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331 lines
12 KiB
Python
331 lines
12 KiB
Python
#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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# netpbmfile.py
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# Copyright (c) 2011-2013, Christoph Gohlke
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# Copyright (c) 2011-2013, The Regents of the University of California
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# Produced at the Laboratory for Fluorescence Dynamics.
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# All rights reserved.
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#
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# Redistribution and use in source and binary forms, with or without
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# modification, are permitted provided that the following conditions are met:
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#
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# * Redistributions of source code must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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# * Redistributions in binary form must reproduce the above copyright
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# notice, this list of conditions and the following disclaimer in the
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# documentation and/or other materials provided with the distribution.
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# * Neither the name of the copyright holders nor the names of any
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# contributors may be used to endorse or promote products derived
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# from this software without specific prior written permission.
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#
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
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# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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# POSSIBILITY OF SUCH DAMAGE.
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"""Read and write image data from respectively to Netpbm files.
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This implementation follows the Netpbm format specifications at
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http://netpbm.sourceforge.net/doc/. No gamma correction is performed.
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The following image formats are supported: PBM (bi-level), PGM (grayscale),
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PPM (color), PAM (arbitrary), XV thumbnail (RGB332, read-only).
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:Author:
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`Christoph Gohlke <http://www.lfd.uci.edu/~gohlke/>`_
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:Organization:
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Laboratory for Fluorescence Dynamics, University of California, Irvine
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:Version: 2013.01.18
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Requirements
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------------
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* `CPython 2.7, 3.2 or 3.3 <http://www.python.org>`_
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* `Numpy 1.7 <http://www.numpy.org>`_
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* `Matplotlib 1.2 <http://www.matplotlib.org>`_ (optional for plotting)
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Examples
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--------
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>>> im1 = numpy.array([[0, 1],[65534, 65535]], dtype=numpy.uint16)
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>>> imsave('_tmp.pgm', im1)
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>>> im2 = imread('_tmp.pgm')
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>>> assert numpy.all(im1 == im2)
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"""
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from __future__ import division, print_function
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import sys
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import re
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import math
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from copy import deepcopy
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import numpy
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__version__ = '2013.01.18'
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__docformat__ = 'restructuredtext en'
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__all__ = ['imread', 'imsave', 'NetpbmFile']
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def imread(filename, *args, **kwargs):
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"""Return image data from Netpbm file as numpy array.
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`args` and `kwargs` are arguments to NetpbmFile.asarray().
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Examples
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--------
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>>> image = imread('_tmp.pgm')
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"""
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try:
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netpbm = NetpbmFile(filename)
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image = netpbm.asarray()
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finally:
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netpbm.close()
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return image
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def imsave(filename, data, maxval=None, pam=False):
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"""Write image data to Netpbm file.
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Examples
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--------
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>>> image = numpy.array([[0, 1],[65534, 65535]], dtype=numpy.uint16)
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>>> imsave('_tmp.pgm', image)
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"""
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try:
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netpbm = NetpbmFile(data, maxval=maxval)
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netpbm.write(filename, pam=pam)
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finally:
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netpbm.close()
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class NetpbmFile(object):
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"""Read and write Netpbm PAM, PBM, PGM, PPM, files."""
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_types = {b'P1': b'BLACKANDWHITE', b'P2': b'GRAYSCALE', b'P3': b'RGB',
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b'P4': b'BLACKANDWHITE', b'P5': b'GRAYSCALE', b'P6': b'RGB',
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b'P7 332': b'RGB', b'P7': b'RGB_ALPHA'}
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def __init__(self, arg=None, **kwargs):
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"""Initialize instance from filename, open file, or numpy array."""
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for attr in ('header', 'magicnum', 'width', 'height', 'maxval',
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'depth', 'tupltypes', '_filename', '_fh', '_data'):
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setattr(self, attr, None)
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if arg is None:
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self._fromdata([], **kwargs)
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elif isinstance(arg, basestring):
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self._fh = open(arg, 'rb')
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self._filename = arg
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self._fromfile(self._fh, **kwargs)
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elif hasattr(arg, 'seek'):
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self._fromfile(arg, **kwargs)
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self._fh = arg
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else:
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self._fromdata(arg, **kwargs)
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def asarray(self, copy=True, cache=False, **kwargs):
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"""Return image data from file as numpy array."""
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data = self._data
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if data is None:
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data = self._read_data(self._fh, **kwargs)
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if cache:
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self._data = data
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else:
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return data
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return deepcopy(data) if copy else data
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def write(self, arg, **kwargs):
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"""Write instance to file."""
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if hasattr(arg, 'seek'):
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self._tofile(arg, **kwargs)
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else:
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with open(arg, 'wb') as fid:
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self._tofile(fid, **kwargs)
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def close(self):
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"""Close open file. Future asarray calls might fail."""
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if self._filename and self._fh:
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self._fh.close()
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self._fh = None
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def __del__(self):
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self.close()
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def _fromfile(self, fh):
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"""Initialize instance from open file."""
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fh.seek(0)
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data = fh.read(4096)
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if (len(data) < 7) or not (b'0' < data[1:2] < b'8'):
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raise ValueError("Not a Netpbm file:\n%s" % data[:32])
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try:
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self._read_pam_header(data)
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except Exception:
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try:
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self._read_pnm_header(data)
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except Exception:
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raise ValueError("Not a Netpbm file:\n%s" % data[:32])
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def _read_pam_header(self, data):
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"""Read PAM header and initialize instance."""
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regroups = re.search(
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b"(^P7[\n\r]+(?:(?:[\n\r]+)|(?:#.*)|"
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b"(HEIGHT\s+\d+)|(WIDTH\s+\d+)|(DEPTH\s+\d+)|(MAXVAL\s+\d+)|"
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b"(?:TUPLTYPE\s+\w+))*ENDHDR\n)", data).groups()
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self.header = regroups[0]
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self.magicnum = b'P7'
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for group in regroups[1:]:
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key, value = group.split()
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setattr(self, unicode(key).lower(), int(value))
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matches = re.findall(b"(TUPLTYPE\s+\w+)", self.header)
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self.tupltypes = [s.split(None, 1)[1] for s in matches]
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def _read_pnm_header(self, data):
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"""Read PNM header and initialize instance."""
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bpm = data[1:2] in b"14"
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regroups = re.search(b"".join((
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b"(^(P[123456]|P7 332)\s+(?:#.*[\r\n])*",
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b"\s*(\d+)\s+(?:#.*[\r\n])*",
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b"\s*(\d+)\s+(?:#.*[\r\n])*" * (not bpm),
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b"\s*(\d+)\s(?:\s*#.*[\r\n]\s)*)")), data).groups() + (1, ) * bpm
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self.header = regroups[0]
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self.magicnum = regroups[1]
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self.width = int(regroups[2])
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self.height = int(regroups[3])
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self.maxval = int(regroups[4])
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self.depth = 3 if self.magicnum in b"P3P6P7 332" else 1
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self.tupltypes = [self._types[self.magicnum]]
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def _read_data(self, fh, byteorder='>'):
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"""Return image data from open file as numpy array."""
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fh.seek(len(self.header))
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data = fh.read()
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dtype = 'u1' if self.maxval < 256 else byteorder + 'u2'
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depth = 1 if self.magicnum == b"P7 332" else self.depth
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shape = [-1, self.height, self.width, depth]
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size = numpy.prod(shape[1:])
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if self.magicnum in b"P1P2P3":
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data = numpy.array(data.split(None, size)[:size], dtype)
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data = data.reshape(shape)
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elif self.maxval == 1:
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shape[2] = int(math.ceil(self.width / 8))
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data = numpy.frombuffer(data, dtype).reshape(shape)
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data = numpy.unpackbits(data, axis=-2)[:, :, :self.width, :]
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else:
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data = numpy.frombuffer(data, dtype)
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data = data[:size * (data.size // size)].reshape(shape)
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if data.shape[0] < 2:
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data = data.reshape(data.shape[1:])
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if data.shape[-1] < 2:
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data = data.reshape(data.shape[:-1])
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if self.magicnum == b"P7 332":
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rgb332 = numpy.array(list(numpy.ndindex(8, 8, 4)), numpy.uint8)
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rgb332 *= [36, 36, 85]
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data = numpy.take(rgb332, data, axis=0)
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return data
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def _fromdata(self, data, maxval=None):
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"""Initialize instance from numpy array."""
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data = numpy.array(data, ndmin=2, copy=True)
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if data.dtype.kind not in "uib":
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raise ValueError("not an integer type: %s" % data.dtype)
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if data.dtype.kind == 'i' and numpy.min(data) < 0:
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raise ValueError("data out of range: %i" % numpy.min(data))
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if maxval is None:
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maxval = numpy.max(data)
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maxval = 255 if maxval < 256 else 65535
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if maxval < 0 or maxval > 65535:
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raise ValueError("data out of range: %i" % maxval)
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data = data.astype('u1' if maxval < 256 else '>u2')
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self._data = data
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if data.ndim > 2 and data.shape[-1] in (3, 4):
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self.depth = data.shape[-1]
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self.width = data.shape[-2]
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self.height = data.shape[-3]
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self.magicnum = b'P7' if self.depth == 4 else b'P6'
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else:
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self.depth = 1
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self.width = data.shape[-1]
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self.height = data.shape[-2]
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self.magicnum = b'P5' if maxval > 1 else b'P4'
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self.maxval = maxval
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self.tupltypes = [self._types[self.magicnum]]
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self.header = self._header()
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def _tofile(self, fh, pam=False):
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"""Write Netbm file."""
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fh.seek(0)
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fh.write(self._header(pam))
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data = self.asarray(copy=False)
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if self.maxval == 1:
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data = numpy.packbits(data, axis=-1)
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data.tofile(fh)
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def _header(self, pam=False):
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"""Return file header as byte string."""
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if pam or self.magicnum == b'P7':
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header = "\n".join((
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"P7",
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"HEIGHT %i" % self.height,
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"WIDTH %i" % self.width,
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"DEPTH %i" % self.depth,
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"MAXVAL %i" % self.maxval,
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"\n".join("TUPLTYPE %s" % unicode(i) for i in self.tupltypes),
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"ENDHDR\n"))
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elif self.maxval == 1:
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header = "P4 %i %i\n" % (self.width, self.height)
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elif self.depth == 1:
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header = "P5 %i %i %i\n" % (self.width, self.height, self.maxval)
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else:
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header = "P6 %i %i %i\n" % (self.width, self.height, self.maxval)
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if sys.version_info[0] > 2:
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header = bytes(header, 'ascii')
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return header
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def __str__(self):
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"""Return information about instance."""
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return unicode(self.header)
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if sys.version_info[0] > 2:
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basestring = str
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unicode = lambda x: str(x, 'ascii')
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if __name__ == "__main__":
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# Show images specified on command line or all images in current directory
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from glob import glob
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from matplotlib import pyplot
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files = sys.argv[1:] if len(sys.argv) > 1 else glob('*.p*m')
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for fname in files:
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try:
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pam = NetpbmFile(fname)
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img = pam.asarray(copy=False)
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if False:
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pam.write('_tmp.pgm.out', pam=True)
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img2 = imread('_tmp.pgm.out')
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assert numpy.all(img == img2)
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imsave('_tmp.pgm.out', img)
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img2 = imread('_tmp.pgm.out')
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assert numpy.all(img == img2)
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pam.close()
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except ValueError as e:
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print(fname, e)
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continue
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_shape = img.shape
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if img.ndim > 3 or (img.ndim > 2 and img.shape[-1] not in (3, 4)):
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img = img[0]
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cmap = 'gray' if pam.maxval > 1 else 'binary'
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pyplot.imshow(img, cmap, interpolation='nearest')
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pyplot.title("%s %s %s %s" % (fname, unicode(pam.magicnum),
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_shape, img.dtype))
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pyplot.show()
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