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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.
#
"""Eiger data/master file reader for FabIO
Eiger data files are HDF5 files with one group called "entry" and a dataset
called "data" in it (now in a data group).
Those dataset are usually compressed using LZ4 and/or bitshuffle compression:
* https://github.com/nexusformat/HDF5-External-Filter-Plugins/tree/master/LZ4
* https://github.com/kiyo-masui/bitshuffle
H5py (>2.5) and libhdf5 (>1.8.10) with the corresponding compression plugin are needed to
actually read the data.
Under windows, those plugins can easily be installed via this repository:
https://github.com/silx-kit/hdf5plugin
"""
__authors__ = ["Jérôme Kieffer"]
__contact__ = "jerome.kieffer@esrf.fr"
__license__ = "MIT"
__copyright__ = "ESRF"
__date__ = "03/04/2020"
import logging
logger = logging.getLogger(__name__)
try:
import h5py
except ImportError:
h5py = None
from .fabioimage import FabioImage
from .fabioutils import NotGoodReader
class EigerImage(FabioImage):
"""
FabIO image class for Images from Eiger data files (HDF5)
"""
DESCRIPTION = "Eiger data files based on HDF5"
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 "Eiger 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()
infile.seek(0)
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
lstds = []
# read the image data
self.h5 = h5py.File(fname, mode="r")
if "entry" in self.h5:
entry = self.h5["entry"]
if "data" in entry:
data = entry["data"]
if isinstance(data, h5py.Group):
"Newer format /entry/data/data_1"
datasets = [i for i in data.keys() if i.startswith("data")]
datasets.sort()
try:
for i in datasets:
lstds.append(data[i])
except KeyError:
pass
else:
lstds = [data]
else:
"elder format entry/data_01"
datasets = [i for i in entry.keys() if i.startswith("data")]
datasets.sort()
try:
for i in datasets:
lstds.append(entry[i])
except KeyError:
pass
if not lstds:
raise NotGoodReader("HDF5 file does not contain an Eiger-like structure.")
self.dataset = lstds
self._nframes = sum(i.shape[0] for i in lstds)
if frame is not None:
return self.getframe(int(frame))
else:
self.currentframe = 0
self.data = self.dataset[0][self.currentframe, :, :]
self._shape = None
return self
def write(self, fname):
"""
try to write image
:param fname: name of the file
"""
if len(self.dataset.shape) == 2:
self.dataset.shape = (1,) + self.dataset.shape
with h5py.File(fname, mode="w") as h5file:
grp = h5file.require_group("entry/data")
if len(self.dataset) > 1:
for i, ds in enumerate(self.dataset):
grp["data_%06i" % i] = ds
else:
grp["data"] = self.dataset
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:
if isinstance(self.dataset, list):
nfr = num
for ds in self.dataset:
if nfr < ds.shape[0]:
data = ds[nfr]
break
else:
nfr -= ds.shape[0]
else:
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
eigerimage = EigerImage
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