/ord >=5 + VarMesh=5*ord; + elseif VarMesh/ord >=2 + VarMesh=2*ord; + else + VarMesh=ord; + end + Amin=VarMesh*(ceil(Amin/VarMesh)); + Amax=VarMesh*(floor(Amax/VarMesh)); + end Histo.(FieldName)=Amin:VarMesh:Amax; %absissa values for histo if isfield(Field,'NbDim') && isequal(Field.NbDim,3) @@ -4521,15 +4530,17 @@ for col=1:size(FieldHisto,3) B=FieldHisto(:,:,col); - C=reshape(double(B),1,nxy(1)*nxy(2));% reshape in a vector + C=reshape(B,1,nxy(1)*nxy(2));% reshape in a vector + Histo.histo(:,col)=hist(C, Histo.(FieldName)); %calculate histogram + % Histo.histo(:,col)=histogram(C); %calculate histogram switch get(handles.LogLinHisto,'Value') case 1 PlotParam.Type='plot'; case 2 - PlotParam.Type='semilogy'; + PlotParam.Type='semilogy'; case 3 - PlotParam.Type='semilogx'; + PlotParam.Type='semilogx'; case 4 - PlotParam.Type='loglog'; + PlotParam.Type='loglog'; end end @@ -5180,8 +5191,11 @@ imax=6; end - case {'civdata','civdata_3D','pivdata_fluidimage'} + case {'civdata','civdata_compress','civdata_3D','pivdata_fluidimage'} menu={'civ1';'filter1';'civ2';'filter2'}; imax=[0 1 1 2 3 3 4 5 5 6]; imax=imax(min(CivStage+1,10)); + if strcmp(FileType,'civdata_compress')&& CivStage>=4 + imin=3; + end end menu=menu(imin:imax);