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#!/usr/bin/env python3
# coding: utf-8
#
# Project: Azimuthal integration
# https://github.com/silx-kit/pyFAI
#
# Copyright (C) 2013-2020 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.
"""Module containing holder classes, like returned objects."""
__author__ = "Valentin Valls"
__contact__ = "valentin.valls@esrf.eu"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__date__ = "02/10/2020"
__status__ = "development"
from collections import namedtuple
Integrate1dtpl = namedtuple("Integrate1dtpl", "position intensity error signal variance normalization count")
Integrate2dtpl = namedtuple("Integrate2dtpl", "radial azimuthal intensity error signal variance normalization count")
class IntegrateResult(tuple):
"""
Class defining shared information between Integrate1dResult and Integrate2dResult.
"""
def __init__(self):
self._sum_signal = None # sum of signal
self._sum_variance = None # sum of variance
self._sum_normalization = None # sum of all normalization SA, pol, ...
self._count = None # sum of counts, from signal/norm
self._count2 = None # sum of counts squared, from variance
self._unit = None
self._has_mask_applied = None
self._has_dark_correction = None
self._has_flat_correction = None
self._normalization_factor = None
self._polarization_factor = None
self._metadata = None
self._npt_azim = None
self._percentile = None
self._method = None
self._method_called = None
self._compute_engine = None
@property
def method(self):
"""return the name of the integration method _actually_ used,
represented as a 4-tuple (dimention, splitting, algorithm, implementation)
"""
return self._method
def _set_method(self, value):
self._method = value
@property
def method_called(self):
"return the name of the method called"
return self._method_called
def _set_method_called(self, value):
self._method_called = value
@property
def compute_engine(self):
"return the name of the compute engine, like CSR"
return self._compute_engine
def _set_compute_engine(self, value):
self._compute_engine = value
@property
def sum(self):
"""Sum of all signal
:rtype: numpy.ndarray
"""
return self._sum_signal
def _set_sum(self, sum_):
"""Set the sum_signal information
:type count: numpy.ndarray
"""
self._sum_signal = sum_
@property
def sum_signal(self):
"""Sum_signal information
:rtype: numpy.ndarray
"""
return self._sum_signal
def _set_sum_signal(self, sum_):
"""Set the sum_signal information
:type count: numpy.ndarray
"""
self._sum_signal = sum_
@property
def sum_variance(self):
"""Sum of all variances information
:rtype: numpy.ndarray
"""
return self._sum_variance
def _set_sum_variance(self, sum_):
"""Set the sum of all variance information
:type count: numpy.ndarray
"""
self._sum_variance = sum_
@property
def sum_normalization(self):
"""Sum of all normalization information
:rtype: numpy.ndarray
"""
return self._sum_normalization
def _set_sum_normalization(self, sum_):
"""Set the sum of all normalization information
:type count: numpy.ndarray
"""
self._sum_normalization = sum_
@property
def count(self):
"""Count information
:rtype: numpy.ndarray
"""
return self._count
def _set_count(self, count):
"""Set the count information
:type count: numpy.ndarray
"""
self._count = count
@property
def unit(self):
"""Radial unit
:rtype: string
"""
return self._unit
def _set_unit(self, unit):
"""Define the radial unit
:type unit: str
"""
self._unit = unit
@property
def has_mask_applied(self):
"""True if a mask was applied
:rtype: bool
"""
return self._has_mask_applied
def _set_has_mask_applied(self, has_mask):
"""Define if dark correction was applied
:type has_mask: bool (or string)
"""
self._has_mask_applied = has_mask
@property
def has_dark_correction(self):
"""True if a dark correction was applied
:rtype: bool
"""
return self._has_dark_correction
def _set_has_dark_correction(self, has_dark_correction):
"""Define if dark correction was applied
:type has_dark_correction: bool
"""
self._has_dark_correction = has_dark_correction
@property
def has_flat_correction(self):
"""True if a flat correction was applied
:rtype: bool
"""
return self._has_flat_correction
def _set_has_flat_correction(self, has_flat_correction):
"""Define if flat correction was applied
:type has_flat_correction: bool
"""
self._has_flat_correction = has_flat_correction
@property
def normalization_factor(self):
"""The normalisation factor used
:rtype: float
"""
return self._normalization_factor
def _set_normalization_factor(self, normalization_factor):
"""Define the used normalisation factor
:type normalization_factor: float
"""
self._normalization_factor = normalization_factor
@property
def polarization_factor(self):
"""The polarization factor used
:rtype: float
"""
return self._polarization_factor
def _set_polarization_factor(self, polarization_factor):
"""Define the used polarization factor
:type polarization_factor: float
"""
self._polarization_factor = polarization_factor
@property
def metadata(self):
"""Metadata associated with the input frame
:rtype: JSON serializable dict object
"""
return self._metadata
def _set_metadata(self, metadata):
"""Define the metadata associated with the input frame
:type metadata: JSON serializable dict object
"""
self._metadata = metadata
@property
def percentile(self):
"for median filter along the azimuth, position of the centile retrieved"
return self._percentile
def _set_percentile(self, value):
self._percentile = value
@property
def npt_azim(self):
"for median filter along the azimuth, number of azimuthal bin initially used"
return self._npt_azim
def _set_npt_azim(self, value):
self._npt_azim = value
class Integrate1dResult(IntegrateResult):
"""
Result of an 1D integration. Provide a tuple access as a simple way to reach main attrbutes.
Default result, extra results, and some interagtion parameters are available from attributes.
For compatibility with older API, the object can be read as a tuple in different ways:
.. codeblock::
result = ai.integrate1d(...)
if result.sigma is None:
radial, I = result
else:
radial, I, sigma = result
"""
def __new__(self, radial, intensity, sigma=None):
if sigma is None:
t = radial, intensity
else:
t = radial, intensity, sigma
return IntegrateResult.__new__(Integrate1dResult, t)
def __init__(self, radial, intensity, sigma=None):
super(Integrate1dResult, self).__init__()
@property
def radial(self):
"""
Radial positions (q/2theta/r)
:rtype: numpy.ndarray
"""
return self[0]
@property
def intensity(self):
"""
Regrouped intensity
:rtype: numpy.ndarray
"""
return self[1]
@property
def sigma(self):
"""
Error array if it was requested
:rtype: numpy.ndarray, None
"""
if len(self) == 2:
return None
return self[2]
class Integrate2dResult(IntegrateResult):
"""
Result of an 2D integration. Provide a tuple access as a simple way to reach main attrbutes.
Default result, extra results, and some interagtion parameters are available from attributes.
For compatibility with older API, the object can be read as a tuple in different ways:
.. codeblock::
result = ai.integrate2d(...)
if result.sigma is None:
I, radial, azimuthal = result
else:
I, radial, azimuthal, sigma = result
"""
def __new__(self, intensity, radial, azimuthal, sigma=None):
if sigma is None:
t = intensity, radial, azimuthal
else:
t = intensity, radial, azimuthal, sigma
return IntegrateResult.__new__(Integrate2dResult, t)
def __init__(self, intensity, radial, azimuthal, sigma=None):
super(Integrate2dResult, self).__init__()
@property
def intensity(self):
"""
Azimuthaly regrouped intensity
:rtype: numpy.ndarray
"""
return self[0]
@property
def radial(self):
"""
Radial positions (q/2theta/r)
:rtype: numpy.ndarray
"""
return self[1]
@property
def azimuthal(self):
"""
Azimuthal positions (chi)
:rtype: numpy.ndarray
"""
return self[2]
@property
def sigma(self):
"""
Error array if it was requested
:rtype: numpy.ndarray, None
"""
if len(self) == 3:
return None
return self[3]
class SeparateResult(tuple):
"""
Class containing the result of AzimuthalIntegrator.separte which separates the
* Amorphous isotropic signal (from a median filter or a sigma-clip)
* Bragg peaks (signal > amorphous)
* Shadow areas (signal < amorphous)
"""
def __new__(self, bragg, amorphous):
return tuple.__new__(SeparateResult, (bragg, amorphous))
def __init__(self, bragg, amorphous):
# tuple.__init__(self, (bragg, amorphous))
self._radial = None
self._intensity = None
self._sigma = None
self._sum_signal = None # sum of signal
self._sum_variance = None # sum of variance
self._sum_normalization = None # sum of all normalization SA, pol, ...
self._count = None # sum of counts, from signal/norm
self._unit = None
self._has_mask_applied = None
self._has_dark_correction = None
self._has_flat_correction = None
self._normalization_factor = None
self._polarization_factor = None
self._metadata = None
self._npt_rad = None
self._npt_azim = None
self._percentile = None
self._method = None
self._method_called = None
self._compute_engine = None
self._shadow = None
@property
def bragg(self):
"""
Contains the bragg peaks
:rtype: numpy.ndarray
"""
return self[0]
@property
def amorphous(self):
"""
Contains the amorphous (isotropic) signal
:rtype: numpy.ndarray
"""
return self[1]
@property
def shadow(self):
"""
Contains the shadowed (weak) signal part
:rtype: numpy.ndarray
"""
return self._shadow
@property
def radial(self):
"""
Radial positions (q/2theta/r)
:rtype: numpy.ndarray
"""
return self._radial
@property
def intensity(self):
"""
Regrouped intensity
:rtype: numpy.ndarray
"""
return self._intensity
@property
def sigma(self):
"""
Error array if it was requested
:rtype: numpy.ndarray, None
"""
return self._sigma
@property
def method(self):
"""return the name of the integration method _actually_ used,
represented as a 4-tuple (dimention, splitting, algorithm, implementation)
"""
return self._method
def _set_method(self, value):
self._method = value
@property
def method_called(self):
"return the name of the method called"
return self._method_called
def _set_method_called(self, value):
self._method_called = value
@property
def compute_engine(self):
"return the name of the compute engine, like CSR"
return self._compute_engine
def _set_compute_engine(self, value):
self._compute_engine = value
@property
def sum(self):
"""Sum of all signal
:rtype: numpy.ndarray
"""
return self._sum_signal
def _set_sum(self, sum_):
"""Set the sum_signal information
:type count: numpy.ndarray
"""
self._sum_signal = sum_
@property
def sum_signal(self):
"""Sum_signal information
:rtype: numpy.ndarray
"""
return self._sum_signal
def _set_sum_signal(self, sum_):
"""Set the sum_signal information
:type count: numpy.ndarray
"""
self._sum_signal = sum_
@property
def sum_variance(self):
"""Sum of all variances information
:rtype: numpy.ndarray
"""
return self._sum_variance
def _set_sum_variance(self, sum_):
"""Set the sum of all variance information
:type count: numpy.ndarray
"""
self._sum_variance = sum_
@property
def sum_normalization(self):
"""Sum of all normalization information
:rtype: numpy.ndarray
"""
return self._sum_normalization
def _set_sum_normalization(self, sum_):
"""Set the sum of all normalization information
:type count: numpy.ndarray
"""
self._sum_normalization = sum_
@property
def count(self):
"""Count information
:rtype: numpy.ndarray
"""
return self._count
def _set_count(self, count):
"""Set the count information
:type count: numpy.ndarray
"""
self._count = count
@property
def unit(self):
"""Radial unit
:rtype: string
"""
return self._unit
def _set_unit(self, unit):
"""Define the radial unit
:type unit: str
"""
self._unit = unit
@property
def has_mask_applied(self):
"""True if a mask was applied
:rtype: bool
"""
return self._has_mask_applied
def _set_has_mask_applied(self, has_mask):
"""Define if dark correction was applied
:type has_mask: bool (or string)
"""
self._has_mask_applied = has_mask
@property
def has_dark_correction(self):
"""True if a dark correction was applied
:rtype: bool
"""
return self._has_dark_correction
def _set_has_dark_correction(self, has_dark_correction):
"""Define if dark correction was applied
:type has_dark_correction: bool
"""
self._has_dark_correction = has_dark_correction
@property
def has_flat_correction(self):
"""True if a flat correction was applied
:rtype: bool
"""
return self._has_flat_correction
def _set_has_flat_correction(self, has_flat_correction):
"""Define if flat correction was applied
:type has_flat_correction: bool
"""
self._has_flat_correction = has_flat_correction
@property
def normalization_factor(self):
"""The normalisation factor used
:rtype: float
"""
return self._normalization_factor
def _set_normalization_factor(self, normalization_factor):
"""Define the used normalisation factor
:type normalization_factor: float
"""
self._normalization_factor = normalization_factor
@property
def polarization_factor(self):
"""The polarization factor used
:rtype: float
"""
return self._polarization_factor
def _set_polarization_factor(self, polarization_factor):
"""Define the used polarization factor
:type polarization_factor: float
"""
self._polarization_factor = polarization_factor
@property
def metadata(self):
"""Metadata associated with the input frame
:rtype: JSON serializable dict object
"""
return self._metadata
def _set_metadata(self, metadata):
"""Define the metadata associated with the input frame
:type metadata: JSON serializable dict object
"""
self._metadata = metadata
@property
def percentile(self):
"for median filter along the azimuth, position of the centile retrieved"
return self._percentile
def _set_percentile(self, value):
self._percentile = value
@property
def npt_azim(self):
"for median filter along the azimuth, number of azimuthal bin initially used"
return self._npt_azim
def _set_npt_azim(self, value):
self._npt_azim = value
class SparseFrame(tuple):
"""Result of the sparsification of a diffraction frame"""
def __new__(self, index, intensity):
return tuple.__new__(SparseFrame, (index, intensity))
def __init__(self, index, intensity):
self._shape = None
self._dtype = None
self._mask = None
self._dummy = None
self._radial = None
self._background_avg = None
self._background_std = None
self._unit = None
self._has_dark_correction = None
self._has_flat_correction = None
self._normalization_factor = None
self._polarization_factor = None
self._metadata = None
self._percentile = None
self._method = None
self._method_called = None
self._compute_engine = None
self._cutoff = None
self._background_cycle = None
self._noise = None
self._radial_range = None
@property
def index(self):
"""
Contains the index position of bragg peaks
:rtype: numpy.ndarray
"""
return self[0]
@property
def intensity(self):
"""
Contains the intensity of bragg peaks
:rtype: numpy.ndarray
"""
return self[1]
@property
def mask(self):
"""
Contains the mask used (encodes for the shape of the image as well)
:rtype: numpy.ndarray
"""
return self._mask
@property
def x(self):
if self._shape is None:
return self[0]
else:
return self[0] % self._shape[-1]
@property
def y(self):
if self._shape is None:
return 0
else:
return self[0] // self._shape[-1]
@property
def cutoff(self):
return self._cutoff
@property
def noise(self):
return self._noise
@property
def radius(self):
return self._radius
@property
def background_avg(self):
return self._background_avg
@property
def background_std(self):
return self._background_std
@property
def shape(self):
return self._shape
@property
def dtype(self):
return self._dtype
@property
def dummy(self):
return self._dummy
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