Index: /trunk/src/civ.m =================================================================== --- /trunk/src/civ.m (revision 173) +++ /trunk/src/civ.m (revision 174) @@ -267,15 +267,24 @@ oldfile=filebase; end -testall=get(handles.ImaDoc,'UserData'); +% testall=get(handles.ImaDoc,'UserData'); ind_opening=1;%default browse.incr_pair=[0 0]; %default -if testall - menu={'*.*', 'All Files (*.*)'; '*.xml; *.avi;*.AVI;*.nc','(*.xml,*.avi,*.nc)'; ... - '*.xml', '.xml files';'*.avi;*.AVI', '.avi files';'*.nc','.nc files'}; -else % menu selecting only .civ or .avi files - menu={'*.xml;*.avi;*.AVI;*.nc','(*.xml,*.avi,*.nc)'; ... - '*.xml', '.xml files';'*.avi;*.AVI', '.avi files';'*.nc', '.nc files';... - '*.*', 'All Files (*.*)'}; -end +% if testall +% menu={'*.*', 'All Files (*.*)'; '*.xml; *.avi;*.AVI;*.nc','(*.xml,*.avi,*.nc)'; ... +% '*.xml', '.xml files';'*.avi;*.AVI', '.avi files';'*.nc','.nc files'}; +% else % menu selecting only .civ or .avi files + menu={'*.xml;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.nc;', ' (*.xml,*.civ,*.png,*.jpg ,.tif, *.avi,*.nc)'; + '*.xml', '.xml files '; ... + '*.civ', '.civ files '; ... + '*.png','.png image files'; ... + '*.jpg',' jpeg image files'; ... + '*.tif','.tif image files'; ... + '*.avi;*.AVI','.avi movie files'; ... + '*.nc','.netcdf files'; ... + '*.*', 'All Files (*.*)'}; + % menu={'*.xml;*.avi;*.AVI;*.nc','(*.xml,*.avi,*.nc)'; ... + % '*.xml', '.xml files';'*.avi;*.AVI', '.avi files';'*.nc', '.nc files';... + % '*.*', 'All Files (*.*)'}; +% end [FileName, PathName, filtindex] = uigetfile( menu, 'Pick a file',oldfile); fileinput=[PathName FileName];%complete file name @@ -431,6 +440,6 @@ end set(handles.browse_root,'UserData',browse);% store information from browser -testall=isequal(menu(filtindex,1),{'*.*'}); -set(handles.ImaDoc,'UserData',testall); +% testall=isequal(menu(filtindex,1),{'*.*'}); +% set(handles.ImaDoc,'UserData',testall); RootName_Callback(hObject, eventdata, handles); @@ -1868,13 +1877,14 @@ civAllxml=set(civAllxml,1,'name','CivDoc'); end - filename_cmx=filecell.nc.civ1{ifile,j};%output netcdf file - filename_cmx(end-1:end+1)='cmx';%name of cmx file + %filename_cur=filecell.nc.civ1{ifile,j};%output netcdf file + [Rootbat,Filebat]=fileparts(filecell.nc.civ1{ifile,j});%output netcdf file (without extention) + %filename_cmx(end-1:end+6)='civ1.cmx';%name of cmx file if batch - [Rootbat,Filebat,extbat]=fileparts(filename_cmx); - filename_bat=fullfile(Rootbat,['job_' Filebat extbat]); +% [Rootbat,Filebat,extbat]=fileparts(filename_cmx); + filename_bat=fullfile(Rootbat,['job_' Filebat]); else - filename_bat=filename_cmx; - end - filename_bat(end-2:end)='bat'; + filename_bat=fullfile(Rootbat,Filebat); + end + filename_bat=[filename_bat '.bat']; %CIV1 @@ -1882,5 +1892,5 @@ par_civ1.filename_ima_a=filecell.ima1.civ1{ifile,j}; par_civ1.filename_ima_b=filecell.ima2.civ1{ifile,j}; - namelog=[filename_cmx([1:end-3]) 'log']; + namelog=[fullfile(Rootbat,Filebat) '.civ1.log']; par_civ1.Dt=num2str(time(num2_civ1(ifile),num_b_civ1(j))-time(num1_civ1(ifile),num_a_civ1(j))); par_civ1.T0=num2str((time(num2_civ1(ifile),num_b_civ1(j))+time(num1_civ1(ifile),num_a_civ1(j)))/2); @@ -1935,8 +1945,8 @@ i_cmd=i_cmd+1; if isequal(civAll,0) - cmd=[cmd CIV1_CMD(filename_cmx(1:end-4),namelog,par_civ1,handles,sparam) '\n']; + cmd=[cmd CIV1_CMD(fullfile(Rootbat,Filebat),'',par_civ1,handles,sparam) '\n']; else civAllCmd=[civAllCmd ' civ1 ']; - str=CIV1_CMD_Unified(filename_cmx([1:end-4]),namelog,par_civ1); + str=CIV1_CMD_Unified(fullfile(Rootbat,Filebat),'',par_civ1); fieldnames=fields(str); [civAllxml,uid_civ1]=add(civAllxml,1,'element','civ1'); @@ -2054,5 +2064,6 @@ par_civ2.filename_ima_b=filecell.ima2.civ2{ifile,j}; %par_civ2.filename_ima_b([end-3:end])=[];%remove .png extension - namelog=[filename_cmx([1:end-3]) 'log']; + [Rootbat,Filebat]=fileparts(filecell.nc.civ2{ifile,j});%output netcdf file (without extention) + namelog=[fullfile(Rootbat,Filebat) '.civ2.log']; par_civ2.Dt=num2str(time(num2_civ2(ifile),num_b_civ2(j))-time(num1_civ2(ifile),num_a_civ2(j))); par_civ2.T0=num2str((time(num2_civ1(ifile),num_b_civ2(j))+time(num1_civ2(ifile),num_a_civ2(j)))/2); @@ -2108,11 +2119,12 @@ %endTESTgrid i_cmd=i_cmd+1; - cmd_CIV2=CIV2_CMD(filename_cmx(1:end-4),namelog,par_civ2,sparam); + cmd_CIV2=CIV2_CMD(fullfile(Rootbat,Filebat),[],par_civ2,sparam);%creates the cmx file [fullfile(Rootbat,Filebat) '.civ2.cmx] if isequal(civAll,0) + flname=fullfile(Rootbat,Filebat); if(isunix) - cmd=[cmd 'cp -f ' filename_cmx '2 ' filename_cmx '\n' cmd_CIV2 '\n']; + cmd=[cmd 'cp -f ' flname '.civ2.cmx ' flname '.cmx\n' cmd_CIV2 '\n']; else - filename_cmx=regexprep(filename_cmx,'\\','\\\\'); - cmd=[cmd 'copy /Y "' filename_cmx '2" "' filename_cmx '"\n' cmd_CIV2 '\n']; + flname=regexprep(flname,'\\','\\\\'); + cmd=[cmd 'copy /Y "' flname '.civ2.cmx" "' flname '.cmx"\n' cmd_CIV2 '\n']; end else @@ -2253,5 +2265,4 @@ end super_cmd=[super_cmd cmd_str '\n']; - % eval(cmd_str); disp(cmd_str); end @@ -2478,5 +2489,5 @@ subdir_civ1=get(handles.subdir_civ1,'String');%subdirectory subdir_civ1 for the netcdf output data subdir_civ2=get(handles.subdir_civ2,'String'); -if isequal(subdir_civ1,''),subdir_civ1='A'; end% put default subdir +if isequal(subdir_civ1,''),subdir_civ1='CIV'; end% put default subdir if isequal(subdir_civ2,''),subdir_civ2=subdir_civ1; end% put default subdir currentdir=pwd;%store the current working directory @@ -2708,5 +2719,5 @@ %create the new subdir_civ2_new if ~exist(fullfile(Path_ima,subdir_civ2_new),'dir') - [xx,m2]=mkdir(subdir_civ2_new); + [xx,m2]=mkdir(fullfile(Path_ima,subdir_civ2_new)); [xx,msg2] = fileattrib(subdir_civ2_new,'+w','g'); %yield writing access (+w) to user group (g) if ~isequal(m2,'') @@ -4043,5 +4054,5 @@ %changes : filename_cmx -> filename ( no extension ) - +% input namelog not used if isequal(par.Dt,'0') par.Dt='1' ;%case of 'displacement' mode @@ -4086,13 +4097,19 @@ % namelog=regexprep(namelog,'\\','\\\\'); if(isunix) - [Rootbat,Filebat,extbat]=fileparts(namelog); - ncName=fullfile(Rootbat,[ Filebat '.nc']); - cmd_CIV1=[sparam.Civ1Bin ' -f ' filename '.cmx >' filename '.log' ]; % redirect standard output to the log file - cmd_CIV1=[cmd_CIV1 '\n' 'mv ' namelog ' ' regexprep(namelog,'\.log','') '.civ1.log' '\n' 'chmod g+w ' ncName]; +% filename +% namelog +% +% [Rootbat,Filebat,extbat]=fileparts(namelog); +% ncName=fullfile(Rootbat,[ Filebat '.nc']); + cmd_CIV1=[sparam.Civ1Bin ' -f ' filename '.cmx >' filename '.log' ]; % redirect standard output to the log file, the result file is named [filename '.nc'] by CIVx + cmd_CIV1=[cmd_CIV1 '\n' 'mv ' filename '.log' ' ' filename '.civ1.log' '\n' 'chmod g+w ' filename '.nc'];%rename .log as .civ1.log and set the netcdf result file for group user writting + cmd_CIV1=[cmd_CIV1 '\n' 'mv ' filename '.cmx' ' ' filename '.civ1.cmx' '\n'];%rename .cmx as .civ1.cmx else %Windows system + filename=regexprep(filename,'\\','\\\\'); cmd_CIV1=['"' sparam.Civ1Bin '" -f "' filename '.cmx" >"' filename '.log"' ]; % redirect standard output to the log file cmd_CIV1=regexprep(cmd_CIV1,'\\','\\\\'); namelog=regexprep(namelog,'\\','\\\\'); - cmd_CIV1=[cmd_CIV1 '\n' 'copy /Y "' namelog '" "' regexprep(namelog,'\.log','') '.civ1.log"']; + cmd_CIV1=[cmd_CIV1 '\n' 'copy /Y "' filename '.log' '" "' filename '.civ1.log"']; + cmd_CIV1=[cmd_CIV1 '\n' 'copy /Y "' filename '.cmx' '" "' filename '.civ1.cmx"']; end @@ -4197,8 +4214,12 @@ par.Dt='1' ;%case of 'displacement' mode end - par.filename_ima_a=regexprep(par.filename_ima_a,'.png',''); par.filename_ima_b=regexprep(par.filename_ima_b,'.png','');% bug : .png appears two times ? -fid=fopen([filename '.cmx2'],'w'); +[fid,errormsg]=fopen([filename '.civ2.cmx'],'w'); +if isequal(fid,-1) + msgbox_uvmat('ERROR',errormsg) + cmd_CIV2=''; + return +end fprintf(fid,['############## CMX file' '\n' ]); fprintf(fid, ['FirstImage ' regexprep(par.filename_ima_a,'\\','\\\\') '\n' ]);% for windows compatibility @@ -4234,13 +4255,20 @@ if(isunix) - cmd_CIV2=[sparam.Civ2Bin ' -f ' filename '.cmx >' filename '.log' ]; % redirect standard output to the log file - [Rootbat,Filebat,extbat]=fileparts(namelog); - ncName=fullfile(Rootbat,[ Filebat '.nc']); - cmd_CIV2=[cmd_CIV2 '\n' 'mv ' namelog ' ' regexprep(namelog,'\.log','') '.civ2.log' '\n' 'chmod g+w ' ncName]; +% cmd_CIV1=[sparam.Civ1Bin ' -f ' filename '.cmx >' filename '.log' ]; % redirect standard output to the log file, the result file is named [filename '.nc'] by CIVx +% cmd_CIV1=[cmd_CIV1 '\n' 'mv ' filename '.log' ' ' filename '.civ1.log' '\n' 'chmod g+w ' filename '.nc']; +% cmd_CIV1=[cmd_CIV1 '\n' 'mv ' filename '.cmx' ' ' filename '.civ1.cmx' '\n'];%rename .cmx as .civ1.cmx, the result file is named [filename '.nc'] by CIVx + + cmd_CIV2=[sparam.Civ2Bin ' -f ' filename '.cmx >' filename '.log' ]; % redirect standard output to the log file, the result file is named [filename '.nc'] by CIVx + cmd_CIV2=[cmd_CIV2 '\n' 'mv ' filename '.log' ' ' filename '.civ2.log' '\n' 'chmod g+w ' filename '.nc']; + cmd_CIV2=[cmd_CIV2 '\n' 'mv ' filename '.cmx' ' ' filename '.civ2.cmx' '\n'];%rename .cmx as .civ2.cmx, the result file is named [filename '.nc'] by CIVx +% [Rootbat,Filebat,extbat]=fileparts(namelog); +% ncName=fullfile(Rootbat,[ Filebat '.nc']); +% cmd_CIV2=[cmd_CIV2 '\n' 'mv ' namelog ' ' regexprep(namelog,'\.log','') '.civ2.log' '\n' 'chmod g+w ' ncName]; else + filename=regexprep(filename,'\\','\\\\'); cmd_CIV2=['"' sparam.Civ2Bin '" -f "' filename '.cmx" >"' filename '.log"' ]; % redirect standard output to the log file cmd_CIV2=regexprep(cmd_CIV2,'\\','\\\\'); - namelog=regexprep(namelog,'\\','\\\\'); - cmd_CIV2=[cmd_CIV2 '\n' 'copy /Y "' namelog '" "' regexprep(namelog,'\.log','') '.civ2.log"']; + cmd_CIV2=[cmd_CIV2 '\n' 'copy /Y "' filename '.log' '" "' filename '.civ2.log"']; + cmd_CIV2=[cmd_CIV2 '\n' 'copy /Y "' filename '.cmx' '" "' filename '.civ2.cmx"']; end Index: /trunk/src/proj_field.m =================================================================== --- /trunk/src/proj_field.m (revision 173) +++ /trunk/src/proj_field.m (revision 174) @@ -918,6 +918,5 @@ %----------------------------------------------------------------- -%initialisation of the input parameters of the projection plane -%----------------------------------------------------------------- +%% initialisation of the input parameters of the projection plane ProjMode='projection';%direct projection by default if isfield(ObjectData,'ProjMode'),ProjMode=ObjectData.ProjMode; end; @@ -948,11 +947,4 @@ NormVec_Y=cos(Phi)*sin(Theta); NormVec_Z=cos(Theta); - -% test for 3D fields -test3D=0; -if isfield(FieldData,'nb_dim') - test3D=isequal(FieldData.nb_dim,3); -end -test3C=test3D; %default 3 vel components %mesh sizes DX and DY @@ -1248,5 +1240,5 @@ Coord_y=[]; Coord_x=[]; - nb_dim=numel(size(DimValue)); + nb_dim=numel(DimValue); for idim=1:nb_dim %loop on space dimensions test_interp(idim)=0;%test for coordiate interpolation (non regular grid), =0 by default @@ -1296,5 +1288,5 @@ if nb_dim==3 DZ=abs(DCoord_min(1)); - Coord_z=linspace(Coord{1}(1),Coord{1}(end),npz); + Coord_z=linspace(Coord{1}(1),Coord{1}(end),DimValue(1)); test_direct_z=test_direct(1); end @@ -1342,5 +1334,5 @@ % case with no rotation and interpolation if isequal(ProjMode,'projection') && isequal(Phi,0) && isequal(Theta,0) && isequal(Psi,0) - if ~testXMin && ~testXMax && ~testYMin && ~testYMax + if ~testXMin && ~testXMax && ~testYMin && ~testYMax && nb_dim==2 ProjData=FieldData; else @@ -1367,4 +1359,10 @@ Xbound(1)=Coord{2}(1)+DXinit*(min_ind2-1); end + if nb_dim==3 %TODO: to update + min_ind3=ceil((Coord{1}(1)-ZMax)/DZinit)+1; + max_ind2=floor((Coord{1}(2)-XMin)/DZinit)+1; + Zbound(2)=Coord{1}(1)+DXinit*(max_ind2-1); + Zbound(1)=Coord{1}(1)+DXinit*(min_ind2-1); + end min_ind1=max(min_ind1,1);% deals with margin (bound lower than the first index) min_ind2=max(min_ind2,1); Index: /trunk/src/uvmat.m =================================================================== --- /trunk/src/uvmat.m (revision 173) +++ /trunk/src/uvmat.m (revision 174) @@ -426,5 +426,5 @@ end [FileName, PathName] = uigetfile( ... - {'*.xml;*.xls;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol;*.nc;*.cmx;*.fig;*.log;*.dat;*.bat;', ' (*.xml,*.xls,*.civ,*.jpg ,*.png, .tif, *.avi,*.vol,*.nc,*.cmx ,*.fig,*.log,*.dat,*.bat)'; + {'*.xml;*.xls;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol;*.nc;*.cmx;*.fig;*.log;*.dat;*.bat;', ' (*.xml,*.xls,*.civ,*.jpg ,*.png, .tif, *.avi,*.vol,*.nc,*.cmx,*.fig,*.log,*.dat,*.bat)'; '*.xml', '.xml files '; ... '*.xls', '.xls files '; ... @@ -437,6 +437,5 @@ '*.nc','.netcdf files'; ... '*.cdf','.netcdf files'; ... - '*.cmx','.cmx text files';... - '*.cmx2','.cmx2 text files';... + '*.cmx','.cmx text files ';... '*.fig','.fig files (matlab fig)';... '*.log','.log text files ';... @@ -2205,4 +2204,5 @@ %read images if ~isempty(filename) && isequal(FieldName,'image') + Npz=1;%default switch FileType case 'movie' @@ -2223,4 +2223,8 @@ case 'vol' A=imread(filename); + if isfield(UvData.XmlData,'Npy') + Npz=size(A,1)/UvData.XmlData.Npy; + A=reshape(A,Npz,UvData.XmlData.Npy,UvData.XmlData.Npx); + end case 'multimage' A=imread(filename,num_i1); @@ -2235,13 +2239,22 @@ Field{1}.AName='image'; Field{1}.ListVarName={'AY','AX','A'}; % - if size(A,3)==3;%color - Field{1}.VarDimName={'AY','AX',{'AY','AX','rgb'}}; % + if ndims(A)==3 + if Npz==1;%color + Field{1}.VarDimName={'AY','AX',{'AY','AX','rgb'}}; % + Field{1}.AY=[npxy(1)-0.5 0.5]; + Field{1}.AX=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers + else + Field{1}.ListVarName=['AZ' Field{1}.ListVarName]; + Field{1}.VarDimName={'AZ','AY','AX',{'AZ','AY','AX'}}; + Field{1}.AZ=[0.5 npxy(1)-0.5]; + Field{1}.AY=[npxy(2)-0.5 0.5]; + Field{1}.AX=[0.5 npxy(3)-0.5]; % coordinates of the first and last pixel centers + end else Field{1}.VarDimName={'AY','AX',{'AY','AX'}}; % - end - Field{1}.AY=Rangy; - Field{1}.AX=Rangx; + Field{1}.AY=[npxy(1)-0.5 0.5]; + Field{1}.AX=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers + end Field{1}.A=A; - % Field{1}.CoordType='px'; %used for mouse_motion Field{1}.CoordUnit='pixel'; %used for mouse_motion end @@ -2488,6 +2501,6 @@ test_x=0; test_z=0;% test for unstructured z coordinate -UvData.ZMax=0; -UvData.ZMin=0;%default +% UvData.ZMax=0; +% UvData.ZMin=0;%default %UvData.Mesh=1; %default [UvData.Field,errormsg]=check_field_structure(UvData.Field); @@ -2522,6 +2535,7 @@ YName=UvData.Field.ListVarName{VarType{imax}.coord(2)}; XName=UvData.Field.ListVarName{VarType{imax}.coord(3)}; -end - + eval(['ZMax=max(UvData.Field.' ZName ');']) + eval(['ZMin=min(UvData.Field.' ZName ');']) +end eval(['XMax=max(UvData.Field.' XName ');']) eval(['XMin=min(UvData.Field.' XName ');']) @@ -2565,5 +2579,5 @@ UvData.Field.YMax=XMax; UvData.Field.YMin=XMin; -if test_z +if NbDim==3 UvData.Field.ZMax=ZMax; UvData.Field.ZMin=ZMin; @@ -2642,6 +2656,6 @@ if NbDim==3 && UvData.NewSeries UvData.Object{1}.NbDim=UvData.NbDim;%test for 3D objects - UvData.Object{1}.RangeZ=Field.Mesh;%main plotting plane - UvData.Object{1}.Coord(1,3)=(UvData.ZMin+UvData.ZMax)/2;%section at a middle plane chosen + 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}.Phi=0; UvData.Object{1}.Theta=0; @@ -2649,6 +2663,6 @@ UvData.Object{1}.HandlesDisplay=plot(0,0,'Tag','proj_object');% A REVOIR PlotHandles=get_plot_handles(handles); - ZBounds(1)=UvData.ZMin; %minimum for the Z slider - ZBounds(2)=UvData.ZMax;%maximum for the Z slider + ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider + ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider UvData.Object{1}.Name='1-PLANE'; UvData.Object{1}.enable_plot=1;