Index: /trunk/src/calc_field.m =================================================================== --- /trunk/src/calc_field.m (revision 398) +++ /trunk/src/calc_field.m (revision 399) @@ -1,5 +1,5 @@ %'calc_field': defines fields (velocity, vort, div...) from civx data and calculate them %--------------------------------------------------------------------- -% [DataOut,errormsg]=calc_field(FieldName,DataIn) +% [DataOut,errormsg]=calc_field(FieldList,DataIn,Coord_interp) % % OUTPUT: @@ -16,6 +16,7 @@ % % INPUT: -% FieldName: string representing the name of the field +% FieldList: cell array of strings representing the name(s) of the field(s) to calculate % DataIn: structure representing the field, as defined in check_field_srtructure.m +% Coord_interp(:,nb_coord) optional set of coordinates to interpolate the field (use with thin plate shell) % % FUNCTION related @@ -23,5 +24,5 @@ % file, depending on the scalar -function [DataOut,errormsg]=calc_field(FieldName,DataIn,Coord_interp) +function [DataOut,errormsg]=calc_field(FieldList,DataIn,Coord_interp) %list of defined scalars to display in menus (in addition to 'ima_cor'). @@ -46,5 +47,5 @@ 'error'}; %error associated to a vector (for stereo or patch) errormsg=[]; %default error message -if ~exist('FieldName','var') +if ~exist('FieldList','var') DataOut=list_field;% gives the list of possible fields in the absence of input else @@ -52,6 +53,6 @@ DataIn=[]; end - if ischar(FieldName) - FieldName={FieldName};%convert a string input to a cell with one string element + if ischar(FieldList) + FieldList={FieldList};%convert a string input to a cell with one string element end if isfield(DataIn,'Z')&& isequal(size(DataIn.Z),size(DataIn.X)) @@ -78,39 +79,29 @@ XMin=min(min(DataIn.SubRange(1,:,:))); YMin=min(min(DataIn.SubRange(2,:,:))); - % if ~exist('Coord_interp','var') - % Mesh=sqrt((YMax-YMin)*(XMax-XMin)/numel(DataIn.Coord_tps(:,1,:)));%2D - % xI=XMin:Mesh:XMax; - % yI=YMin:Mesh:YMax; - % [XI,YI]=meshgrid(xI,yI);% interpolation grid - % Coord_interp(:,1)=reshape(XI,[],1); - % Coord_interp(:,2)=reshape(YI,[],1); - % DataOut.coord_y=[yI(1) yI(end)]; - % DataOut.coord_x=[xI(1) xI(end)]; - % end check_der=0; check_val=0; - for ilist=1:length(FieldName) - switch FieldName{ilist} + nb_sites=size(Coord_interp,1); + nb_coord=size(Coord_interp,2); + for ilist=1:length(FieldList) + switch FieldList{ilist} case 'velocity' check_val=1; - DataOut.U=zeros(size(Coord_interp,1)); - DataOut.V=zeros(size(Coord_interp,1)); + DataOut.U=zeros(nb_sites,1); + DataOut.V=zeros(nb_sites,1); case{'vort','div','strain'}% case of spatial derivatives check_der=1; - DataOut.(FieldName{ilist})=zeros(size(Coord_interp,1)); - otherwise % case of a scalar - check_val=1; - DataOut.(FieldName{ilist})=zeros(size(Coord_interp,1)); - end - end - nbval=zeros(size(Coord_interp,1)); + DataOut.(FieldList{ilist})=zeros(nb_sites,1); +% otherwise % case of a scalar +% check_val=1; +% DataOut.(FieldList{ilist})=zeros(size(Coord_interp,1)); + end + end + nbval=zeros(nb_sites,1); NbSubDomain=size(DataIn.SubRange,3); + %DataIn.Coord_tps=DataIn.Coord_tps(1:end-3,:,:);% suppress the 3 zeros used to fit with the dimensions of variables for isub=1:NbSubDomain - if isfield(DataIn,'NbSites') - nbvec_sub=DataIn.NbSites(isub); - else - nbvec_sub=numel(find(DataIn.Indices_tps(:,isub))); - end - ind_sel=find(Coord_interp>=DataIn.SubRange(:,1,isub) & Coord_interp<=DataIn.SubRange(:,2,isub)); + nbvec_sub=DataIn.NbSites(isub); + check_range=(Coord_interp >=ones(nb_sites,1)*DataIn.SubRange(:,1,isub)' & Coord_interp<=ones(nb_sites,1)*DataIn.SubRange(:,2,isub)'); + ind_sel=find(sum(check_range,2)==nb_coord); %rho smoothing parameter % epoints = Coord_interp(ind_sel) ;% coordinates of interpolation sites @@ -118,11 +109,11 @@ nbval(ind_sel)=nbval(ind_sel)+1;% records the number of values for eacn interpolation point (in case of subdomain overlap) if check_val - EM = tps_eval(Coord_interp(ind_sel),DataIn.Coord_tps(1:nbvec_sub,:,isub));%kernels for calculating the velocity from tps 'sources' + EM = tps_eval(Coord_interp(ind_sel,:),DataIn.Coord_tps(1:nbvec_sub,:,isub));%kernels for calculating the velocity from tps 'sources' end if check_der - [EMDX,EMDY] = tps_eval_dxy(Coord_interp(ind_sel),DataIn.Coord_tps(1:nbvec_sub,:,isub));%kernels for calculating the spatial derivatives from tps 'sources' - end - for ilist=1:length(FieldName) - switch FieldName{ilist} + [EMDX,EMDY] = tps_eval_dxy(Coord_interp(ind_sel,:),DataIn.Coord_tps(1:nbvec_sub,:,isub));%kernels for calculating the spatial derivatives from tps 'sources' + end + for ilist=1:length(FieldList) + switch FieldList{ilist} case 'velocity' ListFields={'U', 'V'}; @@ -154,17 +145,17 @@ end DataOut.FF=nbval==0; %put errorflag to 1 for points outside the interpolation rang - DataOut.FF=reshape(DataOut.FF,numel(yI),numel(xI)); +% DataOut.FF=reshape(DataOut.FF,numel(yI),numel(xI)); nbval(nbval==0)=1; - switch FieldName{1} - case {'velocity','u','v'} - DataOut.U=reshape(DataOut.U./nbval,numel(yI),numel(xI)); - DataOut.V=reshape(DataOut.V./nbval,numel(yI),numel(xI)); - case 'vort' - DataOut.vort=reshape(DataOut.vort,numel(yI),numel(xI)); - case 'div' - DataOut.div=reshape(DataOut.div,numel(yI),numel(xI)); - case 'strain' - DataOut.strain=reshape(DataOut.strain,numel(yI),numel(xI)); - end +% switch FieldList{1} +% case {'velocity','u','v'} +% DataOut.U=reshape(DataOut.U./nbval,numel(yI),numel(xI)); +% DataOut.V=reshape(DataOut.V./nbval,numel(yI),numel(xI)); +% case 'vort' +% DataOut.vort=reshape(DataOut.vort,numel(yI),numel(xI)); +% case 'div' +% DataOut.div=reshape(DataOut.div,numel(yI),numel(xI)); +% case 'strain' +% DataOut.strain=reshape(DataOut.strain,numel(yI),numel(xI)); +% end DataOut.ListVarName=[DataOut.ListVarName ListFields]; for ilist=3:numel(DataOut.ListVarName) @@ -179,7 +170,7 @@ %% civx data DataOut=DataIn; - for ilist=1:length(FieldName) - if ~isempty(FieldName{ilist}) - [VarName,Value,Role,units]=feval(FieldName{ilist},DataIn);%calculate field with appropriate function named FieldName{ilist} + for ilist=1:length(FieldList) + if ~isempty(FieldList{ilist}) + [VarName,Value,Role,units]=feval(FieldList{ilist},DataIn);%calculate field with appropriate function named FieldList{ilist} ListVarName=[ListVarName VarName]; ValueList=[ValueList Value]; Index: /trunk/src/civ.m =================================================================== --- /trunk/src/civ.m (revision 398) +++ /trunk/src/civ.m (revision 399) @@ -1239,6 +1239,8 @@ end 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) @@ -1390,6 +1392,8 @@ end Param.Civ2.Time=(time(i2_civ2(ifile)+1,j2_civ2(j)+1)+time(i1_civ2(ifile)+1,j1_civ2(j)+1))/2; + if strcmp(CivMode,'CivX') Param.Civ2.term_a=num2stra(j1_civ2(j),nom_type_nc); Param.Civ2.term_b=num2stra(j2_civ2(j),nom_type_nc); + end Param.Civ2.filename_nc1=filecell.nc.civ1{ifile,j}; Param.Civ2.filename_nc1(end-2:end)=[]; % remove '.nc' Index: /trunk/src/civ_matlab.m =================================================================== --- /trunk/src/civ_matlab.m (revision 398) +++ /trunk/src/civ_matlab.m (revision 399) @@ -108,5 +108,5 @@ Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ1_param];% {'Civ1_Time','Civ1_Dt'}]; Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_F','Civ1_C'};% cell array containing the names of the fields to record - Data.VarDimName={'NbVec1','NbVec1','NbVec1','NbVec1','NbVec1','NbVec1'}; + Data.VarDimName={'nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1'}; Data.VarAttribute{1}.Role='coord_x'; Data.VarAttribute{2}.Role='coord_y'; @@ -159,5 +159,5 @@ else Data.ListVarName=[Data.ListVarName {'Civ1_FF'}]; - Data.VarDimName=[Data.VarDimName {'NbVec1'}]; + Data.VarDimName=[Data.VarDimName {'nb_vec_1'}]; nbvar=length(Data.ListVarName); Data.VarAttribute{nbvar}.Role='errorflag'; @@ -179,6 +179,6 @@ 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 {'NbVec1','NbVec1',{'NbCoord','Two','NbSubDomain1'},{'NbSubDomain1'},... - {'NbVec1Sub','NbCoord','NbSubDomain1'},{'Nbtps1','NbSubDomain1'},{'Nbtps1','NbSubDomain1'}}]; + 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'; @@ -195,6 +195,6 @@ [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); -% Data.Civ1_U_Diff(ind_good)=Data.Civ1_U(ind_good)-Ures; -% Data.Civ1_V_Diff(ind_good)=Data.Civ1_V(ind_good)-Vres; + 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; @@ -305,5 +305,5 @@ 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 - Data.VarDimName=[Data.VarDimName {'NbVec2','NbVec2','NbVec2','NbVec2','NbVec2','NbVec2'}]; + Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2'}]; Data.VarAttribute{nbvar+1}.Role='coord_x'; Data.VarAttribute{nbvar+2}.Role='coord_y'; @@ -339,5 +339,5 @@ else Data.ListVarName=[Data.ListVarName {'Civ2_FF'}]; - Data.VarDimName=[Data.VarDimName {'NbVec2'}]; + Data.VarDimName=[Data.VarDimName {'nb_vec_2'}]; nbvar=length(Data.ListVarName); Data.VarAttribute{nbvar}.Role='errorflag'; @@ -356,9 +356,6 @@ nbvar=length(Data.ListVarName); 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 {'NbVec2','NbVec2',{'NbCoord','Two','NbSubDomain2'},{'NbSubDomain2'},... - {'NbVec2Sub','NbCoord','NbSubDomain2'},{'Nbtps2','NbSubDomain2'},{'Nbtps2','NbSubDomain2'}}]; -% Data.ListVarName=[Data.ListVarName {'Civ2_U_Diff','Civ2_V_Diff','Civ2_X_SubRange','Civ2_Y_SubRange','Civ2_X_tps','Civ2_Y_tps','Civ2_U_tps','Civ2_V_tps','Civ2_Indices_tps'}]; -% Data.VarDimName=[Data.VarDimName {'NbVec2','NbVec2',{'NbSubDomain2','Two'},{'NbSubDomain2','Two'},... -% {'NbVec2Sub','NbSubDomain2'},{'NbVec2Sub','NbSubDomain2'},{'Nbtps2','NbSubDomain2'},{'Nbtps2','NbSubDomain2'},{'NbVec2Sub','NbSubDomain2'}}]; + 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'; @@ -376,4 +373,6 @@ [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); Data.Civ2_U_smooth(ind_good)=Ures; Data.Civ2_V_smooth(ind_good)=Vres; Index: /trunk/src/find_field_indices.m =================================================================== --- /trunk/src/find_field_indices.m (revision 398) +++ /trunk/src/find_field_indices.m (revision 399) @@ -58,5 +58,4 @@ VarDimIndex=[]; VarDimName={}; - if ~isfield(Data,'VarDimName') errormsg='missing .VarDimName'; @@ -64,5 +63,5 @@ end -%loop on the list of variables +%% loop on the list of variables, group them by common dimensions for ivar=1:nbvar DimCell=Data.VarDimName{ivar}; %dimensions associated with the variable #ivar @@ -85,5 +84,5 @@ CellVarIndex{icell}=ivar;%put the current variabl index in the new cell end - + %look for dimension variables if numel(DimCell)==1% if the variable has a single dimension @@ -100,7 +99,8 @@ end -% find the spatial dimensions and vector components +%% find the spatial dimensions and vector components ListRole={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','warnflag','errorflag',... 'ancillary','image','color','discrete','scalar','coord_tps'}; +NbDim=zeros(size(CellVarIndex));%default for icell=1:length(CellVarIndex) for ilist=1:numel(ListRole) @@ -142,13 +142,4 @@ return end -% if ivar_vector_x>1 -% ivar_vector_x=ivar_vector_x(1); -% end -% if ivar_vector_y>1 -% ivar_vector_y=ivar_vector_y(1); -% end -% if ivar_vector_z>1 -% ivar_vector_z=ivar_vector_z(1); -% end if numel(ivar_errorflag)>1 errormsg='multiply defined error flag in the same cell'; @@ -159,7 +150,4 @@ return end - %NbDim(icell)=0;% nbre of space dimensions -% NbDim(icell)=numel(DimCell); - NbDim(icell)=0; test_coord=0; if numel(VarIndex)>1 @@ -193,3 +181,20 @@ NbDim(icell)=2; end + %look for tps data + if ~isempty(VarType{icell}.coord_tps) + VarType{icell}.var_tps=[]; + tps_dimnames=Data.VarDimName{VarType{icell}.coord_tps}; + if length(tps_dimnames)==3 + for ilist=1:length(Data.VarDimName) + if strcmp(tps_dimnames{1},Data.VarDimName{ilist}{1}) && strcmp(tps_dimnames{3},Data.VarDimName{ilist}{2})% identify the variables corresponding to the tps site coordinates coord_tps + VarType{icell}.var_tps=[VarType{icell}.var_tps ilist]; + elseif length(Data.VarDimName{ilist})==1 && strcmp(tps_dimnames{3},Data.VarDimName{ilist}{1})% identify the variable corresponding to nbsites + VarType{icell}.nbsites_tps= ilist; + elseif length(Data.VarDimName{ilist})==3 && strcmp(tps_dimnames{2},Data.VarDimName{ilist}{1})&& strcmp(tps_dimnames{3},Data.VarDimName{ilist}{3})% identify the variable subrange + VarType{icell}.subrange_tps= ilist; + end + end + end + NbDim(icell)=2; + end end Index: /trunk/src/find_file_series.m =================================================================== --- /trunk/src/find_file_series.m (revision 398) +++ /trunk/src/find_file_series.m (revision 399) @@ -110,8 +110,9 @@ if ~isempty(r) sep1=r.sep1; - if strcmp(lower(r.j1),r.j1) + i1_str='(?\d+)'; + if strcmp(lower(r.j1),r.j1)% lower case index j1_str='(?[a-z])'; else - j1_str='(?[A-Z])'; + j1_str='(?[A-Z])'; % upper case index end j1_star='*'; Index: /trunk/src/griddata_uvmat.m =================================================================== --- /trunk/src/griddata_uvmat.m (revision 398) +++ /trunk/src/griddata_uvmat.m (revision 399) @@ -1,6 +1,6 @@ %'griddata_uvmat': function griddata_uvmat(vec2_X,vec2_Y,vec2_U,vec_X,vec_Y,'linear') %adapt the input of the matlab function griddata to the appropriate version of Matlab -function ZI = griddata_uvmat(X,Y,Z,XI,YI,rho) -if ~exist('rho','var')|| isequal(rho,0) +function ZI = griddata_uvmat(X,Y,Z,XI,YI) +% if ~exist('rho','var')|| isequal(rho,0) txt=ver('MATLAB'); Release=txt.Release; @@ -13,15 +13,15 @@ ZI=griddata(X,Y,Z,XI,YI,'linear'); end -else %smooth with thin plate spline - [ZI,Z_diff]=patch_uvmat(X,Y,Z,XI,YI,rho); - diff_norm=mean(Z_diff.*Z_diff) - ind_good=find(abs(Z_diff)<5*diff_norm); - nb_remove=numel(Z_diff)-numel(ind_good) - if nb_remove>0 - X=X(ind_good); - Y=Y(ind_good); - Z=Z(ind_good); - [ZI,Z_diff]=patch_uvmat(X,Y,Z,XI,YI,rho); - diff_norm_new=mean(Z_diff.*Z_diff) - end -end +% else %smooth with thin plate spline +% [ZI,Z_diff]=patch_uvmat(X,Y,Z,XI,YI,rho); +% diff_norm=mean(Z_diff.*Z_diff) +% ind_good=find(abs(Z_diff)<5*diff_norm); +% nb_remove=numel(Z_diff)-numel(ind_good) +% if nb_remove>0 +% X=X(ind_good); +% Y=Y(ind_good); +% Z=Z(ind_good); +% [ZI,Z_diff]=patch_uvmat(X,Y,Z,XI,YI,rho); +% diff_norm_new=mean(Z_diff.*Z_diff) +% end +% end Index: /trunk/src/mouse_motion.m =================================================================== --- /trunk/src/mouse_motion.m (revision 398) +++ /trunk/src/mouse_motion.m (revision 399) @@ -151,5 +151,5 @@ end end - elseif numel(VarType{icell}.coord) >=2 %structured coordinates + elseif numel(VarType{icell}.coord) >=2 & VarType{icell}.coord > 0 %structured coordinates yName=Field.ListVarName{VarType{icell}.coord(1)}; xName=Field.ListVarName{VarType{icell}.coord(2)}; Index: /trunk/src/proj_field.m =================================================================== --- /trunk/src/proj_field.m (revision 398) +++ /trunk/src/proj_field.m (revision 399) @@ -1,5 +1,5 @@ %'proj_field': projects the field on a projection object %-------------------------------------------------------------------------- -% function [ProjData,errormsg]=proj_field(FieldData,ObjectData,FieldName) +% function [ProjData,errormsg]=proj_field(FieldData,ObjectData) % % OUTPUT: @@ -27,5 +27,5 @@ %FieldData: data of the field to be projected on the projection object, with optional fields % .Txt: error message, transmitted to the projection -% .CoordType: 'px' or 'phys' type of coordinates of the field, must be the same as for the projection object, transmitted +% .FieldList: cell array of strings representing the fields to calculate % .Mesh: typical distance between data points (used for mouse action or display), transmitted % .CoordUnit, .TimeUnit, .dt: transmitted @@ -80,5 +80,5 @@ %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -function [ProjData,errormsg]=proj_field(FieldData,ObjectData,FieldName) +function [ProjData,errormsg]=proj_field(FieldData,ObjectData) errormsg='';%default if ~exist('FieldName','var') @@ -87,9 +87,5 @@ %% case of no projection (object is used only as graph display) if isfield(ObjectData,'ProjMode') && (isequal(ObjectData.ProjMode,'none')||isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside')) - if ~isempty(FieldName) - [ProjData,errormsg]=calc_field(FieldName,FieldData); - else ProjData=[]; - end return end @@ -143,5 +139,5 @@ end case 'plane' - [ProjData,errormsg] = proj_plane(FieldData,ObjectData,FieldName); + [ProjData,errormsg] = proj_plane(FieldData,ObjectData); case 'volume' [ProjData,errormsg] = proj_volume(FieldData,ObjectData); @@ -892,5 +888,5 @@ %project on a plane % AJOUTER flux,circul,error - function [ProjData,errormsg] = proj_plane(FieldData, ObjectData,FieldName) + function [ProjData,errormsg] = proj_plane(FieldData, ObjectData) %----------------------------------------------------------------- @@ -994,5 +990,5 @@ % CellVarIndex=cells of variable index arrays ivar_new=0; % index of the current variable in the projected field -icoord=0; +% icoord=0; nbcoord=0;%number of added coordinate variables brought by projection nbvar=0; @@ -1000,5 +996,5 @@ NbDim=NbDimVec(icell); if NbDim<2 - continue + continue % only cells represnting 2D or 3D fields are involved end VarIndex=CellVarIndex{icell};% indices of the selected variables in the list FieldData.ListVarName @@ -1010,5 +1006,5 @@ ivar_V=VarType.vector_y; ivar_W=VarType.vector_z; - ivar_C=VarType.scalar ; + % ivar_C=VarType.scalar ; ivar_Anc=VarType.ancillary; test_anc=zeros(size(VarIndex)); @@ -1016,5 +1012,5 @@ ivar_F=VarType.warnflag; ivar_FF=VarType.errorflag; - testX=~isempty(ivar_X) && ~isempty(ivar_Y); + check_unstructured_coord=(~isempty(ivar_X) && ~isempty(ivar_Y))||~isempty(VarType.coord_tps); DimCell=FieldData.VarDimName{VarIndex(1)}; if ischar(DimCell) @@ -1024,148 +1020,138 @@ %% case of input fields with unstructured coordinates coord_z=0;%default - if testX - XName=FieldData.ListVarName{ivar_X}; - YName=FieldData.ListVarName{ivar_Y}; - coord_x=FieldData.(XName); - coord_y=FieldData.(YName); - if length(ivar_Z)==1 - ZName=FieldData.ListVarName{ivar_Z}; - coord_z=FieldData.(ZName); - end - - % translate initial coordinates - coord_x=coord_x-ObjectData.Coord(1,1); - coord_y=coord_y-ObjectData.Coord(1,2); - if ~isempty(ivar_Z) - coord_z=coord_z-ObjectData.Coord(1,3); - end - - % selection of the vectors in the projection range (3D case) - if length(ivar_Z)==1 && width > 0 - %components of the unitiy vector normal to the projection plane - fieldZ=norm_plane(1)*coord_x + norm_plane(2)*coord_y+ norm_plane(3)*coord_z;% distance to the plane - indcut=find(abs(fieldZ) <= width); - size(indcut) - for ivar=VarIndex - VarName=FieldData.ListVarName{ivar}; - eval(['FieldData.' VarName '=FieldData.' VarName '(indcut);']) - % A VOIR : CAS DE VAR STRUCTUREE MAIS PAS GRILLE REGULIERE : INTERPOLER SUR GRILLE REGULIERE - end - coord_x=coord_x(indcut); - coord_y=coord_y(indcut); - coord_z=coord_z(indcut); - end - - %rotate coordinates if needed: - Psi=PlaneAngle(1); - Theta=PlaneAngle(2); - Phi=PlaneAngle(3); - if testangle && ~test90y && ~test90x;%=1 for slanted plane - coord_X=(coord_x *cos(Phi) + coord_y* sin(Phi)); - coord_Y=(-coord_x *sin(Phi) + coord_y *cos(Phi))*cos(Theta); - coord_Y=coord_Y+coord_z *sin(Theta); - coord_X=(coord_X *cos(Psi) - coord_Y* sin(Psi));%A VERIFIER - - coord_Y=(coord_X *sin(Psi) + coord_Y* cos(Psi)); - else - coord_X=coord_x; - coord_Y=coord_y; - end - - %restriction to the range of x and y if imposed - testin=ones(size(coord_X)); %default - testbound=0; - if testXMin - testin=testin & (coord_X >= XMin); - testbound=1; - end - if testXMax - testin=testin & (coord_X <= XMax); - testbound=1; - end - if testYMin - testin=testin & (coord_Y >= YMin); - testbound=1; - end - if testYMin - testin=testin & (coord_Y <= YMax); - testbound=1; - end - if testbound - indcut=find(testin); - for ivar=VarIndex - VarName=FieldData.ListVarName{ivar}; - eval(['FieldData.' VarName '=FieldData.' VarName '(indcut);']) - end - coord_X=coord_X(indcut); - coord_Y=coord_Y(indcut); + if check_unstructured_coord + if ~isempty(ivar_X)% case of tps excluded. TODO similar procedure + XName=FieldData.ListVarName{ivar_X}; + YName=FieldData.ListVarName{ivar_Y}; + coord_x=FieldData.(XName); + coord_y=FieldData.(YName); if length(ivar_Z)==1 - coord_Z=coord_Z(indcut); + ZName=FieldData.ListVarName{ivar_Z}; + coord_z=FieldData.(ZName); + end + + % translate initial coordinates + coord_x=coord_x-ObjectData.Coord(1,1); + coord_y=coord_y-ObjectData.Coord(1,2); + if ~isempty(ivar_Z) + coord_z=coord_z-ObjectData.Coord(1,3); + end + + % selection of the vectors in the projection range (3D case) + if length(ivar_Z)==1 && width > 0 + %components of the unitiy vector normal to the projection plane + fieldZ=norm_plane(1)*coord_x + norm_plane(2)*coord_y+ norm_plane(3)*coord_z;% distance to the plane + indcut=find(abs(fieldZ) <= width); + size(indcut) + for ivar=VarIndex + VarName=FieldData.ListVarName{ivar}; + eval(['FieldData.' VarName '=FieldData.' VarName '(indcut);']) + % A VOIR : CAS DE VAR STRUCTUREE MAIS PAS GRILLE REGULIERE : INTERPOLER SUR GRILLE REGULIERE + end + coord_x=coord_x(indcut); + coord_y=coord_y(indcut); + coord_z=coord_z(indcut); + end + + %rotate coordinates if needed: + Psi=PlaneAngle(1); + Theta=PlaneAngle(2); + Phi=PlaneAngle(3); + if testangle && ~test90y && ~test90x;%=1 for slanted plane + coord_X=(coord_x *cos(Phi) + coord_y* sin(Phi)); + coord_Y=(-coord_x *sin(Phi) + coord_y *cos(Phi))*cos(Theta); + coord_Y=coord_Y+coord_z *sin(Theta); + coord_X=(coord_X *cos(Psi) - coord_Y* sin(Psi));%A VERIFIER + + coord_Y=(coord_X *sin(Psi) + coord_Y* cos(Psi)); + else + coord_X=coord_x; + coord_Y=coord_y; + end + + %restriction to the range of x and y if imposed + testin=ones(size(coord_X)); %default + testbound=0; + if testXMin + testin=testin & (coord_X >= XMin); + testbound=1; + end + if testXMax + testin=testin & (coord_X <= XMax); + testbound=1; + end + if testYMin + testin=testin & (coord_Y >= YMin); + testbound=1; + end + if testYMin + testin=testin & (coord_Y <= YMax); + testbound=1; + end + if testbound + indcut=find(testin); + for ivar=VarIndex + VarName=FieldData.ListVarName{ivar}; + eval(['FieldData.' VarName '=FieldData.' VarName '(indcut);']) + end + coord_X=coord_X(indcut); + coord_Y=coord_Y(indcut); + if length(ivar_Z)==1 + coord_Z=coord_Z(indcut); + end end end % different cases of projection - if isequal(ObjectData.ProjMode,'projection') - %the list of dimension - %ProjData.ListDimName=[ProjData.ListDimName FieldData.VarDimName(VarIndex(1))];%add the point index to the list of dimensions - %ProjData.DimValue=[ProjData. - %length(coord_X)]; - - for ivar=VarIndex %transfer variables to the projection plane - VarName=FieldData.ListVarName{ivar}; - if ivar==ivar_X %x coordinate - eval(['ProjData.' VarName '=coord_X;']) - elseif ivar==ivar_Y % y coordinate - eval(['ProjData.' VarName '=coord_Y;']) - elseif isempty(ivar_Z) || ivar~=ivar_Z % other variables (except Z coordinate wyhich is not reproduced) - eval(['ProjData.' VarName '=FieldData.' VarName ';']) - end - if isempty(ivar_Z) || ivar~=ivar_Z - ProjData.ListVarName=[ProjData.ListVarName VarName]; - ProjData.VarDimName=[ProjData.VarDimName DimCell]; - nbvar=nbvar+1; - if isfield(FieldData,'VarAttribute') && length(FieldData.VarAttribute) >=ivar - ProjData.VarAttribute{nbvar}=FieldData.VarAttribute{ivar}; - end - end - end - elseif isequal(ObjectData.ProjMode,'interp')||isequal(ObjectData.ProjMode,'filter')%interpolate data on a regular grid - if isequal(ObjectData.ProjMode,'filter') - rho=1000;%smoothing parameter, (small for strong smoothing) - else - rho=0; - end - coord_x_proj=XMin:DX:XMax; - coord_y_proj=YMin:DY:YMax; - if isfield(FieldData,[VarName '_tps']) - [XI,YI]=meshgrid(coord_x_proj,coord_y_proj'); - XI=reshape(XI,[],1); - YI=reshape(YI,[],1); - end - DimCell={'coord_y','coord_x'}; - ProjData.ListVarName={'coord_y','coord_x'}; - ProjData.VarDimName={'coord_y','coord_x'}; - nbcoord=2; - ProjData.coord_y=[YMin YMax]; - ProjData.coord_x=[XMin XMax]; - if isempty(ivar_X), ivar_X=0; end; - if isempty(ivar_Y), ivar_Y=0; end; - if isempty(ivar_Z), ivar_Z=0; end; - if isempty(ivar_U), ivar_U=0; end; - if isempty(ivar_V), ivar_V=0; end; - if isempty(ivar_W), ivar_W=0; end; - if isempty(ivar_F), ivar_F=0; end; - if isempty(ivar_FF), ivar_FF=0; end; - if ~isequal(ivar_FF,0) - VarName_FF=FieldData.ListVarName{ivar_FF}; - eval(['indsel=find(FieldData.' VarName_FF '==0);']) - coord_X=coord_X(indsel); - coord_Y=coord_Y(indsel); - end - FF=zeros(1,length(coord_y_proj)*length(coord_x_proj)); - testFF=0; - FieldName - if ~isempty(FieldName) - ProjData=calc_field(FieldName,FieldData,[XI YI]); - else + switch ObjectData.ProjMode + case 'projection' + %the list of dimension + %ProjData.ListDimName=[ProjData.ListDimName FieldData.VarDimName(VarIndex(1))];%add the point index to the list of dimensions + %ProjData.DimValue=[ProjData. + %length(coord_X)]; + + for ivar=VarIndex %transfer variables to the projection plane + VarName=FieldData.ListVarName{ivar}; + if ivar==ivar_X %x coordinate + eval(['ProjData.' VarName '=coord_X;']) + elseif ivar==ivar_Y % y coordinate + eval(['ProjData.' VarName '=coord_Y;']) + elseif isempty(ivar_Z) || ivar~=ivar_Z % other variables (except Z coordinate wyhich is not reproduced) + eval(['ProjData.' VarName '=FieldData.' VarName ';']) + end + if isempty(ivar_Z) || ivar~=ivar_Z + ProjData.ListVarName=[ProjData.ListVarName VarName]; + ProjData.VarDimName=[ProjData.VarDimName DimCell]; + nbvar=nbvar+1; + if isfield(FieldData,'VarAttribute') && length(FieldData.VarAttribute) >=ivar + ProjData.VarAttribute{nbvar}=FieldData.VarAttribute{ivar}; + end + end + end + case 'interp'%interpolate data on a regular grid + coord_x_proj=XMin:DX:XMax; + coord_y_proj=YMin:DY:YMax; + DimCell={'coord_y','coord_x'}; + ProjData.ListVarName={'coord_y','coord_x'}; + ProjData.VarDimName={'coord_y','coord_x'}; + nbcoord=2; + ProjData.coord_y=[YMin YMax]; + ProjData.coord_x=[XMin XMax]; + if isempty(ivar_X), ivar_X=0; end; + if isempty(ivar_Y), ivar_Y=0; end; + if isempty(ivar_Z), ivar_Z=0; end; + if isempty(ivar_U), ivar_U=0; end; + if isempty(ivar_V), ivar_V=0; end; + if isempty(ivar_W), ivar_W=0; end; + if isempty(ivar_F), ivar_F=0; end; + if isempty(ivar_FF), ivar_FF=0; end; + if ~isequal(ivar_FF,0) + VarName_FF=FieldData.ListVarName{ivar_FF}; + eval(['indsel=find(FieldData.' VarName_FF '==0);']) + coord_X=coord_X(indsel); + coord_Y=coord_Y(indsel); + end + + FF=zeros(1,length(coord_y_proj)*length(coord_x_proj)); + testFF=0; for ivar=VarIndex VarName=FieldData.ListVarName{ivar}; @@ -1180,10 +1166,5 @@ FieldData.(VarName)=FieldData.(VarName)(indsel); end - % if isfield(FieldData,[VarName '_tps']) - % [XI,YI]=meshgrid(coord_x_proj,coord_y_proj'); - % XI=reshape(XI,[],1); - % YI=reshape(YI,[],1); - % - ProjData.(VarName)=griddata_uvmat(double(coord_X),double(coord_Y),double(FieldData.(VarName)),coord_x_proj,coord_y_proj',rho); + ProjData.(VarName)=griddata_uvmat(double(coord_X),double(coord_Y),double(FieldData.(VarName)),coord_x_proj,coord_y_proj'); varline=reshape(ProjData.(VarName),1,length(coord_y_proj)*length(coord_x_proj)); FFlag= isnan(varline); %detect undefined values NaN @@ -1212,7 +1193,23 @@ ProjData.VarAttribute{ivar_new+1+nbcoord}.Role='errorflag'; end - end - end - + case 'filter' + if ~isempty(VarType.coord_tps) + VarType.coord_tps + coord_x_proj=XMin:DX:XMax; + coord_y_proj=YMin:DY:YMax; + np_x=numel(coord_x_proj); + np_y=numel(coord_y_proj); + [XI,YI]=meshgrid(coord_x_proj,coord_y_proj'); + XI=reshape(XI,[],1); + YI=reshape(YI,[],1); + ProjData=calc_field(FieldData.FieldList,FieldData,[XI YI]); + for ilist=3:length(ProjData.ListVarName)% reshape data, excluding coordinates (ilist=1-2), TODO: rationalise + VarName=ProjData.ListVarName{ilist}; + ProjData.(VarName)=reshape(ProjData.(VarName),np_y,np_x); + end + ProjData.coord_x=[XMin XMax]; + ProjData.coord_y=[YMin YMax]; + end + end %% case of input fields defined on a structured grid else @@ -1352,5 +1349,5 @@ % case with no interpolation if isequal(ProjMode,'projection') && (~testangle || test90y || test90x) - if NbDim==2 && ~testXMin && ~testXMax && ~testYMin && ~testYMax + if NbDim==2 && ~testXMin && ~testXMax && ~testYMin && ~testYMax ProjData=FieldData;% no change by projection else @@ -1375,14 +1372,14 @@ min_indx=ceil((Coord{NbDim}(1)-XMax)/DXinit)+1; max_indx=floor((Coord{NbDim}(1)-XMin)/DXinit)+1; - Xbound(2)=Coord{NbDim}(1)+DXinit*(max_indx-1); + Xbound(2)=Coord{NbDim}(1)+DXinit*(max_indx-1); Xbound(1)=Coord{NbDim}(1)+DXinit*(min_indx-1); end min_indy=max(min_indy,1);% deals with margin (bound lower than the first index) min_indx=max(min_indx,1); - + if test90y ind_new=[3 2 1]; DimCell={AYProjName,AXProjName}; -% DimValue=DimValue(ind_new); + % DimValue=DimValue(ind_new); iz=ceil((ObjectData.Coord(1,1)-Coord{3}(1))/DX)+1; for ivar=VarIndex @@ -1656,5 +1653,5 @@ ivar_F=VarType.warnflag; ivar_FF=VarType.errorflag; - testX=~isempty(ivar_X) && ~isempty(ivar_Y); + check_unstructured_coord=~isempty(ivar_X) && ~isempty(ivar_Y); DimCell=FieldData.VarDimName{VarIndex(1)}; if ischar(DimCell) @@ -1663,5 +1660,5 @@ %% case of input fields with unstructured coordinates - if testX + if check_unstructured_coord XName=FieldData.ListVarName{ivar_X}; YName=FieldData.ListVarName{ivar_Y}; Index: /trunk/src/series.m =================================================================== --- /trunk/src/series.m (revision 398) +++ /trunk/src/series.m (revision 399) @@ -1054,5 +1054,5 @@ if ~isempty(SeriesData.i2_series)||~isempty(SeriesData.j2_series) if isequal(mode,'series(Di)') - find_netcpair_civ(handles,Val);% update the menu of pairs depending on the available netcdf files + find_netcpair_civ(handles);% update the menu of pairs depending on the available netcdf files end end @@ -1069,5 +1069,5 @@ if ~isempty(SeriesData.i2_series)||~isempty(SeriesData.j2_series) if isequal(mode,'series(Di)') - find_netcpair_civ(handles,Val);% update the menu of pairs depending on the available netcdf files + find_netcpair_civ(handles);% update the menu of pairs depending on the available netcdf files end end Index: /trunk/src/uvmat.m =================================================================== --- /trunk/src/uvmat.m (revision 398) +++ /trunk/src/uvmat.m (revision 399) @@ -310,5 +310,4 @@ end if isfield(input,'FieldsString') -% set(handles.Fields,'Value',1) UvData.FieldsString=input.FieldsString; end @@ -486,5 +485,5 @@ handles_NomType=handles.NomType; handles_FileExt=handles.FileExt; - handles_Fields=handles.Fields; +% handles_Fields=handles.Fields; elseif index==2 handles_RootPath=handles.RootPath_1; @@ -494,5 +493,5 @@ handles_NomType=handles.NomType_1; handles_FileExt=handles.FileExt_1; - handles_Fields=handles.Fields_1; +% handles_Fields=handles.Fields_1; set(handles.RootPath_1,'Visible','on') set(handles.RootFile_1,'Visible','on') @@ -504,15 +503,8 @@ %% detect root name, nomenclature and indices in the input file name: -%[RootPath,SubDir]=fileparts_uvmat(fileinput); [FilePath,FileName,FileExt]=fileparts(fileinput); % detect the file type, get the movie object if relevant, and look for the corresponding file series: % the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]); -% if strcmp(NomType,'*')% movies will be opened at the first frame -% i1=1; -% i2=[]; -% j1=[]; -% j2=[]; -% end %% open the file or fill the GUI uvmat according to the detected file type @@ -1964,5 +1956,5 @@ FieldName=[];%default VelType=[];%default - FileExt=get(handles.FileExt,'String'); + % FileExt=get(handles.FileExt,'String'); FileType=UvData.FileType{1}; switch FileType @@ -2234,4 +2226,5 @@ UvData.Field=Field{1}; end +UvData.Field.FieldList={FieldName}; % TODO: to generalise, used for proj_field with tps interpolation %% get bounds and mesh (needed for mouse action and to open set_object) @@ -3818,5 +3811,5 @@ AxeData=UvData.axes3;% retrieve the current plotted data PlotParam=read_GUI(handles.uvmat); -[PP,PlotParamOut]= plot_field(AxeData,handles.axes3,PlotParam); +[tild,PlotParamOut]= plot_field(AxeData,handles.axes3,PlotParam); write_plot_param(handles,PlotParamOut); %update the auto plot parameters @@ -3826,6 +3819,5 @@ %------------------------------------------------------------------- UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface -test=get(handles.edit_object,'Value'); -if test +if get(handles.edit_object,'Value') set(handles.edit_object,'BackgroundColor',[1,1,0]) %suppress the other options @@ -3838,16 +3830,18 @@ set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7]) end + hset_object=findobj(allchild(0),'Tag','set_object'); + if isempty(hset_object)% open the GUI set_object with data of the currently selected object + ViewObject_Callback(hObject, eventdata, handles) + hset_object=findobj(allchild(0),'Tag','set_object'); + end + hhset_object=guidata(hset_object); + set(hhset_object.PLOT,'enable','on'); else UvData.MouseAction='none'; - set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) -end -set(handles.uvmat,'UserData',UvData); -hset_object=findobj(allchild(0),'Tag','set_object'); -if ~isempty(hset_object) - hhset_object=guidata(hset_object); - if test - set(hhset_object.PLOT,'enable','on'); - else - set(hhset_object.PLOT,'enable','off'); + set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) + hset_object=findobj(allchild(0),'Tag','set_object'); + if ~isempty(hset_object)% open the + hhset_object=guidata(hset_object); + set(hhset_object.PLOT,'enable','off'); end end @@ -4567,6 +4561,8 @@ end +%------------------------------------------------------------------------ % --- Executes on button press in ViewObject. function ViewObject_Callback(hObject, eventdata, handles) +%------------------------------------------------------------------------ IndexObj=get(handles.ListObject,'Value'); IndexObj=IndexObj(end); %keeps only the secodn value