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# coding: utf-8
#
# Project: X-ray image reader
# https://github.com/silx-kit/fabio
#
#
# Copyright (C) European Synchrotron Radiation Facility, Grenoble, France
#
# Principal author: Jérôme Kieffer (Jerome.Kieffer@ESRF.eu)
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE
"""
Authors: Henning O. Sorensen & Erik Knudsen
Center for Fundamental Research: Metal Structures in Four Dimensions
Risoe National Laboratory
Frederiksborgvej 399
DK-4000 Roskilde
email:henning.sorensen@risoe.dk
mods for fabio by JPW
modification for HDF5 by Jérôme Kieffer
"""
# Get ready for python3:
from __future__ import with_statement, print_function, absolute_import
import os.path
import logging
logger = logging.getLogger(__name__)
from . import fabioutils
from .fabioutils import FilenameObject, BytesIO
from .fabioimage import FabioImage
# Make sure to load all formats
from . import fabioformats # noqa
MAGIC_NUMBERS = [
# "\42\5a" : 'bzipped'
# "\1f\8b" : 'gzipped'
(b"FORMAT :100", 'bruker100'),
(b"FORMAT : 86", 'bruker'),
(b"\x4d\x4d\x00\x2a", 'tif'),
# The marCCD and Pilatus formats are both standard tif with a header
# hopefully these byte patterns are unique for the formats
# If not the image will be read, but the is missing
(b"\x49\x49\x2a\x00\x08\x00", 'marccd/tif'),
(b"\x49\x49\x2a\x00\x82\x00", 'pilatus'),
(b"\x49\x49\x2a\x00", 'tif'),
# ADSC must come before edf
(b"{\nHEA", 'adsc'),
(b"{", 'edf'),
(b"\r{", 'edf'),
(b"\n{", 'edf'),
(b"ADEPT", 'GE'),
(b"OD", 'OXD'),
(b"IM", 'HiPiC'),
(b'\x2d\x04', 'mar345'),
(b'\xd2\x04', 'mar345'),
(b'\x04\x2d', 'mar345'), # some machines may need byteswapping
(b'\x04\xd2', 'mar345'),
# hint : MASK in 32 bit
(b'M\x00\x00\x00A\x00\x00\x00S\x00\x00\x00K\x00\x00\x00', 'fit2dmask'),
(b'\x00\x00\x00\x03', 'dm3'),
(b"No", "kcd"),
(b"<", "xsd"),
(b"\n\xb8\x03\x00", 'pixi'),
(b"\x89\x48\x44\x46\x0d\x0a\x1a\x0a", "eiger/hdf5"),
(b"R-AXIS", 'raxis'),
(b"\x93NUMPY", 'numpy'),
(b"\\$FFF_START", 'fit2d'),
# Raw JPEG
(b"\xFF\xD8\xFF\xDB", "jpeg"),
# JFIF format
(b"\xFF\xD8\xFF\xE0", "jpeg"),
# Exif format
(b"\xFF\xD8\xFF\xE1", "jpeg"),
# JPEG 2000 (from RFC 3745)
(b"\x00\x00\x00\x0C\x6A\x50\x20\x20\x0D\x0A\x87\x0A", "jpeg2k"),
]
def do_magic(byts, filename):
""" Try to interpret the bytes starting the file as a magic number """
for magic, format_type in MAGIC_NUMBERS:
if byts.startswith(magic):
if "/" in format_type:
if format_type == "eiger/hdf5":
if "::" in filename:
return "hdf5"
else:
return "eiger"
elif format_type == "marccd/tif":
if "mccd" in filename.split("."):
return "marccd"
else:
return "tif"
return format_type
raise Exception("Could not interpret magic string")
def openimage(filename, frame=None):
""" Try to open an image """
if isinstance(filename, fabioutils.PathTypes):
if not isinstance(filename, fabioutils.StringTypes):
filename = str(filename)
if isinstance(filename, FilenameObject):
try:
logger.debug("Attempting to open %s" % (filename.tostring()))
obj = _openimage(filename.tostring())
logger.debug("Attempting to read frame %s from %s with reader %s" % (frame, filename.tostring(), obj.classname))
obj = obj.read(filename.tostring(), frame)
except Exception as ex:
# multiframe file
# logger.debug( "DEBUG: multiframe file, start # %d"%(
# filename.num)
logger.debug("Exception %s, trying name %s" % (ex, filename.stem))
obj = _openimage(filename.stem)
logger.debug("Reading frame %s from %s" % (filename.num, filename.stem))
obj.read(filename.stem, frame=filename.num)
else:
logger.debug("Attempting to open %s" % (filename))
obj = _openimage(filename)
logger.debug("Attempting to read frame %s from %s with reader %s" % (frame, filename, obj.classname))
obj = obj.read(obj.filename, frame)
return obj
def openheader(filename):
""" return only the header"""
if isinstance(filename, fabioutils.PathTypes):
if not isinstance(filename, fabioutils.StringTypes):
filename = str(filename)
obj = _openimage(filename)
obj.readheader(obj.filename)
return obj
def _openimage(filename):
"""
determine which format for a filename
and return appropriate class which can be used for opening the image
:param filename: can be an url like:
hdf5:///example.h5?entry/instrument/detector/data/data#slice=[:,:,5]
"""
if hasattr(filename, "seek") and hasattr(filename, "read"):
# Looks to be a file containing filenames
if not isinstance(filename, BytesIO):
filename.seek(0)
actual_filename = BytesIO(filename.read())
else:
if os.path.exists(filename):
# Already a valid filename
actual_filename = filename
elif "::" in filename:
actual_filename = filename.split("::")[0]
else:
actual_filename = filename
try:
imo = FabioImage()
with imo._open(actual_filename) as f:
magic_bytes = f.read(18)
except IOError as error:
logger.debug("%s: File probably does not exist", error)
raise error
else:
imo = None
filetype = None
try:
filetype = do_magic(magic_bytes, filename)
except Exception:
logger.debug("Backtrace", exc_info=True)
try:
file_obj = FilenameObject(filename=filename)
if file_obj is None:
raise Exception("Unable to deconstruct filename")
if (file_obj.format is not None) and\
len(file_obj.format) != 1 and \
isinstance(file_obj.format, list):
# one of OXD/ADSC - should have got in previous
raise Exception("openimage failed on magic bytes & name guess")
filetype = file_obj.format
except Exception as error:
logger.debug("Backtrace", exc_info=True)
raise IOError("Fabio could not identify " + filename)
if filetype is None:
raise IOError("Fabio could not identify " + filename)
klass_name = "".join(filetype) + 'image'
try:
obj = fabioformats.factory(klass_name)
except (RuntimeError, Exception):
logger.debug("Backtrace", exc_info=True)
raise IOError("Filename %s can't be read as format %s" % (filename, klass_name))
obj.filename = filename
# skip the read for read header
return obj
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