Plotting with axes in different units

In this example we demonstrate how to plot intensity data with detector axes expressed in different units. It serves as a supporting example to the Accessing simulation results tutorial.

  • The standard “Cylinders in DWBA” sample (see this example) is used to setup the simulation.
  • When the simulation is completed, the Simulation::result() method is used to get a SimulationResult object.
  • Depending on an additional parameter IDetector2D.NBINS, IDetector2D.DEGREES, IDetector2D.QYQZ, it will be plotted with axes defined either in millimeters (default units of RectangularDetector), detector bins, degrees or in $Q$-space.
  • Please note, that the given parameter only affects min/max values of histogram axes (there is no rebinning involved).

Intensity images

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#!/usr/bin/env python3
"""
In this example we demonstrate how to plot simulation results with
axes in different units (nbins, mm, degs and QyQz).
"""
import bornagain as ba
from bornagain import angstrom, deg, nm, nm2, kvector_t
import ba_plot
from matplotlib import pyplot as plt
from matplotlib import rcParams


def get_sample():
    """
    Returns a sample with uncorrelated cylinders on a substrate.
    """

    # Define materials
    material_Particle = ba.HomogeneousMaterial("Particle", 0.0006, 2e-08)
    material_Substrate = ba.HomogeneousMaterial("Substrate", 6e-06, 2e-08)
    material_Vacuum = ba.HomogeneousMaterial("Vacuum", 0.0, 0.0)

    # Define form factors
    ff = ba.FormFactorCylinder(5.0*nm, 5.0*nm)

    # Define particles
    particle = ba.Particle(material_Particle, ff)

    # Define particle layouts
    layout = ba.ParticleLayout()
    layout.addParticle(particle, 1.0)
    layout.setWeight(1)
    layout.setTotalParticleSurfaceDensity(0.01)

    # Define layers
    layer_1 = ba.Layer(material_Vacuum)
    layer_1.addLayout(layout)
    layer_2 = ba.Layer(material_Substrate)

    # Define sample
    sample = ba.MultiLayer()
    sample.addLayer(layer_1)
    sample.addLayer(layer_2)

    return sample


def get_simulation(sample):
    beam = ba.Beam(1.0, 1.0*angstrom, ba.Direction(0.2*deg, 0.0*deg))

    # PILATUS detector
    detector_distance = 2000.0  # in mm
    pilatus_pixel_size = 0.172  # in mm
    pilatus_npx, pilatus_npy = 981, 1043  # number of pixels
    width = pilatus_npx*pilatus_pixel_size
    height = pilatus_npy*pilatus_pixel_size
    detector = ba.RectangularDetector(pilatus_npx, width, pilatus_npy, height)
    detector.setPerpendicularToSampleX(detector_distance, width/2., 0.0)

    simulation = ba.GISASSimulation(beam, sample, detector)
    return simulation


def run_simulation():
    simulation = get_simulation(get_sample())
    simulation.runSimulation()
    return simulation.result()


def plot(result):
    """
    Plots simulation results for different detectors.
    """
    # set plotting parameters
    rcParams['image.cmap'] = 'jet'
    rcParams['image.aspect'] = 'auto'

    fig = plt.figure(figsize=(12.80, 10.24))

    plt.subplot(2, 2, 1)
    # default units for rectangular detector are millimeters

    ba_plot.plot_colormap(result,
                     title="In default units",
                     xlabel=r'$X_{mm}$',
                     ylabel=r'$Y_{mm}$',
                     zlabel=None)

    plt.subplot(2, 2, 2)
    ba_plot.plot_colormap(result,
                     units=ba.Axes.NBINS,
                     title="In number of bins",
                     xlabel=r'$X_{nbins}$',
                     ylabel=r'$Y_{nbins}$',
                     zlabel=None)

    plt.subplot(2, 2, 3)
    ba_plot.plot_colormap(result,
                     units=ba.Axes.DEGREES,
                     title="In degs",
                     xlabel=r'$\phi_f ^{\circ}$',
                     ylabel=r'$\alpha_f ^{\circ}$',
                     zlabel=None)

    plt.subplot(2, 2, 4)
    ba_plot.plot_colormap(result,
                     units=ba.Axes.QSPACE,
                     title="Q-space",
                     xlabel=r'$Q_{y} [1/nm]$',
                     ylabel=r'$Q_{z} [1/nm]$',
                     zlabel=None)

    plt.subplots_adjust(left=0.07, right=0.97, top=0.9, bottom=0.1, hspace=0.25)
    plt.show()


if __name__ == '__main__':
    result = run_simulation()
    plot(result)
AxesInDifferentUnits.py