netpbmfile.py

#!/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.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright
#   notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright
#   notice, this list of conditions and the following disclaimer in the
#   documentation and/or other materials provided with the distribution.
# * Neither the name of the copyright holders nor the names of any
#   contributors may be used to endorse or promote products derived
#   from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.

"""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']


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


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()


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)

    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

    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)

    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()