From 8066dd645617d7febcabd239cc60727efe0bfbe5 Mon Sep 17 00:00:00 2001
From: Olivier Sauter <olivier.sauter@epfl.ch>
Date: Sun, 9 Feb 2025 09:30:34 +0100
Subject: [PATCH] fix reading netcdf with units not defined (e.g. fi cdf), add
shot as input
---
matlab/CHDF/cdf2mat.m | 18 ++++++++++++++++--
1 file changed, 16 insertions(+), 2 deletions(-)
diff --git a/matlab/CHDF/cdf2mat.m b/matlab/CHDF/cdf2mat.m
index c9d7a14e..270ded91 100644
--- a/matlab/CHDF/cdf2mat.m
+++ b/matlab/CHDF/cdf2mat.m
@@ -1,4 +1,5 @@
-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);
--
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