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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
#
# 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.
"""
Basic read support for HDF5 files saved by LImA.
"""
__authors__ = ["Jérôme Kieffer"]
__contact__ = "jerome.kieffer@esrf.fr"
__license__ = "MIT"
__copyright__ = "ESRF"
__date__ = "16/11/2020"
import logging
logger = logging.getLogger(__name__)
from .fabioimage import FabioImage
from .fabioutils import NotGoodReader
try:
import h5py
except ImportError:
h5py = None
class LimaImage(FabioImage):
"""FabIO image class for images acquired with the LIMA framwork
LIMA is the Library for Image Acquisition,
https://github.com/esrf-bliss/LImA
"""
DESCRIPTION = "HDF5 file produces by LImA"
DEFAULT_EXTENSIONS = ["h5", "hdf5"]
def __init__(self, data=None, header=None):
"""
Set up initial values
"""
if not h5py:
raise RuntimeError("fabio.EigerImage cannot be used without h5py. Please install h5py and restart")
FabioImage.__init__(self, data, header)
self.dataset = [data]
self.h5 = None
def __repr__(self):
if self.h5 is not None:
return "LImA-HDF5 dataset with %i frames from %s" % (self.nframes, self.h5.filename)
else:
return "%s object at %s" % (self.__class__.__name__, hex(id(self)))
def _readheader(self, infile):
"""
Read and decode the header of an image:
:param infile: Opened python file (can be stringIO or bzipped file)
"""
# list of header key to keep the order (when writing)
self.header = self.check_header()
def read(self, fname, frame=None):
"""
Try to read image
:param fname: name of the file
:param frame: number of the frame
"""
self.resetvals()
with self._open(fname) as infile:
self._readheader(infile)
# read the image data and declare it
self.dataset = None
# read the image data
self.h5 = h5py.File(fname, mode="r")
entry_name = self.h5.attrs.get("default")
if entry_name is None:
raise NotGoodReader("HDF5 file does not contain any default entry.")
if entry_name in self.h5:
entry = self.h5[entry_name]
else:
raise NotGoodReader("HDF5's default entry does not exist.")
if "measurement" in entry:
measurement = entry["measurement"]
else:
raise NotGoodReader("HDF5's default entry has no measurement group.")
if "data" in measurement:
ds = measurement["data"]
else:
raise NotGoodReader("HDF5's measurement group has no dataset.")
self.dataset = ds
self._nframes = ds.shape[0]
if frame is not None:
return self.getframe(int(frame))
else:
self.currentframe = 0
self.data = self.dataset[self.currentframe]
self._shape = None
return self
def getframe(self, num):
""" returns the frame numbered 'num' in the stack if applicable"""
if self.nframes > 1:
new_img = None
if (num >= 0) and num < self.nframes:
data = self.dataset[num]
new_img = self.__class__(data=data, header=self.header)
new_img.dataset = self.dataset
new_img.h5 = self.h5
new_img._nframes = self.nframes
new_img.currentframe = num
else:
raise IOError("getframe %s out of range [%s %s[" % (num, 0, self.nframes))
else:
new_img = FabioImage.getframe(self, num)
return new_img
def previous(self):
""" returns the previous frame in the series as a fabioimage """
return self.getframe(self.currentframe - 1)
def next(self):
""" returns the next frame in the series as a fabioimage """
return self.getframe(self.currentframe + 1)
def close(self):
if self.h5 is not None:
self.h5.close()
self.dataset = None
# This is not compatibility with old code:
limaimage = LimaImage
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