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# coding: utf-8
#
# Project: FabIO X-ray image reader
#
# Copyright (C) 2010-2016 European Synchrotron Radiation Facility
# Grenoble, France
#
# 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.
#
"""
FabIO class for dealing with JPEG 2000 images.
"""
__authors__ = ["Valentin Valls"]
__date__ = "06/04/2020"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__status__ = "stable"
import logging
logger = logging.getLogger(__name__)
try:
import PIL
import PIL.Image
except ImportError:
PIL = None
try:
import glymur
except ImportError:
glymur = None
from .fabioimage import FabioImage
from .fabioutils import OrderedDict
from .utils import pilutils
class Jpeg2KImage(FabioImage):
"""
Images in JPEG 2000 format.
It uses PIL or glymur libraries.
"""
DESCRIPTION = "JPEG 2000 format"
DEFAULT_EXTENSIONS = ["jp2", "jpx", "j2k", "jpf", "jpg2"]
_need_a_seek_to_read = True
def __init__(self, *args, **kwds):
""" Tifimage constructor adds an nbits member attribute """
self.nbits = None
FabioImage.__init__(self, *args, **kwds)
self.lib = ""
self._decoders = OrderedDict()
if PIL is not None:
self._decoders["PIL"] = self._readWithPil
if glymur is not None:
self._decoders["glymur"] = self._readWithGlymur
def _readWithPil(self, filename, infile):
"""Read data using PIL"""
pilimage = PIL.Image.open(infile)
data = pilutils.get_numpy_array(pilimage)
self.data = data
if pilimage and pilimage.info:
for k, v in pilimage.info.items():
self.header[k] = v
def _loadGlymurImage(self, filename, infile):
"""
Hack to use Glymur with Python file object
This code was tested with all release 0.8.x
"""
# image = glymur.Jp2k(filename)
version = tuple(int(i) for i in glymur.__version__.split(".")[:2])
if version == (0, 7):
image = glymur.Jp2k(filename=filename)
elif version >= (0,8):
# inject a shape to avoid calling the read function
image = glymur.Jp2k(filename=filename, shape=(1, 1))
else:
raise IOError("Glymur version %s is not supported" % glymur.__version__)
# Move to the end of the file to know the size
infile.seek(0, 2)
length = infile.tell()
infile.seek(0)
# initialize what it should already be done
image.length = length
image._shape = None
# It is not the only one format supported by Glymur
# but it is a simplification
image._codec_format = glymur.lib.openjp2.CODEC_JP2
# parse the data
image.box = image.parse_superbox(infile)
try:
image._validate()
except Exception:
logger.debug("Backtrace", exc_info=True)
raise IOError("File %s is not a valid format" % filename)
# Now the image can be used normaly
return image
def _readWithGlymur(self, filename, infile):
"""Read data using Glymur"""
image = self._loadGlymurImage(filename, infile)
self.data = image.read()
def read(self, filename, frame=None):
infile = self._open(filename, "rb")
self.data = None
for name, read in self._decoders.items():
try:
infile.seek(0)
read(filename, infile)
self.lib = name
break
except IOError as e:
self.data = None
self.header = OrderedDict()
logger.debug("Error while using %s library: %s" % (name, e), exc_info=True)
if self.data is None:
infile.seek(0)
raise IOError("No decoder available for the file %s." % filename)
self.resetvals()
return self
jpeg2kimage = Jpeg2KImage
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