Index: /trunk/src/series.m =================================================================== --- /trunk/src/series.m (revision 918) +++ /trunk/src/series.m (revision 919) @@ -1764,6 +1764,7 @@ -%% direct processing on the current Matlab session -% if strcmp (RunMode,'local') +%% direct processing on the current Matlab session or creation of command files +filexml=cell(1,NbProcess);% initialisation of the names of the files containing the processing parameters +extxml=cell(1,NbProcess); % initialisation of the set of labels used for the files documenting each process for iprocess=1:NbProcess if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action @@ -1773,5 +1774,5 @@ if isempty(Param.IndexRange.NbSlice) Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i; -% Param.IndexRange.first_i=ref_i(1+(iprocess-1)*BlockLength); + % Param.IndexRange.first_i=ref_i(1+(iprocess-1)*BlockLength); if Param.IndexRange.first_i>last_i NbProcess=iprocess-1;% leave the loop, we are at the end of the calculation @@ -1782,6 +1783,6 @@ Param.IndexRange.last_i=min(last_i,first_i+(iprocess)*BlockLength*incr_i-1); else %multislices (then incr_i is not empty) -% Param.IndexRange.first_i= first_i+incr_i*(iprocess-1); -% Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice; + % Param.IndexRange.first_i= first_i+incr_i*(iprocess-1); + % Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice; Param.IndexRange.first_i= first_i+iprocess-1; Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice; @@ -1809,6 +1810,13 @@ extxml{iprocess}=fullfile_uvmat('','',Param.InputTable{1,3},'.xml',OutputNomType,... Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j); - filexml{iprocess}=fullfile(OutputDir,'0_XML',extxml{iprocess}) - save(t, filexml{iprocess});% save the xml file containing the processing parameters + filexml{iprocess}=fullfile(OutputDir,'0_XML',extxml{iprocess}); + try + save(t, filexml{iprocess});% save the xml file containing the processing parameters + catch ME + if ~strcmp (RunMode,'local') + errormsg=['error writting ' filexml{iprocess} ': ' ME.message]; + return + end + end end if strcmp (RunMode,'local') @@ -1827,4 +1835,5 @@ end end + if ~strcmp (RunMode,'local') && ~strcmp(RunMode,'python') %% processing on a different session of the same computer (background) or cluster, create executable files Index: /trunk/src/set_grid.m =================================================================== --- /trunk/src/set_grid.m (revision 918) +++ /trunk/src/set_grid.m (revision 919) @@ -194,7 +194,7 @@ YA=grid_pix_A(:,2); unitcolumn=32*ones(size(XA)); -Xchar=num2str(XA,2); +Xchar=num2str(XA,'%1.1f');% write x coordinate in px, rounded at the first decimal blanc=char(unitcolumn); -Ychar=num2str(YA,2); +Ychar=num2str(YA,'%1.1f');% write y coordinate in px, rounded at the first decimal tete=['1 ' num2str(nbpointsA(1))]; txt=[Xchar blanc Ychar]; Index: /trunk/src/struct2nc.m =================================================================== --- /trunk/src/struct2nc.m (revision 918) +++ /trunk/src/struct2nc.m (revision 919) @@ -49,5 +49,6 @@ return end -%check the validity of the input field structure + +%% check the validity of the input field structure [errormsg,ListDimName,DimValue,VarDimIndex]=check_field_structure(Data); if ~isempty(errormsg) @@ -56,11 +57,12 @@ end ListVarName=Data.ListVarName; -%nc=netcdf.create(flname,'NC_CLOBBER');%,'clobber'); %create the netcdf file with name flname + +%% create the netcdf file with name flname in format NETCDF4 cmode = netcdf.getConstant('NETCDF4'); cmode = bitor(cmode, netcdf.getConstant('CLASSIC_MODEL')); cmode = bitor(cmode, netcdf.getConstant('CLOBBER')); -nc = netcdf.create(flname, cmode) - -%write global constants +nc = netcdf.create(flname, cmode); + +%% write global constants if isfield(Data,'ListGlobalAttribute') keys=Data.ListGlobalAttribute; @@ -84,5 +86,6 @@ end end -%create dimensions + +%% create the dimensions dimid=zeros(1,length(ListDimName)); for idim=1:length(ListDimName) @@ -95,12 +98,30 @@ testattr=1; end -varid=zeros(1,length(Data.ListVarName)); + + +%% create the variables +varid=nan(1,length(Data.ListVarName)); for ivar=1:length(ListVarName) - varid(ivar)=netcdf.defVar(nc,ListVarName{ivar},'nc_double',dimid(VarDimIndex{ivar}));%define variable -end - %write variable attributes + if isfield(Data,ListVarName{ivar}) + VarClass=class(Data.(ListVarName{ivar})); + VarType=''; + switch VarClass + case {'single','double'} + VarType='nc_float'; % store all floating reals as single + case {'uint8','int16','uint16','int32','uint32','int64','uint64'} + VarType='nc_int'; + case 'logical' + VarType='nc_byte'; + end + if ~isempty(VarType) + varid(ivar)=netcdf.defVar(nc,ListVarName{ivar},VarType,dimid(VarDimIndex{ivar}));%define variable + end + end +end + +%% write variable attributes if testattr for ivar=1:min(numel(VarAttribute),numel(ListVarName)) - if isstruct(VarAttribute{ivar}) + if isstruct(VarAttribute{ivar}) && ~isnan(varid(ivar)) attr_names=fields(VarAttribute{ivar}); for iattr=1:length(attr_names) @@ -114,9 +135,10 @@ end netcdf.endDef(nc); %put in data mode + +%% fill the variables with input data for ivar=1:length(ListVarName) - if isfield(Data,ListVarName{ivar}) + if ~isnan(varid(ivar)) VarVal=Data.(ListVarName{ivar}); %varval=values of the current variable -% VarDimIndex=Data.VarDimIndex{ivar}; %indices of the variable dimensions in the list of dimensions VarDimName=Data.VarDimName{ivar}; if ischar(VarDimName) @@ -126,9 +148,5 @@ testrange=(numel(VarDimName)==1 && strcmp(VarDimName{1},ListVarName{ivar}) && numel(VarVal)==2);% case of a coordinate defined on a regular mesh by the first and last values. testline=isequal(length(siz),2) && isequal(siz(1),1)&& isequal(siz(2), DimValue(VarDimIndex{ivar}));%matlab vector - testcolumn=isequal(length(siz),2) && isequal(siz(1), DimValue(VarDimIndex{ivar}))&& isequal(siz(2),1);%matlab column vector -% if ~testrange && ~testline && ~testcolumn && ~isequal(siz,DimValue(VarDimIndex)) -% errormsg=['wrong dimensions declared for ' ListVarName{ivar} ' in struct2nc.m']; -% break -% end + %testcolumn=isequal(length(siz),2) && isequal(siz(1), DimValue(VarDimIndex{ivar}))&& isequal(siz(2),1);%matlab column vector if testline || testrange if testrange Index: /trunk/src/struct2xml.m =================================================================== --- /trunk/src/struct2xml.m (revision 918) +++ /trunk/src/struct2xml.m (revision 919) @@ -1,15 +1,20 @@ -%'struct2xml': transform a matlab structure to a xml tree. +%'struct2xml': transforms a matlab structure to a xml tree. %-------------------------------------------------------------- +% % each field with char string or num vector is transformed into a corresponding xml element % each field with a matrix containing n lines is transformed into a xml element repeated n times -% WARNING: PROBLEM WITH HIERARCHICAL structures +% each substructure of the input matlab structure is translateed into a subtree in the xml object +% it is also possible to append a subtree to an existing xml object t +% +% t=struct2xml(Object,t,root_uid) %%%%%%%%%%%%%%%%%%%%%%% % OUTPUT: % t: xmltree reproducing the structure of Object % type 'save(t)' to visualize the xml text and save(filename,t) to save it in a file +% to set the title tag of the file, type t=set(t,1,'name','titletag') % % INPUT: % Object: matlab structure, possibly hierarchical -% t: optional input xml tree in which a new branch needs to be appended +% t: optional input xml tree in which a subtree needs to be appended % root_uid: optional uid of the xml element under which the new subtree must be appended