From 838e6822d8dcfa62011f0ff11bbae2a83d0c8bcc Mon Sep 17 00:00:00 2001 From: Ricardo Date: Tue, 28 Jan 2014 13:34:20 +0000 Subject: [PATCH] Relocated --- GPy/plotting/matplot_dep/netpbmfile.py | 331 +++++++++++++++++++++++++ 1 file changed, 331 insertions(+) create mode 100644 GPy/plotting/matplot_dep/netpbmfile.py diff --git a/GPy/plotting/matplot_dep/netpbmfile.py b/GPy/plotting/matplot_dep/netpbmfile.py new file mode 100644 index 00000000..030bd574 --- /dev/null +++ b/GPy/plotting/matplot_dep/netpbmfile.py @@ -0,0 +1,331 @@ +#!/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()