#! /usr/bin/env python
# -*- coding: utf-8 -*-
# netpbmfile.py
# Copyright (c) 2011-2018, Christoph Gohlke
# Copyright (c) 2011-2018, 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
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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).
Only one image per file is supported.
:Author:
`Christoph Gohlke <https://www.lfd.uci.edu/~gohlke/>`_
:Organization:
Laboratory for Fluorescence Dynamics, University of California, Irvine
:Version: 2018.02.07
Requirements
------------
* `CPython 2.7 or 3.6 <https://www.python.org>`_
* `Numpy 1.13 <http://www.numpy.org>`_
* `Matplotlib 2.1 <http://www.matplotlib.org>`_ (optional for plotting)
Revisions
---------
2018.02.07
Style fixes.
2016.02.24
Use 'fromdata' classmethod to initialize from data.
Support 'with' statement.
Scale RGB images to maxval for display.
Make keyword arguments explicit.
Support numpy 1.10.
Examples
--------
>>> im1 = numpy.array([[0, 1], [65534, 65535]], dtype='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
import warnings
from copy import deepcopy
import numpy
__version__ = '2018.02.07'
__docformat__ = 'restructuredtext en'
__all__ = 'imread', 'imsave', 'NetpbmFile'
def imread(filename, copy=True, cache=False, byteorder='>'):
"""Return image data from Netpbm file as numpy array.
`args` and `kwargs` are arguments to NetpbmFile.asarray().
Examples
--------
>>> image = imread('_tmp.pgm')
"""
with NetpbmFile(filename) as netpbm:
image = netpbm.asarray(copy=copy, cache=cache, byteorder=byteorder)
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='uint16')
>>> imsave('_tmp.pgm', image)
"""
NetpbmFile.fromdata(data, maxval=maxval).write(filename, pam=pam)
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, filename):
"""Initialize instance from filename or open file."""
for attr in ('header', 'magicnum', 'width', 'height', 'maxval',
'depth', 'tupltypes', '_filename', '_fh', '_data'):
setattr(self, attr, None)
if filename is None:
return
if hasattr(filename, 'seek'):
self._fh = filename
else:
self._fh = open(filename, 'rb')
self._filename = filename
self._fh.seek(0)
data = self._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])
@classmethod
def fromdata(cls, 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 = cls(None)
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()
return self
def asarray(self, copy=True, cache=False, byteorder='>'):
"""Return image data from file as numpy array."""
data = self._data
if data is None:
data = self._read_data(self._fh, byteorder=byteorder)
if cache:
self._data = data
else:
return data
return deepcopy(data) if copy else data
def write(self, filename, pam=False):
"""Write instance to file."""
if hasattr(filename, 'seek'):
self._tofile(filename, pam=pam)
else:
with open(filename, 'wb') as fh:
self._tofile(fh, pam=pam)
def close(self):
"""Close open file. Future asarray calls might fail."""
if self._filename and self._fh:
self._fh.close()
self._fh = None
def __enter__(self):
return self
def __exit__(self, exc_type, exc_value, traceback):
self.close()
def __str__(self):
"""Return information about instance."""
return unicode(self.header)
def _read_pam_header(self, data):
"""Read PAM header and initialize instance."""
regroups = re.search(
br'(^P7[\n\r]+(?:(?:[\n\r]+)|(?:#.*)|'
br'(HEIGHT\s+\d+)|(WIDTH\s+\d+)|(DEPTH\s+\d+)|(MAXVAL\s+\d+)|'
br'(?: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(br'(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((
br'(^(P[123456]|P7 332)\s+(?:#.*[\r\n])*',
br'\s*(\d+)\s+(?:#.*[\r\n])*',
br'\s*(\d+)\s+(?:#.*[\r\n])*' * (not bpm),
br'\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:], dtype='int64')
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:
size *= numpy.dtype(dtype).itemsize
data = numpy.frombuffer(data[:size], dtype).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 *= numpy.array([36, 36, 85], numpy.uint8)
data = numpy.take(rgb332, data, axis=0)
return data
def _tofile(self, fh, pam=False):
"""Write Netpbm 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 main(argv=None):
"""Command line usage main function.
Show images specified on command line or all images in current directory.
"""
from glob import glob
from matplotlib import pyplot
if argv is None:
argv = sys.argv
if len(argv) > 1 and 'doctest' in argv:
import doctest
doctest.testmod()
return
files = argv[1:] if len(argv) > 1 else glob('*.p*m')
for fname in files:
try:
with NetpbmFile(fname) as pam:
img = pam.asarray(copy=False)
if False: # enable for testing
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)
except ValueError as e:
# raise # enable for debugging
print(fname, e)
continue
cmap = 'gray' if pam.maxval > 1 else 'binary'
shape = img.shape
if img.ndim > 3 or (img.ndim > 2 and img.shape[-1] not in (3, 4)):
warnings.warn('displaying first image only')
img = img[0]
if img.shape[-1] in (3, 4) and pam.maxval != 255:
warnings.warn('converting RGB image for display')
img = img / float(pam.maxval)
img *= 255
numpy.rint(img, out=img)
numpy.clip(img, 0, 255, out=img)
img = img.astype('uint8')
pyplot.imshow(img, cmap, interpolation='nearest')
pyplot.title('"%s %s %s %s' % (fname, unicode(pam.magicnum),
shape, img.dtype))
pyplot.show()
if sys.version_info[0] > 2:
basestring = str
def unicode(x):
return str(x, 'ascii')
if __name__ == '__main__':
sys.exit(main())