XMCD Projection¶
Projection simulation of the PEEM structures
Installation¶
The project is available on PyPi:
pip install xmcd-projection
In order to run the example notebooks, jupyter also needs to be installed:
pip install jupyter
Usage¶
See the docs for details and examples:
If running in Jupyter, make sure you use qt gui for the visualizer to work:
%gui qt
%matplotlib qt
From GMSH .msh file and magnetisation in .csv exported from Magnumfe data¶
To do this, have .msh file exported by GMSH and the magnetisation data
by importing the data in Paraview and going to Save Data… and
exporting to .csv. See examples/example_script.py:
from xmcd_projection import *
msh_file = "example_mesh.msh"
mag_file = "mag_data.csv"
# get the mesh
msh = Mesh.from_file(msh_file)
# get the projection vector
p = get_projection_vector(90, 16)
# prepare raytracing object
raytr = RayTracing(msh, p)
raytr.get_piercings()
struct = raytr.struct
struct_projected = raytr.struct_projected
# load magnetization and make sure the indices are not shuffled
magnetisation, mag_points = load_mesh_magnetisation(mag_file)
shuffle_indx = msh.get_shuffle_indx(mag_points)
magnetisation = magnetisation[shuffle_indx, :]
# get the colours and xmcd values
xmcd_value = raytr.get_xmcd(magnetisation)
mag_colors = get_struct_face_mag_color(struct, magnetisation)
# define the visualizer parameters and show
azi = 90
center_struct = [0, 0, 0]
dist_struct = 2e4
center_peem = [0, -1000, 0]
dist_peem = 2e5
vis = MeshVisualizer(struct, struct_projected,
projected_xmcd=xmcd_value, struct_colors=mag_colors)
vis.show(azi=azi, center=center_peem, dist=dist_peem)
vis.start()
From .vtk generated from Mumax data¶
Import .vtk file in Paraview, go to Saving Data… and export to .vtu
format for the mesh, and .csv format for the magnetization. Ensure that
you are only exporting the part with nonzero magnetization. This can be
achieved by setting a threshold in Paraview. Then, it is very similar to
Magnum.fe, only care needs to be taken to set the appropriate scale. See
examples/mumax_example_script.py:
from xmcd_projection import *
msh_file = "mumax_mesh.vtu"
mag_file = "mumax_mag.csv"
# need to scale points to get them in nm
scale = 1e9
# get the mesh
msh = Mesh.from_file(msh_file, scale=scale)
print(msh.cells)
# get the projection vector
p = get_projection_vector(90, 16)
# prepare raytracing object
raytr = RayTracing(msh, p)
raytr.get_piercings()
struct = raytr.struct
struct_projected = raytr.struct_projected
# load magnetization and make sure the indices are not shuffled
magnetisation, mag_points = load_mesh_magnetisation(mag_file, scale=scale)
shuffle_indx = msh.get_shuffle_indx(mag_points)
magnetisation = magnetisation[shuffle_indx, :]
# get the colours and xmcd values
xmcd_value = raytr.get_xmcd(magnetisation)
mag_colors = get_struct_face_mag_color(struct, magnetisation)
# define the visualizer parameters and show
azi = 90
center_struct = [0, 0, 0]
dist_struct = 1e4
center_peem = [100, -200, 0]
dist_peem = 8e4
vis = MeshVisualizer(struct, struct_projected,
projected_xmcd=xmcd_value, struct_colors=mag_colors)
vis.show(azi=azi, center=center_peem, dist=dist_peem)
vis.start()
From STL file and magnetisation as numpy array¶
This is older version of the library, so might not work as well. Here just in case it is needed in the future
%gui qt
%matplotlib qt
from xmcd_projection import *
from xmcd_projection.stl_visualisation import *
import trimesh
structure_file = r"testing\SOL6-1-3.stl"
magnetisation_file = r"testing\SOL6-1-3_uniform_mag.p"
struct = trimesh.load(structure_file)
magnetisation = np.zeros(struct.vertices.shape)
magnetisation[:, 1] = 1
# define projection vector
p = get_projection_vector(90, 15)
# create visualisation
v = Visualizer(struct, magnetisation, p)
v.generate_view()
v.show()
v.save_render('test1.png')