core.recip Module¶
This module is for functions and classes specific to reciprocal space calculations.
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skbeam.core.recip.calibrated_pixels_to_q(detector_size, pyfai_kwargs)¶ For a given detector and pyfai calibrated geometry give back the q value for each pixel in the detector.
- Parameters
- detector_sizetuple
2 element tuple defining the number of pixels in the detector. Order is (num_columns, num_rows)
- pyfai_kwargs: dict
The dictionary of pyfai geometry kwargs, given by pyFAI’s calibration Ex: dist, poni1, poni2, rot1, rot2, rot3, splineFile, wavelength, detector, pixel1, pixel2
- Returns
- q_valndarray
Reciprocal values for each pixel shape is [num_rows * num_columns]
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skbeam.core.recip.gisaxs(incident_beam, reflected_beam, pixel_size, detector_size, dist_sample, wavelength, theta_i=0.0)¶ This function will provide scattering wave vector(q) components(x, y, z), q parallel and incident and reflected angles for grazing-incidence small angle X-ray scattering (GISAXS) geometry.
- Parameters
- incident_beamtuple
x and y co-ordinates of the incident beam in pixels
- reflected_beamtuple
x and y co-ordinates of the reflected beam in pixels
- pixel_sizetuple
pixel_size in um
- detector_size: tuple
2 element tuple defining no. of pixels(size) in the detector X and Y direction
- dist_samplefloat
sample to detector distance, in meters
- wavelengthfloat
wavelength of the x-ray beam in Angstroms
- theta_ifloat, optional
out of plane angle, default 0.0
- Returns
- namedtuple
gisaxs_output object is returned This gisaxs_output object contains, in this order:
alpha_i : float incident angle
theta_f : array out of plane angle shape (detector_size[0], detector_size[1])
alpha_f : array exit angle shape (detector_size[0], detector_size[1])
tilt_angle : float tilt angle
qx : array x component of the scattering wave vector shape (detector_size[0], detector_size[1])
qy : array y component of the scattering wave vector shape (detector_size[0], detector_size[1])
qz : array z component of the scattering wave vector shape (detector_size[0], detector_size[1])
qr : array q parallel component shape (detector_size[0], detector_size[1])
Notes
This implementation is based on published work. [1]
References
- 1
R. Lazzari, “IsGISAXS: a program for grazing-incidence small- angle X-ray scattering analysis of supported islands,” J. Appl. Cryst., vol 35, p 406-421, 2002.
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class
skbeam.core.recip.gisaxs_output(alpha_i, theta_f, alpha_f, tilt_angle, qx, qy, qz, qr)¶ Bases:
tuple-
property
alpha_f¶ Alias for field number 2
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property
alpha_i¶ Alias for field number 0
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property
qr¶ Alias for field number 7
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property
qx¶ Alias for field number 4
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property
qy¶ Alias for field number 5
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property
qz¶ Alias for field number 6
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property
theta_f¶ Alias for field number 1
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property
tilt_angle¶ Alias for field number 3
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property
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skbeam.core.recip.hkl_to_q(hkl_arr)¶ This module compute the reciprocal space (q) values from known HKL array for each pixel of the detector for all the images
- Parameters
- hkl_arrndarray
(Qx, Qy, Qz) - HKL array shape is [num_images * num_rows * num_columns][3]
- Returns
- q_valndarray
Reciprocal values for each pixel for all images shape is [num_images * num_rows * num_columns]
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skbeam.core.recip.process_to_q(setting_angles, detector_size, pixel_size, calibrated_center, dist_sample, wavelength, ub, frame_mode=None)¶ This will compute the hkl values for all pixels in a shape specified by detector_size.
- Parameters
- setting_anglesndarray
six angles of all the images - Required shape is [num_images][6] and required type is something that can be cast to a 2D numpy array Angle order: delta, theta, chi, phi, mu, gamma (degrees)
- detector_sizetuple
2 element tuple defining the number of pixels in the detector. Order is (num_columns, num_rows)
- pixel_sizetuple
2 element tuple defining the size of each pixel in mm. Order is (column_pixel_size, row_pixel_size). If not in mm, must be in the same units as dist_sample
- calibrated_centertuple
2 element tuple defining the center of the detector in pixels. Order is (column_center, row_center)(x y)
- dist_samplefloat
distance from the sample to the detector (mm). If not in mm, must be in the same units as pixel_size
- wavelengthfloat
wavelength of incident radiation (Angstroms)
- ubndarray
UB matrix (orientation matrix) 3x3 matrix
- frame_modestr, optional
Frame mode defines the data collection mode and thus the desired output from this function. Defaults to hkl mode (frame_mode=4) ‘theta’ : Theta axis frame. ‘phi’ : Phi axis frame. ‘cart’ : Crystal cartesian frame. ‘hkl’ : Reciprocal lattice units frame. See the process_to_q.frame_mode attribute for an exact list of valid options.
- Returns
- hklndarray
(Qx, Qy, Qz) - HKL values shape is [num_images * num_rows * num_columns][3]
Notes
Six angles of an image: (delta, theta, chi, phi, mu, gamma ) These axes are defined according to the following references.