diff --git a/GPy/plotting/matplot_dep/netpbmfile.py b/GPy/plotting/matplot_dep/netpbmfile.py
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+++ b/GPy/plotting/matplot_dep/netpbmfile.py
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+#!/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 `_
+
+:Organization:
+ Laboratory for Fluorescence Dynamics, University of California, Irvine
+
+:Version: 2013.01.18
+
+Requirements
+------------
+* `CPython 2.7, 3.2 or 3.3 `_
+* `Numpy 1.7 `_
+* `Matplotlib 1.2 `_ (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()