Source code for GPy.util.netpbmfile

#!/usr/bin/env python
# -*- coding: utf-8 -*-
# netpbmfile.py

# Copyright (c) 2011-2013, Christoph Gohlke
# Copyright (c) 2011-2013, The Regents of the University of California
# Produced at the Laboratory for Fluorescence Dynamics.
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"""Read and write image data from respectively to Netpbm files.

This implementation follows the Netpbm format specifications at
http://netpbm.sourceforge.net/doc/. No gamma correction is performed.

The following image formats are supported: PBM (bi-level), PGM (grayscale),
PPM (color), PAM (arbitrary), XV thumbnail (RGB332, read-only).

:Author:
  `Christoph Gohlke <http://www.lfd.uci.edu/~gohlke/>`_

:Organization:
  Laboratory for Fluorescence Dynamics, University of California, Irvine

:Version: 2013.01.18

Requirements
------------
* `CPython 2.7, 3.2 or 3.3 <http://www.python.org>`_
* `Numpy 1.7 <http://www.numpy.org>`_
* `Matplotlib 1.2 <http://www.matplotlib.org>`_  (optional for plotting)

Examples
--------
>>> im1 = numpy.array([[0, 1],[65534, 65535]], dtype=numpy.uint16)
>>> imsave('_tmp.pgm', im1)
>>> im2 = imread('_tmp.pgm')
>>> assert numpy.all(im1 == im2)

"""

from __future__ import division, print_function

import sys
import re
import math
from copy import deepcopy

import numpy

__version__ = '2013.01.18'
__docformat__ = 'restructuredtext en'
__all__ = ['imread', 'imsave', 'NetpbmFile']


[docs]def imread(filename, *args, **kwargs): """Return image data from Netpbm file as numpy array. `args` and `kwargs` are arguments to NetpbmFile.asarray(). Examples -------- >>> image = imread('_tmp.pgm') """ try: netpbm = NetpbmFile(filename) image = netpbm.asarray() finally: netpbm.close() return image
[docs]def imsave(filename, data, maxval=None, pam=False): """Write image data to Netpbm file. Examples -------- >>> image = numpy.array([[0, 1],[65534, 65535]], dtype=numpy.uint16) >>> imsave('_tmp.pgm', image) """ try: netpbm = NetpbmFile(data, maxval=maxval) netpbm.write(filename, pam=pam) finally: netpbm.close()
[docs]class NetpbmFile(object): """Read and write Netpbm PAM, PBM, PGM, PPM, files.""" _types = {b'P1': b'BLACKANDWHITE', b'P2': b'GRAYSCALE', b'P3': b'RGB', b'P4': b'BLACKANDWHITE', b'P5': b'GRAYSCALE', b'P6': b'RGB', b'P7 332': b'RGB', b'P7': b'RGB_ALPHA'} def __init__(self, arg=None, **kwargs): """Initialize instance from filename, open file, or numpy array.""" for attr in ('header', 'magicnum', 'width', 'height', 'maxval', 'depth', 'tupltypes', '_filename', '_fh', '_data'): setattr(self, attr, None) if arg is None: self._fromdata([], **kwargs) elif isinstance(arg, basestring): self._fh = open(arg, 'rb') self._filename = arg self._fromfile(self._fh, **kwargs) elif hasattr(arg, 'seek'): self._fromfile(arg, **kwargs) self._fh = arg else: self._fromdata(arg, **kwargs)
[docs] def asarray(self, copy=True, cache=False, **kwargs): """Return image data from file as numpy array.""" data = self._data if data is None: data = self._read_data(self._fh, **kwargs) if cache: self._data = data else: return data return deepcopy(data) if copy else data
[docs] def write(self, arg, **kwargs): """Write instance to file.""" if hasattr(arg, 'seek'): self._tofile(arg, **kwargs) else: with open(arg, 'wb') as fid: self._tofile(fid, **kwargs)
[docs] def close(self): """Close open file. Future asarray calls might fail.""" if self._filename and self._fh: self._fh.close() self._fh = None
def __del__(self): self.close() def _fromfile(self, fh): """Initialize instance from open file.""" fh.seek(0) data = fh.read(4096) if (len(data) < 7) or not (b'0' < data[1:2] < b'8'): raise ValueError("Not a Netpbm file:\n%s" % data[:32]) try: self._read_pam_header(data) except Exception: try: self._read_pnm_header(data) except Exception: raise ValueError("Not a Netpbm file:\n%s" % data[:32]) def _read_pam_header(self, data): """Read PAM header and initialize instance.""" regroups = re.search( b"(^P7[\n\r]+(?:(?:[\n\r]+)|(?:#.*)|" b"(HEIGHT\s+\d+)|(WIDTH\s+\d+)|(DEPTH\s+\d+)|(MAXVAL\s+\d+)|" b"(?:TUPLTYPE\s+\w+))*ENDHDR\n)", data).groups() self.header = regroups[0] self.magicnum = b'P7' for group in regroups[1:]: key, value = group.split() setattr(self, unicode(key).lower(), int(value)) matches = re.findall(b"(TUPLTYPE\s+\w+)", self.header) self.tupltypes = [s.split(None, 1)[1] for s in matches] def _read_pnm_header(self, data): """Read PNM header and initialize instance.""" bpm = data[1:2] in b"14" regroups = re.search(b"".join(( b"(^(P[123456]|P7 332)\s+(?:#.*[\r\n])*", b"\s*(\d+)\s+(?:#.*[\r\n])*", b"\s*(\d+)\s+(?:#.*[\r\n])*" * (not bpm), b"\s*(\d+)\s(?:\s*#.*[\r\n]\s)*)")), data).groups() + (1, ) * bpm self.header = regroups[0] self.magicnum = regroups[1] self.width = int(regroups[2]) self.height = int(regroups[3]) self.maxval = int(regroups[4]) self.depth = 3 if self.magicnum in b"P3P6P7 332" else 1 self.tupltypes = [self._types[self.magicnum]] def _read_data(self, fh, byteorder='>'): """Return image data from open file as numpy array.""" fh.seek(len(self.header)) data = fh.read() dtype = 'u1' if self.maxval < 256 else byteorder + 'u2' depth = 1 if self.magicnum == b"P7 332" else self.depth shape = [-1, self.height, self.width, depth] size = numpy.prod(shape[1:]) if self.magicnum in b"P1P2P3": data = numpy.array(data.split(None, size)[:size], dtype) data = data.reshape(shape) elif self.maxval == 1: shape[2] = int(math.ceil(self.width / 8)) data = numpy.frombuffer(data, dtype).reshape(shape) data = numpy.unpackbits(data, axis=-2)[:, :, :self.width, :] else: data = numpy.frombuffer(data, dtype) data = data[:size * (data.size // size)].reshape(shape) if data.shape[0] < 2: data = data.reshape(data.shape[1:]) if data.shape[-1] < 2: data = data.reshape(data.shape[:-1]) if self.magicnum == b"P7 332": rgb332 = numpy.array(list(numpy.ndindex(8, 8, 4)), numpy.uint8) rgb332 *= [36, 36, 85] data = numpy.take(rgb332, data, axis=0) return data def _fromdata(self, data, maxval=None): """Initialize instance from numpy array.""" data = numpy.array(data, ndmin=2, copy=True) if data.dtype.kind not in "uib": raise ValueError("not an integer type: %s" % data.dtype) if data.dtype.kind == 'i' and numpy.min(data) < 0: raise ValueError("data out of range: %i" % numpy.min(data)) if maxval is None: maxval = numpy.max(data) maxval = 255 if maxval < 256 else 65535 if maxval < 0 or maxval > 65535: raise ValueError("data out of range: %i" % maxval) data = data.astype('u1' if maxval < 256 else '>u2') self._data = data if data.ndim > 2 and data.shape[-1] in (3, 4): self.depth = data.shape[-1] self.width = data.shape[-2] self.height = data.shape[-3] self.magicnum = b'P7' if self.depth == 4 else b'P6' else: self.depth = 1 self.width = data.shape[-1] self.height = data.shape[-2] self.magicnum = b'P5' if maxval > 1 else b'P4' self.maxval = maxval self.tupltypes = [self._types[self.magicnum]] self.header = self._header() def _tofile(self, fh, pam=False): """Write Netbm file.""" fh.seek(0) fh.write(self._header(pam)) data = self.asarray(copy=False) if self.maxval == 1: data = numpy.packbits(data, axis=-1) data.tofile(fh) def _header(self, pam=False): """Return file header as byte string.""" if pam or self.magicnum == b'P7': header = "\n".join(( "P7", "HEIGHT %i" % self.height, "WIDTH %i" % self.width, "DEPTH %i" % self.depth, "MAXVAL %i" % self.maxval, "\n".join("TUPLTYPE %s" % unicode(i) for i in self.tupltypes), "ENDHDR\n")) elif self.maxval == 1: header = "P4 %i %i\n" % (self.width, self.height) elif self.depth == 1: header = "P5 %i %i %i\n" % (self.width, self.height, self.maxval) else: header = "P6 %i %i %i\n" % (self.width, self.height, self.maxval) if sys.version_info[0] > 2: header = bytes(header, 'ascii') return header def __str__(self): """Return information about instance.""" return unicode(self.header)
if sys.version_info[0] > 2: basestring = str unicode = lambda x: str(x, 'ascii') if __name__ == "__main__": # Show images specified on command line or all images in current directory from glob import glob from matplotlib import pyplot files = sys.argv[1:] if len(sys.argv) > 1 else glob('*.p*m') for fname in files: try: pam = NetpbmFile(fname) img = pam.asarray(copy=False) if False: pam.write('_tmp.pgm.out', pam=True) img2 = imread('_tmp.pgm.out') assert numpy.all(img == img2) imsave('_tmp.pgm.out', img) img2 = imread('_tmp.pgm.out') assert numpy.all(img == img2) pam.close() except ValueError as e: print(fname, e) continue _shape = img.shape if img.ndim > 3 or (img.ndim > 2 and img.shape[-1] not in (3, 4)): img = img[0] cmap = 'gray' if pam.maxval > 1 else 'binary' pyplot.imshow(img, cmap, interpolation='nearest') pyplot.title("%s %s %s %s" % (fname, unicode(pam.magicnum), _shape, img.dtype)) pyplot.show()