Index: /trunk/src/civ.m =================================================================== --- /trunk/src/civ.m (revision 434) +++ /trunk/src/civ.m (revision 435) @@ -1,2 +1,3 @@ + %'civ': function associated with the interface 'civ.fig' for PIV, spline interpolation and stereo PIV (patch) %------------------------------------------------------------------------ @@ -63,6 +64,6 @@ t=xmltree(xmlfile); sparam=convert(t); - catch - errormsg={' Unable to read the file PARAM.xml defining the civx binaries:'; lasterr}; + catch ME + errormsg={' Unable to read the file PARAM.xml defining the civx binaries:';ME.message}; end else @@ -409,5 +410,5 @@ % end switch FileType - case {'image','multimage','video'} + case {'image','multimage','video','mmreader'} otherwise errormsg='invalid input file: enter an image, a movie or civ .nc file'; @@ -1059,5 +1060,5 @@ -%------------------------------------------------------------------------ +%--------------orm---------------------------------------------------------- % --- Main lauch command, called by RUN and BATCH function errormsg=launch_jobs(hObject, eventdata, handles, batch) @@ -1227,10 +1228,10 @@ if ~strcmp(CivMode,'CivX') if Param.CheckCiv1 - [Param.Civ1.FileTypeA,FileInfo,Param.Civ1.ImageA]=get_file_type(filecell.ima1.civ1{1}); - [Param.Civ1.FileTypeB,FileInfo,Param.Civ1.ImageB]=get_file_type(filecell.ima2.civ1{1}); + [Param.Civ1.FileTypeA,FileInfo,Param.Civ1.ImageA]=get_file_type(filecell.ima1.civ1{1}); + [Param.Civ1.FileTypeB,FileInfo,Param.Civ1.ImageB]=get_file_type(filecell.ima2.civ1{1}); end if Param.CheckCiv2 - [Param.Civ2.FileTypeA,FileInfo,Param.Civ2.ImageA]=get_file_type(filecell.ima1.civ2{1}); - [Param.Civ2.FileTypeB,FileInfo,Param.Civ2.ImageB]=get_file_type(filecell.ima2.civ2{1}); + [Param.Civ2.FileTypeA,FileInfo,Param.Civ2.ImageA]=get_file_type(filecell.ima1.civ2{1}); + [Param.Civ2.FileTypeB,FileInfo,Param.Civ2.ImageB]=get_file_type(filecell.ima2.civ2{1}); end end @@ -1271,6 +1272,5 @@ if Param.CheckCiv1 % read image-dependent parameters - Param.Civ1.ImageA=filecell.ima1.civ1{ifile,j}; - Param.Civ1.ImageB=filecell.ima2.civ1{ifile,j}; + if ~checkframe% && size(time,1)>=i2_civ1(ifile) && size(time,2)>=j2_civ1(j) Param.Civ1.Dt=(time(i2_civ1(ifile)+1,j2_civ1(j)+1)-time(i1_civ1(ifile)+1,j1_civ1(j)+1)); @@ -1280,20 +1280,30 @@ Param.Civ1.Time=((time(i2_civ1(ifile)+1,j2_civ1(j)+1)+time(i1_civ1(ifile)+1,j1_civ1(j)+1))/2); if strcmp(CivMode,'CivX') - Param.Civ1.term_a=num2stra(j1_civ1(j),nom_type_nc);%UTILITE? - Param.Civ1.term_b=num2stra(j2_civ1(j),nom_type_nc);% - end - form=imformats(regexprep(get(handles.ImaExt,'String'),'^.',''));%look for image formats - if isempty(form) - ImageInfo=get(VideoReader(filecell.ima1.civ1{1,1})); + Param.Civ1.term_a=num2stra(j1_civ1(j),nom_type_nc);%UTILITE? + Param.Civ1.term_b=num2stra(j2_civ1(j),nom_type_nc);% + end + if strcmp(Param.Civ1.FileTypeA,'video')|| strcmp(Param.Civ1.FileTypeA,'mmreader') + % ImageInfo=get(VideoReader(fullfile(Param.RootPath,[Param.RootFile Param.ImaExt]))); + ImageInfo=get(Param.Civ1.ImageA); + % elseif strcmp(Param.Civ1.FileTypeA,'mmreader') + % ImageInfo=get(mmreader(fullfile(Param.RootPath,[Param.RootFile Param.ImaExt]))); Param.Civ1.ImageBitDepth=ImageInfo.BitsPerPixel/3; + if batch + Param.Civ1.ImageA=filecell.ima1.civ1{ifile,j};%file name must be used for batch instead of video object + Param.Civ1.ImageB=filecell.ima2.civ1{ifile,j}; + end else + Param.Civ1.ImageA=filecell.ima1.civ1{ifile,j}; + Param.Civ1.ImageB=filecell.ima2.civ1{ifile,j}; + form=imformats(regexprep(get(handles.ImaExt,'String'),'^.',''));%look for image formats ImageInfo=imfinfo(filecell.ima1.civ1{1,1});%read the first image to get the size Param.Civ1.ImageBitDepth=ImageInfo.BitDepth; end + Param.Civ1.ImageWidth=ImageInfo.Width; Param.Civ1.ImageHeight=ImageInfo.Height; - Param.Civ1.i1=i1_civ1(ifile); - Param.Civ1.i2=i2_civ1(ifile); - % read mask parameters + Param.Civ1.FrameIndexA=i1_civ1(ifile); + Param.Civ1.FrameIndexB=i2_civ1(ifile); + % read mask )parameters if Param.Civ1.CheckMask % the lines below should be changed with the new gui if ~exist(Param.Civ1.Mask,'file') @@ -1312,5 +1322,5 @@ i1_grid=mod(i1_civ1(ifile)-1,nbslice_grid)+1; Param.Civ1.Grid=[filecell.filebase '_' fullfile_uvmat('','',Param.Civ1.Grid,'.grid','_1',i1_grid)]; -% Param.Civ1.Grid=[filecell.filebase '_' name_generator(Param.Civ1.Grid,i1_grid,1,'.grid','_i')]; + % Param.Civ1.Grid=[filecell.filebase '_' name_generator(Param.Civ1.Grid,i1_grid,1,'.grid','_i')]; if ~exist(Param.Civ1.GridName,'file') errormsg='grid file absent for civ1'; @@ -1424,6 +1434,22 @@ end if Param.CheckCiv2==1 - Param.Civ2.ImageA=filecell.ima1.civ2{ifile,j}; - Param.Civ2.ImageB=filecell.ima2.civ2{ifile,j}; + if strcmp(Param.Civ2.FileTypeA,'video')|| strcmp(Param.Civ2.FileTypeA,'mmreader') + % ImageInfo=get(VideoReader(fullfile(Param.RootPath,[Param.RootFile Param.ImaExt]))); + ImageInfo=get(Param.Civ2.ImageA); + % elseif strcmp(Param.Civ1.FileTypeA,'mmreader') + % ImageInfo=get(mmreader(fullfile(Param.RootPath,[Param.RootFile Param.ImaExt]))); + Param.Civ2.ImageBitDepth=ImageInfo.BitsPerPixel/3; + if batch + Param.Civ2.ImageA=filecell.ima1.civ2{ifile,j};%file name must be used for batch instead of video object + Param.Civ2.ImageB=filecell.ima2.civ2{ifile,j}; + end + else + Param.Civ2.ImageA=filecell.ima1.civ2{ifile,j}; + Param.Civ2.ImageB=filecell.ima2.civ2{ifile,j}; + form=imformats(regexprep(get(handles.ImaExt,'String'),'^.',''));%look for image formats + ImageInfo=imfinfo(filecell.ima1.civ2{1,1});%read the first image to get the size + Param.Civ2.ImageBitDepth=ImageInfo.BitDepth; + end + if ~checkframe %&& size(time,1)>=i2_civ2(ifile) && size(time,2)>=j2_civ2(j) Param.Civ2.Dt=time(i2_civ2(ifile)+1,j2_civ2(j)+1)-time(i1_civ2(ifile)+1,j1_civ2(j)+1); @@ -1463,5 +1489,5 @@ form=imformats(regexprep(get(handles.ImaExt,'String'),'^.',''));%look for image formats if isempty(form) - ImageInfo=get(VideoReader(filecell.ima1.civ2{1,1})); + % ImageInfo=get(VideoReader(fullfile()); Param.Civ2.ImageBitDepth=ImageInfo.BitsPerPixel/3; else @@ -1471,6 +1497,8 @@ Param.Civ2.ImageWidth=ImageInfo.Width; Param.Civ2.ImageHeight=ImageInfo.Height; - Param.Civ2.i1=i1_civ2(ifile); - Param.Civ2.i2=i2_civ2(ifile); + Param.Civ2.FrameIndexA=i1_civ2(ifile); + Param.Civ2.FrameIndexB=i2_civ2(ifile); +% Param.Civ2.i1=i1_civ2(ifile); +% Param.Civ2.i2=i2_civ2(ifile); switch CivMode case 'CivX' @@ -4000,6 +4028,6 @@ par_civ1.ImageHeight=size(Data.A,1); par_civ1.Mask='all';% will provide only the grid set for PIV, no image correlation - par_civ1.i1=i1; - par_civ1.i2=i2; + par_civ1.FrameIndexA=num2str(i1); + par_civ1.FrameIndexB=num2str(i2); Param.Civ1=par_civ1; Grid=civ_matlab(Param);% get the grid of x, y positions set for PIV Index: /trunk/src/civ_matlab.m =================================================================== --- /trunk/src/civ_matlab.m (revision 434) +++ /trunk/src/civ_matlab.m (revision 435) @@ -52,11 +52,36 @@ check_patch1=0;%default +% case of input Param set by an xml file (batch mode) if ischar(Param) Param=xml2struct(Param); %if Param is the name of an xml file, read this file as a Matlab structure + if isfield(Param,'Civ1') + if strcmp(Param.Civ1.FileTypeA,'video') + Param.Civ1.ImageA=VideoReader(Param.Civ1.ImageA); + elseif strcmp(Param.Civ1.FileTypeA,'mmreader') + Param.Civ1.ImageA=mmreader(Param.Civ1.ImageA); + end + if strcmp(Param.Civ1.FileTypeB,'video') + Param.Civ1.ImageB=VideoReader(Param.Civ1.ImageB); + elseif strcmp(Param.Civ1.FileTypeB,'mmreader') + Param.Civ1.ImageB=mmreader(Param.Civ1.ImageB); + end + end + if isfield(Param,'Civ2') + if strcmp(Param.Civ2.FileTypeA,'video') + Param.Civ2.ImageA=VideoReader(Param.Civ2.ImageA); + elseif strcmp(Param.Civ2.FileTypeA,'mmreader') + Param.Civ2.ImageA=mmreader(Param.Civ2.ImageA); + end + if strcmp(Param.Civ2.FileTypeB,'video') + Param.Civ2.ImageB=VideoReader(Param.Civ2.ImageB); + elseif strcmp(Param.Civ2.FileTypeB,'mmreader') + Param.Civ2.ImageB=mmreader(Param.Civ2.ImageB); + end + end end %% Civ1 if isfield (Param,'Civ1') -% check_civ1=1;% test for further use of civ1 results + % check_civ1=1;% test for further use of civ1 results % %% prepare images par_civ1=Param.Civ1; @@ -72,11 +97,20 @@ end else - if isfield(par_civ1,'ImageA')&&(ischar(par_civ1.ImageA)||strcmp(class(par_civ1.ImageA),'VideoReader')) % case with no image: only the PIV grid is calculated - [Field,ParamOut,errormsg] = read_field(par_civ1.ImageA,par_civ1.FileTypeA,[],par_civ1.i1); - par_civ1.ImageA=Field.A;%imread(par_civ1.ImageA);%[Field,ParamOut,errormsg] = read_field(ObjectName,FileType,ParamIn,num) - end - if isfield(par_civ1,'ImageB')&& (ischar(par_civ1.ImageB)||strcmp(class(par_civ1.ImageA),'VideoReader')) - [Field,ParamOut,errormsg] = read_field(par_civ1.ImageB,par_civ1.FileTypeB,[],par_civ1.i2); - par_civ1.ImageB=Field.A;%=imread(par_civ1.ImageB); + if isfield(par_civ1,'ImageA')%&&(ischar(par_civ1.ImageA)||strcmp(class(par_civ1.ImageA),'VideoReader')) % case with no image: only the PIV grid is calculated + + [Field,ParamOut,errormsg] = read_field(par_civ1.ImageA,par_civ1.FileTypeA,[],par_civ1.FrameIndexA); + if ~isempty(errormsg) + errormsg=['error in civ_matlab/read_field:' errormsg]; + return + end + par_civ1.ImageA=Field.A;%= image matrix A in the first input field + end + if isfield(par_civ1,'ImageB')%&& (ischar(par_civ1.ImageB)||strcmp(class(par_civ1.ImageA),'VideoReader')) + [Field,ParamOut,errormsg] = read_field(par_civ1.ImageB,par_civ1.FileTypeB,[],par_civ1.FrameIndexB); + if ~isempty(errormsg) + errormsg=['error in civ_matlab/read_field:' errormsg]; + return + end + par_civ1.ImageB=Field.A;%= image matrix A in the second input field end end @@ -121,5 +155,5 @@ Data.Civ1_C=reshape(ctable,[],1); Data.Civ1_F=reshape(F,[],1); - Data.CivStage=1; + Data.CivStage=1; else if exist('ncfile','var') @@ -162,9 +196,9 @@ Data.VarDimName=[Data.VarDimName {'nb_vec_1'}]; nbvar=length(Data.ListVarName); - Data.VarAttribute{nbvar}.Role='errorflag'; + Data.VarAttribute{nbvar}.Role='errorflag'; Data.Civ1_FF=fix(Param.Fix1,Data.Civ1_F,Data.Civ1_C,Data.Civ1_U,Data.Civ1_V); - Data.CivStage=2; - end -end + Data.CivStage=2; + end +end %% Patch1 if isfield (Param,'Patch1') @@ -180,6 +214,6 @@ nbvar=length(Data.ListVarName); Data.ListVarName=[Data.ListVarName {'Civ1_U_smooth','Civ1_V_smooth','Civ1_SubRange','Civ1_NbSites','Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps'}]; - Data.VarDimName=[Data.VarDimName {'nb_vec_1','nb_vec_1',{'nb_coord','nb_bounds','nb_subdomain_1'},{'nb_subdomain_1'},... - {'nb_tps_1','nb_coord','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'}}]; + Data.VarDimName=[Data.VarDimName {'nb_vec_1','nb_vec_1',{'nb_coord','nb_bounds','nb_subdomain_1'},{'nb_subdomain_1'},... + {'nb_tps_1','nb_coord','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'}}]; Data.VarAttribute{nbvar+1}.Role='vector_x'; Data.VarAttribute{nbvar+2}.Role='vector_y'; @@ -191,16 +225,16 @@ if isfield(Data,'Civ1_FF') ind_good=find(Data.Civ1_FF==0); - else + else ind_good=1:numel(Data.Civ1_X); end [Data.Civ1_SubRange,Data.Civ1_NbSites,Data.Civ1_Coord_tps,Data.Civ1_U_tps,Data.Civ1_V_tps,tild,Ures, Vres,tild,FFres]=... - filter_tps([Data.Civ1_X(ind_good) Data.Civ1_Y(ind_good)],Data.Civ1_U(ind_good),Data.Civ1_V(ind_good),[],Data.Patch1_SubDomain,Data.Patch1_Rho,Data.Patch1_Threshold); - fill=zeros(3,2,size(Data.Civ1_SubRange,3)); %matrix of zeros to complement the matrix Data.Civ1_Coord_tps (conveninent for file storage) - Data.Civ1_Coord_tps=cat(1,Data.Civ1_Coord_tps,fill); - Data.Civ1_U_smooth(ind_good)=Ures; - Data.Civ1_V_smooth(ind_good)=Vres; - Data.Civ1_FF(ind_good)=FFres; - Data.CivStage=3; -end + filter_tps([Data.Civ1_X(ind_good) Data.Civ1_Y(ind_good)],Data.Civ1_U(ind_good),Data.Civ1_V(ind_good),[],Data.Patch1_SubDomain,Data.Patch1_Rho,Data.Patch1_Threshold); + fill=zeros(3,2,size(Data.Civ1_SubRange,3)); %matrix of zeros to complement the matrix Data.Civ1_Coord_tps (conveninent for file storage) + Data.Civ1_Coord_tps=cat(1,Data.Civ1_Coord_tps,fill); + Data.Civ1_U_smooth(ind_good)=Ures; + Data.Civ1_V_smooth(ind_good)=Vres; + Data.Civ1_FF(ind_good)=FFres; + Data.CivStage=3; +end %% Civ2 @@ -209,5 +243,9 @@ if ~isfield (Param,'Civ1') || ~strcmp(Param.Civ1.ImageA,par_civ2.ImageA) %read first image if not already done for civ1 - [Field,ParamOut,errormsg] = read_field(par_civ2.ImageA,par_civ2.FileTypeA,[],par_civ2.i1); + [Field,ParamOut,errormsg] = read_field(par_civ2.ImageA,par_civ2.FileTypeA,[],par_civ2.FrameIndexA); + if ~isempty(errormsg) + errormsg=['error in civ_matlab/read_field:' errormsg]; + return + end par_civ2.ImageA=Field.A; else @@ -216,5 +254,9 @@ if ~isfield (Param,'Civ1') || ~strcmp(Param.Civ1.ImageB,par_civ2.ImageB) %read first image if not already done for civ1 - [Field,ParamOut,errormsg] = read_field(par_civ2.ImageB,par_civ2.FileTypeB,[],par_civ2.i2); + [Field,ParamOut,errormsg] = read_field(par_civ2.ImageB,par_civ2.FileTypeB,[],par_civ2.FrameIndexB); + if ~isempty(errormsg) + errormsg=['error in civ_matlab/read_field:' errormsg]; + return + end par_civ2.ImageB=Field.A; else @@ -233,5 +275,5 @@ [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy); GridX=reshape(GridX,[],1); - GridY=reshape(GridY,[],1); + GridY=reshape(GridY,[],1); Shiftx=zeros(size(GridX));% shift expected from civ1 data Shifty=zeros(size(GridX)); @@ -270,5 +312,5 @@ par_civ2.Shiftx=Shiftx(nbval>=1)./nbval(nbval>=1); par_civ2.Shifty=Shifty(nbval>=1)./nbval(nbval>=1); - par_civ2.Grid=[GridX(nbval>=1)-par_civ2.Shiftx/2 GridY(nbval>=1)-par_civ2.Shifty/2];% grid taken at the extrapolated origin of the displacement vectors + par_civ2.Grid=[GridX(nbval>=1)-par_civ2.Shiftx/2 GridY(nbval>=1)-par_civ2.Shifty/2];% grid taken at the extrapolated origin of the displacement vectors if par_civ2.CheckDeformation par_civ2.DUDX=DUDX./nbval; @@ -279,6 +321,6 @@ % caluclate velocity data (y and v in indices, reverse to y component) [xtable ytable utable vtable ctable F] = civ (par_civ2); -% diff_squared=(utable-par_civ2.Shiftx).*(utable-par_civ2.Shiftx)+(vtable+par_civ2.Shifty).*(vtable+par_civ2.Shifty); -% F(diff_squared>=4)=4; %flag vectors whose distance to the guess exceeds 2 pixels + % diff_squared=(utable-par_civ2.Shiftx).*(utable-par_civ2.Shiftx)+(vtable+par_civ2.Shifty).*(vtable+par_civ2.Shifty); + % F(diff_squared>=4)=4; %flag vectors whose distance to the guess exceeds 2 pixels list_param=(fieldnames(Param.Civ2))'; list_remove={'pxcmx','pxcmy','npx','npy','gridflag','maskflag','term_a','term_b','T0'}; @@ -300,6 +342,6 @@ end Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param {'Civ2_Time','Civ2_Dt'}]; -% Data.Civ2_Time=par_civ2.Time; -% Data.Civ2_Dt=par_civ2.Dt; + % Data.Civ2_Time=par_civ2.Time; + % Data.Civ2_Dt=par_civ2.Dt; nbvar=numel(Data.ListVarName); Data.ListVarName=[Data.ListVarName {'Civ2_X','Civ2_Y','Civ2_U','Civ2_V','Civ2_F','Civ2_C'}];% cell array containing the names of the fields to record @@ -340,10 +382,10 @@ Data.VarDimName=[Data.VarDimName {'nb_vec_2'}]; nbvar=length(Data.ListVarName); - Data.VarAttribute{nbvar}.Role='errorflag'; + Data.VarAttribute{nbvar}.Role='errorflag'; Data.Civ2_FF=fix(Param.Fix2,Data.Civ2_F,Data.Civ2_C,Data.Civ2_U,Data.Civ2_V); - Data.CivStage=Data.CivStage+1; + Data.CivStage=Data.CivStage+1; end -end +end %% Patch2 @@ -356,7 +398,7 @@ Data.ListVarName=[Data.ListVarName {'Civ2_U_smooth','Civ2_V_smooth','Civ2_SubRange','Civ2_NbSites','Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps'}]; Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2',{'nb_coord','nb_bounds','nb_subdomain_2'},{'nb_subdomain_2'},... - {'nb_tps_2','nb_coord','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'}}]; - - Data.VarAttribute{nbvar+1}.Role='vector_x'; + {'nb_tps_2','nb_coord','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'}}]; + + Data.VarAttribute{nbvar+1}.Role='vector_x'; Data.VarAttribute{nbvar+2}.Role='vector_y'; Data.VarAttribute{nbvar+5}.Role='coord_tps'; @@ -369,14 +411,14 @@ else ind_good=1:numel(Data.Civ2_X); - end + end [Data.Civ2_SubRange,Data.Civ2_NbSites,Data.Civ2_Coord_tps,Data.Civ2_U_tps,Data.Civ2_V_tps,tild,Ures, Vres,tild,FFres]=... - filter_tps([Data.Civ2_X(ind_good) Data.Civ2_Y(ind_good)],Data.Civ2_U(ind_good),Data.Civ2_V(ind_good),[],Data.Patch2_SubDomain,Data.Patch2_Rho,Data.Patch2_Threshold); - fill=zeros(3,2,size(Data.Civ2_SubRange,3)); %matrix of zeros to complement the matrix Data.Civ1_Coord_tps (conveninent for file storage) - Data.Civ2_Coord_tps=cat(1,Data.Civ2_Coord_tps,fill); + filter_tps([Data.Civ2_X(ind_good) Data.Civ2_Y(ind_good)],Data.Civ2_U(ind_good),Data.Civ2_V(ind_good),[],Data.Patch2_SubDomain,Data.Patch2_Rho,Data.Patch2_Threshold); + fill=zeros(3,2,size(Data.Civ2_SubRange,3)); %matrix of zeros to complement the matrix Data.Civ1_Coord_tps (conveninent for file storage) + Data.Civ2_Coord_tps=cat(1,Data.Civ2_Coord_tps,fill); Data.Civ2_U_smooth(ind_good)=Ures; Data.Civ2_V_smooth(ind_good)=Vres; Data.Civ2_FF(ind_good)=FFres; - Data.CivStage=Data.CivStage+1; -end + Data.CivStage=Data.CivStage+1; +end %% write result in a netcdf file if requested Index: /trunk/src/find_file_series.m =================================================================== --- /trunk/src/find_file_series.m (revision 434) +++ /trunk/src/find_file_series.m (revision 435) @@ -52,5 +52,5 @@ % ifile_min=1;%default [FileType,FileInfo,Object]=get_file_type(fullfileinput); -if strcmp( FileType,'multimage')||strcmp( FileType,'video') +if strcmp( FileType,'multimage')||strcmp( FileType,'video')||strcmp( FileType,'mmreader') NomType='*'; i1_series=(1:FileInfo.NumberOfFrames)'; Index: /trunk/src/get_file_type.m =================================================================== --- /trunk/src/get_file_type.m (revision 434) +++ /trunk/src/get_file_type.m (revision 435) @@ -74,4 +74,8 @@ FileInfo.NumberOfFrames=get(VideoObject,'NumberOfFrames'); FileType='video'; + elseif exist('mmreader.m','file')% Matlab 2009a + VideoObject=mmreader(fileinput); + FileInfo.NumberOfFrames=get(VideoObject,'NumberOfFrames'); + FileType='mmreader'; end end Index: /trunk/src/read_field.m =================================================================== --- /trunk/src/read_field.m (revision 434) +++ /trunk/src/read_field.m (revision 435) @@ -150,9 +150,9 @@ % % ParamOut.FieldList={'get_field...'}; % end - case 'video' + case {'video','mmreader'} try A=read(ObjectName,num); catch ME - errormsg=ME.message + errormsg=ME.message; return end Index: /trunk/src/uvmat.m =================================================================== --- /trunk/src/uvmat.m (revision 434) +++ /trunk/src/uvmat.m (revision 435) @@ -1528,5 +1528,5 @@ UvData=get(handles.uvmat,'UserData'); -while get(handles.speed,'Value')~=0 && isequal(get(handles.Movie,'BusyAction'),'queue') % enable STOP command +while get(handles.Movie,'Value')==1 && get(handles.speed,'Value')~=0 && isequal(get(handles.Movie,'BusyAction'),'queue') % enable STOP command errormsg=runpm(hObject,eventdata,handles,increment); if ~isempty(errormsg) @@ -1555,5 +1555,5 @@ UvData=get(handles.uvmat,'UserData'); -while get(handles.speed,'Value')~=0 && isequal(get(handles.MovieBackward,'BusyAction'),'queue') % enable STOP command +while get(handles.MovieBackward,'Value')==1 && get(handles.speed,'Value')~=0 && isequal(get(handles.MovieBackward,'BusyAction'),'queue') % enable STOP command errormsg=runpm(hObject,eventdata,handles,increment); if ~isempty(errormsg) @@ -2034,5 +2034,5 @@ end end - case 'video' + case {'video','mmreader'} ObjectName=UvData.MovieObject{1}; case 'vol' %TODO: update @@ -2094,5 +2094,5 @@ end end - case 'video' + case {'video','mmreader'} Name=UvData.MovieObject{2}; case 'vol' %TODO: update @@ -2406,12 +2406,10 @@ %% get bounds and mesh (needed for mouse action and to open set_object) -XName=''; %default -YName=''; -if ~isempty(VarType{imax}.coord_x) - XName=UvData.Field.ListVarName{VarType{imax}.coord_x}; - DimIndex=VarDimIndex{CellVarIndex{imax}(1)}; %list of dim indices for the variable - nbpoints_x=DimValue(DimIndex(NbDim)); - %unstructured coordinates - if ~isempty(VarType{imax}.coord_y) +if NbDim>1 + XName=''; %default + YName=''; + %unstructured coordinates + if ~isempty(VarType{imax}.coord_x)&&~isempty(VarType{imax}.coord_y) + XName=UvData.Field.ListVarName{VarType{imax}.coord_x}; YName=UvData.Field.ListVarName{VarType{imax}.coord_y}; %nbvec=length(UvData.Field.(XName));%nbre of measurement points (e.g. vectors) @@ -2422,131 +2420,132 @@ NbDim=2; end - end -%structured coordinate -elseif numel(VarType)>=imax && numel(VarType{imax}.coord)>=NbDim && VarType{imax}.coord(NbDim)>0 - XName=UvData.Field.ListVarName{VarType{imax}.coord(NbDim)}; - if NbDim> 1 && VarType{imax}.coord(NbDim-1)>0 - YName=UvData.Field.ListVarName{VarType{imax}.coord(NbDim-1)}; %structured coordinates - end - % VarIndex=CellVarIndex{imax}; % list of variable indices - DimIndex=VarDimIndex{CellVarIndex{imax}(1)}; %list of dim indices for the variable - nbpoints_x=DimValue(DimIndex(NbDim)); - XMax=nbpoints_x;%default - XMin=1;%default -end - -if NbDim==3 - if ~test_x - ZName=UvData.Field.ListVarName{VarType{imax}.coord(1)};%structured coordinates in 3D - end - ZMax=max(UvData.Field.(ZName)); - ZMin=min(UvData.Field.(ZName)); - UvData.Field.ZMax=ZMax; - UvData.Field.ZMin=ZMin; - test_z=1; - if isequal(ZMin,ZMax)%no z dependency - NbDim=2; - test_z=0; - end -end -if ~isempty (XName) - XMax=max(max(UvData.Field.(XName))); - XMin=min(min(UvData.Field.(XName))); - UvData.Field.NbDim=NbDim; - UvData.Field.XMax=XMax; - UvData.Field.XMin=XMin; - if NbDim >1&& ~isempty(YName) - YMax=max(max(UvData.Field.(YName))); - YMin=min(min(UvData.Field.(YName))); - UvData.Field.YMax=YMax; - UvData.Field.YMin=YMin; - end - nbvec=length(UvData.Field.(XName)); - if test_x %unstructured coordinates - if test_z - UvData.Field.Mesh=((XMax-XMin)*(YMax-YMin)*(ZMax-ZMin))/nbvec;% volume per vector - UvData.Field.Mesh=(UvData.Field.Mesh)^(1/3); - else - UvData.Field.Mesh=sqrt((XMax-XMin)*(YMax-YMin)/nbvec);%2D - end - end -end -% case of structured coordinates -if ~test_x - DX=(XMax-XMin)/(nbpoints_x-1); - if NbDim >1 - nbpoints_y=DimValue(DimIndex(NbDim-1)); - if isempty(YName)% if the y coordinate is not expressed, it is taken as the matrix index - DY=1; - UvData.Field.YMax=nbpoints_y; - UvData.Field.YMin=1; - else - DY=(YMax-YMin)/(nbpoints_y-1); - end - end + %structured coordinate + elseif numel(VarType)>=imax && numel(VarType{imax}.coord)>=NbDim && VarType{imax}.coord(NbDim)>0 + XName=UvData.Field.ListVarName{VarType{imax}.coord(NbDim)}; + if NbDim> 1 && VarType{imax}.coord(NbDim-1)>0 + YName=UvData.Field.ListVarName{VarType{imax}.coord(NbDim-1)}; %structured coordinates + end + % VarIndex=CellVarIndex{imax}; % list of variable indices + DimIndex=VarDimIndex{CellVarIndex{imax}(1)}; %list of dim indices for the variable + nbpoints_x=DimValue(DimIndex(NbDim)); + XMax=nbpoints_x;%default + XMin=1;%default + end + if NbDim==3 - nbpoints_z=DimValue(DimIndex(1)); - DZ=(ZMax-ZMin)/(nbpoints_z-1); - UvData.Field.Mesh=(DX*DY*DZ)^(1/3); + if ~test_x + ZName=UvData.Field.ListVarName{VarType{imax}.coord(1)};%structured coordinates in 3D + end + ZMax=max(UvData.Field.(ZName)); + ZMin=min(UvData.Field.(ZName)); UvData.Field.ZMax=ZMax; UvData.Field.ZMin=ZMin; + test_z=1; + if isequal(ZMin,ZMax)%no z dependency + NbDim=2; + test_z=0; + end + end + if ~isempty (XName) + XMax=max(max(UvData.Field.(XName))); + XMin=min(min(UvData.Field.(XName))); + UvData.Field.NbDim=NbDim; + UvData.Field.XMax=XMax; + UvData.Field.XMin=XMin; + if NbDim >1&& ~isempty(YName) + YMax=max(max(UvData.Field.(YName))); + YMin=min(min(UvData.Field.(YName))); + UvData.Field.YMax=YMax; + UvData.Field.YMin=YMin; + end + nbvec=length(UvData.Field.(XName)); + if test_x %unstructured coordinates + if test_z + UvData.Field.Mesh=((XMax-XMin)*(YMax-YMin)*(ZMax-ZMin))/nbvec;% volume per vector + UvData.Field.Mesh=(UvData.Field.Mesh)^(1/3); + else + UvData.Field.Mesh=sqrt((XMax-XMin)*(YMax-YMin)/nbvec);%2D + end + end + end + % case of structured coordinates + if ~test_x + DX=(XMax-XMin)/(nbpoints_x-1); + if NbDim >1 + nbpoints_y=DimValue(DimIndex(NbDim-1)); + if isempty(YName)% if the y coordinate is not expressed, it is taken as the matrix index + DY=1; + UvData.Field.YMax=nbpoints_y; + UvData.Field.YMin=1; + else + DY=(YMax-YMin)/(nbpoints_y-1); + end + end + if NbDim==3 + nbpoints_z=DimValue(DimIndex(1)); + DZ=(ZMax-ZMin)/(nbpoints_z-1); + UvData.Field.Mesh=(DX*DY*DZ)^(1/3); + UvData.Field.ZMax=ZMax; + UvData.Field.ZMin=ZMin; + else + UvData.Field.Mesh=DX;%sqrt(DX*DY); + end + end + % adjust the mesh to a value 1, 2 , 5 *10^n + ord=10^(floor(log10(UvData.Field.Mesh)));%order of magnitude + if UvData.Field.Mesh/ord>=5 + UvData.Field.Mesh=5*ord; + elseif UvData.Field.Mesh/ord>=2 + UvData.Field.Mesh=2*ord; else - UvData.Field.Mesh=DX;%sqrt(DX*DY); - end -end -% adjust the mesh to a value 1, 2 , 5 *10^n -ord=10^(floor(log10(UvData.Field.Mesh)));%order of magnitude -if UvData.Field.Mesh/ord>=5 - UvData.Field.Mesh=5*ord; -elseif UvData.Field.Mesh/ord>=2 - UvData.Field.Mesh=2*ord; -else - UvData.Field.Mesh=ord; -end -UvData.Object{1}.Type='plane';%main plotting plane -UvData.Object{1}.ProjMode='projection';%main plotting plane -UvData.Object{1}.DisplayHandle.uvmat=[]; %plane not visible in uvmat -UvData.Object{1}.DisplayHandle.view_field=[]; %plane not visible in uvmat - -%% 3D case (menuvolume) -if NbDim==3% && UvData.NewSeries - test_set_object=1; - hset_object=findobj(allchild(0),'tag','set_object');% look for the set_object GUI - ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider - ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider - if ~isempty(hset_object) %if set_object is detected - delete(hset_object);% delete the GUI set_object if it does not fit - end - if test_set_object% reinitiate the GUI set_object - delete_object(1);% delete the current projection object in the list UvData.Object, delete its graphic representations and update the list displayed in handles.ListObject and 2 - UvData.Object{1}.NbDim=NbDim;%test for 3D objects - UvData.Object{1}.RangeZ=UvData.Field.Mesh;%main plotting plane - UvData.Object{1}.Coord(1,3)=(UvData.Field.ZMin+UvData.Field.ZMax)/2;%section at a middle plane chosen - UvData.Object{1}.Angle=[0 0 0]; - UvData.Object{1}.HandlesDisplay=plot(0,0,'Tag','proj_object');% A REVOIR - UvData.Object{1}.Name='1-PLANE'; - UvData.Object{1}.enable_plot=1; - set_object(UvData.Object{1},handles,ZBounds); - set(handles.ListObject,'Value',1); - set(handles.ListObject,'String',{'1-PLANE'}); - set(handles.edit_object,'Value',1)% put the plane in edit mode to enable the z cursor - edit_object_Callback([],[], handles) - end - %multilevel case (single menuplane in a 3D space) -elseif isfield(UvData,'Z') - if isfield(UvData,'CoordType')&& isequal(UvData.CoordType,'phys') && isfield(UvData,'XmlData') - XmlData=UvData.XmlData{1}; - if isfield(XmlData,'PlanePos') - UvData.Object{1}.Coord=XmlData.PlanePos(UvData.ZIndex,:); - end - if isfield(XmlData,'PlaneAngle') - siz=size(XmlData.PlaneAngle); - indangle=min(siz(1),UvData.ZIndex);%take first angle if a single angle is defined (translating scanning) - UvData.Object{1}.PlaneAngle=XmlData.PlaneAngle(indangle,:); - end - elseif isfield(UvData,'ZIndex') - UvData.Object{1}.ZObject=UvData.ZIndex; - end -end + UvData.Field.Mesh=ord; + end + UvData.Object{1}.Type='plane';%main plotting plane + UvData.Object{1}.ProjMode='projection';%main plotting plane + UvData.Object{1}.DisplayHandle.uvmat=[]; %plane not visible in uvmat + UvData.Object{1}.DisplayHandle.view_field=[]; %plane not visible in uvmat + + %% 3D case (menuvolume) + if NbDim==3% && UvData.NewSeries + test_set_object=1; + hset_object=findobj(allchild(0),'tag','set_object');% look for the set_object GUI + ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider + ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider + if ~isempty(hset_object) %if set_object is detected + delete(hset_object);% delete the GUI set_object if it does not fit + end + if test_set_object% reinitiate the GUI set_object + delete_object(1);% delete the current projection object in the list UvData.Object, delete its graphic representations and update the list displayed in handles.ListObject and 2 + UvData.Object{1}.NbDim=NbDim;%test for 3D objects + UvData.Object{1}.RangeZ=UvData.Field.Mesh;%main plotting plane + UvData.Object{1}.Coord(1,3)=(UvData.Field.ZMin+UvData.Field.ZMax)/2;%section at a middle plane chosen + UvData.Object{1}.Angle=[0 0 0]; + UvData.Object{1}.HandlesDisplay=plot(0,0,'Tag','proj_object');% A REVOIR + UvData.Object{1}.Name='1-PLANE'; + UvData.Object{1}.enable_plot=1; + set_object(UvData.Object{1},handles,ZBounds); + set(handles.ListObject,'Value',1); + set(handles.ListObject,'String',{'1-PLANE'}); + set(handles.edit_object,'Value',1)% put the plane in edit mode to enable the z cursor + edit_object_Callback([],[], handles) + end + %multilevel case (single menuplane in a 3D space) + elseif isfield(UvData,'Z') + if isfield(UvData,'CoordType')&& isequal(UvData.CoordType,'phys') && isfield(UvData,'XmlData') + XmlData=UvData.XmlData{1}; + if isfield(XmlData,'PlanePos') + UvData.Object{1}.Coord=XmlData.PlanePos(UvData.ZIndex,:); + end + if isfield(XmlData,'PlaneAngle') + siz=size(XmlData.PlaneAngle); + indangle=min(siz(1),UvData.ZIndex);%take first angle if a single angle is defined (translating scanning) + UvData.Object{1}.PlaneAngle=XmlData.PlaneAngle(indangle,:); + end + elseif isfield(UvData,'ZIndex') + UvData.Object{1}.ZObject=UvData.ZIndex; + end + end +end + testnewseries=UvData.NewSeries; UvData.NewSeries=0;% put to 0 the test for a new field series (set by RootPath_callback)