def test_cylinder_non_positive_pixels_per_len():
good_diameter = 4 # len, some positive number is good
good_height = 2 * good_diameter # len, a very squat cylinder
bad_pixels_per_len = 0 # should be 1 or greater
with pytest.raises(ValueError):
pixel_cylinder(
diameter_outer=good_diameter,
height=good_height,
pixels_per_len=bad_pixels_per_len,
)
def test_cylinder_hallow_construction():
cylinder = pixel_cylinder(height=1.0,
diameter_inner=6.0,
diameter_outer=12.0,
pixels_per_len=1)
assert cylinder # tests constructor
known_mask = np.array([[
[0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0],
[0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0],
[0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0],
[0, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 0],
[1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1],
[1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1],
[0, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 0],
[0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0],
[0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0],
[0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0],
]])
known_mask_vector = np.ndarray.flatten(known_mask)
calc_mask = cylinder.mask
calc_mask_vector = np.ndarray.flatten(calc_mask)
tolerance = 1e-6 # very small value
abs_error = np.abs(np.linalg.norm(known_mask_vector - calc_mask_vector))
assert abs_error < tolerance
bb = cylinder.bounding_box
assert bb.dx == 1
assert bb.dy == 12
assert bb.dz == 12
# Reference
# https://scikit-image.org/docs/dev/auto_examples/numpy_operations/plot_structuring_elements.html#sphx-glr-auto-examples-numpy-operations-plot-structuring-elements-py
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from ptg.pixel_shape import PixelCube as pixel_cube
from ptg.pixel_shape import PixelCylinder as pixel_cylinder
from ptg.pixel_shape import PixelSphere as pixel_sphere
struc_3d = {
"PixelCube1": pixel_cube(dx=1, pixels_per_len=1),
"PixelCube2": pixel_cube(dx=2, pixels_per_len=1),
"PixelCube3": pixel_cube(dx=3, pixels_per_len=1),
"PixelCylinder3": pixel_cylinder(diameter_outer=3,
height=1,
pixels_per_len=1),
"PixelCylinder5": pixel_cylinder(diameter_outer=5,
height=1,
pixels_per_len=1),
"PixelCylinder7": pixel_cylinder(diameter_outer=7,
height=1,
pixels_per_len=1),
"PixelSphere3": pixel_sphere(diameter=3, pixels_per_len=1),
"PixelSphere5": pixel_sphere(diameter=5, pixels_per_len=1),
"PixelSphere7": pixel_sphere(diameter=7, pixels_per_len=1),
}
fig = plt.figure(figsize=(8, 8))
idx = 1
draw_cylinder = False
if draw_cylinder:
max_len = 12
else:
max_len = 6
ppl = 3 # pixels per length
if draw_cylinder:
# cylinder primitive
pixel_shape = pixel_cylinder(
diameter_inner=6,
diameter_outer=max_len,
height=1,
pixels_per_len=ppl,
anchor_x=offsetx,
anchor_y=offsety,
anchor_z=offsetz,
)
else:
# quarter-cylinder primitive
pixel_shape = pixel_quarter_cylinder(
height=1,
radius_inner=3,
radius_outer=max_len,
pixels_per_len=ppl,
anchor_x=offsetx,
anchor_y=offsety,
anchor_z=offsetz,
)
def test_cylinder_diameter_inner_exceeds_diameter_outer():
ID = 10 # inner diameter
OD = 5 # outer diameter
with pytest.raises(ValueError):
pixel_cylinder(diameter_inner=ID, diameter_outer=OD)
def test_cylinder_non_positive_height():
good_diameter = 10
bad_height = 0 # height should be 1 or greater
with pytest.raises(ValueError):
pixel_cylinder(diameter_outer=good_diameter, height=bad_height)
def test_cylinder_non_positive_diameter():
bad_value = 0 # diamter should be 1 or greater
with pytest.raises(ValueError):
pixel_cylinder(diameter_outer=bad_value)