#
# Project: MXCuBE
# https://github.com/mxcube
#
# This file is part of MXCuBE software.
#
# MXCuBE is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# MXCuBE is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with MXCuBE. If not, see <http://www.gnu.org/licenses/>.
"""AbstractFlux class
Defines get_average_flux_density.
"""
from scipy.interpolate import interp1d
from mxcubecore.HardwareObjects.abstract.AbstractActuator import AbstractActuator
from mxcubecore import HardwareRepository as HWR
__copyright__ = """ Copyright © 2010-2022 by the MXCuBE collaboration """
__license__ = "LGPLv3+"
[docs]class AbstractFlux(AbstractActuator):
"""Class for Flux abstraction"""
def __init__(self, name):
super().__init__(name)
# flux by default is read only
self.read_only = True
[docs] def init(self):
"""Initialise some parameters."""
super().init()
self.read_only = self.get_property("read_only") or True
# Dose rate for a standard composition crystal, in Gy/s
# As a function of energy in keV
#
# NB this can be called as a function, the same as if it was defined thus:
# def get_dose_rate_per_photon_per_mmsq(self, energy):
#
# The interpolation table get_dose_rate_per_photon_per_mmsq was created using
# "Absorbed dose calculations for macromolecular crystals: improvements to RADDOSE"
# Paithankar, K.S., Owen, R.L and Garman, E.F J. Syn. Rad. (2009), 16, 152-162,
# for some sensible crystal composition, by Gleb Bourenkov
#
# The reason for *not* having a get_dose_rate function is that the actual dose rate
# depends heavily on beam profile and crystal size and shape.
# The necessary approximations should be done locally.
# See GphlWorkflow for an example of how to do it.
#
get_dose_rate_per_photon_per_mmsq = interp1d(
[4.0, 6.6, 9.2, 11.8, 14.4, 17.0, 19.6, 22.2, 24.8, 27.4, 30.0],
[
4590.0e-12,
1620.0e-12,
790.0e-12,
457.0e-12,
293.0e-12,
202.0e-12,
146.0e-12,
111.0e-12,
86.1e-12,
68.7e-12,
55.2e-12,
],
)
[docs] def get_average_flux_density(self, transmission=None):
"""Get average flux density over the beam area in photons / mm^2
for a given transmission setting
Args:
transmission (float): Target transmission [%]
(defaults to current value)
Returns:
(float): (photons / mm^2) - average flux density over beam area.
"""
beam_size = HWR.beamline.beam.get_beam_size()
flux = self.get_value()
result = None
if flux and all(beam_size):
result = flux / (beam_size[0] * beam_size[1])
if transmission is not None:
result *= transmission / HWR.beamline.transmission.get_value()
return result