Changed powdersim() to allow for 'custom' peak profile (based on Voigt)

skued/__init__.py

@@ -4,11 +4,12 @@
 __license__ = 'MIT'
 __version__ = '0.4.4' # TODO: automatic versioning?
 
-from .array_utils import repeated_array, mirror
+from .affine import (affine_map, change_basis_mesh, change_of_basis, is_basis,
+ is_rotation_matrix, minimum_image_distance,
+ rotation_matrix, transform, translation_matrix,
+ translation_rotation_matrix)
+from .array_utils import mirror, repeated_array
 from .parallel import pmap, preduce
 from .plot_utils import spectrum_colors
-from .quantities import lorentz, electron_wavelength, interaction_parameter
-from .affine import (affine_map, transform, change_of_basis, is_basis, translation_matrix,
- is_rotation_matrix, rotation_matrix, translation_rotation_matrix,
- change_basis_mesh, minimum_image_distance)
+from .quantities import electron_wavelength, interaction_parameter, lorentz
 from .voigt import gaussian, lorentzian, pseudo_voigt

skued/simulation/powdersim.py

@@ -5,7 +5,7 @@
 from ..voigt import pseudo_voigt
 import numpy as np
 
-def powdersim(crystal, scattering_length, broadening = True, **kwargs):
+def powdersim(crystal, scattering_length, fwhm_g = 0.01, fwhm_l = 0.02, **kwargs):
  """
  Simulates polycrystalline diffraction pattern.
 
@@ -15,9 +15,10 @@ def powdersim(crystal, scattering_length, broadening = True, **kwargs):
  Crystal from which to diffract.
  scattering_length : `~numpy.ndarray`, shape (N,)
  Range of scattering length over which to compute the diffraction pattern [2pi/Angs].
- broadening: bool, optional
- If True (default), returned pattern will display Voigt-related broadening.
-
+ fwhm_g, fwhm_l : float, optional
+ Full-width at half-max of the Gaussian and Lorentzian parts of the Voigt profile.
+ See `skued.pseudo_voigt` for more details.
+
  Returns
  -------
  pattern : `~numpy.ndarray`, shape (N,)
@@ -27,12 +28,10 @@ def powdersim(crystal, scattering_length, broadening = True, **kwargs):
  scatt_length = np.sqrt(Gx**2 + Gy**2 + Gz**2)/(4*np.pi)
  intensities = np.absolute(crystal.structure_factor((Gx, Gy, Gz)))**2
 
+ psf = pseudo_voigt(scattering_length, center = np.mean(scattering_length), fwhm_g = fwhm_g, fwhm_l = fwhm_l)
+
  pattern = np.zeros_like(scattering_length)
- if broadening:
- for s, I in zip(scatt_length, intensities):
- pattern += I * pseudo_voigt(scattering_length, s, 0.01, 0.02)
- else:
- for s, I in zip(scatt_length, intensities):
- pattern += I * pseudo_voigt(scattering_length, s, 1e-5, 1e-5)
+ for s, i in zip(scatt_length, intensities):
+ pattern += i * pseudo_voigt(scattering_length, s, fwhm_g, fwhm_l)
 
  return pattern