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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.
#
"""HDF5 image for FabIO
Authors: Jerome Kieffer
email: Jerome.Kieffer@terre-adelie.org
Specifications:
input should being the form:
filename::path
Only supports ndim=2 or 3 (exposed as a stack of images
"""
# Get ready for python3:
from __future__ import with_statement, print_function, division
__authors__ = ["Jérôme Kieffer"]
__contact__ = "Jerome.Kieffer@terre-adelie.org"
__license__ = "MIT"
__copyright__ = "Jérôme Kieffer"
__date__ = "08/07/2016"
import numpy
import logging
import os
import posixpath
import sys
from .fabioimage import FabioImage
logger = logging.getLogger("hdf5image")
if sys.version_info[0] < 3:
bytes = str
try:
import h5py
except ImportError:
h5py = None
from .fabioutils import previous_filename, next_filename
class Hdf5Image(FabioImage):
"""
FabIO image class for Images from an HDF file
filename::dataset
"""
def __init__(self, *arg, **kwargs):
"""
Generic constructor
"""
if not h5py:
raise RuntimeError("fabio.Hdf5Image cannot be used without h5py. Please install h5py and restart")
FabioImage.__init__(self, *arg, **kwargs)
self.hdf5 = None
self.dataset = None
def read(self, fname, frame=None):
"""
try to read image
@param fname: filename::datasetpath
"""
self.resetvals()
if "::" not in fname:
err = "the '::' separator in mandatory for HDF5 container, absent in %s" % fname
logger.error(err)
raise RuntimeError(err)
filename, datapath = fname.split("::", 1)
self.filename = filename
if os.path.isfile(self.filename):
self.hdf5 = h5py.File(self.filename, "r")
else:
error = "No such file or directory: %s" % self.filename
logger.error(error)
raise RuntimeError(error)
try:
self.dataset = self.hdf5[datapath]
except Exception as err:
logger.error("No such datapath %s in %s, %s", datapath, filename, err)
raise
if isinstance(self.dataset, h5py.Group) and ("data" in self.dataset):
datapath = posixpath.join(datapath, "data")
logger.warning("The actual dataset is ")
self.dataset = self.dataset["data"]
# ndim does not exist for external links ?
ndim = len(self.dataset.shape)
if ndim == 3:
self.nframes = self.dataset.shape[0]
if frame is not None:
self.currentframe = int(frame)
else:
self.currentframe = 0
self.data = self.dataset[self.currentframe, :, :]
elif ndim == 2:
self.data = self.dataset[:, :]
else:
err = "Only 2D and 3D datasets are supported by FabIO, here %sD" % self.dataset.ndim
logger.error(err)
raise RuntimeError(err)
return self
def write(self, fname, force_type=numpy.uint16):
raise NotImplementedError("Write is not implemented")
def getframe(self, num):
"""
Returns a frame as a new FabioImage object
@param num: frame number
"""
if num < 0 or num > self.nframes:
raise RuntimeError("Requested frame number %i is out of range [0, %i[ " % (num, self.nframes))
# Do a deep copy of the header to make a new one
frame = self.__class__(header=self.header)
frame.hdf5 = self.hdf5
frame.dataset = self.dataset
frame.filename = self.filename
frame.nframes = self.nframes
frame.data = self.dataset[num, :, :]
frame.currentframe = num
return frame
def next(self):
"""
Get the next image in a series as a fabio image
"""
if self.currentframe < (self.nframes - 1):
return self.getframe(self.currentframe + 1)
else:
newobj = Hdf5Image()
newobj.read(next_filename(self.filename))
return newobj
def previous(self):
"""
Get the previous image in a series as a fabio image
"""
if self.currentframe > 0:
return self.getframe(self.currentframe - 1)
else:
newobj = Hdf5Image()
newobj.read(previous_filename(self.filename))
return newobj
hdf5image = Hdf5Image
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