My tools of the trade for python programming.
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#!/usr/bin/python
# $Id: text_input.py,v 1.6 2011-09-16 21:21:23 wirawan Exp $
#
# wpylib.iofmt.text_input module
# Quick-n-dirty text input utilities
#
# Wirawan Purwanto
# Created: 20090601
#
# Routines put here are commonly used in my own scripts.
# They are not necessarily suitable for general-purpose uses; evaluate
# your needs and see if they can them as well.
#
# 20090601: Created as pyqmc.utils.text_input .
# 20100927: Moved to wpylib.iofmt.text_input .
#
# TODO
# - book-keep the line number. Also note superfile must have its own line
# number keeping.
#
"""
Simple text-based input reader.
This module is part of wpylib project.
"""
import re
import numpy
from wpylib.sugar import zip_gen
from wpylib.file.file_utils import open_input_file
from wpylib.py import make_unbound_instance_method
import wpylib.py.im_weakref
def make_match_proc(match):
"""Make matching procedure: simple string becomes regexp,
regexp remains regexp, and other callable object is passed as is."""
if isinstance(match, basestring):
Regexp = re.compile(match)
match_proc = lambda x: Regexp.search(x)
elif hasattr(getattr(match, "search", None), "__call__"):
Regexp = match
match_proc = lambda x: Regexp.search(x)
else:
match_proc = match
return match_proc
class text_input(object):
'''Text input reader with support for UNIX-style comment marker (#) and
standard field separation (tabs and whitespaces).
Used for quick and dirty data reading (iterating only once in forward
direction without the need of rewinding or skipping).
This object can be treated like an input file, e.g. used as an iterator,
etc.
To support more fancy options (e.g., rewinding), use "superize=1" when
creating the instance.
Other valid constructor flags:
- expand_errorbar (default: False)
- comment_char (default: "#")
- skip_blank_lines (default: True)
'''
def __init__(self, fname, **opts):
if opts.get("superize", 0):
open_opts = { "superize" : opts["superize"] }
del opts["superize"]
else:
open_opts = {}
self.file = open_input_file(fname, **open_opts)
# Do NOT touch the "next_" field below unless you know what you're doing:
self.set_next_proc(self.next_line)
# field_filtering_proc field can be used to filter unwanted fields, or do
# some additional transformations before final feed to the main iteration.
self.field_filtering_proc = lambda flds : flds
# Default fancy options:
self.skip_blank_lines = True
if len(opts) > 0:
self.set_options(**opts)
self.lineno = 0
def __del__(self):
if getattr(self, "file", None):
self.file.close()
def close(self):
if getattr(self, "file", None):
self.file.close()
del self.file
def __iter__(self):
return self
"""
def next(self):
while True:
L = self.file.next()
F = self.field_filtering_proc(L.split("#")[0].split())
if len(F) > 0:
return F
"""
def next_rec(self):
'''Yields the next record, which is already separated into fields.'''
comment_char = getattr(self, "comment_char", "#")
while True:
self.lineno += 1
L = self.file.next()
F = self.field_filtering_proc(L.split(comment_char)[0].split())
if len(F) > 0 or not self.skip_blank_lines:
return F
def next_line(self):
'''Yields the next line, which is already separated into fields.'''
comment_char = getattr(self, "comment_char", "#")
while True:
self.lineno += 1
L = self.file.next()
F = self.field_filtering_proc(L.split(comment_char)[0].rstrip())
if len(F) > 0 or not self.skip_blank_lines:
return F
def set_next_proc(self, proc):
self.next_ = make_unbound_instance_method(proc)
def next(self):
return self.next_(self)
def seek_text(self, regex=None, match=None):
'''Seeks the file until a particular piece text is encountered.
We ignore all comments.
The `regex' argument can be either a regex string or a standard python
regular expression object.'''
if regex:
if isinstance(regex, basestring):
Regexp = re.compile(regex)
else:
Regexp = regex
match_proc = lambda x: Regexp.search(x)
else:
match_proc = match
while True:
L = self.next_line()
if match_proc(L):
return L
def read_floats(self, *cols, **kwd):
"""Quickly reads a set of floats from a text file.
Returns a numpy array of the values in double precision.
Example usage:
>>> arr = text_input("/tmp/file.txt").read_floats(0, 2, 3)
to read columns 1, 3, and 4 of the text file /tmp/file.txt, while disregarding
comments.
"""
# float_fields extracts the desired columns and converts them to floats
float_fields = lambda vals : [ float(vals[col]) for col in cols ]
if "maxcount" in kwd:
rslt = [ float_fields(vals.split()) for (c,vals) in zip(xrange(kwd['maxcount']),self) ]
else:
rslt = [ float_fields(vals.split()) for vals in self ]
# finally convert them to a numpy ndarray:
return numpy.array(rslt)
def read_items(self, *col_desc, **kwd):
"""Quickly reads a set of items from records of whitespace-separated fields
in a text file.
Returns a structured numpy array of the values read.
Example usage:
>>> arr = text_input("/tmp/file.txt").read_items(0, (2, int), (3, "S10", "Atom"))
reads columns 1 (as floats, by default), 3 (as integers), and 4 (as strings of
max length of 10, which field is named "Atom") from the text file /tmp/file.txt,
while disregarding comments.
If the tuple contains the third field, it is used as the name of the field;
otherwise the fields are named f0, f1, f2, ....
Preliminary ability to read in complex data has been added!
Complex data (floating-point only) must be specified as a tuple of two columns
containing the real and imaginary data, like this:
((2, 3), complex, 'ampl')
or
((7, 9), complex) # fine to interleave column with something else
Additional keyword options:
* deftype: default datatype
* maxcount: maximum number of records to be read
* end_line_match: a regular expression or test subroutine accepting a
single argument (i.e. the text line) marking the end boundary of the list
to be read (i.e. one line past the list contents)
* last_line_match: a regular expression or test subroutine accepting a
single argument (i.e. the text line) marking the last element of the list
to be read
"""
deftype = kwd.get("deftype", float)
class register_item_t:
flds = []
cols = []
complex_types = (complex, numpy.complexfloating)
def add(self, col, fldname, type):
dtype = numpy.dtype(type)
t = dtype.type
dsamp = t() # create a sample
# Special handling for complex:
# -- unfortunately this detection fails because even real
# numbers have its 'imag' attribute:
#dattrs = dir(dsamp)
#if "imag" in dattrs and "real" in dattrs:
if isinstance(dsamp, numpy.complexfloating):
dtype_elem = dsamp.real.dtype
t_elem = dtype_elem.type
conv_func = lambda v, c: t(t_elem(v[c[0]]) + 1j*t_elem(v[c[1]]))
self.cols.append((conv_func, col))
self.flds.append((fldname, dtype))
else:
# other datatypes: much easier
# Simply get the string, and use numpy to convert to the datatype
# on-the-fly
conv_func = lambda v, c: t(v[c])
self.cols.append((conv_func, col))
self.flds.append((fldname, dtype))
reg = register_item_t()
for (i,c) in zip(xrange(len(col_desc)), col_desc):
if type(c) == int:
reg.add(c, 'f' + str(i), deftype)
elif len(c) == 1:
reg.add(c[0], 'f' + str(i), deftype)
elif len(c) == 2:
reg.add(c[0], 'f' + str(i), c[1])
elif len(c) == 3:
reg.add(c[0], c[2], c[1])
else:
raise ValueError, \
"Invalid column specification: %s" % (c,)
cols = reg.cols
flds = reg.flds
get_fields = lambda vals : tuple([ filt(vals,col) for (filt,col) in cols ])
if "maxcount" in kwd:
src_iter = zip_gen(xrange(kwd['maxcount']),self)
else:
src_iter = enumerate(self)
# FIXME below: zip() evaluates the function before the loop, thus may
# eat a lot of memory.
if 'end_line_match' in kwd:
rslt = []
match = make_match_proc(kwd['end_line_match'])
for (c,vals) in src_iter:
if match(vals):
break
rslt.append(get_fields(vals.split()))
elif 'last_line_match' in kwd:
rslt = []
match = make_match_proc(kwd['end_line_match'])
for (c,vals) in src_iter:
rslt.append(get_fields(vals.split()))
if match(vals):
break
elif "maxcount" in kwd:
#print "hello"
rslt = [ get_fields(vals.split()) for (c,vals) in zip(xrange(kwd['maxcount']),self) ]
else:
rslt = [ get_fields(vals.split()) for vals in self ]
#print rslt
# finally convert them to a numpy ndarray:
return numpy.array(rslt, dtype=flds)
# Sets fancy options
def set_options(self, **opts):
for (o,v) in opts.iteritems():
if o == "expand_errorbar":
self.expand_errorbar(v)
elif o == "skip_blank_lines":
self.skip_blank_lines = v
elif o == "comment_char":
self.comment_char = v
else:
raise ValueError, "Invalid option: %s" % (o,)
return self
# Option for errorbar expansion:
def expand_errorbar(self, v=True):
'''Enables or disables errorbar expansion.'''
from wpylib.py.im_weakref import im_ref
if v:
self.opt_expand_errorbar = True
self.field_filtering_proc = im_ref(self.expand_errorbar_hook)
else:
self.opt_expand_errorbar = False
self.field_filtering_proc = lambda flds : flds
return self
def expand_errorbar_hook(self, F):
# A hook for field_filtering_proc for expanding errorbars:
from pyqmc.stats.errorbar import expand
return expand(F, flatten=True)
# Various sundry tools
def head(filename, maxlines):
"""Emulates UNIX head(1) command by reading at most `maxlines`
text lines.
It is intended for plain text files only!
It also supports compressed files through text_input() facility.
"""
# head is easy to implement. But how about tail?
F = text_input(filename, skip_blank_lines=False, comment_char='\0')
out = []
try:
for x in xrange(maxlines):
out.append(F.next())
except StopIteration:
pass
return out
def tail(filename, maxlines):
"""Emulates UNIX tail(1) command by reading at most `maxlines`
text lines at the end of a text file.
It is intended for plain text files only!
It also supports compressed files through text_input() facility.
Warning: this algorithm is far less optimal than head() since it
has to read the whole file.
It's okay for moderately small files.
"""
F = text_input(filename, skip_blank_lines=False, comment_char='\0')
out = []
lines2read = max(2*maxlines, 100)
try:
while True:
for x in xrange(lines2read):
out.append(F.next())
out = out[-maxlines:]
except StopIteration:
pass
return out[-maxlines:]