def save_to_mesh(file_path, v, f):
"""
v : vertex data.
f : face data.
"""
igl.write_triangle_mesh(file_path, v, f)
def transform(self, v: np.ndarray, f: np.ndarray) -> Tuple[np.ndarray, np.ndarray]:
# nv, nf, _, _, _ = igl.offset_surface(v, f, 0, 64, SIGNED_DISTANCE_TYPE_PSEUDONORMAL)
igl.write_triangle_mesh("/home/zgong8/temp/mc_tmp_in.obj", v, f)
subprocess.run(["/home/zgong8/libigl/tutorial/build/bin/705_MarchingCubes", "/home/zgong8/temp/mc_tmp_in.obj", "/home/zgong8/temp/mc_tmp_out_1.obj", "/home/zgong8/temp/mc_tmp_out_2.obj"])
nv, nf = igl.read_triangle_mesh("/home/zgong8/temp/mc_tmp_out_2.obj", np.float64)
return nv, nf
def write_mesh(data_dir, vert, face, input_name):
mesh_dir = os.path.join(data_dir, "meshes/")
sysutil.mkdirs(mesh_dir)
if vert.shape[0] < 10:
vert, face = np.array([[0, 0, 0.]]), np.array([[0, 0, 0]])
igl.write_triangle_mesh(os.path.join(mesh_dir, input_name + ".ply"),
vert,
face,
force_ascii=False)
def process_shape_file(self, in_file: str, out_file: str):
assert self.is_full()
vertices, faces = igl.read_triangle_mesh(in_file, np.float64)
new_vertices, new_faces = self.process_shape_data(vertices, faces)
if new_faces is not None:
if len(new_faces) < max_output_faces:
igl.write_triangle_mesh(out_file, new_vertices, new_faces)
return True
else:
print("Too large, bad for connection, dropped in the end.")
return False
def inner_surface(in_path, out_path, depth=1, nsteps=1):
'''compute inner surfaces from mesh at in_path, save results'''
# load input mesh
v, f = igl.read_triangle_mesh(in_path)
v2array = inner_surface_mesh(v, f, depth=depth, nsteps=nsteps)
if nsteps == 1:
igl.write_triangle_mesh(out_path, v2array[0], f, force_ascii=False)
else:
split = out_path.split(".")
for step in range(nsteps):
step_str = "%03i" % (step + 1)
out_path_step = ".".join([*(split[:-2]), step_str, split[-1]])
igl.write_triangle_mesh(out_path_step,
v2array[step],
f,
force_ascii=False)
try:
# get binary mask
nii = nib.load(in_file)
binary_mask = nii.get_fdata()
# get affine translation
dx = nii.affine[0][3]
dy = nii.affine[1][3]
dz = nii.affine[2][3]
aff = np.asarray([-dx, -dy, dz])
# print(nii.affine)
# create mesh
distance = distance_transform_edt(binary_mask)
verts, faces, _, _ = measure.marching_cubes(
distance,
0,
spacing=(abs(nii.affine[0][0]), abs(nii.affine[1][1]),
abs(nii.affine[2][2])),
gradient_direction="ascent",
method='lewiner')
# apply affine translation to vertices
verts2 = [v + aff for v in verts]
verts2 = np.asarray(verts2)
# save
igl.write_triangle_mesh(out_file, verts2, faces)
except:
print('ERROR: cannot create ' + sys.argv[2])
# make apex covariance sharper
c[0] *= 0.001
vs2, fs2 = loop_gps(v, f, c, 5)
# make apex covariance vertically anisotropic (reduce variance in x direction)
c[0] = [[0.001, 0, 0], [0, 0.01, 0], [0, 0, 0.01]]
vs3, fs3 = loop_gps(v, f, c, 5)
# make apex covariance horizontally anisotropic (reduce variance in y direction)
c[0] = [[0.01, 0, 0], [0, 0.001, 0], [0, 0, 0.01]]
vs4, fs4 = loop_gps(v, f, c, 5)
# make apex covariance horizontally anisotropic and super flat
c[0] = [[1, 0, 0], [0, 0.00001, 0], [0, 0, 1]]
vs5, fs5 = loop_gps(v, f, c, 5)
# save meshes to .off files
igl.write_triangle_mesh(os.path.join(root_folder, "data", "cone.off"), v, f)
print("Wrote control mesh to", os.path.join(root_folder, "data", "cone.off"))
igl.write_triangle_mesh(
os.path.join(root_folder, "data", "cone-pointy-gps.off"), vs2, fs2)
igl.write_triangle_mesh(
os.path.join(root_folder, "data", "cone-concave-gps.off"), vs3, fs3)
igl.write_triangle_mesh(
os.path.join(root_folder, "data", "cone-plateau-gps.off"), vs4, fs4)
igl.write_triangle_mesh(
os.path.join(root_folder, "data", "cone-cylinder-gps.off"), vs5, fs5)
print("Wrote GPS meshes to",
os.path.join(root_folder, "data", "cone-<variant>-gps.off"))
def main():
parser = argparse.ArgumentParser()
parser.add_argument('model_weights_path',
type=str,
help='path to the model checkpoint')
parser.add_argument('input_path', type=str, help='path to the input')
parser.add_argument('--disable_cuda',
action='store_true',
help='disable cuda')
parser.add_argument('--sample_cloud',
type=int,
help='run on sampled points')
parser.add_argument('--n_rounds',
type=int,
default=5,
help='number of rounds')
parser.add_argument('--prob_thresh',
type=float,
default=.9,
help='threshold for final surface')
parser.add_argument(
'--output',
type=str,
help='path to save the resulting high prob mesh to. also disables viz')
parser.add_argument('--output_trim_unused',
action='store_true',
help='trim unused vertices when outputting')
# Parse arguments
args = parser.parse_args()
set_args_defaults(args)
viz = not args.output
args.polyscope = False
# Initialize polyscope
if viz:
polyscope.init()
# === Load the input
if args.input_path.endswith(".npz"):
record = np.load(args.input_path)
verts = torch.tensor(record['vert_pos'],
dtype=args.dtype,
device=args.device)
surf_samples = torch.tensor(record['surf_pos'],
dtype=args.dtype,
device=args.device)
samples = verts.clone()
faces = torch.zeros((0, 3), dtype=torch.int64, device=args.device)
polyscope.register_point_cloud("surf samples", toNP(surf_samples))
if args.input_path.endswith(".xyz"):
raw_pts = np.loadtxt(args.input_path)
verts = torch.tensor(raw_pts, dtype=args.dtype, device=args.device)
samples = verts.clone()
faces = torch.zeros((0, 3), dtype=torch.int64, device=args.device)
polyscope.register_point_cloud("surf samples", toNP(verts))
else:
print("reading mesh")
verts, faces = utils.read_mesh(args.input_path)
print(" {} verts {} faces".format(verts.shape[0], faces.shape[0]))
verts = torch.tensor(verts, dtype=args.dtype, device=args.device)
faces = torch.tensor(faces, dtype=torch.long, device=args.device)
# verts = verts[::10,:]
if args.sample_cloud:
samples = mesh_utils.sample_points_on_surface(
verts, faces, args.sample_cloud)
else:
samples = verts.clone()
# === Load the model
print("loading model weights")
model = PointTriNet_Mesher()
model.load_state_dict(torch.load(args.model_weights_path))
model.eval()
with torch.no_grad():
# Sample lots of faces from the vertices
print("predicting")
candidate_triangles, candidate_probs = model.predict_mesh(
samples.unsqueeze(0), n_rounds=args.n_rounds)
candidate_triangles = candidate_triangles.squeeze(0)
candidate_probs = candidate_probs.squeeze(0)
print("done predicting")
# Visualize
high_prob = args.prob_thresh
high_faces = candidate_triangles[candidate_probs > high_prob]
closed_faces = mesh_utils.fill_holes_greedy(high_faces)
if viz:
polyscope.register_point_cloud("input points", toNP(samples))
spmesh = polyscope.register_surface_mesh("all faces",
toNP(samples),
toNP(candidate_triangles),
enabled=False)
spmesh.add_scalar_quantity("probs",
toNP(candidate_probs),
defined_on='faces')
spmesh = polyscope.register_surface_mesh(
"high prob mesh " + str(high_prob), toNP(samples),
toNP(high_faces))
spmesh.add_scalar_quantity(
"probs",
toNP(candidate_probs[candidate_probs > high_prob]),
defined_on='faces')
spmesh = polyscope.register_surface_mesh("hole-closed mesh " +
str(high_prob),
toNP(samples),
toNP(closed_faces),
enabled=False)
polyscope.show()
# Save output
if args.output:
high_prob = args.prob_thresh
out_verts = toNP(samples)
out_faces = toNP(high_faces)
out_faces_closed = toNP(closed_faces)
if args.output_trim_unused:
out_verts, out_faces, _, _ = igl.remove_unreferenced(
out_verts, out_faces)
igl.write_triangle_mesh(args.output + "_mesh.ply", out_verts,
out_faces)
write_ply_points(args.output + "_samples.ply", toNP(samples))
igl.write_triangle_mesh(args.output + "_pred_mesh.ply", out_verts,
out_faces)
igl.write_triangle_mesh(args.output + "_pred_mesh_closed.ply",
out_verts, out_faces_closed)
write_ply_points(args.output + "_samples.ply", toNP(samples))
# 1. Install miniconda (python 3.7 version, windows 64 bits)
# 2. In a miniconda terminal run conda install igl
# 3. Swap to this python compiler in pycharm
import igl
import numpy as np
import os
#Change this to point to your subject folder
root_folder = '.'
subject_id_usr = os.path.join(root_folder, 'subjects folder', 'subject_01')
#Make sure you've at least simplified the mesh of the subject
vertices = np.load(os.path.join(subject_id_usr, 'vertices_simple.npy'))
faces = np.load(os.path.join(subject_id_usr, 'faces_simple.npy'))
ret = igl.write_triangle_mesh(os.path.join(subject_id_usr, "bunny_out.obj"),
vertices, faces)
v, f = igl.read_triangle_mesh(os.path.join(subject_id_usr, "bunny_out.obj"))
[pd1, pd2, pv1, pv2] = igl.principal_curvature(v, f, radius=5, use_k_ring=True)
#Mean curvature is (pv1+pv2)/2 and Gaussian curvature is pv1*pv2
# k = igl.gaussian_curvature(v, f)
np.save(os.path.join(subject_id_usr, 'mean_curv_simple.npy'), (pv1 + pv2) / 2)
#Deletes temporary object
os.remove(os.path.join(subject_id_usr, "bunny_out.obj"))
def test_write_triangle_mesh(self):
ok = igl.write_triangle_mesh("out.obj", self.v, self.f)
self.assertEqual(ok, True)
def mesh_model(model, res_path, convert=True, all_edges=True):
fil = model.split("/")[-1][:-5]
folder = "/".join(model.split("/")[:-1])
with fileinput.FileInput(model, inplace=True) as fi:
for line in fi:
print(line.replace(
"UNCERTAINTY_MEASURE_WITH_UNIT( LENGTH_MEASURE( 1.00000000000000E-06 )",
"UNCERTAINTY_MEASURE_WITH_UNIT( LENGTH_MEASURE( 1.00000000000000E-17 )"
),
end='')
occ_steps = read_step_file(model)
bt = BRep_Tool()
for occ_cnt in range(len(occ_steps)):
if convert:
try:
nurbs_converter = BRepBuilderAPI_NurbsConvert(
occ_steps[occ_cnt])
nurbs_converter.Perform(occ_steps[occ_cnt])
nurbs = nurbs_converter.Shape()
except:
print("Conversion failed")
continue
else:
nurbs = occ_steps[occ_cnt]
mesh = BRepMesh_IncrementalMesh(occ_steps[occ_cnt], 0.9, False, 0.5,
True)
mesh.Perform()
if not mesh.IsDone():
print("Mesh is not done.")
continue
occ_topo = TopologyExplorer(nurbs)
occ_top = Topo(nurbs)
occ_topo1 = TopologyExplorer(occ_steps[occ_cnt])
occ_top1 = Topo(occ_steps[occ_cnt])
d1_feats = []
d2_feats = []
t_curves = []
tr_curves = []
stats = {}
stats["model"] = model
total_edges = 0
total_surfs = 0
stats["curves"] = []
stats["surfs"] = []
c_cnt = 0
t_cnt = 0
# Iterate over edges
for edge in occ_topo.edges():
curve = BRepAdaptor_Curve(edge)
stats["curves"].append(edge_map[curve.GetType()])
d1_feat = convert_curve(curve)
if edge_map[curve.GetType()] == "Other":
continue
for f in occ_top.faces_from_edge(edge):
if f == None:
print("Broken face")
continue
su = BRepAdaptor_Surface(f)
c = BRepAdaptor_Curve2d(edge, f)
t_curve = {
"surface": f,
"3dcurve": edge,
"3dcurve_id": c_cnt,
"2dcurve_id": t_cnt
}
t_curves.append(t_curve)
tr_curves.append(convert_2dcurve(c))
t_cnt += 1
d1_feats.append(d1_feat)
c_cnt += 1
total_edges += 1
patches = []
faces1 = list(occ_topo1.faces())
# Iterate over faces
for fci, face in enumerate(occ_topo.faces()):
surf = BRepAdaptor_Surface(face)
stats["surfs"].append(surf_map[surf.GetType()])
d2_feat = convert_surface(surf)
if surf_map[surf.GetType()] == "Other":
continue
for tc in t_curves:
if tc["surface"] == face:
patch = {
"3dcurves": [],
"2dcurves": [],
"orientations": [],
"surf_orientation": face.Orientation(),
"wire_ids": [],
"wire_orientations": []
}
for wc, fw in enumerate(occ_top.wires_from_face(face)):
patch["wire_orientations"].append(fw.Orientation())
if all_edges:
edges = [
i for i in WireExplorer(fw).ordered_edges()
]
else:
edges = list(occ_top.edges_from_wire(fw))
for fe in edges:
for ttc in t_curves:
if ttc["3dcurve"].IsSame(fe) and tc[
"surface"] == ttc["surface"]:
patch["3dcurves"].append(ttc["3dcurve_id"])
patch["2dcurves"].append(ttc["2dcurve_id"])
patch["wire_ids"].append(wc)
orientation = fe.Orientation()
patch["orientations"].append(orientation)
patches.append(patch)
break
location = TopLoc_Location()
facing = (bt.Triangulation(faces1[fci], location))
if facing != None:
tab = facing.Nodes()
tri = facing.Triangles()
verts = []
for i in range(1, facing.NbNodes() + 1):
verts.append(list(tab.Value(i).Coord()))
faces = []
for i in range(1, facing.NbTriangles() + 1):
index1, index2, index3 = tri.Value(i).Get()
faces.append([index1 - 1, index2 - 1, index3 - 1])
os.makedirs(res_path, exist_ok=True)
igl.write_triangle_mesh(
"%s/%s_%03i_mesh_%04i.obj" % (res_path, fil, occ_cnt, fci),
np.array(verts), np.array(faces))
d2_feat["faces"] = faces
d2_feat["verts"] = verts
else:
print("Missing triangulation")
continue
d2_feats.append(d2_feat)
total_surfs += 1
bbox = get_boundingbox(occ_steps[occ_cnt], use_mesh=False)
xmin, ymin, zmin, xmax, ymax, zmax = bbox[:6]
bbox1 = [
"%.2f" % xmin,
"%.2f" % ymin,
"%.2f" % zmin,
"%.2f" % xmax,
"%.2f" % ymax,
"%.2f" % zmax,
"%.2f" % (xmax - xmin),
"%.2f" % (ymax - ymin),
"%.2f" % (zmax - zmin)
]
stats["#edges"] = total_edges
stats["#surfs"] = total_surfs
# Fix possible orientation problems
if convert:
for p in patches:
# Check orientation of first curve
if len(p["2dcurves"]) >= 2:
cur = tr_curves[p["2dcurves"][0]]
nxt = tr_curves[p["2dcurves"][1]]
c_ori = p["orientations"][0]
n_ori = p["orientations"][1]
if c_ori == 0:
pole0 = np.array(cur["poles"][0])
pole1 = np.array(cur["poles"][-1])
else:
pole0 = np.array(cur["poles"][-1])
pole1 = np.array(cur["poles"][0])
if n_ori == 0:
pole2 = np.array(nxt["poles"][0])
pole3 = np.array(nxt["poles"][-1])
else:
pole2 = np.array(nxt["poles"][-1])
pole3 = np.array(nxt["poles"][0])
d02 = np.abs(pole0 - pole2)
d12 = np.abs(pole1 - pole2)
d03 = np.abs(pole0 - pole3)
d13 = np.abs(pole1 - pole3)
amin = np.argmin([d02, d12, d03, d13])
if amin == 0 or amin == 2: # Orientation of first curve incorrect, fix
p["orientations"][0] = abs(c_ori - 1)
# Fix all orientations
for i in range(len(p["2dcurves"]) - 1):
cur = tr_curves[p["2dcurves"][i]]
nxt = tr_curves[p["2dcurves"][i + 1]]
c_ori = p["orientations"][i]
n_ori = p["orientations"][i + 1]
if c_ori == 0:
pole1 = np.array(cur["poles"][-1])
else:
pole1 = np.array(cur["poles"][0])
if n_ori == 0:
pole2 = np.array(nxt["poles"][0])
pole3 = np.array(nxt["poles"][-1])
else:
pole2 = np.array(nxt["poles"][-1])
pole3 = np.array(nxt["poles"][0])
d12 = np.abs(pole1 - pole2)
d13 = np.abs(pole1 - pole3)
amin = np.min([d12, d13])
if amin == 1: # Incorrect orientation, flip
p["orientations"][i + 1] = abs(n_ori - 1)
features = {
"curves": d1_feats,
"surfaces": d2_feats,
"trim": tr_curves,
"topo": patches,
"bbox": bbox1
}
os.makedirs(res_path, exist_ok=True)
fip = fil + "_features2"
with open("%s/%s_%03i.yml" % (res_path, fip, occ_cnt), "w") as fili:
yaml.dump(features, fili, indent=2)
fip = fil + "_features"
with open("%s/%s_%03i.yml" % (res_path, fip, occ_cnt), "w") as fili:
features2 = copy.deepcopy(features)
for sf in features2["surfaces"]:
del sf["faces"]
del sf["verts"]
yaml.dump(features2, fili, indent=2)
# res_path = folder.replace("/step/", "/stat/")
# fip = fil + "_stats"
# with open("%s/%s_%03i.yml"%(res_path, fip, occ_cnt), "w") as fili:
# yaml.dump(stats, fili, indent=2)
print("Writing results for %s with %i parts." % (model, len(occ_steps)))
# 3. perform Gaussian-product subdivision
# note: igl.loop only handles 3D subdivs -> split the 9D mesh into three 3D ones
for _ in range(4):
qq1, f = igl.loop(qq1, cm.f)
qq2, f = igl.loop(qq2, cm.f)
qlin, cm.f = igl.loop(qlin, cm.f)
# 4. transform back to 3D
cm.v = np.zeros((len(qlin),3))
for i, ql in enumerate(qlin):
icov = [qq1[i],
[qq1[i][1], qq2[i][0], qq2[i][1]],
[qq1[i][2], qq2[i][1], qq2[i][2]]]
cm.v[i] = np.linalg.inv(icov) @ ql
#------------------------------------------------------------------------------------------
# save meshes to .off file
path = os.path.join(root_folder, "data", "tweety-loop.off")
igl.write_triangle_mesh(path, lmesh.v, lmesh.f)
print("Wrote Loop mesh to", path)
path = os.path.join(root_folder, "data", "tweety-gps.off")
igl.write_triangle_mesh(path, cm.v, cm.f)
print("Wrote GPS mesh to", path)
