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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
mods for APS GE by JVB
"""
import os.path
import logging
from . import fabioutils
from .fabioutils import FilenameObject, BytesIO
from .fabioimage import FabioImage
# Make sure to load all formats
from . import fabioformats # noqa
logger = logging.getLogger(__name__)
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'),
# d*TREK must come before edf
(b"{\nHEA", 'dtrek'),
# EDF_ types
(b"\r\n{\r\nEDF", 'edf'), # EDF3 (can be interpreted like EDF1 but refused by fit2d)
(b"\n{\r\nEDF", 'edf'), # EDF2 (can be interpreted like EDF1 but refused by fit2d)
(b"{\r\nEDF", 'edf'), # EDF1 (EDF >=V2.4 starting with EDF_, fit2d friendly, without starting newline)
(b"{\n", 'edf'), # EDF0 (EDF V1.xx "standard", without additional EDF_ structure information)
(b"\n{\n", 'edf'), # EDFU (EDF unknown source, V1.xx)
# conventional
(b"{", 'edf'),
(b"\r{", 'edf'),
(b"\n{", 'edf'),
# had to add a special case for GE here because they blanked out
# the default header for the GE's at APS with the firmware
# update as of 2018
(b"ADEPT", 'GE'),
(b"\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00", '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/lima/sparse/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"),
(b"ESPERANTO FORMAT", "esperanto"),
(b'###CBF: VERSION', "cbf")
]
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/lima/sparse/hdf5":
if "::" in filename:
return "hdf5"
else:
# check if the creator is LIMA
import h5py
with h5py.File(filename, "r") as h:
creator = h.attrs.get("creator")
if str(creator).startswith("LIMA"):
return "lima"
elif str(creator).startswith("pyFAI"):
return "sparse"
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):
"""Open an image.
It returns a FabioImage-class instance which can be used as a context
manager to close the file at the termination.
.. code-block:: python
with fabio.open("image.edf") as i:
print(i.nframes)
print(i.data)
:param Union[str,FilenameObject] filename: A filename or a filename
iterator.
:param Union[int,None] frame: A specific frame inside this file.
:rtype: FabioImage
"""
if isinstance(filename, fabioutils.PathTypes):
if not isinstance(filename, fabioutils.StringTypes):
filename = str(filename)
if isinstance(filename, FilenameObject):
try:
actual_filename = filename.tostring()
logger.debug("Attempting to open %s", actual_filename)
obj = _openimage(actual_filename)
logger.debug("Attempting to read frame %s from %s with reader %s", frame, actual_filename, obj.classname)
obj = obj.read(actual_filename, 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"):
# Data stream without filename
filename.seek(0)
data = filename.read()
actual_filename = BytesIO(data)
# Back to the location before the read
filename.seek(0)
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:
logger.debug("Backtrace", exc_info=True)
raise
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:
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
def open_series(filenames=None, first_filename=None,
single_frame=None, fixed_frames=None, fixed_frame_number=None):
"""
Create an object to iterate frames through a file series.
This function is a wrapper over :class:`~file_series.FileSeries` to facilitate
simple uses of file series iterations.
:param Union[Generator,Iterator,List] filenames: Ordered list of filenames
to process as a file series. It also can be a generator, and
iterator, or :class:`~fabio.file_series.filename_series` or
:class:`~fabio.file_series.file_series` objects.
:param str first_filename: If provided iterate filenames from this filename
and try to consecutivelly open next files. If this argument is specified
the `filenames` have to unspecified. Internally it uses
:class:`~fabio.file_series.filename_series` to iterate the filenames.
:param Union[Bool,None] single_frame: If True, all files are supposed to
contain only one frame.
:param Union[Bool,None] fixed_frames: If True, all files are supposed to
contain the same amount of frames (this fixed amount will be reached
from the first file of the serie).
:param Union[Integer,None] fixed_frame_number: If set, all files are
supposed to contain the same amount of frames (sepecified by this
argument)
:rtype: :class:`~file_series.FileSeries`
"""
# Here to avoid recursive import
from . import file_series
if filenames is not None and first_filename is not None:
raise ValueError("'filenames' and 'first_filename' are mutual exclusive")
if first_filename is not None:
filenames = file_series.filename_series(filename=first_filename)
return file_series.FileSeries(filenames=filenames,
single_frame=single_frame,
fixed_frames=fixed_frames,
fixed_frame_number=fixed_frame_number)
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