#!/usr/bin/env python
# -*- coding: utf8 -*-
#
# Copyright or © or Copr. Actimar/IFREMER (2010-2015)
#
# This software is a computer program whose purpose is to provide
# utilities for handling oceanographic and atmospheric data,
# with the ultimate goal of validating the MARS model from IFREMER.
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# ==================================================================================================
import os, re, StringIO, sys
# ==================================================================================================
__author__ = 'Jonathan Wilkins'
__email__ = 'wilkins@actimar.fr'
__date__ = '2011-03-01'
__doc__ = 'Load / save fortran namelist string / file.'
# ==================================================================================================
# FIXME:
# - [Check if still applicable] Fix badly handled comment when comment characters are in a quoted (string) value
# TODO:
# - Recheck namelist format(s?) and allow specifying differents characters for namelist start/end,
# comments start and array indexing.
# - Allow N-dimensionnal arrays (1d currently).
# - Allow store of arrays into python lists rather than dicts.
# - Store namelist and variables in python lists (keep order)
# - Eventually store comments ?
# ==================================================================================================
[docs]class Namelist(dict):
'''Handles the fortran namelist format as below:
.. code-block:: none
! header comment
&namelist1 b=.true. i=0,f=0.1, s="ab" , ss="abcd" / ! inline comment
! standalone comment
# another "comment"
&namelist2
integer=1500, float=1.5e3 ! inline comment
str1="A : B"
str2="/path/to/file.txt"
array(0)=0
array(1)=1
/
Empty lines, spaces and comments (from ":", "!" or "#" characters to the end of line) are allowed.
Namelists start tag is the "&" character and end tag is "/", both on their own line or not.
Variables are delimited with space(s) or comma.
Namelists (sections) are stored and made accessible in a dictionnary fashion as this class
inherit from dict.
- Keys are the namelists names, values are the variables of the corresponding namelist.
- Namelist variables are also stored in dicts.
- If the variable is an array like variable, values are also stored in a dict.
Variables types are automatically handled, available types are:
- boolean: stored as bool python variable
- integer: as int
- real/scientific: as float
- array: as dict
.. note:
- When loading namelists, previously loaded namelists are overriden, not cleared (use the parent class clear method if needed).
- Only 1-dimensionnal array like variables are allowed
.. note::
- **Variables cannot be inserted directly into the Namelist**, you must access/setup the namelist level before (see examples)
that's because there is no global variable in a namelist file !
:Examples:
>>> n = Namelist()
>>> # The following is not correct and would results in a ValueError:
>>> n['myvar'] = 0
... ValueError: Cannot set a global variable in namelist, value must be a dict
>>> # That's the good way to do things:
>>> n['mynamelist'] = {}
>>> n['mynamelist']['myvar'] = 0
>>> n = Namelist()
>>> n['namelist1'] = dict(integer=1, real=1.0, string='hello', array=dict(a=0,b=1))
>>> print n.save_string()
... &namelist1
... real = 1.0
... integer = 1
... array(a) = 0
... array(b) = 1
... string = "hello"
... /
>>> n = Namelist.from_file('mynamelist.txt')
'''
_maxreadsize = 2 * (2**20) # n * Mio
def __init__(self):
dict.__init__(self)
def __str__(self):
return '\n\n'.join('%s:\n%s'%(namelist, '\n'.join((' %s = %s (%s)'%(k,v,v.__class__.__name__) for k,v in variables.iteritems()))) for namelist, variables in self.iteritems())
def __setitem__(self, key, value):
if not isinstance(value, dict):
raise ValueError('Cannot set a global variable in namelist, value must be a dict')
dict.__setitem__(self, key, value)
[docs] @classmethod
def from_file(cls, filepath, *a, **k):
'''Factory method populating the created namelist with a file.'''
o = cls(*a, **k)
o.load_file(filepath)
return o
[docs] @classmethod
def from_string(cls, string, *a, **k):
'''Factory method populating the created namelist with a string.'''
o = cls(*a, **k)
o.load_string(string)
return o
[docs] def load_string(self, string):
'''Load namelists from a string.'''
#print '[start of raw namelist]\n%s\n[end of raw namelist]'%(s)
# Clean comments / spaces / empty lines
s = self.remove_comments(string)
#print '[start of filtered namelist]\n%s\n[end of filtered namelist]'%(s)
# Patterns
namelist = re.compile(r'''\s*&(?P<namelist>[a-zA-Z][a-zA-Z0-9_]*)\s+(?P<statements>(?:(?:"|').*?(?:"|')|[^/])*)/''', re.MULTILINE|re.DOTALL|re.VERBOSE)
variable = re.compile(r'\s*(?P<variable>[a-zA-Z][a-zA-Z0-9_]*)(?:\((?P<index>\d+)\))?\s*=\s*(?P<value>[^\s,]+)(?:\s+|,)', re.MULTILINE|re.DOTALL|re.VERBOSE)
boolean = re.compile(r'\.?(?P<boolean>true|false|t|f)\.?', re.I)
integer = re.compile(r'(?P<integer>[-+]?\d+)')
real = re.compile(r'(?P<real>[-+]?(\d+\.\d*|\.\d+)([eE][-+]?\d+)?)')
string = re.compile(r'''(?:"|')(?P<string>.*?)(?:"|')''')
# Values converters. Order is important !
casts = ((string,str), (boolean,lambda v: v.lower().strip().startswith('t') and True or False), (real,float), (integer,int))
# Loop on namelists
for nm in namelist.finditer(s):
ngd = nm.groupdict()
#print (' namelist: %s '%(ngd['namelist'])).center(80, '=')
#print 'start:', vm.start(), 'end:', vm.end()
#print 'groups:', vm.groups(), 'groupdict:', vgd
self[ngd['namelist']] = {}
# Loop on variables
for vm in variable.finditer(ngd['statements']):
vgd = vm.groupdict()
#print (' variable: %s '%(vgd['variable'])).center(80, '-')
#print 'start:', vm.start(), 'end:', vm.end()
#print 'groups:', vm.groups(), 'groupdict:', vgd
index = vgd.get('index', None)
# Initialize array (dict) if needed
if index is not None and vgd['variable'] not in self[ngd['namelist']]:
self[ngd['namelist']][vgd['variable']] = {}
# Find and convert value
for p,c in casts:
m = p.search(vgd['value'])
if m:
if index is not None:
self[ngd['namelist']][vgd['variable']][index] = c(m.groups()[0])
else:
self[ngd['namelist']][vgd['variable']] = c(m.groups()[0])
break
[docs] def save_string(self):
'''Return the (fortran) formated namelists'''
s = StringIO.StringIO()
for namelist,variables in self.iteritems():
s.write('&%s\n'%namelist)
for vn,vv in variables.iteritems():
if isinstance(vv, dict):
for i,vi in vv.iteritems():
if isinstance(vi, (str,unicode)):
s.write(' %s(%s) = "%s"\n'%(vn,i,vi))
elif isinstance(vi, bool):
s.write(' %s(%s) = .%s.\n'%(vn,i,str(vi).lower()))
else:
s.write(' %s(%s) = %s\n'%(vn,i,vi))
else:
if isinstance(vv, (str,unicode)):
s.write(' %s = "%s"\n'%(vn,vv))
elif isinstance(vv, bool):
s.write(' %s = .%s.\n'%(vn,str(vv).lower()))
else:
s.write(' %s = %s\n'%(vn,vv))
s.write('/\n\n')
r = s.getvalue()
s.close()
return r
[docs] def load_file(self, filepath):
'''Load namelists from a text file'''
self._filepath = filepath
fh = file(self._filepath, 'rU')
fc = fh.read(self._maxreadsize)
fh.close()
self.load_string(fc)
[docs] def save_file(self, filename, append=False):
'''Save the (fortran) formatted namelists to a file'''
fh = file(filename, append and 'a' or 'w')
fh.write(self.save_string())
fh.close()
# ==================================================================================================
if __name__ == '__main__':
'''Test this module'''
namelist = '''\
! header comment
&namelist1 b=.true. i=0,f=0.1, s="ab" , ss="abcd" / ! inline comment
# standalone &n a="comment" /
&namelist2
integer=1500, float=1.5e3 ! inline comment
str1 = "A : B"
str2="/path/to/file.txt"
array(0)=0
array(1) = 1 /
&namfine
head_fine = './IN/head.quib3'/
'''
namelist = '''\
! header comment
&namelist1 b=.true. i=0,f=0.1, s="ab" , ss="abcd" / ! inline comment
&namelist2
integer=1500, float=1.5e3 ! inline comment
str1 = "A:B"
str2='./path/to/file.txt'
array(0)=0
array(1) = 1 /
'''
if len(sys.argv) == 2 and sys.argv[1] in ('-t', '-test', '--test'):
print ' namelist in input '.center(80, '=')
print namelist
print
nf = Namelist.from_string(namelist)
elif len(sys.argv) == 2:
nf = Namelist.from_file(sys.argv[1])
else:
print 'usage: %(prog)s (namelistfile|--test)'%dict(prog=os.path.split(sys.argv[0])[1])
sys.exit(1)
print ' namelist as a descriptive string (__str__ method) '.center(80, '=')
print nf
print
print ' namelist as formated string (save_string method) '.center(80, '=')
print nf.save_string()
print
