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# !/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Project: Azimuthal integration
# https://github.com/silx-kit/pyFAI
#
# Copyright (C) 2019 European Synchrotron Radiation Facility, Grenoble, France
#
# Principal author: Jérôme Kieffer (Jerome.Kieffer@ESRF.eu)
#
# 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.
"""This modules contains helper function relative to image header.
"""
__author__ = "Valentin Valls"
__contact__ = "valentin.valls@esrf.eu"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__date__ = "16/10/2020"
import logging
import fabio
_logger = logging.getLogger(__name__)
class MonitorNotFound(Exception):
"""Raised when monitor information in not found or is not valid."""
pass
def _get_monitor_value_from_edf(image, monitor_key):
"""Return the monitor value from an EDF image using an header key.
Take care of the counter and motor syntax using for example 'counter/bmon'
which reach 'bmon' value from 'counter_pos' key using index from
'counter_mne' key.
:param fabio.fabioimage.FabioImage image: Image containing the header
:param str monitor_key: Key containing the monitor
:return: returns the monitor else raise a MonitorNotFound
:rtype: float
:raise MonitorNotFound: when the expected monitor is not found on the
header
"""
keys = image.header
if "/" in monitor_key:
base_key, mnemonic = monitor_key.split('/', 1)
mnemonic_values_key = base_key + "_mne"
mnemonic_values = keys.get(mnemonic_values_key, None)
if mnemonic_values is None:
raise MonitorNotFound("Monitor mnemonic key '%s' not found in the header" % (mnemonic_values_key))
mnemonic_values = mnemonic_values.split()
pos_values_key = base_key + "_pos"
pos_values = keys.get(pos_values_key)
if pos_values is None:
raise MonitorNotFound("Monitor pos key '%s' not found in the header" % (pos_values_key))
pos_values = pos_values.split()
try:
index = mnemonic_values.index(mnemonic)
except ValueError:
_logger.debug("Exception", exc_info=1)
raise MonitorNotFound("Monitor mnemonic '%s' not found in the header key '%s'" % (mnemonic, mnemonic_values_key))
if index >= len(pos_values):
raise MonitorNotFound("Monitor value '%s' not found in '%s'. Not enougth values." % (pos_values_key))
monitor = pos_values[index]
else:
if monitor_key not in keys:
raise MonitorNotFound("Monitor key '%s' not found in the header" % (monitor_key))
monitor = keys[monitor_key]
try:
monitor = float(monitor)
except ValueError as _e:
_logger.debug("Exception", exc_info=1)
raise MonitorNotFound("Monitor value '%s' is not valid" % (monitor))
return monitor
def _get_monitor_value_from_hdf5(image, monitor_key):
"""Return the monitor value from an HDF5 image using an header key.
The monotor_key is a path from the image path containing:
- A dataset containing a scalar (a constant monitor)
- A dataset containing a vector of values (it must containes enougth values
than the amount of frames)
:param fabio.fabioimage.FabioImage image: Image containing the header
:param str monitor_key: Key identify the path of the monitor
:return: returns the monitor else raise a MonitorNotFound
:rtype: float
:raise MonitorNotFound: when the expected monitor is not found on the
header
"""
if monitor_key not in image.hdf5:
raise MonitorNotFound("Monitor path '%s' not found" % (monitor_key))
monitor_dataset = image.hdf5[monitor_key]
if not hasattr(monitor_dataset, "dtype"):
raise MonitorNotFound("Monitor path '%s' is not a datatset" % (monitor_key))
if monitor_dataset.dtype.kind not in "fiu":
raise MonitorNotFound("Monitor path '%s' does not contain a numerical value" % (monitor_key))
if monitor_dataset.shape == tuple():
# A constant monitor
return monitor_dataset[()]
if len(monitor_dataset.shape) != 1:
raise MonitorNotFound("Monitor path '%s' expect a vector of values" % (monitor_key))
if image.currentframe >= monitor_dataset.size:
raise MonitorNotFound("Monitor path '%s' does not provide enougth values" % (monitor_key))
return monitor_dataset[image.currentframe]
def get_monitor_value(image, monitor_key):
"""Return the monitor value from an image using an header key.
:param fabio.fabioimage.FabioImage image: Image containing the header
:param str monitor_key: Key containing the monitor
:return: returns the monitor else raise an exception
:rtype: float
:raise MonitorNotFound: when the expected monitor is not found on the
header
"""
if monitor_key is None:
return Exception("No monitor defined")
if fabio.version_info[0:2] < (0, 9):
# FIXME: Remove this dead code by upgrading the dependancy to fabio>=0.9
if isinstance(image, fabio.edfimage.EdfImage):
return _get_monitor_value_from_edf(image, monitor_key)
elif isinstance(image, fabio.numpyimage.NumpyImage):
return _get_monitor_value_from_edf(image, monitor_key)
elif isinstance(image, fabio.hdf5image.Hdf5Image):
return _get_monitor_value_from_hdf5(image, monitor_key)
else:
if isinstance(image, (fabio.edfimage.EdfImage, fabio.edfimage.EdfFrame)):
return _get_monitor_value_from_edf(image, monitor_key)
elif isinstance(image, fabio.numpyimage.NumpyImage):
return _get_monitor_value_from_edf(image, monitor_key)
elif isinstance(image, (fabio.hdf5image.Hdf5Image, fabio.hdf5image.Hdf5Frame)):
return _get_monitor_value_from_hdf5(image, monitor_key)
raise Exception("File format '%s' unsupported" % type(image))
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