Mumax projection¶

[1]:

%gui qt
%matplotlib qt
from glob import glob
import os, sys
# only necessary if using without installing
sys.path.append("..")
from xmcd_projection import *
from skimage.io import imread, imsave
from PIL import Image
import meshio
import trimesh

c:\users\lukas\miniconda3\lib\site-packages\numpy\_distributor_init.py:30: UserWarning: loaded more than 1 DLL from .libs:
c:\users\lukas\miniconda3\lib\site-packages\numpy\.libs\libopenblas.GK7GX5KEQ4F6UYO3P26ULGBQYHGQO7J4.gfortran-win_amd64.dll
c:\users\lukas\miniconda3\lib\site-packages\numpy\.libs\libopenblas.NOIJJG62EMASZI6NYURL6JBKM4EVBGM7.gfortran-win_amd64.dll
  warnings.warn("loaded more than 1 DLL from .libs:"

Get file paths¶

[ ]:

msh_file = "mumax_mesh.vtu"
mag_file = "mumax_mag.csv"
# scale for the points
scale = 1e9

Generate raytracing - skip if generated¶

[ ]:

# get the mesh, scale the points to nm
msh = Mesh.from_file(msh_file, scale=scale)

Make sure that the projection vector is correct and that the structure is oriented well¶

[4]:

# get the projection vector
p = get_projection_vector(90, 0) # direction of xrays
n = [0, 1, 1] # normal to the projection plane
x0 = [-100, 0, 0] # point on the projection plane

# prepare raytracing object
raytr = RayTracing(msh, p, n=n, x0=x0)
struct = raytr.struct
struct_projected = raytr.struct_projected

[14]:

vis = MeshVisualizer(struct, struct_projected)
vis.set_camera(dist=2e5)
vis.show()

If raytracing file generated - skip if not¶

[ ]:

# load raytracing if exists
raytr = np.load("raytracing.npy", allow_pickle=True).item()
struct = raytr.struct
struct_projected = raytr.struct_projected

Generate and save raytracing¶

[5]:

raytr.get_piercings()
np.save("raytracing.npy", raytr, allow_pickle=True)

  0%|                                                                               | 1/3320 [00:03<3:19:32,  3.61s/it]c:\users\lukas\documents\xmcd-projection\xmcd_projection\raytracing.py:142: UserWarning: Wrong number of intersections! Ensure that tetrahedra are valid and that the projection plane does not intersect the structure. If this happens rarely, it could be a numerical artefact.
  warn(
100%|█████████████████████████████████████████████████████████████████████████████| 3320/3320 [00:08<00:00, 373.87it/s]

Get the xmcd¶

Get magnetisation, fix vertex shuffling¶

Note: sometimes if the mesh file has multiple parts, the paraview export and the original mesh coordinates are not in the same order. I add a function to fix that when necessary

[6]:

magnetisation, mag_points = load_mesh_magnetisation(mag_file, scale=scale)
shuffle_file = "shuffle_indx.npy"
try:
    shuffle_indx = np.load(shuffle_file)
except FileNotFoundError:
    print('File not found. Generating shuffle indx')
    shuffle_indx = msh.get_shuffle_indx(mag_points)
    np.save(shuffle_file, shuffle_indx)
magnetisation = magnetisation[shuffle_indx, :]

Get the colours and XMCD values¶

[7]:

xmcd_value = raytr.get_xmcd(magnetisation)
mag_colors = get_struct_face_mag_color(struct, magnetisation)

[8]:

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)
Image.fromarray(vis.get_image_np())

[8]:

../_images/examples_mumax_projection_18_0.png

[9]:

vis.update_colors(xmcd_value, mag_colors)
vis.view_both(azi=azi, center=center_peem, dist=dist_peem)
Image.fromarray(vis.get_image_np())

[9]:

../_images/examples_mumax_projection_21_0.png

[10]:

vis.view_projection(azi=azi, center=center_peem, dist=dist_peem)
Image.fromarray(vis.get_image_np())

[10]:

../_images/examples_mumax_projection_23_0.png

[11]:

center_struct = [75, 50, 0]
dist_struct = 1e4
vis.view_struct(azi=azi, center=center_struct, dist=dist_struct)
Image.fromarray(vis.get_image_np())

[11]:

../_images/examples_mumax_projection_25_0.png

[12]:

vis.view_projection(azi=azi, center=center_peem, dist=dist_peem)
Image.fromarray((vis.get_blurred_image(desired_background=0.7)*255).astype(np.uint8))

[12]:

../_images/examples_mumax_projection_27_0.png

[13]:

vis.view_both(azi=azi, center=center_peem, dist=dist_peem)
vis.save_render('mumax_shadow.png')
vis.view_projection()
blurred = vis.get_blurred_image(desired_background=0.7)
imsave('mumax_shadow_blurred.png', (blurred*255).astype(np.uint8), check_contrast=False)

vis.view_struct(azi=azi, center=center_struct, dist=dist_struct)
vis.save_render('mumax_structure_view.png')

[ ]: