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# fmt: off
from subprocess import DEVNULL, check_call
import numpy as np
import pytest
from ase import Atoms
from ase.build import molecule
from ase.cell import Cell
from ase.io import write
from ase.io.pov import (
POVRAYIsosurface,
get_bondpairs,
set_high_bondorder_pairs,
write_pov,
)
def test_povray_io(testdir, povray_executable):
H2 = molecule('H2')
write_pov('H2.pov', H2)
check_call([povray_executable, 'H2.pov'], stderr=DEVNULL)
def test_povray_highorder(testdir, povray_executable):
atoms = molecule('CH4')
radii = [0.2] * len(atoms)
bondpairs = get_bondpairs(atoms, radius=1.0)
assert len(bondpairs) == 4
high_bondorder_pairs = {}
def setbond(target, order):
high_bondorder_pairs[(0, target)] = ((0, 0, 0), order, (0.1, -0.2, 0))
setbond(2, 2)
setbond(3, 3)
bondpairs = set_high_bondorder_pairs(bondpairs, high_bondorder_pairs)
renderer = write_pov(
'atoms.pov', atoms,
povray_settings=dict(canvas_width=50, bondatoms=bondpairs),
radii=radii,
)
# XXX Not sure how to test that the bondpairs data processing is correct.
pngfile = renderer.render()
assert pngfile.is_file()
print(pngfile.absolute())
def test_deprecated(testdir):
with pytest.warns(FutureWarning):
write_pov('tmp.pov', molecule('H2'), run_povray=True)
@pytest.fixture()
def skimage():
return pytest.importorskip('skimage')
@pytest.fixture()
def isosurface_things(skimage):
rng = np.random.RandomState(42)
cell = Cell(rng.random((3, 3)))
values = np.zeros((3, 5, 7))
values[1, 2, 3] = 1
center_cell_position = cell.cartesian_positions([1 / 3, 2 / 5, 3 / 7])
# This is the step which requires scikit-image:
surface = POVRAYIsosurface(
density_grid=values,
cut_off=0.12345,
cell=cell,
cell_origin=(0, 0, 0))
return cell, center_cell_position, surface
def test_compute_isosurface(isosurface_things):
cell, center_cell_position, isosurf = isosurface_things
vert_centroid = np.mean(isosurf.verts @ cell, axis=0)
assert np.allclose(vert_centroid, center_cell_position)
def test_render_isosurface(testdir, isosurface_things, povray_executable):
cell, _center_cell_position, isosurf = isosurface_things
atoms = Atoms(
'H3',
scaled_positions=[[0, 0, 0], [1 / 3, 0, 0], [2 / 3, 0, 0]],
cell=cell)
renderer = write('tmp.pov', atoms, isosurface_data=[isosurf])
png_path = renderer.render(povray_executable=povray_executable)
# does the diamond appear over the second hydrogen atom?
assert png_path.is_file()
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