KGeoBag Visualization

The KGeoBag module provides a set of stand-alone visualization tools that are described under tools-label. These are suited to display the simulation geometry and other geometric elements, such as the mesh used for field calculation and/or navigation.

In addition, the geometry visualization can also be defined in the configuration file. In this case, output files may be produced before or after performing the simulation, and a visualization window can be shown as well. Note that the visualization window blocks the application until it is closed, so it is not advised to use this feature in a scripted environment. The examples in this section are based on the DipoleTrapSimulation.xml file, which may be extended accordingly to test the features explained here and in the following chapters. The commandline option -b (or -batch) will prevent any visualization windows to appear regardless of the setting in the configuration file, e.g.:

Kassiopeia -b DipoleTrapSimulation.xml

The KGeoBag module provides painter classes for the geometry which are covered below in the Kassiopeia section. In addition, the mesh geometry can be viewed as well:

<vtk_window
        name="vtk_window"
        enable_display="true"
        enable_write="true"
        frame_title="KGeoBag Visualization"
    >
    <vtk_axial_mesh_painter
        name="vtk_axial_mesh_painter"
        surfaces="world/dipole_trap/@electrode_tag"
        color_mode="area"
    />
</vtk_window>

The axial mesh painter needs a defined mesh (<axial_mesh> XML element, see Configuring Your Own Simulation). An <vtk_mesh_painter> exists as well, to be used with an asymmetric mesh (defined via <mesh>).

Using Python

It is possible to draw a geometry visualization in Python. This is especially useful if you run your analysis in Python as well (see Understanding Simulation Output for examples.)

The PyVista Python package makes it easy to operate on the VTK output files that are produced by KGeoBag and the other Kasper modules. (Note that this method only works if VTK was enabled at build time.) In the XML snippets above, the different VTK painters will produce output files if the enable_write attribute is set. These files contain the 3D geometry in the vtp format and can be read in Python. In order to get a 2D view of the geometry, one also needs to create a slice that transforms the 3D surfaces into 2D lines.

import pyvista as pv
import matplotlib as mpl
import matplotlib.pyplot as plt

# Open geometry file
dataset = pv.read('geometry_painter.vtp')

# Produce a slice along the x-z axis
mesh = dataset.slice(normal=[0,1,0])

# Draw lines in each slice cell
plt.figure()
xlim, ylim = (0,0), (0,0)
for ind in range(mesh.n_cells):
    x, y, z = mesh.cell_points(ind).T

    if mesh.cell_type(ind) == 3:  # VTK_LINE
        line = mpl.lines.Line2D(z, x, lw=2, c='k')
        plt.gca().add_artist(line)
        xlim = (min(xlim[0],z.min()), max(xlim[1],z.max()))
        ylim = (min(ylim[0],x.min()), max(ylim[1],x.max()))
plt.xlim(xlim)
plt.ylim(ylim)