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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 TIFF images.
In facts wraps TiffIO from V. Armando Solé (available in PyMca) or falls back to PIL
Authors:
........
* Henning O. Sorensen & Erik Knudsen:
Center for Fundamental Research: Metal Structures in Four Dimensions;
Risoe National Laboratory;
Frederiksborgvej 399;
DK-4000 Roskilde;
email:erik.knudsen@risoe.dk
* Jérôme Kieffer:
European Synchrotron Radiation Facility;
Grenoble (France)
"""
__authors__ = ["Jérôme Kieffer", "Henning O. Sorensen", "Erik Knudsen"]
__date__ = "03/04/2020"
__license__ = "MIT"
__copyright__ = "ESRF, Grenoble & Risoe National Laboratory"
__status__ = "stable"
import time
import logging
logger = logging.getLogger(__name__)
try:
import PIL
except ImportError:
PIL = None
import numpy
from .utils import pilutils
from . import fabioimage
from . import TiffIO
_USE_TIFFIO = True
"""Uses TiffIO library if available"""
_USE_PIL = True
"""Uses PIL library if available"""
class TiffFrame(fabioimage.FabioFrame):
"""Frame container for TIFF format"""
def __init__(self, data, tiff_header):
super(TiffFrame, self).__init__(data, tiff_header)
# also expose the tiff header as 'tiff header' attribute
self.tiff_header = tiff_header
class TifImage(fabioimage.FabioImage):
"""
Images in TIF format
Wraps TiffIO
"""
DESCRIPTION = "Tagged image file format"
DEFAULT_EXTENSIONS = ["tif", "tiff"]
_need_a_seek_to_read = True
def __init__(self, *args, **kwds):
""" Tifimage constructor adds an nbits member attribute """
self.nbits = None
fabioimage.FabioImage.__init__(self, *args, **kwds)
self._tiffio = None
self.lib = None
def _readheader(self, infile):
"""
Try to read Tiff images header...
"""
header = numpy.frombuffer(infile.read(64), numpy.uint16)
# TODO: this values dim1/dim2 looks to be wrong
dim1 = int(header[9])
dim2 = int(header[15])
self._shape = dim2, dim1
# nbits is not a FabioImage attribute...
self.nbits = int(header[21]) # number of bits
def _create_frame(self, image_data, tiff_header):
"""Create exposed data from TIFF information"""
return TiffFrame(image_data, tiff_header)
def _read_header_from_pil(self, image):
header = self.check_header()
for num, name in TiffIO.TAG_ID.items():
if num in image.tag:
name = name[0].lower() + name[1:]
value = image.tag[num]
# For some PIL version the tag content is a tuple
if isinstance(value, tuple) and len(value) == 1:
value = value[0]
header[name] = value
return header
def _read_with_tiffio(self, infile):
tiffIO = TiffIO.TiffIO(infile)
self._nframes = tiffIO.getNumberOfImages()
if self.nframes > 0:
# No support for now of multi-frame tiff images
header = tiffIO.getInfo(0)
data = tiffIO.getData(0)
frame = self._create_frame(data, header)
self.header = frame.header
self.data = frame.data
self._tiffio = tiffIO
if self.data.ndim == 2:
self._shape = None
elif self.data.ndim == 3:
logger.warning("Third dimension is the color")
self._shape = None
else:
logger.warning("dataset has %s dimensions (%s), check for errors !!!!", self.data.ndim, self.data.shape)
self.lib = "TiffIO"
def _read_with_pil(self, infile):
pilimage = PIL.Image.open(infile)
header = self._read_header_from_pil(pilimage)
data = pilutils.get_numpy_array(pilimage)
frame = self._create_frame(data, header)
self.header = frame.header
self.data = frame.data
self._shape = None
self.lib = "PIL"
def read(self, fname, frame=None):
"""
Wrapper for TiffIO.
"""
infile = self._open(fname, "rb")
self._readheader(infile)
self.lib = None
infile.seek(0)
if _USE_TIFFIO:
try:
self._read_with_tiffio(infile)
except Exception as error:
logger.warning("Unable to read %s with TiffIO due to %s, trying PIL", fname, error)
logger.debug("Backtrace", exc_info=True)
infile.seek(0)
if self.lib is None:
if _USE_PIL and PIL is not None:
try:
self._read_with_pil(infile)
except Exception as error:
logger.error("Error in opening %s with PIL: %s", fname, error)
logger.debug("Backtrace", exc_info=True)
if infile.closed:
infile = self._open(fname, "rb")
else:
infile.close()
if self.lib is None:
logger.error("Error in opening %s: no tiff reader managed to read the file.", fname)
self.resetvals()
return self
def write(self, fname):
"""
Overrides the FabioImage.write method and provides a simple TIFF image writer.
:param str fname: name of the file to save the image to
"""
with TiffIO.TiffIO(fname, mode="w") as tiff_file:
tiff_file.writeImage(self.data,
info=self.header,
software="fabio.tifimage",
date=time.ctime())
def close(self):
if self._tiffio is not None:
self._tiffio.close()
self._tiffio = None
super(TifImage, self).close()
def _get_frame(self, num):
"""Inherited function returning a FabioFrame"""
if 0 <= num < self.nframes:
frame = self.getframe(num)
frame._set_container(self, num)
frame._set_file_container(self, num)
return frame
raise IndexError("getframe out of range")
def getframe(self, num):
"""Returns the frame `num`.
This frame is not cached on the image structure.
"""
if self._tiffio is None:
raise NotImplementedError("getframe is only implemented for TiffIO lib")
if 0 <= num < self.nframes:
image_data = self._tiffio.getData(num)
tiff_header = self._tiffio.getInfo(num)
return self._create_frame(image_data, tiff_header)
raise Exception("getframe out of range")
tifimage = TifImage
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