fix reading netcdf with units not defined (e.g. fi cdf), add shot as input

matlab/CHDF/cdf2mat.m

-function cdf2mat_out = cdf2mat(pfname)
+function cdf2mat_out = cdf2mat(pfname,varargin)
+% cdf2mat_out = cdf2mat(pfname,varargin)
 %
 % reads all variables and coordinates from netcdf
 % some trials with netcdf, using 50725c01.cdf as test
@@ -7,6 +8,9 @@ function cdf2mat_out = cdf2mat(pfname)
 %
 % Uses matlab netcdf.open, ncinfo, netcdf.inqVarIDs, netcd.getVar, etc
 %
+% varargin{1}: shot number to add (in particular when cdf file does not have it defined
+%              shot from file: allinfo=ncinfo(pfname);if ~isempty(allinfo.Attributes),top_attr_names = {allinfo.Attributes(:).Name};allinfo.Attributes(strmatch('shot',top_attr_names,'exact')).Value, else, disp('no Attributes'),end
+%
 
 %
 if ~exist(pfname,'file')
@@ -33,6 +37,7 @@ if length(allvarnames) ~= length(allvarids)
 end
 
 [varnames_sorted,~]=sort(allvarnames);
+cdf2mat_out.allvarnames_sorted = varnames_sorted;
 
 % to find a variable:
 % strmatch('GFUN',allvarnames,'exact')
@@ -56,6 +61,8 @@ for i=1:length(coordnames_sorted)
     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
+    matcdf.coords(i).units = '';
+    matcdf.coords(i).long_name = [matcdf.coords(i).name ' empty'];
     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);
@@ -80,6 +87,7 @@ 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 i==strmatch('ZEFFC',varnames_sorted,'exact'), keyboard; end
   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');
@@ -89,6 +97,8 @@ for i=1:length(varnames_sorted)
     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
+    matcdf.vars(i).units = '';
+    matcdf.vars(i).long_name = [matcdf.vars(i).name ' empty'];
     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);
@@ -128,7 +138,11 @@ if ~isempty(allinfo.Attributes)
   ij = strmatch('shot',top_attr_names,'exact');
   cdf2mat_out.shot = allinfo.Attributes(ij).Value;
 else
-  cdf2mat_out.shot = NaN;
+  if nargin>1 && isnumeric(varargin{1})
+    cdf2mat_out.shot = varargin{1};
+  else
+    cdf2mat_out.shot = NaN;
+  end
 end
 cdf2mat_out.fname = pfname;
 [a1,a2,a3]=fileparts(pfname);