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NF: adding primitive stars, 3D stars, rhombi. #170

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NF: adding primitive stars, 3D stars, rhombi. #170

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f2faa07
adding stars, 3D, rhombi
lidonohu Feb 27, 2020
cf93bee
fixed pep8
lidonohu Feb 27, 2020
fef0bae
prim test
lidonohu Feb 27, 2020
24ca40b
test_prim
lidonohu Mar 5, 2020
88bf418
pep8 prim name
lidonohu Mar 5, 2020
c990dfd
new line fix
lidonohu Mar 5, 2020
90806ad
last PEP8
lidonohu Mar 5, 2020
795551e
added missing line
lidonohu Mar 5, 2020
b0dc9ed
added missing line
lidonohu Mar 5, 2020
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195 changes: 181 additions & 14 deletions fury/primitive.py
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Expand Up @@ -33,7 +33,7 @@ def faces_from_sphere_vertices(vertices):
"""
hull = ConvexHull(vertices, qhull_options='Qbb Qc')
faces = np.ascontiguousarray(hull.simplices)
if len(vertices) < 2**16:
if len(vertices) < 2 ** 16:
return np.asarray(faces, np.uint16)
else:
return faces
Expand Down Expand Up @@ -117,18 +117,19 @@ def repeat_primitive(vertices, faces, centers, directions=(1, 0, 0),
Expanded triangles that composed our shape to duplicate
big_colors : ndarray
Expanded colors applied to all vertices/faces
big_centers : ndarray
Expanded centers for all vertices/faces
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Can you explain why you remove this docstring ?


"""
# duplicated vertices if needed
if not have_tiled_verts:
vertices = np.tile(vertices, (centers.shape[0], 1))
big_vertices = vertices

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Can you explain why do you remove big_vertices?

# Get unit shape
unit_verts_size = vertices.shape[0] // centers.shape[0]
unit_triangles_size = faces.shape[0]

big_centers = np.repeat(centers, unit_verts_size, axis=0)
# apply centers position
big_vertices = vertices + big_centers
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Same questions as above, I don't understand why you add this part? Please, can you explain ?

# scale them
if isinstance(scale, (list, tuple, np.ndarray)):
scale = np.repeat(scale, unit_verts_size, axis=0)
Expand All @@ -137,16 +138,16 @@ def repeat_primitive(vertices, faces, centers, directions=(1, 0, 0),

# update triangles
big_triangles = np.array(np.tile(faces,
(centers.shape[0], 1)),
(centers.shape[0], 1)),
dtype=np.int32)
big_triangles += np.repeat(np.arange(0, centers.shape[0] *
unit_verts_size, step=unit_verts_size),
unit_verts_size, step=unit_verts_size),
unit_triangles_size,
axis=0).reshape((big_triangles.shape[0], 1))

def normalize_input(arr, arr_name=''):
if isinstance(arr, (tuple, list, np.ndarray)) and len(arr) == 3 and \
not all(isinstance(i, (list, tuple, np.ndarray)) for i in arr):
not all(isinstance(i, (list, tuple, np.ndarray)) for i in arr):
return np.array([arr] * centers.shape[0])
elif isinstance(arr, np.ndarray) and len(arr) == 1:
return np.repeat(arr, centers.shape[0], axis=0)
Expand All @@ -163,20 +164,18 @@ def normalize_input(arr, arr_name=''):

# update orientations
directions = normalize_input(directions, 'directions')
big_vertices -= big_centers
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Same questions as above?

for pts, dirs in enumerate(directions):
ai, aj, ak = transform.Rotation.from_rotvec(np.pi/2 * dirs). \
ai, aj, ak = transform.Rotation.from_rotvec(np.pi / 2 * dirs). \
as_euler('zyx')
rotation_matrix = euler_matrix(ai, aj, ak)
big_vertices[pts * unit_verts_size: (pts+1) * unit_verts_size] = \
big_vertices[pts * unit_verts_size: (pts + 1) * unit_verts_size] = \
np.dot(rotation_matrix[:3, :3],
big_vertices[pts * unit_verts_size:
(pts+1) * unit_verts_size].T).T

# apply centers position
big_centers = np.repeat(centers, unit_verts_size, axis=0)
(pts + 1) * unit_verts_size].T).T
big_vertices += big_centers

return big_vertices, big_triangles, big_colors, big_centers
return big_vertices, big_triangles, big_colors
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Why do you remove big_centers ?



def prim_square():
Expand Down Expand Up @@ -313,6 +312,7 @@ def prim_superquadric(roundness=(1, 1), sphere_name='symmetric362'):
True

"""

def _fexp(x, p):
"""Return a different kind of exponentiation."""
return np.sign(x) * (np.abs(x) ** p)
Expand All @@ -329,3 +329,170 @@ def _fexp(x, p):
vertices = np.ascontiguousarray(xyz)

return vertices, sphere_triangles


def prim_rhombicuboctahedron():
"""Return vertices and triangle for rhombicuboctahedron geometry

Parameters
----------

Returns
-------
my_vertices: ndarray
vertices coords that composed our rhombicuboctahedron
my_triangles: ndarray
Triangles that composed our rhombicuboctahedron
"""
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Missing an empty line

my_vertices = np.array([[-2, 4, 2],
[-4, 2, 2],
[-4, -2, 2],
[-2, -4, 2],
[2, -4, 2],
[4, -2, 2],
[4, 2, 2],
[2, 4, 2],
[-2, 2, 4],
[-2, -2, 4],
[2, -2, 4],
[2, 2, 4],
[-2, 4, -2],
[-4, 2, -2],
[-4, -2, -2],
[-2, -4, -2],
[2, -4, -2],
[4, -2, -2],
[4, 2, -2],
[2, 4, -2],
[-2, 2, -4],
[-2, -2, -4],
[2, -2, -4],
[2, 2, -4]])

my_triangles = np.array([[0, 1, 8],
[1, 2, 9],
[1, 8, 9],
[2, 3, 9],
[3, 9, 10],
[3, 4, 10],
[4, 10, 5],
[5, 11, 10],
[5, 6, 11],
[6, 7, 11],
[7, 8, 11],
[7, 8, 0],
[8, 9, 10],
[8, 10, 11],
[12, 13, 20],
[13, 14, 21],
[13, 20, 21],
[14, 15, 21],
[15, 21, 22],
[15, 16, 22],
[16, 22, 17],
[17, 22, 23],
[17, 23, 18],
[18, 19, 23],
[19, 20, 23],
[19, 20, 12],
[20, 21, 22],
[20, 22, 23],
[7, 18, 19],
[6, 7, 18],
[6, 17, 18],
[5, 6, 17],
[4, 5, 16],
[5, 16, 17],
[0, 1, 12],
[1, 12, 13],
[1, 2, 13],
[2, 13, 14],
[2, 3, 14],
[3, 14, 15],
[0, 7, 12],
[7, 12, 19],
[3, 15, 16],
[3, 4, 16],
], dtype='i8')
return my_vertices, my_triangles


def prim_star(dim=2):
"""Return vertices and triangle for star geometry

Parameters
----------
dim: int
Represents the dimension of the wanted star

Returns
-------
vertices: ndarray
vertices coords that composed our star
triangles: ndarray
Triangles that composed our star

"""
if dim == 2:
vert = np.array([[-2.0, -3.0, 0.0],
[0.0, -2.0, 0.0],
[3.0, -3.0, 0.0],
[2.0, -1.0, 0.0],
[3.0, 1.0, 0.0],
[1.0, 1.0, 0.0],
[0.0, 3.0, 0.0],
[-1.0, 1.0, 0.0],
[-3.0, 1.0, 0.0],
[-2.0, -1.0, 0.0]])

triangles = np.array([[1, 9, 0],
[1, 2, 3],
[3, 4, 5],
[5, 6, 7],
[7, 8, 9],
[1, 9, 3],
[3, 7, 9],
[3, 5, 7]], dtype='i8')

if dim == 3:
vert = np.array([[-3.0, -3.0, 0.0],
[0.0, -2, 0.0],
[3.0, -3.0, 0.0],
[2.0, -1.0, 0.0],
[3.0, 1.0, 0.0],
[1.0, 1.0, 0.0],
[0, 3.0, 0.0],
[-1.0, 1.0, 0.0],
[-3.0, 1.0, 0.0],
[-2.0, -1.0, 0.0],
[2.0, 1.5, 1.0],
[2.0, 1.5, -1.0]])
triangles = np.array([[1, 9, 0],
[1, 2, 3],
[3, 4, 5],
[5, 6, 7],
[7, 8, 9],
[1, 9, 3],
[3, 7, 9],
[3, 5, 7],
[1, 0, 10],
[0, 9, 10],
[10, 9, 8],
[7, 8, 10],
[6, 7, 10],
[5, 6, 10],
[5, 10, 4],
[10, 3, 4],
[3, 10, 2],
[10, 1, 2],
[1, 0, 11],
[0, 9, 11],
[11, 9, 8],
[7, 8, 10],
[6, 7, 11],
[5, 6, 11],
[5, 10, 4],
[11, 3, 4],
[3, 11, 2],
[11, 1, 2]], dtype='i8')
return vert, triangles
22 changes: 14 additions & 8 deletions fury/tests/test_primitive.py
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Expand Up @@ -2,18 +2,24 @@
import numpy.testing as npt
import fury.primitive as fp


def test_vertices_primitives():
l_primitives = [(fp.prim_square, (4, 3)),
(fp.prim_box, (8, 3))]
l_primitives = [(fp.prim_square, (4, 3), -.5, .5, 0),
(fp.prim_box, (8, 3), -.5, .5, 0),
(fp.prim_star, (10, 3), -3, 3, -0.06666666666666667),
(fp.prim_rhombicuboctahedron, (24, 3), -4, 4, 0)]

for func, shape in l_primitives:
for func, shape, min, max, mean in l_primitives:
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min, max, mean are predefined by python so it is better to avoid this variable name. Can you change them? Just put e_min, .... the e is for expected

vertices, _ = func()

npt.assert_equal(vertices.shape, shape)
npt.assert_equal(np.mean(vertices), 0)
npt.assert_equal(vertices.min(), -.5)
npt.assert_equal(vertices.max(), 0.5)
npt.assert_equal(np.mean(vertices), mean)
npt.assert_equal(vertices.min(), min)
npt.assert_equal(vertices.max(), max)

vertices, _ = fp.prim_star(3)
npt.assert_equal(vertices.shape, (12, 3))
npt.assert_equal(np.mean(vertices), 0.1111111111111111)
npt.assert_equal(vertices.min(), -3)
npt.assert_equal(vertices.max(), 3)


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empty line to remove

def test_triangles_primitives():
Expand Down