Source code for flowws_analysis.Diffraction

import flowws
from flowws import Argument as Arg
import plato.draw

from ._diffraction_primitive import Diffraction as DiffractionPrimitive
from ._diffraction_primitive import DEFAULT_COLORMAP

[docs]@flowws.add_stage_arguments class Diffraction(flowws.Stage): """Compute a 3D diffraction pattern of the system and display its slice or projection. This stage computes a 3D histogram of the system based on the given periodic system box and particle coordinates and performs the FFT in 3D. Either a slice or full projection through the Fourier space is displayed with the current system orientation. **Note:** This module should be considered experimental in terms of stability for the time being; the inputs and outputs may change drastically in the future, or the module may be removed entirely. """ ARGS = [ Arg('bin_count', '-b', int, default=128, help='Number of bins to use in the x, y, and z directions'), Arg('projection', '-p', bool, False, help='If True, project the diffraction pattern all the way through fourier space'), Arg('min_value', None, float, 0, help='Minimum value of intensity to clip to'), Arg('max_value', None, float, 1, help='Maximum value of intensity to clip to'), Arg('sigma', None, float, 0, help='Lengthscale of blurring the FFT'), ] def run(self, scope, storage): """Prepare to display the diffraction pattern""" self.positions = scope['position'] = scope['box'] scope.setdefault('visuals', []).append(self) scope.setdefault('visual_link_rotation', []).append(self) def draw_plato(self): prim = DiffractionPrimitive(positions=self.positions, prim.size = self.arguments['bin_count'] prim.sigma = self.arguments['sigma'] prim.vmin = self.arguments['min_value'] prim.vmax = self.arguments['max_value'] prim.projection = self.arguments['projection'] prim.cmap = DEFAULT_COLORMAP return plato.draw.Scene(prim, size=(1, 1), pixel_scale=800)