def far_point_subsample(mesh, n, seed=None, center_scale=False):
# seed should be a dict with key mesh name and value list of seed vertices N x 3 (where N is number of points)
# return val is mesh object that I wrote
v = mesh.vertices
if seed is None:
seed_t = np.empty([0,0])
else:
seed_t = seed[mesh.name]
if n > v.shape[0] or n < seed_t.shape[0]:
raise ValueError('n larger than number of vertices or smaller than number of seed_t points')
if isinstance(seed_t, ndarray) and seed_t.size and v.shape[1] == 3 and v.ndim == 2:
if seed_t.ndim == 1 and seed_t.shape[0] == 3:
seed_t = np.array([seed_t])
# are s in v (or close enough?)
if all([any(all(isclose(x, v), 1)) for x in seed_t]):
# get ind for seed_t points
subidx = [where(all(isclose(x, v), axis=1))[0][0] for x in seed_t]
else:
raise ValueError('seed improperly formed, expecting n x 3 array')
else:
random.seed()
subidx = [random.randint(0, v.shape[0]-1)]
for i in range(len(subidx),n):
subidx.append(argmax(amin(cdist(v[subidx], v), axis=0)))
# list of integers that subsampled
return MeshFactory.mesh_from_data(v[subidx], center_scale=center_scale, name=mesh.name)
def exportAlignedMeshes(Auto3dgmData, exportFolder, phase=2):
from auto3dgm_nazar.mesh.meshexport import MeshExport
from auto3dgm_nazar.mesh.meshfactory import MeshFactory
if phase == 1:
label = "Phase 1"
elif phase == 2:
label = "Phase 2"
else:
raise ValueError(
'Unaccepted phase number passed to Auto3dgmLogic.exportAlignedMeshes'
)
m = Auto3dgmData.datasetCollection.datasets[0]
r = Auto3dgmData.datasetCollection.analysis_sets[
label].globalized_alignment['r']
for idx, mesh in enumerate(m):
new_vertices = np.transpose(r[idx] @ np.transpose(mesh.vertices))
new_faces = mesh.faces.astype('int64')
new_mesh = MeshFactory.mesh_from_data(new_vertices,
faces=new_faces,
name=mesh.name,
center_scale=True,
deep=True)
MeshExport.writeToFile(exportFolder, new_mesh, format='ply')
def ds_from_filelist(filelist):
meshes = []
mesheslist = []
for file in filelist:
meshes.append(MeshFactory.mesh_from_file(file))
mesheslist.append(meshes)
return (DatasetCollection(datasets=mesheslist))
def ds_from_dir(dir_path, center_scale=False):
c = [join(dir_path, x) for x in listdir(dir_path)]
files = [
f for f in c
if isfile(f) and splitext(f)[1] in DatasetFactory.__ftypes
]
if not files:
msg = 'No appropriate files were found in ' + dir_path
raise OSError(msg)
meshes = []
mesheslist = []
for file in files:
meshes.append(MeshFactory.mesh_from_file(file, center_scale))
mesheslist.append(meshes)
return (DatasetCollection(datasets=mesheslist))
def ds_from_meshdata(vertices, faces, deep=True):
for i in range(0, len(vertices)):
meshes.append(
MeshFactory.mesh_from_data(vertices[i], faces[i], deep))
mesheslist.append(meshes)
return (DatasetCollection(datasets=mesheslist))
array([[ 1.38777878e-16, 1.00000000e+00, 2.49800181e-16],
[ -1.11022302e-16, -3.60822483e-16, 1.00000000e+00],
[ 1.00000000e+00, -1.38777878e-17, 1.66533454e-16]]))
'''
print(AA[1])
'''
Out[40]:
array([[ 4.49640325e-15, 1.00000000e+00, -3.87190280e-15],
[ -3.94129174e-15, 3.94129174e-15, 1.00000000e+00],
[ 1.00000000e+00, -4.38538095e-15, 4.21884749e-15]])
'''
# So the alignment works as expected. However, when we integrate the mesh class:
mesh1 = MeshFactory.mesh_from_data(A)
mesh2 = MeshFactory.mesh_from_data(B)
BB = Correspondence.best_pairwise_PCA_alignment(mesh1, mesh2, 0)
print(BB)
'''
Out[45]:
(array([3, 1, 2, 0]), array([[ 0.18660992, -0.95001991, -0.25027765],
[ 0.02395067, -0.25027765, 0.96787781],
[ 0.9821421 , 0.18660992, 0.02395067]]))
'''
AA = Correspondence.locgpd(mesh1, mesh2, 0, 0, 5, 0)
print(AA[1])
#Test script for the mesh factory
from auto3dgm_nazar.mesh.meshfactory import MeshFactory
#Test case 0: Giving out a non-sense file
#Conditions: filestring refers to a non existing file
#Expect: When I try to create a mesh, I get an error
filestring = '/home/safari/Desktop/tutkimus/Slicer/HackathonJAN/testdata/20_Test_Teeth_PLY/Non-existing file.ply'
MeshFactory.mesh_from_file(filestring)
'''
In [27]: filestring='/home/safari/Desktop/tutkimus/Slicer/HackathonJAN/testdata/20_Test_Teeth_PLY/Non-existing file.ply'
In [28]: MeshFactory.mesh_from_file(filestring)
---------------------------------------------------------------------------
OSError Traceback (most recent call last)
<ipython-input-28-dce76620cc80> in <module>()
----> 1 MeshFactory.mesh_from_file(filestring)
/home/safari/Desktop/tutkimus/Slicer/HackathonJAN/gitstuff/auto3dgm/auto3dgm/mesh/meshfactory.py in mesh_from_file(file_path)
52 msg = 'File {} not present or not allowed filetype: {}'.format(
53 file_path, ', '.join(allowed_filetypes))
---> 54 raise OSError(msg)
55
56 @staticmethod
OSError: File /home/safari/Desktop/tutkimus/Slicer/HackathonJAN/testdata/20_Test_Teeth_PLY/Non-existing file.ply not present or not allowed filetype: .ply, .obj, .stl
'''
# Result: Success!
#Test case 1: Giving out an invalid
#Conditions: filestring refers to a file type not supported
#Expect: When I try to create a mesh, I get an error
def print_polyfaces(polydata):
cell_n = polydata.GetNumberOfCells()
point_n = polydata.GetCell(1).GetNumberOfPoints()
faces_new = zeros((cell_n, point_n), dtype=int)
for i in range(cell_n):
print('cell/polygon ' + str(i))
for j in range(point_n):
print(polydata.GetCell(i).GetPointId(j))
vertices = array([[0, 0, 0], [1, 0, 0], [1, 1, 0], [0, 1, 0], [2, 2, 1]],
dtype=int)
faces = array([[0, 1, 2], [1, 2, 3], [1, 3, 4], [2, 3, 0]], dtype=int)
mesh = MeshFactory.mesh_from_data(vertices, faces, False)
print(mesh)
print(mesh.vertices)
print(mesh.faces)
"""
Print output should look like this:
<auto3dgm.mesh.mesh.Mesh object at 0x1048962b0>
[[0. 0. 0.]
[1. 0. 0.]
[1. 1. 0.]
[0. 1. 0.]
[2. 2. 1.]]
[[0 1 2]
[1 2 3]
from auto3dgm_nazar.mesh.meshfactory import MeshFactory from auto3dgm_nazar.mesh.subsample import Subsample from numpy import array vertices = array([[0, 0, 0], [1, 0, 0], [1, 1, 0], [0, 1, 0], [2, 2, 1]]) seed = vertices[[1, 4]] mesh = MeshFactory.mesh_from_data(vertices) submesh_noseed = Subsample.far_point_subsample(mesh, 4) print(submesh_noseed) print(submesh_noseed.vertices) print(submesh_noseed.faces) submesh_seed = Subsample.far_point_subsample(mesh, 4, seed) print(submesh_seed) print(submesh_seed.vertices) print(submesh_seed.faces) """ Print results for first set will be random, but second set will be stable Print results should look something like this: <auto3dgm.mesh.mesh.Mesh object at 0x117cd5518> [[0 0 0] [2 2 1] [1 1 0] [1 0 0]] [] <auto3dgm.mesh.mesh.Mesh object at 0x10f5e31d0> [[1 0 0]