add gas, gash for JET and fix cdf2mat for ASTRA cdf file as well

matlab/CHDF/cdf2mat.m

@@ -47,16 +47,31 @@ for i=1:length(coordnames_sorted)
   matcdf.coords(i).index_allvarnames = strmatch(matcdf.coords(i).name,allvarnames,'exact');
   matcdf.coords(i).index_varnames_sorted = strmatch(matcdf.coords(i).name,varnames_sorted,'exact');
   matcdf.coords(i).varid = allvarids(matcdf.coords(i).index_allvarnames);
-  if strcmp(allinfo.Variables(matcdf.coords(i).index_allvarnames).Datatype,'single')
-    matcdf.coords(i).data = netcdf.getVar(funnetcdf,matcdf.coords(i).varid,'double');
+  if ~isempty(matcdf.coords(i).index_allvarnames)
+    if strcmp(allinfo.Variables(matcdf.coords(i).index_allvarnames).Datatype,'single')
+      matcdf.coords(i).data = netcdf.getVar(funnetcdf,matcdf.coords(i).varid,'double');
+    else
+      matcdf.coords(i).data = netcdf.getVar(funnetcdf,matcdf.coords(i).varid);
+    end
+    for ij=1:length(fields_variables_to_copy)
+      matcdf.coords(i).(fields_variables_to_copy{ij}) = allinfo.Variables(matcdf.coords(i).index_allvarnames).(fields_variables_to_copy{ij});
+    end
+    for jj=1:numel(allinfo.Variables(matcdf.coords(i).index_allvarnames).Attributes)
+      if strcmp(lower(allinfo.Variables(matcdf.coords(i).index_allvarnames).Attributes(jj).Name),'units')
+        matcdf.coords(i).units = strtrim(allinfo.Variables(matcdf.coords(i).index_allvarnames).Attributes(jj).Value);
+      end
+      if strcmp(lower(allinfo.Variables(matcdf.coords(i).index_allvarnames).Attributes(jj).Name),'long_name')
+        matcdf.coords(i).long_name = strtrim(allinfo.Variables(matcdf.coords(i).index_allvarnames).Attributes(jj).Value);
+      end
+    end
   else
-    matcdf.coords(i).data = netcdf.getVar(funnetcdf,matcdf.coords(i).varid);
-  end
-  for ij=1:length(fields_variables_to_copy)
-    matcdf.coords(i).(fields_variables_to_copy{ij}) = allinfo.Variables(matcdf.coords(i).index_allvarnames).(fields_variables_to_copy{ij});
+    matcdf.coords(i).data = [];
+    for ij=1:length(fields_variables_to_copy)
+      matcdf.coords(i).(fields_variables_to_copy{ij}) = [];
+    end
+    matcdf.coords(i).units = '';
+    matcdf.coords(i).long_name = [matcdf.coords(i).name ' empty'];
   end
-  matcdf.coords(i).units = strtrim(allinfo.Variables(matcdf.coords(i).index_allvarnames).Attributes(1).Value);
-  matcdf.coords(i).long_name = strtrim(allinfo.Variables(matcdf.coords(i).index_allvarnames).Attributes(2).Value);
   matcdf.coords(i).label = [matcdf.coords(i).name ' ' num2str(matcdf.coords(i).Size) ': ' matcdf.coords(i).long_name];
   cdf2mat_out.coords.(matcdf.coords(i).name) = matcdf.coords(i);
 end
@@ -65,16 +80,31 @@ for i=1:length(varnames_sorted)
   matcdf.vars(i).name = varnames_sorted{i};
   matcdf.vars(i).index_allvarnames = strmatch(matcdf.vars(i).name,allvarnames,'exact');
   matcdf.vars(i).varid = allvarids(matcdf.vars(i).index_allvarnames);
-  if strcmp(allinfo.Variables(matcdf.vars(i).index_allvarnames).Datatype,'single')
-    matcdf.vars(i).data = netcdf.getVar(funnetcdf,matcdf.vars(i).varid,'double');
+  if ~isempty(matcdf.vars(i).index_allvarnames)
+    if strcmp(allinfo.Variables(matcdf.vars(i).index_allvarnames).Datatype,'single')
+      matcdf.vars(i).data = netcdf.getVar(funnetcdf,matcdf.vars(i).varid,'double');
+    else
+      matcdf.vars(i).data = netcdf.getVar(funnetcdf,matcdf.vars(i).varid);
+    end
+    for ij=1:length(fields_variables_to_copy)
+      matcdf.vars(i).(fields_variables_to_copy{ij}) = allinfo.Variables(matcdf.vars(i).index_allvarnames).(fields_variables_to_copy{ij});
+    end
+    for jj=1:numel(allinfo.Variables(matcdf.vars(i).index_allvarnames).Attributes)
+      if strcmp(lower(allinfo.Variables(matcdf.vars(i).index_allvarnames).Attributes(jj).Name),'units')
+        matcdf.vars(i).units = strtrim(allinfo.Variables(matcdf.vars(i).index_allvarnames).Attributes(jj).Value);
+      end
+      if strcmp(lower(allinfo.Variables(matcdf.vars(i).index_allvarnames).Attributes(jj).Name),'long_name')
+        matcdf.vars(i).long_name = strtrim(allinfo.Variables(matcdf.vars(i).index_allvarnames).Attributes(jj).Value);
+      end
+    end
   else
-    matcdf.vars(i).data = netcdf.getVar(funnetcdf,matcdf.vars(i).varid);
-  end
-  for ij=1:length(fields_variables_to_copy)
-    matcdf.vars(i).(fields_variables_to_copy{ij}) = allinfo.Variables(matcdf.vars(i).index_allvarnames).(fields_variables_to_copy{ij});
+    matcdf.vars(i).data = [];
+    for ij=1:length(fields_variables_to_copy)
+      matcdf.vars(i).(fields_variables_to_copy{ij}) = [];
+    end
+    matcdf.vars(i).units = '';
+    matcdf.vars(i).long_name = [matcdf.vars(i).name ' empty'];
   end
-  matcdf.vars(i).units = strtrim(allinfo.Variables(matcdf.vars(i).index_allvarnames).Attributes(1).Value);
-  matcdf.vars(i).long_name = strtrim(allinfo.Variables(matcdf.vars(i).index_allvarnames).Attributes(2).Value);
   matcdf.vars(i).label = matcdf.vars(i).name;
   for j=1:length(matcdf.vars(i).Dimensions)
     ij = strmatch(matcdf.vars(i).Dimensions(j).Name,coordnames_sorted,'exact');
@@ -93,13 +123,18 @@ for i=1:length(varnames_sorted)
   matcdf.vars(i).label = [matcdf.vars(i).label ': ' matcdf.vars(i).long_name ' [' matcdf.vars(i).units ']'];
   cdf2mat_out.allvars.(matcdf.vars(i).name) = matcdf.vars(i);
 end
-top_attr_names = {allinfo.Attributes(:).Name};
-ij = strmatch('shot',top_attr_names,'exact');
-cdf2mat_out.shot = allinfo.Attributes(ij).Value;
+if ~isempty(allinfo.Attributes)
+  top_attr_names = {allinfo.Attributes(:).Name};
+  ij = strmatch('shot',top_attr_names,'exact');
+  cdf2mat_out.shot = allinfo.Attributes(ij).Value;
+else
+  cdf2mat_out.shot = NaN;
+end
 cdf2mat_out.fname = pfname;
-cdf2mat_out.id = pfname(length(pfname)-11:length(pfname)-4);
+[a1,a2,a3]=fileparts(pfname);
+cdf2mat_out.id = a2;
 
-netcdf.close(funnetcdf);
+  netcdf.close(funnetcdf);
 
 clear matcdf
 return