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simplify fiber integrator #2336

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Nov 20, 2024
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simplify fiber integrator #2336

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simplify fiber integrator
Nov 14, 2024
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171 changes: 24 additions & 147 deletions src/pyFAI/integrator/fiber.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@
__contact__ = "[email protected]"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__date__ = "13/11/2024"
__date__ = "20/11/2024"
__status__ = "stable"
__docformat__ = 'restructuredtext'

Expand Down Expand Up @@ -155,6 +155,8 @@ def integrate_fiber(self, data,
:param pyFAI.units.UnitFiber/str unit_ip: unit to describe the in-plane axis. If not provided, it takes qip_nm^-1
:param list ip_range: The lower and upper range of the in-plane unit. If not provided, range is simply (data.min(), data.max()). Values outside the range are ignored. Optional.
:param bool vertical_integration: If True, integrates along unit_ip; if False, integrates along unit_oop
:param incident_angle: tilting of the sample towards the beam (analog to rot2): in radians
:param tilt_angle: tilting of the sample orthogonal to the beam direction (analog to rot3): in radians
:param int sample_orientation: 1-4, four different orientation of the fiber axis regarding the detector main axis, from 1 to 4 is +90º
:param str filename: output filename in 2/3 column ascii format
:param bool correctSolidAngle: correct for solid angle of each pixel if True
Expand Down Expand Up @@ -183,8 +185,14 @@ def integrate_fiber(self, data,

unit_ip = unit_ip or 'qip_nm^-1'
unit_oop = unit_oop or 'qoop_nm^-1'
unit_ip = parse_fiber_unit(unit=unit_ip, sample_orientation=sample_orientation)
unit_oop = parse_fiber_unit(unit=unit_oop, sample_orientation=unit_ip.sample_orientation)
unit_ip = parse_fiber_unit(unit=unit_ip,
incident_angle=kwargs.get('incident_angle', None),
tilt_angle=kwargs.get('tilt_angle', None),
sample_orientation=sample_orientation)
unit_oop = parse_fiber_unit(unit=unit_oop,
incident_angle=unit_ip.incident_angle,
tilt_angle=unit_ip.tilt_angle,
sample_orientation=unit_ip.sample_orientation)

self.reset_integrator(incident_angle=unit_ip.incident_angle,
tilt_angle=unit_ip.tilt_angle,
Expand Down Expand Up @@ -262,78 +270,7 @@ def integrate_fiber(self, data,

return result

def integrate_grazing_incidence(self, data,
npt_oop=None, unit_oop=None, oop_range=None,
npt_ip=None, unit_ip=None, ip_range=None,
vertical_integration = True,
incident_angle=None, tilt_angle=None, sample_orientation=None,
filename=None,
correctSolidAngle=True,
mask=None, dummy=None, delta_dummy=None,
polarization_factor=None, dark=None, flat=None,
method=("no", "histogram", "cython"),
normalization_factor=1.0,
**kwargs):
"""Calculate the integrated profile curve along a specific FiberUnit, additional inputs for incident angle, tilt angle and sample_orientation
:param ndarray data: 2D array from the Detector/CCD camera
:param int npt_oop: number of points to be used along the out-of-plane axis
:param pyFAI.units.UnitFiber/str unit_oop: unit to describe the out-of-plane axis. If not provided, it takes qoop_nm^-1
:param list oop_range: The lower and upper range of the out-of-plane unit. If not provided, range is simply (data.min(), data.max()). Values outside the range are ignored. Optional.
:param int npt_ip: number of points to be used along the in-plane axis
:param pyFAI.units.UnitFiber/str unit_ip: unit to describe the in-plane axis. If not provided, it takes qip_nm^-1
:param list ip_range: The lower and upper range of the in-plane unit. If not provided, range is simply (data.min(), data.max()). Values outside the range are ignored. Optional.
:param bool vertical_integration: If True, integrates along unit_ip; if False, integrates along unit_oop
:param incident_angle: tilting of the sample towards the beam (analog to rot2): in radians
:param tilt_angle: tilting of the sample orthogonal to the beam direction (analog to rot3): in radians
:param int sample_orientation: 1-4, four different orientation of the fiber axis regarding the detector main axis, from 1 to 4 is +90º
:param str filename: output filename in 2/3 column ascii format
:param bool correctSolidAngle: correct for solid angle of each pixel if True
:param ndarray mask: array (same size as image) with 1 for masked pixels, and 0 for valid pixels
:param float dummy: value for dead/masked pixels
:param float delta_dummy: precision for dummy value
:param float polarization_factor: polarization factor between -1 (vertical) and +1 (horizontal).
* 0 for circular polarization or random,
* None for no correction,
* True for using the former correction
:param ndarray dark: dark noise image
:param ndarray flat: flat field image
:param IntegrationMethod method: IntegrationMethod instance or 3-tuple with (splitting, algorithm, implementation)
:param float normalization_factor: Value of a normalization monitor
:return: chi bins center positions and regrouped intensity
:rtype: Integrate1dResult
"""
deprecated_params = get_deprecated_params_1d(**kwargs)
npt_oop = deprecated_params.get('npt_oop', None) or npt_oop
npt_ip = deprecated_params.get('npt_ip', None) or npt_ip
unit_oop = deprecated_params.get('unit_oop', None) or unit_oop
unit_ip = deprecated_params.get('unit_ip', None) or unit_ip
oop_range = deprecated_params.get('oop_range', None) or oop_range
ip_range = deprecated_params.get('ip_range', None) or ip_range
vertical_integration = deprecated_params.get('vertical_integration', None) or vertical_integration

unit_ip = unit_ip or 'qip_nm^-1'
unit_oop = unit_oop or 'qoop_nm^-1'
unit_ip = parse_fiber_unit(unit=unit_ip, incident_angle=incident_angle, tilt_angle=tilt_angle, sample_orientation=sample_orientation)
unit_oop = parse_fiber_unit(unit=unit_oop, incident_angle=unit_ip.incident_angle, tilt_angle=unit_ip.tilt_angle, sample_orientation=unit_ip.sample_orientation)

self.reset_integrator(incident_angle=unit_ip.incident_angle,
tilt_angle=unit_ip.tilt_angle,
sample_orientation=unit_ip.sample_orientation)

return self.integrate_fiber(data=data,
npt_oop=npt_oop, unit_oop=unit_oop, oop_range=oop_range,
npt_ip=npt_ip, unit_ip=unit_ip, ip_range=ip_range,
vertical_integration=vertical_integration,
sample_orientation=sample_orientation,
filename=filename,
correctSolidAngle=correctSolidAngle,
mask=mask, dummy=dummy, delta_dummy=delta_dummy,
polarization_factor=polarization_factor, dark=dark, flat=flat,
method=method,
normalization_factor=normalization_factor,
)

integrate_grazing_incidence = integrate_fiber
integrate1d_grazing_incidence = integrate_grazing_incidence
integrate1d_fiber = integrate_fiber

Expand All @@ -356,6 +293,8 @@ def integrate2d_fiber(self, data,
:param int npt_oop: number of points to be used along the out-of-plane axis
:param pyFAI.units.UnitFiber/str unit_oop: unit to describe the out-of-plane axis. If not provided, it takes qoop_nm^-1
:param list oop_range: The lower and upper range of the out-of-plane unit. If not provided, range is simply (data.min(), data.max()). Values outside the range are ignored. Optional.
:param incident_angle: tilting of the sample towards the beam (analog to rot2): in radians
:param tilt_angle: tilting of the sample orthogonal to the beam direction (analog to rot3): in radians
:param int sample_orientation: 1-4, four different orientation of the fiber axis regarding the detector main axis, from 1 to 4 is +90º
:param str filename: output filename in 2/3 column ascii format
:param bool correctSolidAngle: correct for solid angle of each pixel if True
Expand Down Expand Up @@ -383,8 +322,15 @@ def integrate2d_fiber(self, data,

unit_ip = unit_ip or 'qip_nm^-1'
unit_oop = unit_oop or 'qoop_nm^-1'
unit_ip = parse_fiber_unit(unit=unit_ip, sample_orientation=sample_orientation)
unit_oop = parse_fiber_unit(unit=unit_oop, sample_orientation=unit_ip.sample_orientation)
unit_ip = parse_fiber_unit(unit=unit_ip,
sample_orientation=sample_orientation,
incident_angle=kwargs.get('incident_angle', None),
tilt_angle=kwargs.get('tilt_angle', None),
)
unit_oop = parse_fiber_unit(unit=unit_oop,
incident_angle=unit_ip.incident_angle,
tilt_angle=unit_ip.tilt_angle,
sample_orientation=unit_ip.sample_orientation)

self.reset_integrator(incident_angle=unit_ip.incident_angle,
tilt_angle=unit_ip.tilt_angle,
Expand All @@ -404,73 +350,4 @@ def integrate2d_fiber(self, data,
unit=(unit_ip, unit_oop),
filename=filename)

def integrate2d_grazing_incidence(self, data,
npt_ip=1000, unit_ip=None, ip_range=None,
npt_oop=1000, unit_oop=None, oop_range=None,
incident_angle=None, tilt_angle=None, sample_orientation=None,
filename=None,
correctSolidAngle=True,
mask=None, dummy=None, delta_dummy=None,
polarization_factor=None, dark=None, flat=None,
method=("no", "histogram", "cython"),
normalization_factor=1.0, **kwargs):
"""Reshapes the data pattern as a function of two FiberUnits, additional inputs for incident angle, tilt angle and sample_orientation
:param ndarray data: 2D array from the Detector/CCD camera
:param int npt_ip: number of points to be used along the in-plane axis
:param pyFAI.units.UnitFiber/str unit_ip: unit to describe the in-plane axis. If not provided, it takes qip_nm^-1
:param list ip_range: The lower and upper range of the in-plane unit. If not provided, range is simply (data.min(), data.max()). Values outside the range are ignored. Optional.
:param int npt_oop: number of points to be used along the out-of-plane axis
:param pyFAI.units.UnitFiber/str unit_oop: unit to describe the out-of-plane axis. If not provided, it takes qoop_nm^-1
:param list oop_range: The lower and upper range of the out-of-plane unit. If not provided, range is simply (data.min(), data.max()). Values outside the range are ignored. Optional.
:param incident_angle: tilting of the sample towards the beam (analog to rot2): in radians
:param tilt_angle: tilting of the sample orthogonal to the beam direction (analog to rot3): in radians
:param int sample_orientation: 1-4, four different orientation of the fiber axis regarding the detector main axis, from 1 to 4 is +90º
:param str filename: output filename in 2/3 column ascii format
:param bool correctSolidAngle: correct for solid angle of each pixel if True
:param ndarray mask: array (same size as image) with 1 for masked pixels, and 0 for valid pixels
:param float dummy: value for dead/masked pixels
:param float delta_dummy: precision for dummy value
:param float polarization_factor: polarization factor between -1 (vertical) and +1 (horizontal).
* 0 for circular polarization or random,
* None for no correction,
* True for using the former correction
:param ndarray dark: dark noise image
:param ndarray flat: flat field image
:param IntegrationMethod method: IntegrationMethod instance or 3-tuple with (splitting, algorithm, implementation)
:param float normalization_factor: Value of a normalization monitor
:return: regrouped intensity and unit arrays
:rtype: Integrate2dResult
"""
deprecated_params = get_deprecated_params_2d(**kwargs)
npt_oop = deprecated_params.get('npt_oop', None) or npt_oop
npt_ip = deprecated_params.get('npt_ip', None) or npt_ip
unit_oop = deprecated_params.get('unit_oop', None) or unit_oop
unit_ip = deprecated_params.get('unit_ip', None) or unit_ip
oop_range = deprecated_params.get('oop_range', None) or oop_range
ip_range = deprecated_params.get('ip_range', None) or ip_range

unit_ip = unit_ip or 'qip_nm^-1'
unit_oop = unit_oop or 'qoop_nm^-1'
unit_ip = parse_fiber_unit(unit=unit_ip, incident_angle=incident_angle, tilt_angle=tilt_angle, sample_orientation=sample_orientation)
unit_oop = parse_fiber_unit(unit=unit_oop, incident_angle=unit_ip.incident_angle, tilt_angle=unit_ip.tilt_angle, sample_orientation=unit_ip.sample_orientation)

self.reset_integrator(incident_angle=unit_ip.incident_angle,
tilt_angle=unit_ip.tilt_angle,
sample_orientation=unit_ip.sample_orientation)

if (isinstance(method, (tuple, list)) and method[0] != "no") or (isinstance(method, IntegrationMethod) and method.split != "no"):
logger.warning(f"Method {method} is using a pixel-splitting scheme. GI integration should be use WITHOUT PIXEL-SPLITTING! The results could be wrong!")

return self.integrate2d_fiber(data=data, npt_ip=npt_ip, npt_oop=npt_oop,
unit_ip=unit_ip, unit_oop=unit_oop,
ip_range=ip_range,
oop_range=oop_range,
sample_orientation=sample_orientation,
filename=filename,
correctSolidAngle=correctSolidAngle,
mask=mask, dummy=dummy, delta_dummy=delta_dummy,
polarization_factor=polarization_factor, dark=dark, flat=flat,
method=method,
normalization_factor=normalization_factor,
)
integrate2d_grazing_incidence = integrate2d_fiber