geom_from_pars#

anri.io.geom_from_pars(pars, y0, sig_wavelength, sig_ky, sig_kz, sig_beam, voxel_size, pol_factor=1.0, sig_psf=0.0, k_in_lab=None, width_beam=0.0, sig_beam_v=0.0, width_beam_v=0.0, voxel_3d=False, sig_omega=0.0)[source]#

Build the geometry dict for anri.fwd.render_row() from ImageD11 parameters.

Combines beam_from_pars(), gonio_from_pars() and detector_from_pars() with the spreads the renderer needs.

Parameters:

  • pars (dict) – ImageD11 parameters: detector geometry (y_center … o22), wavelength, wedge, chi. ImageD11’s wedge has the opposite sign to anri’s, so the returned geometry has -wedge.

  • y0 (float) – dty at which the rotation axis is in the beam

  • sig_wavelength (float) – Standard deviations of the wavelength (angstrom) and of the beam divergence (radians)

  • sig_ky (float) – Standard deviations of the wavelength (angstrom) and of the beam divergence (radians)

  • sig_kz (float) – Standard deviations of the wavelength (angstrom) and of the beam divergence (radians)

  • sig_beam (float) – The beam’s profile across it, horizontally: a flat top of width_beam (default 0: a Gaussian) blurred by a Gaussian of standard deviation sig_beam (same units as dty; must be > 0), see anri.fwd.beam_weight(). A pencil beam is narrow, a box or horizontal line beam wider than the sample.

  • width_beam (float, default: 0.0) – The beam’s profile across it, horizontally: a flat top of width_beam (default 0: a Gaussian) blurred by a Gaussian of standard deviation sig_beam (same units as dty; must be > 0), see anri.fwd.beam_weight(). A pencil beam is narrow, a box or horizontal line beam wider than the sample.

  • voxel_size (float) – Side length of the voxels (same units as dty)

  • pol_factor (float, default: 1.0) – Degree of horizontal polarisation, see anri.fwd.polarisation()

  • sig_psf (float, default: 0.0) – Standard deviation of the detector point spread, in pixels. Spots much narrower than a pixel have intensity-weighted centroids snapped towards pixel centres (by up to ~0.3 px at 0.1 px wide); a real detector’s point spread prevents that.

  • k_in_lab (Array | ndarray | bool | number | bool | int | float | complex | None, default: None) – [3] Direction of the incoming beam (default lab x), see beam_from_pars()

  • sig_beam_v (float, default: 0.0) – The beam’s profile across it, vertically, as for sig_beam and width_beam. Only used for cubes: for columns (2D maps) the whole vertical profile crosses the voxel.

  • width_beam_v (float, default: 0.0) – The beam’s profile across it, vertically, as for sig_beam and width_beam. Only used for cubes: for columns (2D maps) the whole vertical profile crosses the voxel.

  • voxel_3d (bool, default: False) – Whether the voxels are cubes (a 3D map) rather than columns (a 2D map, e.g. a TensorMap layer)

  • sig_omega (float, default: 0.0) – Extra standard deviation of every peak in omega, in degrees (default 0): a simple stand-in for mosaicity, and a way to smooth the loss at the start of a refinement.

Return type:

dict