Index: /trunk/src/civ.m =================================================================== --- /trunk/src/civ.m (revision 247) +++ /trunk/src/civ.m (revision 248) @@ -2152,4 +2152,7 @@ Param.Patch1.SubDomain=subdomain_patch1; end + if box_test(4)==1 + Param.Civ2=par_civ2; + end [Data,erromsg]=civ_uvmat(Param,filecell.nc.civ1{ifile,j}); if isempty(errormsg) @@ -2705,6 +2708,10 @@ if ~testdiff % civ2 or patch2 are written in the same file as civ1 if box_test(4)==0 ; %check the existence of civ2 if it is not calculated - Data=nc2struct(filename,'ListGlobalAttribute','civ2'); - if isempty(Data.civ2)||isequal(Data.civ2,0) + Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2'); + if ~isempty(Data.CivStage) && Data.CivStage<4 %test for civ files + msgbox_uvmat('ERROR',['no civ2 data in ' filename]) + filecell=[]; + return + elseif isempty(Data.civ2)||isequal(Data.civ2,0) msgbox_uvmat('ERROR',['no civ2 data in ' filename]) filecell=[]; @@ -2712,6 +2719,12 @@ end elseif box_test(3)==0; %check the existence of patch if it is not calculated - Data=nc2struct(filename,'ListGlobalAttribute','patch'); - if isempty(Data.patch)||isequal(Data.patch,0) + Data=nc2struct(filename,'ListGlobalAttribute','CivStage','patch') + if ~isempty(Data.CivStage) + if Data.CivStage<3 %test for civ files + msgbox_uvmat('ERROR',['no patch data in ' filename]) + filecell=[]; + return + end + elseif isempty(Data.patch)||isequal(Data.patch,0) msgbox_uvmat('ERROR',['no patch data in ' filename]) filecell=[]; @@ -2801,6 +2814,10 @@ return else - Data=nc2struct(filename,'ListGlobalAttribute','civ2'); - if isempty(Data.civ2)||isequal(Data.civ2,0) + Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2'); + if ~isempty(Data.CivStage) && Data.CivStage<4 %test for civ files + msgbox_uvmat('ERROR',['no civ2 data in ' filename]) + filecell=[]; + return + elseif isempty(Data.civ2)||isequal(Data.civ2,0) msgbox_uvmat('ERROR',['no civ2 data in ' filename]) filecell=[]; @@ -4677,5 +4694,5 @@ end [filecell,num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2,nom_type_nc,file_ref_fix1,file_ref_fix2]=... - set_civ_filenames(handles,ref_i,ref_j,[1 0 0 0 0 0]); + set_civ_filenames(handles,ref_i,ref_j,[1 0 0 0 0 0]) Data.ListVarName={'ny','nx','A'}; Data.VarDimName={'ny','nx',{'ny','nx'}}; Index: /trunk/src/civ_uvmat.m =================================================================== --- /trunk/src/civ_uvmat.m (revision 247) +++ /trunk/src/civ_uvmat.m (revision 248) @@ -8,9 +8,10 @@ ListVarCiv1={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_F'}; ListVarFix1={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_F','Civ1_FF'}; +mask=''; +maskname='';%default %% Civ1 if isfield (Param,'Civ1') par_civ1=Param.Civ1; - str2num(par_civ1.rho) image1=imread(par_civ1.filename_ima_a); image2=imread(par_civ1.filename_ima_b); @@ -30,7 +31,10 @@ PointCoord(:,1)=reshape(GridX,[],1); PointCoord(:,2)=reshape(GridY,[],1); - + if ~isempty(par_civ1.maskname) + maskname=par_civ1.maskname; + mask=imread(maskname); + end % caluclate velocity data (y and v in indices, reverse to y component) - [xtable ytable utable vtable ctable F] = pivlab (image1,image2,ibx2,iby2,isx2,isy2,shiftx,-shifty,PointCoord,str2num(par_civ1.rho), []); + [xtable ytable utable vtable ctable F] = pivlab (image1,image2,ibx2,iby2,isx2,isy2,shiftx,-shifty,PointCoord,str2num(par_civ1.rho), mask); list_param=(fieldnames(par_civ1))'; list_remove={'pxcmx','pxcmy','npx','npy','gridflag','maskflag','term_a','term_b','T0'}; @@ -148,4 +152,68 @@ Data.CivStage=3; end + +%% Civ2 +if isfield (Param,'Civ2') + par_civ2=Param.Civ2 + image1=imread(par_civ2.filename_ima_a); + image2=imread(par_civ2.filename_ima_b); + stepx=str2num(par_civ2.dx); + stepy=str2num(par_civ2.dy); + ibx2=ceil(str2num(par_civ2.ibx)/2); + iby2=ceil(str2num(par_civ2.iby)/2); + isx2=4; + isy2=4; +% shiftx=str2num(par_civ1.shiftx); +% shifty=str2num(par_civ1.shifty); +% TO GET shift from par_civ2.filename_nc1 + miniy=max(1+isy2+shifty,1+iby2); + minix=max(1+isx2-shiftx,1+ibx2); + maxiy=min(size(image1,1)-isy2+shifty,size(image1,1)-iby2); + maxix=min(size(image1,2)-isx2-shiftx,size(image1,2)-ibx2); + [GridX,GridY]=meshgrid(minix:stepx:maxix,miniy:stepy:maxiy); + PointCoord(:,1)=reshape(GridX,[],1); + PointCoord(:,2)=reshape(GridY,[],1); + if ~isempty(par_civ2.maskname)&& ~strcmp(maskname,par_civ2.maskname)% mask exist, not already read in civ1 + mask=imread(par_civ2.maskname); + end + % caluclate velocity data (y and v in indices, reverse to y component) + [xtable ytable utable vtable ctable F] = pivlab (image1,image2,ibx2,iby2,isx2,isy2,shiftx,-shifty,PointCoord,str2num(par_civ1.rho),mask); + list_param=(fieldnames(par_civ1))'; + list_remove={'pxcmx','pxcmy','npx','npy','gridflag','maskflag','term_a','term_b','T0'}; + index=zeros(size(list_param)); + for ilist=1:length(list_remove) + index=strcmp(list_remove{ilist},list_param); + if ~isempty(find(index,1)) + list_param(index)=[]; + end + end + for ilist=1:length(list_param) + Civ1_param{ilist}=['Civ1_' list_param{ilist}]; + eval(['Data.Civ1_' list_param{ilist} '=Param.Civ1.' list_param{ilist} ';']) + end + if isfield(Data,'Civ1_gridname') && strcmp(Data.Civ1_gridname(1:6),'noFile') + Data.Civ1_gridname=''; + end + if isfield(Data,'Civ1_maskname') && strcmp(Data.Civ1_maskname(1:6),'noFile') + Data.Civ1_maskname=''; + end + Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ1_param {'Civ1_Time','Civ1_Dt'}]; + Data.Civ1_Time=str2double(par_civ1.T0); + Data.Civ1_Dt=str2double(par_civ1.Dt); + Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_F'};% cell array containing the names of the fields to record + Data.VarDimName={'nbvec1','nbvec1','nbvec1','nbvec1','nbvec1','nbvec1'}; + Data.VarAttribute{1}.Role='coord_x'; + Data.VarAttribute{2}.Role='coord_y'; + Data.VarAttribute{3}.Role='vector_x'; + Data.VarAttribute{4}.Role='vector_y'; + Data.VarAttribute{5}.Role='warnflag'; + Data.Civ1_X=reshape(xtable,[],1); + Data.Civ1_Y=reshape(size(image1,1)-ytable+1,[],1); + Data.Civ1_U=reshape(utable,[],1); + Data.Civ1_V=reshape(-vtable,[],1); + Data.Civ1_C=reshape(ctable,[],1); + Data.Civ1_F=reshape(F,[],1); + Data.CivStage=Data.CivStage+1; +end %% write result % 'TESTcalc' Index: /trunk/src/editxml.m =================================================================== --- /trunk/src/editxml.m (revision 247) +++ /trunk/src/editxml.m (revision 248) @@ -330,7 +330,7 @@ head_name=get(t,1,'name'); %Path to shemas: -% path_uvmat=which('editxml');% check the path detected for source file uvmat -% path_UVMAT=fileparts(path_uvmat); %path to UVMAT -% xmlparam=fullfile(path_UVMAT,'PARAM.xml'); + path_uvmat=which('editxml');% check the path detected for source file uvmat + path_UVMAT=fileparts(path_uvmat); %path to UVMAT + % xmlparam=fullfile(path_UVMAT,'PARAM.xml'); xmlparam='PARAM.xml'; %will find PARAM.xml whose path is set in priority if exist(xmlparam,'file') @@ -338,23 +338,23 @@ sparam=convert(tparam); if isfield(sparam,'SchemaPath') - schemafile=[fullfile(sparam.SchemaPath,head_name) '.xsd']; - end - if ~exist(schemafile,'file') - schemafile=fullfile(path_UVMAT,schemafile);%look for relative path definition - end - if exist(schemafile,'file') - xs=xmltree(schemafile); - else - msgbox_uvmat('ERROR',['The xml schema for ' CurrentFile ' is unknown, check the schema path set in the file PARAM.xml']) - [FileName, PathName]=uigetfile( ... - {'*.xsd', '(*.xsd)'; - '*.xsd', '.xsd files '; ... - '*.*', 'All Files (*.*)'}, ... - 'Pick a .xsd schema' ,schemafile); %file browser - if ischar(PathName) && ischar(FileName) && exist(fullfile(PathName,FileName),'file') - DataIn.Schema=fullfile(PathName,FileName); - xs=xmltree(DataIn.Schema);%open the associated schema file + schemafile=[fullfile(sparam.SchemaPath,head_name) '.xsd']; + if ~exist(schemafile,'file') + schemafile=fullfile(path_UVMAT,schemafile);%look for relative path definition + end + if exist(schemafile,'file') + xs=xmltree(schemafile); else - xs=[]; + msgbox_uvmat('ERROR',['The needed xml schema ' sparam.SchemaPath ' is not found, check the file PARAM.xml']) + [FileName, PathName]=uigetfile( ... + {'*.xsd', '(*.xsd)'; + '*.xsd', '.xsd files '; ... + '*.*', 'All Files (*.*)'}, ... + 'Pick a .xsd schema' ,schemafile); %file browser + if ischar(PathName) && ischar(FileName) && exist(fullfile(PathName,FileName),'file') + DataIn.Schema=fullfile(PathName,FileName); + xs=xmltree(DataIn.Schema);%open the associated schema file + else + xs=[]; + end end end Index: /trunk/src/mouse_motion.m =================================================================== --- /trunk/src/mouse_motion.m (revision 247) +++ /trunk/src/mouse_motion.m (revision 248) @@ -224,5 +224,4 @@ xround=Field.X(ind_pt); yround=Field.Y(ind_pt); -% if isfield(Field,'A') % dx=str2double(par.dx); % dy=str2double(par.dy); @@ -253,5 +252,5 @@ set(hhhh,'Position',[xround-isx2+shiftx yround-isy2+shifty 2*isx2 2*isy2]) end - [xtable ytable utable vtable ctable typevector result_conv] = pivlab (Field.A,Field.B,ibx2,iby2,isx2,isy2,shiftx,shifty,[xround yround], 1, []); + [xtable ytable utable vtable ctable typevector result_conv] = pivlab (Field.A,Field.B,ibx2,iby2,isx2,isy2,shiftx,shifty,[xround size(Field.A,1)-yround+1], 1, []); % Asub=Field.A(yround-iby2:yround+iby2,xround-ibx2:xround+ibx2);%first sub-image % Asub=reshape(Asub,[],1);%first sub-image reshaped as matlab vector Index: /trunk/src/pivlab.m =================================================================== --- /trunk/src/pivlab.m (revision 247) +++ /trunk/src/pivlab.m (revision 248) @@ -42,4 +42,6 @@ %% mask testmask=0; +image1=double(image1); +image2=double(image2); if exist('mask','var') && ~isempty(mask) testmask=1; @@ -54,11 +56,9 @@ % 100>=mask> 20: velocity not calculated, impermeable (no flux through mask boundaries) % 20>=mask: velocity=0 - test_noflux=(mask<=100) ; - test_undefined=(mask<=200 & mask>100 ); - image1(test_undefined)=min(min(image1))*ones(size(image1));% put image to zero in the undefined area - image2(test_undefined)=min(min(image1))*ones(size(image1));% put image to zero in the undefined area + test_noflux=(mask<100) ; + test_undefined=(mask<200 & mask>=100 ); + image1(test_undefined)=min(min(image1));% put image to zero in the undefined area + image2(test_undefined)=min(min(image2));% put image to zero in the undefined area end -image1=double(image1); -image2=double(image2); %% calculate correlations: MAINLOOP Index: /trunk/src/proj_field.m =================================================================== --- /trunk/src/proj_field.m (revision 247) +++ /trunk/src/proj_field.m (revision 248) @@ -1772,5 +1772,5 @@ testbound=1; end - if testYMin + if testYMax testin=testin & (coord_Y <= YMax); testbound=1; Index: /trunk/src/series.m =================================================================== --- /trunk/src/series.m (revision 247) +++ /trunk/src/series.m (revision 248) @@ -2167,7 +2167,10 @@ %check the current path to the selected function +if ~isempty(list_transform{ind_coord}) func=functions(list_transform{ind_coord}); set(handles.path_transform,'String',fileparts(func.file)); %show the path to the senlected function - +else + set(handles.path_transform,'String',''); %show the path to the senlected function +end %------------------------------------------------------------------------ % --- generates a series of file names with reference numbers between range1 and Index: /trunk/src/uvmat.m =================================================================== --- /trunk/src/uvmat.m (revision 247) +++ /trunk/src/uvmat.m (revision 248) @@ -1494,8 +1494,9 @@ maskname=maskfiles(ilist).name;% take the first mask file in the list [rr,ff,x1,x2,xa,xb,xext,Mask_NomType{ilist}]=name2display(maskname); - if ~strcmp(Mask_NomType{ilist},Mask_NomType{1}) - msgbox_uvmat('ERROR',['inconsistent mask types ' Mask_NomType{1} Mask_NomType{ilist } ' coexist in the current image directory']) - return - end +% +% if ~strcmp(Mask_NomType{ilist},Mask_NomType{1}) +% msgbox_uvmat('ERROR',['inconsistent mask types ' Mask_NomType{1} ' and ' Mask_NomType{ilist } ' coexist in the current image directory']) +% return +% end [Path2,Name,ext]=fileparts(maskname); Namedouble=double(Name); @@ -1521,5 +1522,5 @@ Mask.NbSlice=nbslice; num_i1=mod(num_i1-1,nbslice)+1; - Mask.NomType=Mask_NomType{1}; + Mask.NomType=regexprep(Mask_NomType{1},'0','');%remove '0' in nom type for masks [maskname,mdetect]=name_generator(Mask.Base,num_i1,num_j1,'.png',Mask.NomType);% mdetect=exist(maskname,'file'); @@ -2147,5 +2148,4 @@ ParamIn.GUIName='get_field'; [Field{1},ParamOut,errormsg] = read_field(ObjectName,FileType,ParamIn,num_i1); - Field{1} if ~isempty(errormsg) errormsg=['error in reading ' filename ': ' errormsg]; @@ -2594,5 +2594,5 @@ %% Plot the projections on the selected projection objects -'PLOT' + % main projection object (uvmat display) list_object=get(handles.list_object_1,'String');