#!/usr/bin/python # $Id: text_input.py,v 1.1 2010-09-27 19:54:05 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.file.file_utils import open_input_file 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.''' 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) # 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) def __del__(self): if getattr(self, "file", None): self.file.close() 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.''' while True: L = self.file.next() F = self.field_filtering_proc(L.split("#")[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.''' while True: L = self.file.next() F = self.field_filtering_proc(L.split("#")[0].rstrip()) if len(F) > 0 or not self.skip_blank_lines: return F # Do NOT touch the "next" field below unless you know what you're doing: next = next_line 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, str): 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, .... Additional keyword options: * deftype: default datatype * maxcount: maximum number of records to be read TODO: Needs ability to read in complex data. """ deftype = kwd.get("deftype", float) # float_fields extracts the desired columns and converts them to floats flds = [] cols = [] for (i,c) in zip(xrange(len(col_desc)), col_desc): if type(c) == int: cols.append(c) flds.append(('f' + str(i), deftype)) elif len(c) == 1: cols.append(c[0]) flds.append(('f' + str(i), deftype)) elif len(c) == 2: cols.append(c[0]) flds.append(('f' + str(i), c[1])) elif len(c) == 3: cols.append(c[0]) flds.append((c[2], c[1])) #print cols #print flds get_fields = lambda vals : tuple([ vals[col] for col in cols ]) if "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) if o == "skip_blank_lines": self.skip_blank_lines = 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.''' if v: self.opt_expand_errorbar = True self.field_filtering_proc = 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)