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# yanny.py
#
# Python library for reading & writing yanny files.
#
# B. A. Weaver, NYU, 2008-10-20
#
# $Id: yanny.py 128984 2011-12-22 19:52:34Z weaver $
#
"""Python library for reading & writing yanny files.
yanny is an object-oriented interface to FTCL/yanny data files following
these specifications_.
The format of the returned object is similar to that returned by
``read_yanny()`` in the efftickle perl package (in the yannytools product).
Currently multidimensional arrays are only supported for type ``char``, but a
close reading of the specifications indicates that multidimensional arrays
were only ever intended to be supported for type ``char``.
.. _specifications: http://www.sdss3.org/dr8/software/par.php
"""
__author__ = 'Benjamin Weaver <benjamin.weaver@nyu.edu>'
__version__ = '$Revision: 128984 $'.split(': ')[1].split()[0]
__all__ = [ 'yanny', 'read_yanny', 'write_yanny', 'write_yanny_append' ]
__docformat__ = "restructuredtext en"
#
# Modules
#
import re
import os
import os.path
import datetime
import numpy
#
# Classes
#
class yanny(dict):
"""An object interface to a yanny file.
Most users will use the convenience functions defined in this package, but
this object provides a somewhat more powerful way of reading &
writing the data in a yanny file.
Attributes
----------
np : bool
If True, data in a yanny file will be converted into a NumPy record
array.
debug : bool
If True, some simple debugging statements will be turned on.
_filename : str
The name of a yanny parameter file.
_contents : str
The complete contents of a yanny parameter file.
_struct_type_caches : dict
A dictionary of dictionaries, one dictionary for every structure
definition in a yanny parameter file. Contains the types of
each column
_struct_isarray_caches : dict
A dictionary of dictionaries, one dictionary for every structure
definition in a yanny parameter file. Contains a boolean value
for every column.
_enum_cache : dict
Initially ``None``, this attribute is initialized the first time
the ``isenum()`` method is called. The keyword is the name of the
enum type, the value is a list of the possible values of that type.
Parameters
----------
filename : str
The name of a yanny file.
np : bool, optional
If True, data in a yanny file will be converted into a NumPy record
array. Default is False
debug : bool, optional
If True, some simple debugging statements will be turned on. Default
is False.
"""
@staticmethod
def get_token(string):
"""Removes the first 'word' from string.
If the 'word' is enclosed in double quotes, it returns the
contents of the double quotes. If the 'word' is enclosed in
braces, it returns the contents of the braces, but does not
attempt to split the array. If the 'word' is the last word of the
string, remainder is set equal to the empty string. This is
basically a wrapper on some convenient regular expressions.
"""
if string[0] == '"':
(word, remainder) = re.search(r'^"([^"]*)"\s*(.*)',
string).groups()
elif string[0] == '{':
(word, remainder) = re.search(r'^\{\s*([^}]*)\s*\}\s*(.*)',
string).groups()
else:
try:
(word, remainder) = re.split(r'\s+',string,1)
except ValueError:
#print "Problem with string: %s" % string
(word, remainder) = (string, '')
if remainder is None:
remainder = ''
return (word,remainder)
@staticmethod
def protect(x):
"""Used to appropriately quote string that might contain whitespace.
This method is mostly for internal use by the yanny object.
"""
s = str(x)
if len(s) == 0 or re.search(r'\s+',s) is not None:
return '"' + s + '"'
else:
return s
@staticmethod
def dtype_to_struct(dt,structname='mystruct',enums=dict()):
"""Convert a NumPy dtype object describing a record array to
a typedef struct statement.
The second argument is the name of the structure.
If any of the columns are enum types, enums must
be a dictionary with the keys the column names, and the values
are a tuple containing the name of the enum type as the first item
and a tuple or list of possible values as the second item.
"""
dtmap = {'i2':'short','i4':'int','i8':'long','f4':'float',
'f8':'double'}
lines = list()
for e in enums:
lines.append('typedef enum {')
for n in enums[e][1]:
lines.append(" %s,"%n)
lines[-1] = lines[-1].strip(',')
lines.append('} %s;' % enums[e][0].upper())
lines.append('')
lines.append('typedef struct {')
for c in dt.names:
if dt[c].kind == 'V':
t = dt[c].subdtype[0].str[1:]
l = dt[c].subdtype[1][0]
s = dt[c].subdtype[0].itemsize
else:
t = dt[c].str[1:]
l = 0
s = dt[c].itemsize
line = ' '
if t[0] == 'S':
if c in enums:
line += enums[c][0].upper()
else:
line += 'char'
else:
line += dtmap[t]
line += ' %s' % c
if l > 0:
line += "[%d]" % l
if t[0] == 'S' and c not in enums:
line += "[%d]" % s
line += ';'
lines.append(line)
lines.append('} %s;' % structname.upper())
return "\n".join(lines)
def __init__(self,filename=None,np=False,debug=False):
"""Create a yanny object using a yanny file.
Create a yanny object using a yanny file, filename. If the file exists,
it is read, & the dict structure of the object will be basically the
same as that returned by ``read_yanny()`` in the efftickle package.
If the file does not exist, or if no filename is given, a blank
structure is returned. Other methods allow for subsequent writing
to the file.
"""
#
# The symbol hash is inherited from the old read_yanny
#
self['symbols'] = dict()
#
# Create special attributes that contain the internal status of the object
# this should prevent overlap with keywords in the data files
#
self._filename = ''
self._contents = ''
#
# Since the re is expensive, cache the structure types keyed by the field.
# Create a dictionary for each structure found.
#
self._struct_type_caches = dict()
self._struct_isarray_caches = dict()
self._enum_cache = None
#
# Optionally convert numeric data into NumPy arrays
#
self.np = np
#
# Turn on simple debugging
#
self.debug = debug
#
# If the file exists, read it
#
if filename is not None:
if os.access(filename,os.R_OK):
self._filename = filename
f = open(filename,'r')
self._contents = f.read()
f.close()
self._parse()
return
def __str__(self):
"""Implement the ``str()`` function for yanny objects.
Simply prints the current contents of the yanny file.
"""
return self._contents
def __eq__(self,other):
"""Test two yanny objects for equality.
Two yanny objects are assumed to be equal if their contents are equal.
"""
if isinstance(other,yanny):
return str(other) == str(self)
return False
def type(self,structure,variable):
"""Returns the type of a variable defined in a structure.
Returns ``None`` if the structure or the variable is undefined.
"""
if structure not in self:
return None
if variable not in self.columns(structure):
return None
defl = filter(lambda x: x.find(structure.lower()) > 0,
self['symbols']['struct'])
defu = filter(lambda x: x.find(structure.upper()) > 0,
self['symbols']['struct'])
if len(defl) != 1 and len(defu) != 1:
return None
elif len(defl) == 1:
definition = defl
else:
definition = defu
#
# Added code to cache values to speed up parsing large files.
# 2009.05.11 / Demitri Muna, NYU
# Find (or create) the cache for this structure.
#
try:
cache = self._struct_type_caches[structure]
except KeyError:
self._struct_type_caches[structure] = dict()
cache = self._struct_type_caches[structure] # cache for one struct type
#
# Lookup (or create) the value for this variable
#
try:
var_type = cache[variable]
except KeyError:
if self.debug:
print variable
typere = re.compile(r'(\S+)\s+%s([[<].*[]>]|);' % variable)
(typ,array) = typere.search(definition[0]).groups()
var_type = typ + array.replace('<','[').replace('>',']')
cache[variable] = var_type
return var_type
def basetype(self,structure,variable):
"""Returns the bare type of a variable, stripping off any array
information."""
typ = self.type(structure,variable)
if self.debug:
print variable, typ
try:
return typ[0:typ.index('[')]
except ValueError:
return typ
def isarray(self,structure,variable):
"""Returns True if the variable is an array type.
For character types, this means a two-dimensional array,
*e.g.*: ``char[5][20]``.
"""
try:
cache = self._struct_isarray_caches[structure]
except KeyError:
self._struct_isarray_caches[structure] = dict()
cache = self._struct_isarray_caches[structure]
try:
result = cache[variable]
except KeyError:
typ = self.type(structure,variable)
character_array = re.compile(r'char[[<]\d*[]>][[<]\d*[]>]')
if ((character_array.search(typ) is not None) or
(typ.find('char') < 0 and (typ.find('[') >= 0
or typ.find('<') >= 0))):
cache[variable] = True
else:
cache[variable] = False
result = cache[variable]
return result
def isenum(self,structure,variable):
"""Returns true if a variable is an enum type.
"""
if self._enum_cache is None:
self._enum_cache = dict()
if 'enum' in self['symbols']:
for e in self['symbols']['enum']:
m = re.search(r'typedef\s+enum\s*\{([^}]+)\}\s*(\w+)\s*;',e).groups()
self._enum_cache[m[1]] = re.split(r',\s*',m[0].strip())
else:
return False
return self.basetype(structure,variable) in self._enum_cache
def array_length(self,structure,variable):
"""Returns the length of an array type or 1 if the variable is not
an array.
For character types, this is the length of a two-dimensional
array, *e.g.*, ``char[5][20]`` has length 5.
"""
if self.isarray(structure,variable):
typ = self.type(structure,variable)
return int(typ[typ.index('[')+1:typ.index(']')])
else:
return 1
def char_length(self,structure,variable):
"""Returns the length of a character field.
*e.g.* ``char[5][20]`` is an array of 5 strings of length 20.
Returns ``None`` if the variable is not a character type. If the
length is not specified, *i.e.* ``char[]``, it returns the length of
the largest string.
"""
typ = self.type(structure,variable)
if typ.find('char') < 0:
return None
try:
return int(typ[typ.rfind('[')+1:typ.rfind(']')])
except ValueError:
if self.isarray(structure,variable):
return max([max(map(len,r)) for r in self[structure][variable]])
else:
return max(map(len,self[structure][variable]))
def dtype(self,structure):
"""Returns a NumPy dtype object suitable for describing a table as
a record array.
Treats enums as string, which is what the IDL reader does.
"""
dt = list()
dtmap = {'short':'i2', 'int':'i4', 'long':'i8', 'float':'f',
'double':'d' }
for c in self.columns(structure):
typ = self.basetype(structure,c)
if typ == 'char':
d = "S%d" % self.char_length(structure,c)
elif self.isenum(structure,c):
d = "S%d" % max(map(len,self._enum_cache[typ]))
else:
d = dtmap[typ]
if self.isarray(structure,c):
dt.append((c,d,(self.array_length(structure,c),)))
else:
dt.append((c,d))
dt = numpy.dtype(dt)
return dt
def convert(self,structure,variable,value):
"""Converts value into the appropriate (Python) type.
* ``short`` & ``int`` are converted to Python ``int``.
* ``long`` is converted to Python ``long``.
* ``float`` & ``double`` are converted to Python ``float``.
* Other types are not altered.
There may be further conversions into NumPy types, but this is the
first stage.
"""
typ = self.basetype(structure,variable)
if (typ == 'short' or typ == 'int'):
if self.isarray(structure,variable):
return map(int, value)
else:
return int(value)
if typ == 'long':
if self.isarray(structure,variable):
return map(long, value)
else:
return long(value)
if (typ == 'float' or typ == 'double'):
if self.isarray(structure,variable):
return map(float, value)
else:
return float(value)
return value
def tables(self):
"""Returns a list of all the defined structures.
This is just the list of keys of the object with the 'internal'
keys removed.
"""
foo = self['symbols'].keys()
foo.remove('struct')
foo.remove('enum')
return foo
def columns(self,table):
"""Returns an ordered list of column names associated with a particular
table.
The order is the same order as they are defined in the yanny file.
"""
foo = list()
if table in self['symbols']:
return self['symbols'][table]
return foo
def size(self,table):
"""Returns the number of rows in a table.
"""
foo = self.columns(table)
return len(self[table][foo[0]])
def pairs(self):
"""Returns a list of keys to keyword/value pairs.
Equivalent to doing ``self.keys()``, but with all the data tables &
other control structures stripped out.
"""
p = list()
foo = self.tables()
for k in self.keys():
if k == 'symbols' or k in foo:
continue
p.append(k)
return p
def row(self,table,index):
"""Returns a list containing a single row from a specified table in column order
If index is out of range, it returns an empty list.
If the yanny object instance is set up for NumPy record arrays, then
a single row can be obtained with::
>>> row0 = par['TABLE'][0]
"""
datarow = list()
if table in self and index >= 0 and index < self.size(table):
for c in self.columns(table):
datarow.append(self[table][c][index])
return datarow
def set_filename(self,newfile):
"""Updates the filename associated with the yanny object.
Use this if the object was created with no filename.
"""
self._filename = newfile
return
def list_of_dicts(self, table):
"""Construct a list of dictionaries.
Takes a table from the yanny object and constructs a list object
containing one row per entry. Each item in the list is a dictionary
keyed by the struct value names.
If the yanny object instance is set up for NumPy record arrays, then
the same functionality can be obtained with::
>>> foo = par['TABLE'][0]['column']
"""
return_list = list()
d = dict()
struct_fields = self.columns(table) # I'm assuming these are in order...
for i in range(self.size(table)):
one_row = self.row(table, i) # one row as a list
j = 0
for key in struct_fields:
d[key] = one_row[j]
j = j + 1
return_list.append(dict(d)) # append a new dict (copy of d)
return return_list
def new_dict_from_pairs(self):
"""Returns a new dictionary of keyword/value pairs.
The new dictionary (*i.e.*, not a yanny object) contains the keys
that ``self.pairs()`` returns. There are two reasons this is convenient:
* the key 'symbols' that is part of the yanny object will not be present
* a simple yanny file can be read with no further processing
Example
-------
Read a yanny file and return only the pairs::
>>> new_dict = yanny.yanny(file).new_dict_from_pairs()
added: Demitri Muna, NYU 2009-04-28
"""
new_dictionary = dict()
for key in self.pairs():
new_dictionary[key] = self[key]
return new_dictionary
def write(self,*args):
"""Write a yanny object to a file.
This assumes that the filename used to create the object was not that
of a pre-existing file. If a file of the same name is detected,
this method will *not* attempt to overwrite it, but will print a warning.
This also assumes that the special 'symbols' key has been properly
created. This will not necessarily make the file very human-readable,
especially if the data lines are long. If the name of a new file is
given, it will write to the new file (assuming it doesn't exist).
If the writing is successful, the data in the object will be updated.
"""
if len(args) > 0:
newfile = args[0]
else:
if len(self._filename) > 0:
newfile = self._filename
else:
print "ERROR: No filename specified!"
return
basefile = os.path.basename(newfile)
timestamp = datetime.datetime.utcnow().strftime('%Y-%m-%d %H:%M:%S UTC')
contents = "#\n# %s\n#\n# Created by yanny.py\n#\n# %s\n#\n" % (basefile,timestamp)
#
# Print any key/value pairs
#
for key in self.pairs():
contents += "%s %s\n" % (key,self[key])
#
# Print out enum definitions
#
if len(self['symbols']['enum']) > 0:
contents += "\n" + "\n\n".join(self['symbols']['enum']) + "\n"
#
# Print out structure definitions
#
if len(self['symbols']['struct']) > 0:
contents += "\n" + "\n\n".join(self['symbols']['struct']) + "\n"
contents += "\n"
#
# Print out the data tables
#
for sym in self.tables():
columns = self.columns(sym)
for k in range(self.size(sym)):
line = list()
line.append(sym)
for col in columns:
if self.isarray(sym,col):
datum = '{' + ' '.join(map(self.protect,self[sym][col][k])) + '}'
else:
datum = self.protect(self[sym][col][k])
line.append(datum)
contents += "%s\n" % ' '.join(line)
#
# Actually write the data to file
#
if os.access(newfile,os.F_OK):
print "%s exists, aborting write!" % newfile
print "For reference, here's what would have been written:"
print contents
else:
f = open(newfile,'w')
print >> f, contents
f.close()
self._contents = contents
self._filename = newfile
self._parse()
return
def append(self,datatable):
"""Appends data to an existing FTCL/yanny file.
Tries as much as possible to preserve the ordering & format of the
original file. The datatable should adhere to the format of the
yanny object, but it is not necessary to reproduce the 'symbols'
dictionary. It will not try to append data to a file that does not
exist. If the append is successful, the data in the object will be updated.
"""
if len(self._filename) == 0:
print "No filename is set for this object. Use the set_filename method to set the filename!"
return
if type(datatable) != dict:
print "Data to append is not of the correct type. Use a dict!"
return
timestamp = datetime.datetime.utcnow().strftime('%Y-%m-%d %H:%M:%S UTC')
contents = ''
#
# Print any key/value pairs
#
for key in datatable.keys():
if key.upper() in self.tables() or key == 'symbols':
continue
contents += "%s %s\n" % (key, datatable[key])
#
# Print out the data tables
#
for sym in self.tables():
if sym.lower() in datatable:
datasym = sym.lower()
else:
datasym = sym
if datasym in datatable:
columns = self.columns(sym)
for k in range(len(datatable[datasym][columns[0]])):
line = list()
line.append(sym)
for col in columns:
if self.isarray(sym,col):
datum = '{' + ' '.join(map(self.protect,datatable[datasym][col][k])) + '}'
else:
datum = self.protect(datatable[datasym][col][k])
line.append(datum)
contents += "%s\n" % ' '.join(line)
#
# Actually write the data to file
#
if len(contents) > 0:
contents = ("# Appended by yanny.py at %s.\n" % timestamp) + contents
if os.access(self._filename,os.W_OK):
f = open(self._filename,'a')
print >> f, contents
f.close()
self._contents += contents
self._parse()
else:
print "%s does not exist, aborting append!" % self._filename
print "For reference, here's what would have been written:"
print contents
else:
print "Nothing to be appended!"
return
def _parse(self):
"""Converts text into tables that users can use.
This method is for use internally by the yanny object. It is not
meant to be called by users.
Parsing proceeds in this order:
#. Lines that end with a backslash character ``\`` are reattached
to following lines.
#. Structure & enum definitions are identified, saved into the
'symbols' dictionary & stripped from the contents.
#. Structure definitions are interpreted.
#. At this point, the remaining lines of the original file can only
contain these things:
* 'blank' lines, including lines that only contain comments
* keyword/value pairs
* structure rows
#. The remaining lines are scanned sequentially.
#. 'Blank' lines are identified & ignored.
#. Whitespace & comments are stripped from non-blank lines.
#. Empty double braces ``{{}}`` are converted into empty double
quotes ``""``.
#. If the first word on a line matches the name of a structure,
the line is broken up into tokens & each token or set of tokens
(for arrays) is converted to the appropriate Python type.
#. If the first word on a line does not match the name of a
structure, it must be a keyword, so this line is interpreted
as a keyword/value pair. No further processing is done to
the value.
#. At the conclusion of parsing, if ``self.np`` is ``True``, the
structures are converted into NumPy record arrays.
"""
#
# there are five things we might find
# 1. 'blank' lines including comments
# 2. keyword/value pairs (which may have trailing comments)
# 3. enumeration definitions
# 4. structure definitions
# 5. data
#
lines = self._contents
#
# Reattach lines ending with \
#
lines = re.sub(r'\\\s*\n',' ',lines)
#
# Find structure & enumeration definitions & strip them out
#
self['symbols']['struct'] = re.findall(r'typedef\s+struct\s*\{[^}]+\}\s*\w+\s*;',lines)
self['symbols']['enum'] = re.findall(r'typedef\s+enum\s*\{[^}]+\}\s*\w+\s*;',lines)
lines = re.sub(r'typedef\s+struct\s*\{[^}]+\}\s*\w+\s*;','',lines)
lines = re.sub(r'typedef\s+enum\s*\{[^}]+\}\s*\w+\s*;','',lines)
#
# Interpret the structure definitions
#
typedefre = re.compile(r'typedef\s+struct\s*\{([^}]+)\}\s*(\w*)\s*;')
for typedef in self['symbols']['struct']:
typedefm = typedefre.search(typedef)
(definition,name) = typedefm.groups()
self[name.upper()] = dict()
self['symbols'][name.upper()] = list()
definitions = re.findall(r'\S+\s+\S+;',definition)
for d in definitions:
d = d.replace(';','')
(datatype,column) = re.split(r'\s+',d)
column = re.sub(r'[[<].*[]>]$','',column)
self['symbols'][name.upper()].append(column)
self[name.upper()][column] = list()
comments = re.compile(r'^\s*#') # Remove lines containing only comments
blanks = re.compile(r'^\s*$') # Remove lines containing only whitespace
trailing_comments = re.compile(r'\s*\#.*$') # Remove trailing comments
double_braces = re.compile(r'\{\s*\{\s*\}\s*\}') # Double empty braces get replaced with empty quotes
if len(lines) > 0:
for line in lines.split('\n'):
if self.debug:
print line
if len(line) == 0:
continue
if comments.search(line) is not None:
continue
if blanks.search(line) is not None:
continue
#
# Remove leading & trailing blanks & comments
#
line = line.strip()
line = trailing_comments.sub('',line)
line = double_braces.sub('""',line)
#
# Now if the first word on the line does not match a
# structure definition it is a keyword/value pair
#
(key, value) = self.get_token(line)
uckey = key.upper()
if uckey in self['symbols'].keys():
#
# Structure data
#
for column in self['symbols'][uckey]:
if len(value) > 0 and blanks.search(value) is None:
(data,value) = self.get_token(value)
if self.isarray(uckey,column):
#
# An array value
# if it's character data, it won't be
# delimited by {} unless it is a multidimensional
# string array. It may or may not be delimited
# by double quotes
#
# Note, we're assuming here that the only
# multidimensional arrays are string arrays
#
arraydata = list()
while len(data) > 0:
(token, data) = self.get_token(data)
arraydata.append(token)
self[uckey][column].append(
self.convert(uckey,column,arraydata))
else:
#
# A single value
#
self[uckey][column].append(
self.convert(uckey,column,data))
else:
break
else:
#
# Keyword/value pair
#
self[key] = value
#
# If self.np is True, convert tables into NumPy record arrays
#
if self.np:
for t in self.tables():
record = numpy.zeros((self.size(t),),dtype=self.dtype(t))
for c in self.columns(t):
record[c] = self[t][c]
self[t] = record
return
#
# Functions
#
def read_yanny(filename):
"""Reads the contents of an FTCL/yanny file & returns the data in a hash.
This is just a convenience wrapper on a yanny object, for use when a
user is not interested in changing the contents of a yanny object.
"""
par = yanny(filename)
return par.copy()
def write_yanny(filename,datatable):
"""Writes the contents of a hash to an FTCL/yanny file.
Ideally used in conjunction with read_yanny() to create an initial
dictionary of the appropriate format.
"""
par = yanny(filename)
for key in datatable:
par[key] = datatable[key]
par.write()
return
def write_yanny_append(filename,datatable):
"""Appends the contents of a hash to an existing FTCL/yanny file.
Ideally used in conjunction with read_yanny() to create an initial
dictionary of the appropriate format.
"""
par = yanny(filename)
par.append(datatable)
return
def main():
"""Used to test the yanny class.
"""
par = yanny(os.path.join(os.getenv('YANNYTOOLS_DIR'),'data','test.par'),
np=True,debug=True)
print par.pairs()
for p in par.pairs():
print "%s => %s" % (p, par[p])
print par.keys()
print par['symbols'].keys()
print par['symbols']['struct']
print par['symbols']['enum']
print par.tables()
for t in par.tables():
print par.dtype(t)
print "%s: %d entries" % (t,par.size(t))
print par.columns(t)
for c in par.columns(t):
print "%s: type %s" % (c,par.type(t,c))
print par[t][c]
if par.isenum('MYSTRUCT','new_flag'):
print par._enum_cache
par.write() # This should fail, since test.par already exists.
datatable = {'status_update': {'state':['SUCCESS', 'SUCCESS'],
'timestamp':['2008-06-22 01:27:33','2008-06-22 01:27:36']},
'new_keyword':'new_value'}
par.set_filename(os.path.join(os.getenv('YANNYTOOLS_DIR'),'data','test_append.par'))
par.append(datatable) # This should also fail, because test_append.par does not exist
return
#
# Testing purposes
#
if __name__ == '__main__':
main()
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