![(please configure the [header_logo] section in trac.ini)](/trac/issm/chrome/common/trac_banner.png)
Changeset 19080
- Timestamp:
- 02/03/15 11:06:34 (10 years ago)
- Location:
- issm/trunk-jpl/src/m/contrib/netCDF
- Files:
-
- 2 edited
-
export_netCDF.m (modified) (11 diffs)
-
export_netCDF.py (modified) (2 diffs)
Legend:
- Unmodified
- Added
- Removed
-
issm/trunk-jpl/src/m/contrib/netCDF/export_netCDF.m
r19055 r19080 1 2 1 function export_netCDF(md,filename) 3 2 … … 15 14 end 16 15 %open file and write description 17 mode = netcdf.getConstant('N ETCDF4');18 mode = bitor(mode,netcdf.getConstant('N OCLOBBER'));%NOCLOBBER to avoid overwrite16 mode = netcdf.getConstant('NC_NETCDF4'); 17 mode = bitor(mode,netcdf.getConstant('NC_NOCLOBBER'));%NOCLOBBER to avoid overwrite 19 18 ncid = netcdf.create(filename,mode); 20 19 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Title',['Results for run ' md.miscellaneous.name]); … … 33 32 DimSize(2).index=netcdf.defDim(ncid,'VertNum',md.mesh.numberofvertices); 34 33 DimSize(3).index=netcdf.defDim(ncid,'VertperElt',size(md.mesh.elements,2)); 34 DimSize(4).index=netcdf.defDim(ncid,'Time',StepNum); 35 DimSize(5).index=netcdf.defDim(ncid,'StringLength',20); 36 DimSize(6).index=netcdf.defDim(ncid,'StructLength',2); 35 37 36 38 for i=1:length(DimSize), … … 45 47 groups=fieldnames(md); 46 48 for i=1:length(groups), 47 %disp(sprintf('group name in tree %s ',groups{i}));49 disp(sprintf('group name in tree %s ',groups{i})); 48 50 groupID=netcdf.defGrp(ncid,groups{i}); 49 51 %In each group gather the fields of the class … … 52 54 if strcmp(groups(i),'results'), 53 55 for j=1:length(groupfields)%looping on the different solutions 54 %disp(sprintf('=====Field name in tree %s ',groupfields{j}));56 %disp(sprintf('=====Field name in tree %s ',groupfields{j})); 55 57 if length(md.results.(groupfields{j}))>1, 56 58 %the solution have several timestep get last timesteps and output frequency 57 59 last_step = length(md.results.(groupfields{j})); 58 step_freq = md.settings.output_frequency;59 60 %grab first time step 60 61 subfields=fields(md.results.(groupfields{j})(1)); … … 62 63 netcdf.putAtt(groupID,netcdf.getConstant('NC_GLOBAL'),'classtype','results'); 63 64 if ~strcmp(subfields(k),'errlog') && ~strcmp(subfields(k),'outlog') && ~strcmp(subfields(k),'SolutionType'), 64 disp(sprintf('==========SubField name in tree %s ',subfields{k})); 65 Var=md.results.(groupfields{1})(1).(subfields{k}); 66 [truc,DimSize,DimValue]=DefCreateVar(ncid,Var,groupID,subfields{k},DimSize,DimValue); 67 %CreateVar(Var,True,last_step,step_freq) 65 %disp(sprintf('==========SubField name in tree %s ',subfields{k})); 66 Var=md.results.(groupfields{j})(1).(subfields{k}); 67 [DimSize,DimValue]=DefCreateVar(ncid,Var,groupID,subfields{k},DimSize,DimValue,true,last_step,md,groupfields{j}); 68 68 end 69 69 end … … 72 72 subfields=fields(md.results.(groupfields{j})); 73 73 for k=1:length(subfields), 74 disp(sprintf('==========SubField name in tree %s ',subfields{k}));75 netcdf.putAtt(groupID,netcdf.getConstant(' GLOBAL'),'classtype','results');74 %disp(sprintf('==========SubField name in tree %s ',subfields{k})); 75 netcdf.putAtt(groupID,netcdf.getConstant('NC_GLOBAL'),'classtype','results'); 76 76 if ~strcmp(subfields(k),'errlog') && ~strcmp(subfields(k),'outlog') && ~strcmp(subfields(k),'SolutionType'), 77 77 Var=md.results.(groupfields{1})(1).(subfields{k}); 78 [ truc,DimSize,DimValue]=DefCreateVar(ncid,Var,groupID,subfields{k},DimSize,DimValue);78 [DimSize,DimValue]=DefCreateVar(ncid,Var,groupID,subfields{k},DimSize,DimValue,false); 79 79 end 80 80 end … … 85 85 else 86 86 for j=1:length(groupfields), 87 disp(sprintf('=====Field name in tree %s ',groupfields{j}));88 netcdf.putAtt(groupID,netcdf.getConstant(' GLOBAL'),'classtype',class(md.(groups{i})));87 %disp(sprintf('=====Field name in tree %s ',groupfields{j})); 88 netcdf.putAtt(groupID,netcdf.getConstant('NC_GLOBAL'),'classtype',class(md.(groups{i}))); 89 89 Var=md.(groups{i}).(groupfields{j}); 90 [ truc,DimSize,DimValue]=DefCreateVar(ncid,Var,groupID,groupfields{j},DimSize,DimValue);90 [DimSize,DimValue]=DefCreateVar(ncid,Var,groupID,groupfields{j},DimSize,DimValue,false); 91 91 end 92 92 end … … 95 95 end 96 96 97 function [ varclass,DimSize,DimValue]=DefCreateVar(ncid,Var,groupID,field,DimSize,DimValue)97 function [DimSize,DimValue]=DefCreateVar(ncid,Var,groupID,field,DimSize,DimValue,istime,last,md,midfield) 98 98 varclass=class(Var); 99 99 varsize=size(Var); … … 105 105 LogicString='False'; 106 106 end 107 netcdf.putAtt(groupID,netcdf.getConstant(' GLOBAL'),field,LogicString);107 netcdf.putAtt(groupID,netcdf.getConstant('NC_GLOBAL'),field,LogicString); 108 108 elseif isa(Var,'char'), 109 netcdf.putAtt(groupID,netcdf.getConstant(' GLOBAL'),field,Var);109 netcdf.putAtt(groupID,netcdf.getConstant('NC_GLOBAL'),field,Var); 110 110 elseif isa(Var,'double'), %dealing with arrays 111 [dims,DimSize,DimValue]=GetDims(ncid,Var,groupID,field,DimSize,DimValue); 112 varid = netcdf.defVar(groupID,field,'double',dims); 113 if length(Var)==0, 114 netcdf.putVar(groupID,varid,NaN); 115 else 116 netcdf.putVar(groupID,varid,Var); 117 end 111 [dims,DimSize,DimValue]=GetDims(ncid,Var,groupID,field,DimSize,DimValue,istime); 112 varid = netcdf.defVar(groupID,field,'NC_DOUBLE',dims); 113 if istime, 114 VarTab=Var; 115 for i=2:last, 116 TimeVar=md.results.(midfield)(i).(field); 117 VarTab=[VarTab TimeVar]; 118 end 119 netcdf.putVar(groupID,varid,VarTab); 120 else 121 if length(Var)==0, 122 netcdf.putVar(groupID,varid,NaN); 123 else 124 netcdf.putVar(groupID,varid,Var); 125 end 126 end 118 127 elseif isa(Var,'cell'), 119 disp(sprintf('no support for class %s for field %s so far',varclass,field)); 128 [dims,DimSize,DimValue]=GetDims(ncid,Var,groupID,field,DimSize,DimValue,istime); 129 %dirty hack to be able to pass strings 130 varid = netcdf.defVar(groupID,field,'NC_CHAR',dims); 131 for i=1:length(Var), 132 startpoint=zeros(size(Var)); 133 startpoint(:,i)=i-1; 134 if length(Var)>1, 135 endpoint=[min(length(Var{i}),20) 1]; 136 else 137 endpoint=min(length(Var{i}),20); 138 end 139 if length(Var{i})>20, 140 netcdf.putVar(groupID,varid,startpoint,endpoint,Var{i}(1:20)) 141 else 142 netcdf.putVar(groupID,varid,startpoint,endpoint,Var{i}) 143 end 144 end 120 145 elseif isa(Var,'struct'), 121 disp(sprintf('no support for class %s for field %s so far',varclass,field)); 146 %Start by getting the structure fields and size 147 locfields=fields(Var); 148 [dims,DimSize,DimValue]=GetDims(ncid,Var,groupID,locfields,DimSize,DimValue,istime); 149 varid = netcdf.defVar(groupID,field,'NC_CHAR',dims); 150 for i=1:length(locfields), 151 for j=1:2, 152 if j==1, 153 startpoint=[0,0,i-1]; 154 CharVar=locfields{i}; 155 else 156 startpoint=[0,1,i-1]; 157 if isa(Var.(locfields{i}),'char'), 158 CharVar=Var.(locfields{i}); 159 else 160 CharVar=num2str(Var.(locfields{i})); 161 end 162 end 163 endpoint=[min(length(CharVar),20),1,1]; 164 if length(CharVar)>20, 165 netcdf.putVar(groupID,varid,startpoint,endpoint,CharVar(1:20)) 166 else 167 netcdf.putVar(groupID,varid,startpoint,endpoint,CharVar) 168 end 169 end 170 end 122 171 else 123 172 disp(sprintf('no support for class %s of field %s',varclass,field)); … … 126 175 end 127 176 128 function [dims,DimSize,DimValue]=GetDims(ncid,Var,groupID,field,DimSize,DimValue )177 function [dims,DimSize,DimValue]=GetDims(ncid,Var,groupID,field,DimSize,DimValue,istime) 129 178 dims=[]; 130 varlength=length(Var); 131 varsize=size(Var); 132 MatOrVec=varsize>1; %checking if we have a matrix (1 1) are vector (1 0) 133 for i=1:sum(MatOrVec), %loop on the number of (non 1) dimensions 134 currentdim=varsize(i); 135 dimexist=DimValue==currentdim; 136 if sum(dimexist)==0, %dimension is new to us, need to create it 137 dimname=strcat(field,int2str(i)); 138 dimindex=length(DimSize)+1; 139 DimSize(dimindex).index=netcdf.defDim(ncid,dimname,currentdim); 140 [DimSize(dimindex).name,DimSize(dimindex).value]=netcdf.inqDim(ncid,DimSize(dimindex).index); 179 %specific treatment for structures 180 if isa(Var,'struct') 181 varsize=size(field); %we pass here the fields of the current structure 182 MatOrVec=varsize>1; %checking if we have a matrix (1 1) or vector (1 0) 183 for i=1:sum(MatOrVec), %loop on the number of (non 1) dimensions 184 currentdim=varsize(i); 185 dimexist=DimValue==currentdim; 186 if sum(dimexist)==0, %dimension is new to us, need to create it 187 dimname=strcat(field{1},int2str(i)); 188 dimindex=length(DimSize)+1; 189 DimSize(dimindex).index=netcdf.defDim(ncid,dimname,currentdim); 190 [DimSize(dimindex).name,DimSize(dimindex).value]=netcdf.inqDim(ncid,DimSize(dimindex).index); 191 dims(i)=DimSize(dimindex).index; 192 DimValue(dimindex)=currentdim; 193 else 194 dimindex=find(dimexist); 195 if DimSize(dimindex).value~=currentdim, 196 error('Indexation problem with the dimension structure') 197 end 198 end 141 199 dims(i)=DimSize(dimindex).index; 142 DimValue(dimindex)=currentdim; 143 else 144 dimindex=find(dimexist); 145 if DimSize(dimindex).value~=currentdim, 146 error('Indexation problem with the dimension structure') 147 end 148 end 149 dims(i)=DimSize(dimindex).index; 200 end 201 dims=[DimSize(6).index dims]; 202 else 203 %with a cell array need to grab the transposed size to work 204 if isa(Var,'cell'), 205 varsize=size(Var'); 206 else 207 varsize=size(Var); 208 end 209 MatOrVec=varsize>1; %checking if we have a matrix (1 1) or vector (1 0) 210 for i=1:sum(MatOrVec), %loop on the number of (non 1) dimensions 211 currentdim=varsize(i); 212 dimexist=DimValue==currentdim; 213 if sum(dimexist)==0, %dimension is new to us, need to create it 214 dimname=strcat(field,int2str(i)); 215 dimindex=length(DimSize)+1; 216 DimSize(dimindex).index=netcdf.defDim(ncid,dimname,currentdim); 217 [DimSize(dimindex).name,DimSize(dimindex).value]=netcdf.inqDim(ncid,DimSize(dimindex).index); 218 dims(i)=DimSize(dimindex).index; 219 DimValue(dimindex)=currentdim; 220 else 221 dimindex=find(dimexist); 222 if DimSize(dimindex).value~=currentdim, 223 error('Indexation problem with the dimension structure') 224 end 225 end 226 dims(i)=DimSize(dimindex).index; 227 end 228 end 229 if istime, 230 dims=[dims DimSize(4).index];%adding the time dimension if necessary 231 end 232 %if we have a cell variable we need to add a stringlength dimension 233 if isa(Var,'cell') || isa(Var,'struct'), 234 dims=[DimSize(5).index dims]; 150 235 end 151 236 end -
issm/trunk-jpl/src/m/contrib/netCDF/export_netCDF.py
r19055 r19080 88 88 if time!=0: 89 89 timevar=md.results.__dict__[supfield].__getitem__(time).__dict__[field] 90 #print 'Treating '+str(group)+'.'+str(supfield)+'.'+str(field)+' for time '+str(time)90 print 'Treating '+str(group)+'.'+str(supfield)+'.'+str(field)+' for time '+str(time) 91 91 vartab=numpy.column_stack((vartab,timevar)) 92 print numpy.shape(vartab) 92 93 try: 93 94 ncvar[:,:]=vartab[:,:] … … 129 130 VertNum=NCData.createDimension('VertNum',md.mesh.numberofvertices) 130 131 VertperElt=NCData.createDimension('VertperElt',numpy.shape(md.mesh.elements)[1]) 132 Time=NCData.createDimension('Time',StepNum) 133 DictDim=NCData.createDimension('DictDim',2) 131 134 132 135 DimDict = {len(EltNum):'EltNum', 133 136 len(VertNum):'VertNum', 134 len(VertperElt):'VertperElt'} 137 len(VertperElt):'VertperElt', 138 len(Time):'Time', 139 len(DictDim):'DictDim'} 135 140 136 141 TypeDict = {float:'f8',
Note:
See TracChangeset
for help on using the changeset viewer.
