Index: /trunk/src/find_field_cells.m =================================================================== --- /trunk/src/find_field_cells.m (revision 1057) +++ /trunk/src/find_field_cells.m (revision 1058) @@ -17,5 +17,6 @@ % _image : B/W image, (behaves like scalar) % _vector_x,_y,_z: indices of variables giving the vector components x, y, z -% _warnflag: index of warnflag +% _warnflag: index of warnflag +% _histo: index of variable used as histogram % .DimIndex % .ProjModeRequest= 'interp_lin', 'interp_tps' indicate whether lin interpolation or derivatives (tps) is needed to calculate the requested field @@ -118,7 +119,8 @@ end ind_discrete=find(strcmp('discrete',Role)); -ind_coord_x=find(strcmp('coord_x',Role)); +ind_coord_x=[find(strcmp('coord_x',Role)) find(strcmp('histo',Role))]; ind_coord_y=find(strcmp('coord_y',Role)); ind_coord_z=find(strcmp('coord_z',Role)); +ind_histo=find(strcmp('histo',Role)); ind_coord_tps=find(strcmp('coord_tps',Role)); check_string=cellfun(@ischar,Data.VarDimName)==1; @@ -477,5 +479,5 @@ Cell1DPlot{icell}.YIndex_discrete=[]; DimCell_x=Data.VarDimName{ind_coord_x(icell)}; - for ivar=ind_coord_y + for ivar=[ind_coord_y ind_histo] DimCell=Data.VarDimName{ivar}; if numel(DimCell_x)==1 && strcmp(DimCell_x{1},DimCell{1}) Index: /trunk/src/plot_field.m =================================================================== --- /trunk/src/plot_field.m (revision 1057) +++ /trunk/src/plot_field.m (revision 1058) @@ -585,5 +585,5 @@ TextDisplay=0; for icell=1:numel(CellInfo) - if isfield(CellInfo{icell},'VarIndex_histo') + if isfield(CellInfo{icell},'VarIndex_histo')% case of histogram plot TextDisplay=1; VarName=data.ListVarName{CellInfo{icell}.CoordIndex}; Index: /trunk/src/proj_field.m =================================================================== --- /trunk/src/proj_field.m (revision 1057) +++ /trunk/src/proj_field.m (revision 1058) @@ -509,4 +509,5 @@ if isfield(FieldData,'VarAttribute')&& numel(FieldData.VarAttribute)>=ivar VarAttribute_var=FieldData.VarAttribute{ivar}; + VarAttribute_var.Role='coord_x'; end % VarAttribute_var.Role='coord_x';% the variable is now used as an absissa Index: /trunk/src/read_field.m =================================================================== --- /trunk/src/read_field.m (revision 1057) +++ /trunk/src/read_field.m (revision 1058) @@ -265,5 +265,5 @@ A=imread(FileName); case 'rdvision' - [A,FileInfo,timestamps]=read_rdvision(FileName,num); + [A,FileInfo,timestamps,errormsg]=read_rdvision(FileName,num); case 'image_DaVis' Input=readimx(FileName); Index: /trunk/src/read_rdvision.m =================================================================== --- /trunk/src/read_rdvision.m (revision 1057) +++ /trunk/src/read_rdvision.m (revision 1058) @@ -125,8 +125,13 @@ % binrepertoire='2017-01-19T22.12.182'% EXP14 %%%%%%%%%%%%%%%%%%%%%%%%% binfile=fullfile(RootPath,binrepertoire,sprintf('%s%.5d.bin',bin_file,data(ii).file_idx)); + if ~exist(binfile,'file') + errormsg=[binfile ' does not exist']; + return + else fid=fopen(binfile,'rb'); fseek(fid,data(ii).offset,-1); A(:,:,i)=reshape(fread(fid,w*h,classname),w,h)'; fclose(fid); + end end Index: /trunk/src/series/merge_proj.m =================================================================== --- /trunk/src/series/merge_proj.m (revision 1057) +++ /trunk/src/series/merge_proj.m (revision 1058) @@ -533,9 +533,4 @@ end end -% if isempty(FFName) -% FFName='FF'; -% end -% MergeData.(FFName)(NbAver~=0)=0;% flag to 1 undefined summed data -% MergeData.(FFName)(NbAver==0)=1;% flag to 1 undefined summed data end end Index: /trunk/src/series/merge_proj_polar.m =================================================================== --- /trunk/src/series/merge_proj_polar.m (revision 1057) +++ /trunk/src/series/merge_proj_polar.m (revision 1058) @@ -100,5 +100,6 @@ HeadData.ListVarName= {'radius','azimuth'} ; HeadData.VarDimName={'radius','azimuth'}; -HeadData.VarAttribute={'coord_y','coord_x'} ; +HeadData.VarAttribute{1}.Role='coord_y'; +HeadData.VarAttribute{2}.Role='coord_x'; HeadData.radius=radius_shifted; HeadData.azimuth=azimuth_arclength; @@ -373,5 +374,7 @@ ProjData{iview}.ListVarName= [ProjData{iview}.ListVarName ListVarName]; ProjData{iview}.VarDimName={'radius','azimuth'}; - ProjData{iview}.VarAttribute=[{'coord_x'} {'coord_y'} VarAttribute]; +% ProjData{iview}.VarAttribute{1}.Role='coord_y'; +% ProjData{iview}.VarAttribute{2}.Role='coord_x'; + ProjData{iview}.VarAttribute=[ProjData{iview}.VarAttribute VarAttribute]; for ivar=1:numel(ListVarName) ProjData{iview}.VarDimName{ivar+2}={'radius','azimuth'}; @@ -457,4 +460,75 @@ disp([ num2str(ellapsed_time/(60*NbField),3) ' minutes per iteration']) +% %'merge_field': concatene fields +% %------------------------------------------------------------------------ +% function [MergeData,errormsg]=merge_field(Data) +% %% default output +% if isempty(Data)||~iscell(Data) +% MergeData=[]; +% return +% end +% errormsg=''; +% MergeData=Data{1};% merged field= first field by default, reproduces the global attributes of the first field +% NbView=length(Data); +% if NbView==1% if there is only one field, just reproduce it in MergeData +% return +% end +% +% %% group the variables (fields of 'Data') in cells of variables with the same dimensions +% [CellInfo,NbDim,errormsg]=find_field_cells(Data{1}); +% if ~isempty(errormsg) +% return +% end +% +% %LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS +% for icell=1:length(CellInfo) +% if NbDim(icell)~=1 % skip field cells which are of dim 1 +% switch CellInfo{icell}.CoordType +% case 'scattered' %case of input fields with unstructured coordinates: just concatene data +% for ivar=CellInfo{icell}.VarIndex % indices of the selected variables in the list FieldData.ListVarName +% VarName=Data{1}.ListVarName{ivar}; +% for iview=2:NbView +% MergeData.(VarName)=[MergeData.(VarName); Data{iview}.(VarName)]; +% end +% end +% case 'grid' %case of fields defined on a structured grid +% FFName=''; +% if isfield(CellInfo{icell},'VarIndex_errorflag') && ~isempty(CellInfo{icell}.VarIndex_errorflag) +% FFName=Data{1}.ListVarName{CellInfo{icell}.VarIndex_errorflag};% name of errorflag variable +% MergeData.ListVarName(CellInfo{icell}.VarIndex_errorflag)=[];%remove error flag variable in MergeData (will use NaN instead) +% MergeData.VarDimName(CellInfo{icell}.VarIndex_errorflag)=[]; +% MergeData.VarAttribute(CellInfo{icell}.VarIndex_errorflag)=[]; +% end +% % select good data on each view +% for ivar=CellInfo{icell}.VarIndex % indices of the selected variables in the list FieldData.ListVarName +% VarName=Data{1}.ListVarName{ivar}; +% for iview=1:NbView +% if isempty(FFName) +% check_bad=isnan(Data{iview}.(VarName));%=0 for NaN data values, 1 else +% else +% check_bad=isnan(Data{iview}.(VarName)) | Data{iview}.(FFName)~=0;%=0 for NaN or error flagged data values, 1 else +% end +% Data{iview}.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag +% if iview==1 +% %MergeData.(VarName)=Data{1}.(VarName);% initiate MergeData with the first field +% MergeData.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag +% NbAver=~check_bad;% initiate NbAver: the nbre of good data for each point +% elseif size(Data{iview}.(VarName))~=size(MergeData.(VarName)) +% errormsg='sizes of the input matrices do not agree, need to interpolate on a common grid using a projection object'; +% return +% else +% MergeData.(VarName)=MergeData.(VarName) +double(Data{iview}.(VarName));%add data +% NbAver=NbAver + ~check_bad;% add 1 for good data, 0 else +% end +% end +% MergeData.(VarName)(NbAver~=0)=MergeData.(VarName)(NbAver~=0)./NbAver(NbAver~=0);% take average of defined data at each point +% MergeData.(VarName)(NbAver==0)=NaN;% set to NaN the points with no good data +% end +% end +% +% end +% end + + %'merge_field': concatene fields %------------------------------------------------------------------------ @@ -469,5 +543,5 @@ NbView=length(Data); if NbView==1% if there is only one field, just reproduce it in MergeData - return + return end @@ -514,5 +588,5 @@ errormsg='sizes of the input matrices do not agree, need to interpolate on a common grid using a projection object'; return - else + else MergeData.(VarName)=MergeData.(VarName) +double(Data{iview}.(VarName));%add data NbAver=NbAver + ~check_bad;% add 1 for good data, 0 else @@ -523,12 +597,4 @@ end end - % if isempty(FFName) - % FFName='FF'; - % end - % MergeData.(FFName)(NbAver~=0)=0;% flag to 1 undefined summed data - % MergeData.(FFName)(NbAver==0)=1;% flag to 1 undefined summed data - end -end - - - + end +end Index: /trunk/src/series/sub_background.m =================================================================== --- /trunk/src/series/sub_background.m (revision 1057) +++ /trunk/src/series/sub_background.m (revision 1058) @@ -140,6 +140,7 @@ %% setting of parameters specific to sub_background - nbaver_init=23; %default number of images used for the sliding background: to be adjusted later to include an integer number of bursts - if nbfield_i~=1 + CheckVolume='No'; + nbaver_init=23; %default number of images used for the sliding background: to be adjusted later to include an integer number of bursts + if nbfield_i~=1 nbaver=floor(nbaver_init/nbfield_j); % number of bursts used for the sliding background, if isequal(mod(nbaver,2),0)% if nbaver is even @@ -148,13 +149,32 @@ nbaver_init=nbaver*nbfield_j;%propose by default an integer number of bursts end - + BrightnessRankThreshold=0.1; + CheckSubmedian='No'; + SaturationCoeff=0; + if isfield(Param,'ActionInput') + if isfield(Param.ActionInput,'CheckVolume') && Param.ActionInput.CheckVolume + CheckVolume='Yes'; + end + if isfield(Param.ActionInput,'SlidingSequenceLength') + nbaver_init=Param.ActionInput.SlidingSequenceLength; + end + if isfield(Param.ActionInput,'BrightnessRankThreshold') + BrightnessRankThreshold=Param.ActionInput.BrightnessRankThreshold; + end + if isfield(Param.ActionInput,'CheckSubmedian') && Param.ActionInput.CheckSubmedian + CheckSubmedian='Yes'; + end + if isfield(Param.ActionInput,'SaturationCoeff') + SaturationCoeff=Param.ActionInput.SaturationCoeff; + end + end prompt = {'volume scan mode (Yes/No)';... 'Number of images for the sliding background (MUST FIT IN COMPUTER MEMORY)';... 'the luminosity rank chosen to define the background (0.1=for dense particle seeding, 0.5 (median) for sparse particles';... 'set to 0 image levels below median(Yes/No)';... - 'image rescaling coefficient(high values reduce the influence of bright particles), =0 for no rescaling' }; + 'image rescaling coefficient(=2 to reduce the influence of bright particles), =0 for no rescaling' }; dlg_title = 'get (slice by slice) a sliding background and substract to each image'; num_lines= 5; - def = { 'No';num2str(nbaver_init);'0.1';'No';'2'}; + def = { CheckVolume;num2str(nbaver_init);num2str(BrightnessRankThreshold);CheckSubmedian;num2str(SaturationCoeff)}; answer = inputdlg(prompt,dlg_title,num_lines,def); if isempty(answer) Index: /trunk/src/uvmat.m =================================================================== --- /trunk/src/uvmat.m (revision 1057) +++ /trunk/src/uvmat.m (revision 1058) @@ -2637,5 +2637,9 @@ Mask.NbSlice_j=1; if isempty(j1_series) + if isempty(i1_series) + MaskNomType='*'; + else Mask.NbSlice_i=i1_series(1,2,end); + end else Mask.NbSlice_j=j1_series(1,end,2); @@ -2667,8 +2671,10 @@ MaskIndex_i=str2num(get(handles.z_index,'String')); else - MaskIndex_i=mod(str2num(get(handles.i1,'String')),Mask.NbSlice_i); -end + MaskIndex_i=mod(str2num(get(handles.i1,'String'))-1,Mask.NbSlice_i)+1; +end +MaskIndex_z=MaskIndex_i;%default if Mask.NbSlice_j>1 MaskIndex_j=str2num(get(handles.j1,'String')); + MaskIndex_z=MaskIndex_j; else MaskIndex_j=1; @@ -2702,5 +2708,5 @@ return end - MaskField.ZIndex=MaskIndex_i; + MaskField.ZIndex=MaskIndex_z; %px to phys or other transform on field menu_transform=get(handles.TransformName,'String');