bcdi.simulation: calculation of the diffraction intensity based on FFT or kinematical sum

simulation_utils

In Bragg geometry, calculation of the diffraction intensity based on FFT or kinematical sum. It can include a displacement field, noise, detector gaps etc… See Carnis et al. Scientific Reports 9, 17357 (2019) https://doi.org/10.1038/s41598-019-53774-2

In forward CDI geometry, calculation of the Bragg peak positions in 3D for a mesocrystal, knowing the unit cell and unit cell parameter. It can be used to fit experimental data.

API Reference

supportMaker

This module provides tools to create a simple support using polygons. It is possible to define distances in pixels or nanometers.

API Reference

Make a 3D polygon.

bcdi.simulation.supportMaker.AddPolyCen(array, center, planes)

Make the polygon.

Parameters

  • array – input array

  • center – origin of polygon

  • planes – array of planes

bcdi.simulation.supportMaker.MakePoly(dims, planes)

Make a polygon.

Parameters

  • dims – dimensions of array in pixels

  • planes – array of planes

bcdi.simulation.supportMaker.MakePolyCen(dims, center, planes)

Make the polygon.

Parameters

  • array – input array

  • center – origin of polygon

  • planes – array of planes

bcdi.simulation.supportMaker.generatePlanesCuboid(x, y, z)

Make a cuboid of size x,y,z.

bcdi.simulation.supportMaker.generatePlanesPrism(x, y)

Make a Prism of thickness x, y is somewhat arbitrary.

bcdi.simulation.supportMaker.generatePlanesTetrahedra(x)

Make a tetrahedra of dimension x.

bcdi.simulation.supportMaker.make_poly(dims, planes)

Make a polygon.

Parameters

  • dims – dimensions of array in pixels

  • planes – array of planes

bcdi.simulation.supportMaker.rot_planes(planes, rot)

Rotate planes with some rotation matrix.

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class bcdi.simulation.supportMaker.supportMaker(rawdata, wavelength=None, detector_distance=None, detector_pixel_size=None, ang_step=None, braggAng=None, planes=None, planesDist=None, voxel_size=None)

A masking class for support creation.

Parameters

  • rawdata – raw experimental data

  • wavelength – x-ray wavelength

  • detector_distance – sample to detector (m)

  • detector_pixel_size – detector pixel size - 2D (m)

  • ang_step – angular step (degrees)

  • braggAng – bragg angle (degrees)

  • planes – array of planes np.array([x,y,z])

  • planesDist – array of plane distance to origin (m)

  • voxel_size – set the voxel size to some arbitrary size, np.array([x,y,z]) (m)

calc_voxel_size(wavelength=None, detDist=None, pixel_size=None, ang_step=None, braggAng=None)

Calculate the voxel size.

get_planes()

Return planes array.

get_planesDist()

Return planes distance from origin.

get_support()

Return the generated support.

set_planes(planes_list, plane_distance_origin_list)

Set the planes.

set_support(rawdata)

Set the support to match rawdata dimensions.

set_voxel_size(voxel_size)

Set the voxel size.