# Copyright 2014 Diamond Light Source Ltd.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""
.. module:: base_absorption_correction
:platform: Unix
:synopsis: A set of plugins to correct for absorption effects in xrd and\
xrf ct.
.. moduleauthor:: Aaron D. Parsons <scientificsoftware@diamond.ac.uk>
"""
import logging
from savu.plugins.plugin import Plugin
from savu.plugins.driver.cpu_plugin import CpuPlugin
import xraylib as xl
[docs]class BaseAbsorptionCorrection(Plugin, CpuPlugin):
"""
a base absorption correction for stxm and xrd
:param azimuthal_offset: angle between detectors. Default: -90.0.
:param density: the density. Default: 3.5377.
:param compound: the compount. Default: 'Co0.1Re0.01Ti0.05(SiO2)0.84'.
"""
def __init__(self, name):
logging.debug("Starting Absorption correction")
super(BaseAbsorptionCorrection,
self).__init__(name)
[docs] def setup(self):
logging.debug('setting up the base absorption correction')
in_dataset, out_datasets = self.get_datasets()
in_pData, out_pData = self.get_plugin_datasets()
in_meta_data = in_dataset[0].meta_data
try:
idx = in_meta_data.get('PeakEnergy')
except KeyError:
logging.debug('No PeakEnergy: trying with the fullSpectrum')
try:
in_dataset, out_datasets = self.get_datasets()
in_dataset[0].get_data_patterns()['SPECTRUM']
idx = list(in_meta_data.get('energy'))
except KeyError:
logging.debug("No PeakEnergy or energy axis. This won't work")
raise
self.nChannels = len(idx)
in_pData[0].plugin_data_setup('SINOGRAM', self.get_num_channels())
in_pData[1].plugin_data_setup('SINOGRAM', 'single')
spectra = out_datasets[0]
spectra.create_dataset(in_dataset[0])
out_pData[0].plugin_data_setup('SINOGRAM', self.get_num_channels())
[docs] def get_num_channels(self):
return self.nChannels
[docs] def get_azimuthal_offset(self):
return self.parameters['azimuthal_offset']
[docs] def nOutput_datasets(self):
return 1
[docs] def get_mu(self, compound, energy, density):
'''
returns mu for a compound for a single, or list, of energies
'''
if isinstance(energy, (list)):
op = []
for e in energy:
op.append((xl.CS_Total_CP(compound, e)*density)*1e-2)
return op
else:
return (xl.CS_Total_CP(compound, energy)*density)*1e-2