Index: /trunk/src/find_field_cells.m =================================================================== --- /trunk/src/find_field_cells.m (revision 1008) +++ /trunk/src/find_field_cells.m (revision 1009) @@ -75,12 +75,12 @@ for ilist=1:numel(Data.ListVarName) if ~isfield(Data,Data.ListVarName{ilist}) - check_var=0;% dimensions of data defined, data not needed for this function + check_var=0;% dimensions of array defined, but the corresponding array is not given break end end -if ~check_var && ~(isfield(Data,'ListDimName')&& isfield(Data,'DimValue')&&isequal(numel(Data.ListDimName),numel(Data.DimValue))) - errormsg=['missing variable or values of dimensions' Data.ListVarName{ilist}]; - return -end +% if ~check_var && ~(isfield(Data,'ListDimName')&& isfield(Data,'DimValue')&& isequal(numel(Data.ListDimName),numel(Data.DimValue))) +% errormsg=['missing dimension values']; +% return +% end Index: /trunk/src/find_file_series.m =================================================================== --- /trunk/src/find_file_series.m (revision 1008) +++ /trunk/src/find_file_series.m (revision 1009) @@ -11,11 +11,11 @@ % NomType: nomenclature type corrected after checking the first file (problem of 0 before the number string) % FileInfo: structure containing info on the input files (assumed identical on the whole series) - % FileInfo.FileType: type of file, = - % = 'image', usual image as recognised by Matlab - % = 'multimage', image series stored in a single file - % = 'civx', netcdf file with civx convention - % = 'civdata', civ data with new convention - % = 'netcdf' other netcdf files - % = 'video': movie recognised by VideoReader (e;g. avi) +% FileInfo.FileType: type of file, = +% = 'image', usual image as recognised by Matlab +% = 'multimage', image series stored in a single file +% = 'civx', netcdf file with civx convention +% = 'civdata', civ data with new convention +% = 'netcdf' other netcdf files +% = 'video': movie recognised by VideoReader (e;g. avi) % MovieObject: video object (=[] otherwise % i1_input,i2_input,j1_input,j2_input: indices of the input file, or of the first file in the series if the input file does not exist @@ -23,5 +23,5 @@ %INPUT % FilePath: path to the directory to be scanned -% fileinput: name (without path) of the input file sample +% fileinput: name (without path) of the input file sample % checkxml: =1(default) take into account xml file existence to possibly include indexes in RootFile % =0: do not take into account xml file existence @@ -53,10 +53,9 @@ %% check for particular file types: images, movies, civ data -checkfileindexing=0; if isfield(FileInfo,'FileIndexing') && strcmp(FileInfo.FileIndexing,'on') [RootPath,SubDir,RootFile,i1_input,i2_input,j1_input,j2_input,FileExt,NomType]=fileparts_uvmat(fullfileinput); - if ~isempty(regexp(SubDir,'^level\d+$')) && exist([RootPath '.xml'],'file') - NomType='level'; - end + % if ~isempty(regexp(SubDir,'^level\d+$')) && exist([RootPath '.xml'],'file') + % NomType='level'; + % end i1_series=zeros(1,1,1); i2_series=zeros(1,1,1); @@ -75,4 +74,5 @@ return end + checkfileindexing=0; end if ~exist(FilePath,'dir') @@ -173,145 +173,157 @@ end end - if strcmp(NomType,'level') - star_string=[RootFile '*' FileExt]; - detect_string=['^' RootFile '(?\d+)' FileExt '$'];%string used in regexp to detect file indices - wd=pwd;%current working directory - cd (FilePath)% move to the local dir to save time in the operation dir. - dirpair=dir(star_string);% look for relevant files in the file directory - cd(wd)% back to the working directory - nbpair=numel(dirpair); - i1_series=zeros(1,nbpair); - if nbpair==0% no detected file - RootFile=''; - end - % scan the list of relevant files, extract the indices - for ifile=1:nbpair - rr=regexp(dirpair(ifile).name,detect_string,'names'); - if ~isempty(rr) - i1_series(ifile)=str2num(rr.i1); - end - end - % look for the list of subfolders level# - cd (RootPath)% move to the local dir to save time in the operation dir. - dirpair=dir('level*');% look for relevant subfolders named with leve# - cd(wd) - [RootPath,SubDir]=fileparts(RootPath); - nbpair=numel(dirpair); - jfile=0; - for ifile=1:nbpair - rr=regexp(dirpair(ifile).name,'^level(?\d+)$','names'); - if ~isempty(rr) - jfile=jfile+1; - j1_series(jfile)=str2num(rr.i1); - end - end - [j1_series,i1_series]=meshgrid(j1_series,i1_series); -% i1_series=reshape(i1_series,1,[]); -% j1_series=reshape(j1_series,1,[]); + % if strcmp(NomType,'level') + % star_string=[RootFile '*' FileExt]; + % detect_string=['^' RootFile '(?\d+)' FileExt '$'];%string used in regexp to detect file indices + % wd=pwd;%current working directory + % cd (FilePath)% move to the local dir to save time in the operation dir. + % dirpair=dir(star_string);% look for relevant files in the file directory + % cd(wd)% back to the working directory + % nbpair=numel(dirpair); + % i1_series=zeros(1,nbpair); + % if nbpair==0% no detected file + % RootFile=''; + % end + % % scan the list of relevant files, extract the indices + % for ifile=1:nbpair + % rr=regexp(dirpair(ifile).name,detect_string,'names'); + % if ~isempty(rr) + % i1_series(ifile)=str2num(rr.i1); + % end + % end + % % look for the list of subfolders level# + % cd (RootPath)% move to the local dir to save time in the operation dir. + % dirpair=dir('level*');% look for relevant subfolders named with leve# + % cd(wd) + % [RootPath,SubDir]=fileparts(RootPath); + % nbpair=numel(dirpair); + % jfile=0; + % for ifile=1:nbpair + % rr=regexp(dirpair(ifile).name,'^level(?\d+)$','names'); + % if ~isempty(rr) + % jfile=jfile+1; + % j1_series(jfile)=str2num(rr.i1); + % end + % end + % [j1_series,i1_series]=meshgrid(j1_series,i1_series); + % else + detect_string=['^' RootFile sep1 i1_str i2_str sep2 j1_str j2_str FileExt '$'];%string used in regexp to detect file indices + %find the string used to extract the relevant files with the command dir + star_string=[RootFile sep1 i1_star i2_star sep2 j1_star j2_star FileExt]; + wd=pwd;%current working directory + cd (FilePath)% move to the local dir to save time in the operation dir. + dirpair=dir(star_string);% look for relevant files in the file directory + cd(wd) + nbpair=numel(dirpair); + ref_i_list=zeros(1,nbpair); + ref_j_list=zeros(1,nbpair); + if nbpair==0% no detected file + RootFile=''; + end + % scan the list of relevant files, extract the indices + for ifile=1:nbpair + rr=regexp(dirpair(ifile).name,detect_string,'names'); + if ~isempty(rr) + i1=str2num(rr.i1); + i2=str2num(regexprep(rr.i2,'^-','')); + j1=stra2num(regexprep(rr.j1,'^_','')); + j2=stra2num(regexprep(rr.j2,'^-','')); + ref_i=i1; + if isempty(i2_input) + if ~isempty(i2)% invalid file name if i2 does not exist in the input file + break + end + else + ref_i=floor((i1+i2)/2); + end + ref_j=1; + if isempty(j1_input) + if ~isempty(j1)% invalid file name if j1 does not exist in the input file + break + end + else %j1_input is not empty + if isempty(j1)% the detected name does not fit with the input + break + else + ref_j=j1; + if isempty(j2_input) + if ~isempty(j2)% invalid file name if j2 does not exist in the input file + break + end + else + ref_j=floor((j1+j2)/2); + end + end + end + % update the detected index series + if ~isempty(ref_i)&&~isempty(ref_j) + ref_i_list(ifile)=ref_i; + ref_j_list(ifile)=ref_j; + nb_pairs=0; + if ~isempty(i2_input)|| ~isempty(j2_input) %deals with pairs + if size(i1_series,1)>=ref_i+1 && size(i1_series,2)>=ref_j+1 + nb_pairs=numel(find(i1_series(ref_i+1,ref_j+1,:)~=0)); + end + end + if i1==0 + i1=-1;% set index 0 to -1 to distinguish from the absent index (set to 0) + end + if j1==0 + j1=-1;% set index 0 to -1 to distinguish from the absent index (set to 0) + end + i1_series(ref_i+1,ref_j+1,nb_pairs+1)=i1; + if ~isempty(i2_input) + i2_series(ref_i+1,ref_j+1,nb_pairs+1)=i2; + end + if ~isempty(j1_input) + j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1; + end + if ~isempty(j2_input) + j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1; + j2_series(ref_i+1,ref_j+1,nb_pairs+1)=j2; + end + end + end + end + % look for the numerical string of the first files to update the NomType (take into account the 0 before the number) + max_j=max(ref_j_list); + if isempty(max_j) + ref_ij=ref_i_list; else - detect_string=['^' RootFile sep1 i1_str i2_str sep2 j1_str j2_str FileExt '$'];%string used in regexp to detect file indices - %find the string used to extract the relevant files with the command dir - star_string=[RootFile sep1 i1_star i2_star sep2 j1_star j2_star FileExt]; - wd=pwd;%current working directory - cd (FilePath)% move to the local dir to save time in the operation dir. - dirpair=dir(star_string);% look for relevant files in the file directory - cd(wd) - nbpair=numel(dirpair); - ref_i_list=zeros(1,nbpair); - ref_j_list=zeros(1,nbpair); - if nbpair==0% no detected file - RootFile=''; - end - % scan the list of relevant files, extract the indices - for ifile=1:nbpair - rr=regexp(dirpair(ifile).name,detect_string,'names'); - if ~isempty(rr) - i1=str2num(rr.i1); - i2=str2num(regexprep(rr.i2,'^-','')); - j1=stra2num(regexprep(rr.j1,'^_','')); - j2=stra2num(regexprep(rr.j2,'^-','')); - ref_i=i1; - if isempty(i2_input) - if ~isempty(i2)% invalid file name if i2 does not exist in the input file - break - end - else - ref_i=floor((i1+i2)/2); - end - ref_j=1; - if isempty(j1_input) - if ~isempty(j1)% invalid file name if j1 does not exist in the input file - break - end - else %j1_input is not empty - if isempty(j1)% the detected name does not fit with the input - break - else - ref_j=j1; - if isempty(j2_input) - if ~isempty(j2)% invalid file name if j2 does not exist in the input file - break - end - else - ref_j=floor((j1+j2)/2); - end - end - end - % update the detected index series - if ~isempty(ref_i)&&~isempty(ref_j) - ref_i_list(ifile)=ref_i; - ref_j_list(ifile)=ref_j; - nb_pairs=0; - if ~isempty(i2_input)|| ~isempty(j2_input) %deals with pairs - if size(i1_series,1)>=ref_i+1 && size(i1_series,2)>=ref_j+1 - nb_pairs=numel(find(i1_series(ref_i+1,ref_j+1,:)~=0)); - end - end - if i1==0 - i1=-1;% set index 0 to -1 to distinguish from the absent index (set to 0) - end - if j1==0 - j1=-1;% set index 0 to -1 to distinguish from the absent index (set to 0) - end - i1_series(ref_i+1,ref_j+1,nb_pairs+1)=i1; - if ~isempty(i2_input) - i2_series(ref_i+1,ref_j+1,nb_pairs+1)=i2; - end - if ~isempty(j1_input) - j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1; - end - if ~isempty(j2_input) - j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1; - j2_series(ref_i+1,ref_j+1,nb_pairs+1)=j2; - end - end - end - end - % look for the numerical string of the first files to update the NomType (take into account the 0 before the number) - max_j=max(ref_j_list); - if isempty(max_j) - ref_ij=ref_i_list; - else - ref_ij=ref_i_list*max_j+ref_j_list; % ordered by index i, then by j for a given i. - end - ind_select=find(ref_ij>0); - - if ~isempty(ind_select) - [tild,ifile_min]=min(ref_ij(ind_select)); - [tild,tild,tild,tild,tild,tild,tild,tild,NomType]=fileparts_uvmat(dirpair(ind_select(ifile_min)).name);% 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.FileType) - [FileInfo,MovieObject]=get_file_info(fullfile(FilePath,dirpair(ifile_min).name)); - end - end - end - end - -%% set to empty array the irrelevant index series -if isequal(i1_series,0), i1_series=[]; end -if isequal(i2_series,0), i2_series=[]; end -if isequal(j1_series,0), j1_series=[]; end -if isequal(j2_series,0), j2_series=[]; end + ref_ij=ref_i_list*max_j+ref_j_list; % ordered by index i, then by j for a given i. + end + ind_select=find(ref_ij>0); + + if ~isempty(ind_select) + [tild,ifile_min]=min(ref_ij(ind_select)); + [tild,tild,tild,tild,tild,tild,tild,tild,NomType]=fileparts_uvmat(dirpair(ind_select(ifile_min)).name);% 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.FileType) + [FileInfo,MovieObject]=get_file_info(fullfile(FilePath,dirpair(ifile_min).name)); + end + end + % end + end + + %% set to empty array the irrelevant index series + if isequal(i1_series,0), i1_series=[]; end + if isequal(i2_series,0), i2_series=[]; end + if isequal(j1_series,0), j1_series=[]; end + if isequal(j2_series,0), j2_series=[]; end + + %% case of isolated input file, not member of an indexed series + if isempty(i1_series) + [PathDir,RootFile]=fileparts(fullfileinput); + [RootPath,SubDir,DirExt]=fileparts(PathDir); + SubDir=[SubDir DirExt];% include part after . in the name (considered as a file extension) + NomType='*'; + i2_series=[];j1_series=[];j2_series=[]; +% i1_input=1;i2_input=[];j1_input=[];j2_input=[]; + if ~exist(fullfileinput,'file') + RootFile=''; + return + end + end end % %% detect rdvision format @@ -332,5 +344,5 @@ else % if there is a file index, j denotes the frame index while i denotes the file index if ~isempty(regexp(NomType,'ab$', 'once'))% recognized as a pair - RootFile=fullfile_uvmat('','',RootFile,'',NomType,i1_input,i2_input,j1_input,j2_input);% restitute the root name without the detected indices + RootFile=fullfile_uvmat('','',RootFile,'',NomType,i1_input,i2_input,j1_input,j2_input);% restitute the root name without the detected indices i1_series=zeros(FileInfo.NumberOfFrames+1,2);% first column =0 i1_series(:,2)=(0:FileInfo.NumberOfFrames)'; % second column=frame index -1 @@ -388,6 +400,6 @@ end end -i1_series=permute(i1_series,[3 2 1]);% permute dimensions +i1_series=permute(i1_series,[3 2 1]);% permute dimensions i2_series=permute(i2_series,[3 2 1]);% permute dimensions -j1_series=permute(j1_series,[3 2 1]);% permute dimensions +j1_series=permute(j1_series,[3 2 1]);% permute dimensions j2_series=permute(j2_series,[3 2 1]);% permute dimensions Index: /trunk/src/geometry_calib.m =================================================================== --- /trunk/src/geometry_calib.m (revision 1008) +++ /trunk/src/geometry_calib.m (revision 1009) @@ -220,5 +220,5 @@ %% Apply calibration -[GeometryCalib,index,Z_plane]=calibrate(Coord,CalibFcn,Intrinsic);% apply calibration +[GeometryCalib,index,ind_removed,Z_plane]=calibrate(Coord,CalibFcn,Intrinsic);% apply calibration %% record the coordinate unit @@ -238,5 +238,6 @@ answer=msgbox_uvmat('INPUT_Y-N',{'store calibration data';... ['Error rms (along x,y)=' num2str(GeometryCalib.ErrorRms) ' pixels'];... - ['Error max (along x,y)=' num2str(GeometryCalib.ErrorMax) ' pixels']}); + ['Error max (along x,y)=' num2str(GeometryCalib.ErrorMax) ' pixels']; + [num2str(numel(ind_removed)) ' points removed']}); if strcmp(answer,'Yes') %store the calibration data if strcmp(calib_cell{val}(1:2),'3D')%set the plane position for 3D (projection) calibration @@ -334,5 +335,5 @@ %% Apply calibration -[GeometryCalib,index,Z_plane]=calibrate(Coord,CalibFcn,Intrinsic);% apply calibration +[GeometryCalib,index,ind_removed,Z_plane]=calibrate(Coord,CalibFcn,Intrinsic);% apply calibration @@ -353,5 +354,6 @@ answer=msgbox_uvmat('INPUT_Y-N',{'store calibration data';... ['Error rms (along x,y)=' num2str(GeometryCalib.ErrorRms) ' pixels'];... - ['Error max (along x,y)=' num2str(GeometryCalib.ErrorMax) ' pixels']}); + ['Error max (along x,y)=' num2str(GeometryCalib.ErrorMax) ' pixels'];... + [num2str(numel(ind_removed)) ' points removed']}); if strcmp(answer,'Yes') %store the calibration data if strcmp(calib_cell{val}(1:2),'3D')%set the plane position for 3D (projection) calibration @@ -395,14 +397,13 @@ %------------------------------------------------------------------------ % --- activate calibration and store parameters in ouputfile . -function [GeometryCalib,index,Z_plane]=calibrate(Coord,CalibFcn,Intrinsic) +function [GeometryCalib,ind_max,ind_removed,Z_plane]=calibrate(Coord,CalibFcn,Intrinsic) %------------------------------------------------------------------------ index=[]; - +GeometryCalib=[]; % apply the calibration, whose type is selected in handles.calib_type if ~isempty(Coord) GeometryCalib=feval(CalibFcn,Coord,Intrinsic); else - GeometryCalib=[]; msgbox_uvmat('ERROR','No calibration points, abort') end @@ -411,6 +412,29 @@ end Z_plane=[]; -if ~isempty(Coord) - %check error + +% estimate calibration error rms and max +X=Coord(:,1); +Y=Coord(:,2); +Z=Coord(:,3); +x_ima=Coord(:,4); +y_ima=Coord(:,5); +[Xpoints,Ypoints]=px_XYZ(GeometryCalib,X,Y,Z); +GeometryCalib.ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima))); +GeometryCalib.ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima))); +[ErrorMax(1),index(1)]=max(abs(Xpoints-x_ima)); +[ErrorMax(2),index(2)]=max(abs(Ypoints-y_ima)); +[tild,ind_dim]=max(ErrorMax); +ind_max=index(ind_dim); % mark the index with maximum deviation + +% detect bad calibration points, marked by indices ind_bad, if the +% difference of actual image coordinates and those given by calibration is +% greater than 2 pixels and greater than 4 rms. +check_x=abs(Xpoints-x_ima)>max(2,3*GeometryCalib.ErrorRms(1)); +check_y=abs(Ypoints-y_ima)>max(2,3*GeometryCalib.ErrorRms(2)); +ind_removed=find(check_x | check_y) +% repeat calibration without the excluded points: +if ~isempty(ind_removed) + Coord(ind_removed,:)=[]; + GeometryCalib=feval(CalibFcn,Coord,Intrinsic); X=Coord(:,1); Y=Coord(:,2); @@ -420,15 +444,12 @@ [Xpoints,Ypoints]=px_XYZ(GeometryCalib,X,Y,Z); GeometryCalib.ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima))); - [GeometryCalib.ErrorMax(1),index(1)]=max(abs(Xpoints-x_ima)); GeometryCalib.ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima))); - [GeometryCalib.ErrorMax(2),index(2)]=max(abs(Ypoints-y_ima)); - [tild,ind_dim]=max(GeometryCalib.ErrorMax); - index=index(ind_dim); - %set the Z position of the reference plane used for calibration - if isequal(max(Z),min(Z))%Z constant - Z_plane=Z(1); - GeometryCalib.NbSlice=1; - GeometryCalib.SliceCoord=[0 0 Z_plane]; - end +end +GeometryCalib.ErrorMax=ErrorMax; +%set the Z position of the reference plane used for calibration +if isequal(max(Z),min(Z))%Z constant + Z_plane=Z(1); + GeometryCalib.NbSlice=1; + GeometryCalib.SliceCoord=[0 0 Z_plane]; end Index: /trunk/src/get_field.m =================================================================== --- /trunk/src/get_field.m (revision 1008) +++ /trunk/src/get_field.m (revision 1009) @@ -15,4 +15,12 @@ % INPUT: % FileName: name (including path) of the netcdf file to open +% ParmIn: structure containing parameters for preselecting menus: +% .Title: set the title of the GUI get_field +% .SwitchVarIndexTime='file index','variable' or 'matrix index': select the default option for 'time' +% .TimeAttrName: preselect the name of a global attribute for time +% .SeriesInput=1 if get_field is called by the GUI series,=0 otherwise (plot options provided in the latter case) +% .Coord_x,.Coord_y,.Coord_z, names of the variables used as the three coordinates +% .scalar : set the default choise of the scale variable +% .vector_x, .vector_y : set the default choise for the variables used for the x and y vector components %======================================================================= @@ -85,5 +93,5 @@ end if ~exist('ParamIn','var') - ParamIn=[]; + ParamIn.Coord_z=''; end @@ -151,9 +159,9 @@ time_index=find(~cellfun('isempty',regexp(Field.Display.ListGlobalAttribute,'Time')),1);% look for global attribute containing name 'Time' end -if ~isempty(time_index) +if isempty(time_index) + set(handles.SwitchVarIndexTime,'Value',1); +else set(handles.SwitchVarIndexTime,'Value',2); set(handles.TimeName,'UserData',time_index) -else - set(handles.SwitchVarIndexTime,'Value',1); end set(handles.SwitchVarIndexTime,'String',ListSwitchVarIndexTime) @@ -230,6 +238,11 @@ CoordIndex=CellInfo{imax}.CoordIndex; if numel(CoordIndex)==2 + if isfield(ParamIn,'Coord_x')&& isfield(ParamIn,'Coord_y') + YName=ParamIn.Coord_y; + XName=ParamIn.Coord_x; + else YName=Field.ListVarName{CoordIndex(1)}; XName=Field.ListVarName{CoordIndex(2)}; + end ListCoord=get(handles.Coord_x,'String'); XIndex=find(strcmp(XName,ListCoord)); @@ -259,5 +272,5 @@ %% set z coordinate menu if relevant -if Field.MaxDim>=3 && prod(Field.DimValue)<10^8; % 3D field (with memory content smaller than 400 Mo) +if Field.MaxDim>=3 && prod(Field.DimValue)<10^8 && ~isempty(ParamIn.Coord_z); % 3D field (with memory content smaller than 400 Mo) set(handles.Check3D,'Value',1) else Index: /trunk/src/get_file_info.m =================================================================== --- /trunk/src/get_file_info.m (revision 1008) +++ /trunk/src/get_file_info.m (revision 1009) @@ -6,4 +6,5 @@ % FileInfo: structure containing info on the file (case of images or video), in particular % .FileType: type of file, needed as input of read_field.m +% .FileIndexing='on' for data files (when series of indexed files are expected) % .Height: image height in pixels % .Width: image width in pixels Index: /trunk/src/mouse_motion.m =================================================================== --- /trunk/src/mouse_motion.m (revision 1008) +++ /trunk/src/mouse_motion.m (revision 1009) @@ -129,4 +129,5 @@ if isfield(FigData,tagaxes) Field=FigData.(tagaxes); % the current field is sought as substructure of FigData with key tagaxes + if isfield(Field,'ListVarName') [CellInfo,NbDimArray]=find_field_cells(Field);%analyse the physical fields contained in Field Index: /trunk/src/proj_field.m =================================================================== --- /trunk/src/proj_field.m (revision 1008) +++ /trunk/src/proj_field.m (revision 1009) @@ -730,5 +730,5 @@ if strcmp(ProjData.VarAttribute{nbvar+ivar}.Role,'vector_x'); ivar_U=nbvar+ivar; - elseif strcmp(ProjData.VarAttribute{nbvar+ivar}.Role,'vector_y');TriScatteredInterp + elseif strcmp(ProjData.VarAttribute{nbvar+ivar}.Role,'vector_y'); ivar_V=nbvar+ivar; end @@ -738,6 +738,7 @@ elseif isequal(ProjMode,'interp_lin') %filtering %linear interpolation: if ~check_abscissa - XName=FieldData.ListVarName{CellInfo{icell}.CoordIndex(end)}; - ProjData.ListVarName=[ProjData.ListVarName {XName}];TriScatteredInterp + %XName=FieldData.ListVarName{CellInfo{icell}.CoordIndex(end)}; + XName='X'; + ProjData.ListVarName=[ProjData.ListVarName {XName}]; ProjData.VarDimName=[ProjData.VarDimName {XName}]; nbvar=numel(ProjData.ListVarName); Index: /trunk/src/series.m =================================================================== --- /trunk/src/series.m (revision 1008) +++ /trunk/src/series.m (revision 1009) @@ -642,4 +642,5 @@ RootFile=''; else %scan the input folder + InputTable{iview,3}(1)=[]; [RootPath,~,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileInfo,MovieObject]=... find_file_series(fullfile(InputTable{iview,1},InputTable{iview,2}),[InputTable{iview,3} InputTable{iview,4} InputTable{iview,5}]); Index: /trunk/src/series/stereo_civ.m =================================================================== --- /trunk/src/series/stereo_civ.m (revision 1008) +++ /trunk/src/series/stereo_civ.m (revision 1009) @@ -453,21 +453,5 @@ Data.Civ1_FF(ind_good)=FFres; Data.CivStage=3; - - - - -% -% % get z from u and v (displacements) -% -% tempXmid=Rangx(1)+(Rangx(2)-Rangx(1))*(Data.Civ1_X-0.5)/(Npx-1);%temporary coordinate (velocity taken at the point middle from imgae 1 and 2) -% tempYmid=Rangy(1)+(Rangy(2)-Rangy(1))*(Data.Civ1_Y-0.5)/(Npy-1);%temporary coordinate (velocity taken at the point middle from imgae 1 and 2) -% tempUphys=Data.Civ1_U_smooth*(Rangx(2)-Rangx(1))/(Npx-1); -% tempVphys=Data.Civ1_V_smooth*(Rangy(2)-Rangy(1))/(Npy-1); -% [tempZphys,tempXphys,tempYphys,tempCiv3_E]=shift2z(tempXmid,tempYmid,tempUphys,tempVphys,XmlData); %Data.Xphys and Data.Xphys are real coordinate (geometric correction more accurate than xtemp/ytemp) -% temp=find(Data.Civ1_FF~=0); -% tempXmid(temp)=[]; -% tempYmid(temp)=[]; -% tempZphys(temp)=[]; -% + end @@ -651,18 +635,4 @@ par_civ3.ImageA=par_civ1.ImageA; par_civ3.ImageB=par_civ1.ImageB; - % if ~isfield(Param.Civ1,'ImageA') -% i1=i1_series_Civ3(ifield); -% i2=i1; -% if ~isempty(i2_series_Civ3) -% i2=i2_series_Civ3(ifield); -% end -% j1=1; -% if ~isempty(j1_series_Civ3) -% j1=j1_series_Civ3(ifield); -% end -% j2=j1; -% if ~isempty(j2_series_Civ3) -% j2=j2_series_Civ3(ifield); -% end par_civ3.ImageWidth=size(par_civ3.ImageA,2); par_civ3.ImageHeight=size(par_civ3.ImageA,1); @@ -844,16 +814,23 @@ % else % store only phys data - Data_light.ListVarName={'Xphys','Yphys','Zphys','Civ3_C','Xmid','Ymid','Uphys','Vphys','Error'}; - Data_light.VarDimName={'nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3'}; - temp=find(Data.Civ3_FF==0); - Data_light.Zphys=Data.Zphys(temp); - Data_light.Yphys=Data.Yphys(temp); - Data_light.Xphys=Data.Xphys(temp); - Data_light.Civ3_C=Data.Civ3_C(temp); - Data_light.Xmid=Data.Xmid(temp); - Data_light.Ymid=Data.Ymid(temp); - Data_light.Uphys=Data.Uphys(temp); - Data_light.Vphys=Data.Vphys(temp); - Data_light.Error=Data.Error(temp); + % Data_light.ListVarName={'Xphys','Yphys','Zphys','Civ3_C','Xmid','Ymid','Uphys','Vphys','Error'}; + % Data_light.VarDimName={'nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3'}; + Data_light.ListVarName={'Xphys','Yphys','Zphys','Civ3_C','DX','DY','Error'}; + Data_light.VarDimName={'nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3'}; + Data_light.VarAttribute{1}.Role='coord_x'; + Data_light.VarAttribute{2}.Role='coord_y'; + Data_light.VarAttribute{3}.Role='scalar'; + Data_light.VarAttribute{5}.Role='vector_x'; + Data_light.VarAttribute{6}.Role='vector_y'; + ind_good=find(Data.Civ3_FF==0); + Data_light.Zphys=Data.Zphys(ind_good); + Data_light.Yphys=Data.Yphys(ind_good); + Data_light.Xphys=Data.Xphys(ind_good); + Data_light.Civ3_C=Data.Civ3_C(ind_good); +% Data_light.Xmid=Data.Xmid(ind_good); +% Data_light.Ymid=Data.Ymid(ind_good); + Data_light.DX=Data.Uphys(ind_good); + Data_light.DY=Data.Vphys(ind_good); + Data_light.Error=Data.Error(ind_good); if exist('ncfile2','var') errormsg=struct2nc(ncfile2,Data_light); Index: /trunk/src/uvmat.m =================================================================== --- /trunk/src/uvmat.m (revision 1008) +++ /trunk/src/uvmat.m (revision 1009) @@ -1748,5 +1748,5 @@ [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileInfo,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]); errormsg=''; -if isempty(i1_series) +if isempty(RootFile) fileinput=uigetfile_uvmat('pick an input file',fullfile(RootPath,SubDir)); hh=dir(fileinput); @@ -3819,4 +3819,23 @@ end + %% introduce default projection objects in 3D + for imap=1:numel(IndexObj) + iobj=IndexObj(imap); + if numel(UvData.ProjObject)=3 && UvData.ProjObject{iobj}.Coord(1,3)UvData.Field.ZMin) + UvData.ProjObject{iobj}.Coord(1,3)=(UvData.Field.ZMin+UvData.Field.ZMax)/2;%section at a middle plane chosen + end + end + end + + set(handles.uvmat,'UserData',UvData) + %% loop on the projection objects: one or two for imap=1:numel(IndexObj) @@ -3824,13 +3843,4 @@ if numel(UvData.ProjObject)=3 && UvData.ProjObject{iobj}.Coord(1,3)UvData.Field.ZMin) - UvData.ProjObject{iobj}.Coord(1,3)=(UvData.Field.ZMin+UvData.Field.ZMax)/2;%section at a middle plane chosen - end end [ObjectData,errormsg]=proj_field(UvData.Field,UvData.ProjObject{iobj});% project field on the object @@ -3872,5 +3882,5 @@ ObjectData.A=feval(AClass,ObjectData.A); end - set(handles.uvmat,'UserData',UvData) + if ~isempty(ObjectData) if imap==2 && isempty(view_field_handle) @@ -4362,4 +4372,9 @@ ParamIn.vec_color='Civ2_C'; end + else + ParamIn.TimeAttrName=get(handles.TimeName,'String'); + ParamIn.Coord_x=get(handles.Coord_x,'String'); + ParamIn.Coord_y=get(handles.Coord_y,'String'); + ParamIn.Coord_z=get(handles.Coord_z,'String'); end Index: /trunk/src/view_field.m =================================================================== --- /trunk/src/view_field.m (revision 1008) +++ /trunk/src/view_field.m (revision 1009) @@ -336,5 +336,5 @@ FigName=get(ListFig(ilist),'name'); if isempty(FigName) - FigName=['figure ' num2str(ListFig(ilist))]; + FigName=['figure ' num2str(ListFig(ilist).Number)]; end if ~strcmp(FigName,'uvmat')