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#!/usr/bin/python2
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# -*- coding: utf-8 -*-
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# 3rd attempt
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# 15th Feb 2012, 09:38AM
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# http://eayd.in
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# http://github.com/eaydin/cr2fits
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### This script is redistributable in anyway.
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### But it includes netpbmfile.py which is NOT written by M. Emre Aydin.
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### It has its own copyright and it has been stated in the source code.
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### BUT, there's nothing to worry about usage, laws etc.
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### Enjoy.
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sourceweb = "http://github.com/eaydin/cr2fits"
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version = "1.0.3"
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try :
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from copy import deepcopy
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import numpy, pyfits, subprocess, sys, re, datetime, math
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except :
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print("ERROR : Missing some libraries!")
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print("Check if you have the following :\n\tnumpy\n\tpyfits\n\tdcraw")
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print("For details : %s" % sourceweb)
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raise SystemExit
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### --- NETPBMFILE SOURCE CODE --- ###
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# Copyright (c) 2011, Christoph Gohlke
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# Copyright (c) 2011, The Regents of the University of California
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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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__all__ = ['NetpbmFile']
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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', '_fileid', '_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._fileid = open(arg, 'rb')
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self._filename = arg
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self._fromfile(self._fileid, **kwargs)
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elif hasattr(arg, 'seek'):
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self._fromfile(arg, **kwargs)
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self._fileid = 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._fileid, **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._fileid:
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self._fileid.close()
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self._fileid = None
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def __del__(self):
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self.close()
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def _fromfile(self, fileid):
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"""Initialize instance from open file."""
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fileid.seek(0)
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data = fileid.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, fileid, byteorder='>'):
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"""Return image data from open file as numpy array."""
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fileid.seek(len(self.header))
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data = fileid.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, fileid, pam=False):
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"""Write Netbm file."""
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fileid.seek(0)
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fileid.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(fileid)
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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(("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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### --- END OF NETPBMFILE SOURCE CODE --- ###
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### CR2FITS SOURCE CODE ###
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try :
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cr2FileName = sys.argv[1]
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colorInput = int(sys.argv[2]) # 0=R 1=G 2=B
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except :
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print("ERROR : You probably don't know how to use it?")
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print("./cr2fits.py <cr2filename> <color-index>")
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print("The <color-index> can take 3 values:0,1,2 for R,G,B respectively.")
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print("Example :\n\t$ ./cr2fits.py myimage.cr2 1")
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print("The above example will create 2 outputs.")
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print("\tmyimage.ppm : The PPM, which you can delete.")
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print("\tmyimage-G.fits : The FITS image in the Green channel, which is the purpose!")
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print("For details : http://github.com/eaydin/cr2fits")
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print("Version : %s" % version)
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raise SystemExit
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colors = {0:"Red",1:"Green",2:"Blue"}
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colorState = any([True for i in colors.keys() if i == colorInput])
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if colorState == False :
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print("ERROR : Color value can be set as 0:Red, 1:Green, 2:Blue.")
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raise SystemExit
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print("Reading file %s...") % cr2FileName
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try :
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#Converting the CR2 to PPM
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p = subprocess.Popen(["dcraw","-6","-j","-W",cr2FileName]).communicate()[0]
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#Getting the EXIF of CR2 with dcraw
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p = subprocess.Popen(["dcraw","-i","-v",cr2FileName],stdout=subprocess.PIPE)
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cr2header = p.communicate()[0]
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#Catching the Timestamp
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m = re.search('(?<=Timestamp:).*',cr2header)
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date1=m.group(0).split()
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months = { 'Jan' : 1, 'Feb' : 2, 'Mar' : 3, 'Apr' : 4, 'May' : 5, 'Jun' : 6, 'Jul' : 7, 'Aug' : 8, 'Sep' : 9, 'Oct' : 10, 'Nov' : 11, 'Dec' : 12 }
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date = datetime.datetime(int(date1[4]),months[date1[1]],int(date1[2]),int(date1[3].split(':')[0]),int(date1[3].split(':')[1]),int(date1[3].split(':')[2]))
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date ='{0:%Y-%m-%d %H:%M:%S}'.format(date)
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#Catching the Shutter Speed
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m = re.search('(?<=Shutter:).*(?=sec)',cr2header)
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shutter = m.group(0).strip()
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#Catching the Aperture
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m = re.search('(?<=Aperture: f/).*',cr2header)
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aperture = m.group(0).strip()
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#Catching the ISO Speed
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m = re.search('(?<=ISO speed:).*',cr2header)
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iso = m.group(0).strip()
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#Catching the Focal length
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m = re.search('(?<=Focal length: ).*(?=mm)',cr2header)
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focal = m.group(0).strip()
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#Catching the Original Filename of the cr2
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m = re.search('(?<=Filename:).*',cr2header)
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original_file = m.group(0).strip()
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#Catching the Camera Type
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m = re.search('(?<=Camera:).*',cr2header)
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camera = m.group(0).strip()
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except :
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print("ERROR : Something went wrong with dcraw. Do you even have dcraw?")
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raise SystemExit
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print("Reading the PPM output...")
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try :
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#Reading the PPM
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ppm_name = cr2FileName.split('.')[0] + '.ppm'
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im_ppm = NetpbmFile(ppm_name).asarray()
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except :
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print("ERROR : Something went wrong while reading the PPM file.")
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raise SystemExit
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print("Extracting %s color channels... (may take a while)" % colors[colorInput])
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try :
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#Extracting the Green Channel Only
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im_green = numpy.zeros((im_ppm.shape[0],im_ppm.shape[1]),dtype=numpy.uint16)
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for row in xrange(0,im_ppm.shape[0]) :
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for col in xrange(0,im_ppm.shape[1]) :
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im_green[row,col] = im_ppm[row,col][colorInput]
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except :
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print("ERROR : Something went wrong while extracting color channels.")
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raise SystemExit
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print("Creating the FITS file...")
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try :
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#Creating the FITS File
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hdu = pyfits.PrimaryHDU(im_green)
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hdu.header.set('OBSTIME',date)
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hdu.header.set('EXPTIME',shutter)
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hdu.header.set('APERTUR',aperture)
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hdu.header.set('ISO',iso)
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hdu.header.set('FOCAL',focal)
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hdu.header.set('ORIGIN',original_file)
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hdu.header.set('FILTER',colors[colorInput])
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hdu.header.set('CAMERA',camera)
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hdu.header.add_comment('FITS File Created with cr2fits.py available at %s'%(sourceweb))
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hdu.header.add_comment('cr2fits.py version %s'%(version))
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hdu.header.add_comment('EXPTIME is in seconds.')
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hdu.header.add_comment('APERTUR is the ratio as in f/APERTUR')
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hdu.header.add_comment('FOCAL is in mm')
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except :
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print("ERROR : Something went wrong while creating the FITS file.")
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raise SystemExit
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print("Writing the FITS file...")
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try :
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hdu.writeto(cr2FileName.split('.')[0]+"-"+colors[colorInput][0]+'.fits')
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except :
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print("ERROR : Something went wrong while writing the FITS file. Maybe it already exists?")
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raise SystemExit
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print("Conversion successful!")
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