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