def signedDistance(f, box=None, parallel=False):
if box is not None:
adapt_box_to(f, box)
else:
create_box(f)
ncpus = mp.cpu_count() if parallel else 1
lib_exe.execute( lib_exe.mshdist + "-ncpu " + str(ncpus) + " -noscale box.1.o.mesh " + f + " > /dev/null 2>&1")
if os.path.exists("box.mesh"): os.remove("box.mesh")
if os.path.exists("box.1.mesh"): os.remove("box.1.mesh")
def create_box(f):
mesh = lib_msh.Mesh(f)
cube = lib_msh.Mesh(cube=[mesh.xmin, mesh.xmax, mesh.ymin, mesh.ymax, mesh.zmin, mesh.zmax])
cube.verts[:,:3] -= mesh.center
cube.verts[:,:3] *= 1.25
cube.verts[:,:3] += mesh.center
cube.write("box.mesh")
lib_exe.execute( lib_exe.tetgen + "-pgANEF box.mesh > /dev/null 2>&1" )
hausd = 0.02 * np.max(mesh.dims)
lib_exe.execute( lib_exe.mmg3d + "box.1.mesh -hausd %f -hmax %f > /dev/null 2>&1" % (hausd, hausd) )
def intersects(f):
lib_exe.execute(lib_exe.tetgen + "-d %s > log.txt" % (f))
res = True
with open("log.txt", "r") as f:
lines = f.readlines()
if "No faces are intersecting" in "".join(lines):
res = False
else:
res = True
os.remove("log.txt")
return res
def morph(f):
IN = os.path.join(directories["signed"], f)
OUT = os.path.join(directories["morphed"], f)
TMP = templates["morphing_skull"] if "Skull" in f else templates[
"morphing_face"]
REFS = [10, 2, 0] if "Skull" in f else [10, 2, 3]
with tempfile.TemporaryDirectory() as tmp:
os.chdir(tmp)
lib_exe.execute(
lib_exe.python_cmd("morph.py") +
"-t %s -s %s -o %s --icotris %d --icotets %d --fixtris %d -n %d"
% (TMP, IN, OUT, REFS[0], REFS[1], REFS[2], 250))
def adapt_box_to(f, box, maxNb=20000):
shutil.copyfile(box,"box.mesh")
cube = lib_msh.Mesh("box.mesh")
mesh = lib_msh.Mesh(f)
step = 1 if len(mesh.verts)<maxNb else int(len(mesh.verts)/maxNb)+1
dists, _ = nearest_neighbor(cube.verts[:,:3], mesh.verts[::step,:3])
cube.scalars = np.array(dists)
ABS = np.absolute(cube.scalars)
mini, maxi = 0.005*np.max(cube.dims), 0.5*np.max(cube.dims)
cube.scalars = mini + (maxi-mini) * (ABS - np.min(ABS)) / (np.max(ABS) - np.min(ABS))
cube.write("box.1.mesh")
cube.writeSol("box.1.sol")
lib_exe.execute(lib_exe.mmg3d + "box.1.mesh -hgrad 1.5 > /dev/null 2>&1")
def to_mesh(f, output):
#Convert a stl to mesh with meshlabserver
meshlabScript = os.path.join(os.path.dirname(os.path.abspath(__file__)),
"meshlab_scripts", "cleanSTL.mlx")
tmp = f.replace(".stl", ".obj")
lib_exe.execute(lib_exe.meshlabserver +
"-i %s -o %s -s %s > /dev/null 2>&1" %
(f, tmp, meshlabScript))
f = tmp
#Convert a .obj to .mesh
with open(f, "r") as _f:
LINES = _f.readlines()
mesh = lib_msh.Mesh()
mesh.verts = np.array([[float(x) for x in l.split()[1:]] for l in LINES
if l[0] == "v"])
mesh.tris = np.array([[int(x) - 1 for x in l.split()[1:]]
for l in LINES if l[0] == "f"])
mesh.verts = np.insert(mesh.verts, 3, 0, axis=1)
mesh.tris = np.insert(mesh.tris, 3, 0, axis=1)
mesh.computeBBox()
mesh.write(output)
if not os.path.splitext(args.input)[1] == ".mesh":
print(args.input + " is not a .mesh file")
sys.exit()
if not os.path.splitext(args.output)[1] == ".mesh":
print("Output file must be in the .mesh format")
sys.exit()
if intersects(args.input):
print(args.input + " has intersecting facets")
sys.exit()
mesh = lib_msh.Mesh(args.input)
ico = lib_msh.Mesh(ico=[args.center, args.radius])
ico.tris[:, -1] = 10
mesh.fondre(ico)
mesh.write("out.mesh")
lib_exe.execute(lib_exe.tetgen + "-pgANEYF out.mesh")
lib_exe.execute(lib_exe.mmg3d + "out.1.mesh -nosurf -o " + args.output)
os.remove(args.output.replace(".mesh", ".sol"))
#Make the same references in args.output than in out.mesh
def distance(a, b):
return ((a[0] - b[0])**2 + (a[1] - b[1])**2 + (a[2] - b[2])**2)**0.5
final = lib_msh.Mesh(args.output)
for i, t in enumerate(final.tris):
vert1 = final.verts[t[0]]
if distance(vert1, [0.5, 0.5, 0.65]) < 0.12:
final.tris[i, -1] = 10
final.write(args.output)
os.remove("out.mesh")
"--directory",
type=str,
help="directory containing the data to test",
required=True)
parser.add_argument("-m",
"--medit",
action="store_true",
help="visualize each result with medit")
args = parser.parse_args()
args.directory = os.path.abspath(args.directory)
# 1 - Carve a .mesh object
print("Testing carve.py")
IN = os.path.join(args.directory, "buddha.mesh")
OUT = os.path.join(args.directory, "buddha.carved.mesh")
lib_exe.execute(
lib_exe.python_cmd("carve.py") + "-i %s -o %s -r %d" % (IN, OUT, 31))
if args.medit: lib_exe.execute(lib_exe.medit + "%s" % (OUT))
os.remove(OUT)
# 2 - convert .obj and .stl objects to .mesh
print("Testing convert.py")
IN1 = os.path.join(args.directory, "buddha.obj")
OUT1 = os.path.join(args.directory, "buddha1.mesh")
lib_exe.execute(
lib_exe.python_cmd("convert.py") + "-i %s -o %s" % (IN1, OUT1))
IN2 = os.path.join(args.directory, "buddha.stl")
OUT2 = os.path.join(args.directory, "buddha2.mesh")
lib_exe.execute(
lib_exe.python_cmd("convert.py") + "-i %s -o %s" % (IN2, OUT2))
if args.medit: lib_exe.execute(lib_exe.medit + "%s %s" % (OUT1, OUT2))
buddha1 = lib_msh.Mesh(OUT1)
parser = argparse.ArgumentParser(description="Warps a mesh with a baloon-like object")
parser.add_argument("-i", "--input", type=str, help="Mesh to wrap", required=True)
parser.add_argument("-o", "--output", type=str, help="Output mesh", required=True)
parser.add_argument("-t", "--template", type=str, help="Template to wrap", required=True)
args = parser.parse_args(sys.argv[1:])
#checks
args.template = os.path.abspath(args.template) if args.template else None
args.input = os.path.abspath(args.input)
args.output = os.path.abspath(args.output)
#Copy the template to warp
shutil.copyfile(args.template, "sphere.mesh")
#Warp
lib_exe.execute(lib_paths.wrapping + " %s -p -nit %d -load %f > /dev/null 2>&1" % (args.input, 150, 40) )
#Clean the mesh and extract the surface
final = None
try:
number_max=-1
for f in [x for x in os.listdir(".") if "sphere.d." in x and ".mesh" in x]:
number = int(f.split(".")[2])
if number>number_max:
final = f
except:
final = "sphere.d.mesh"
warped = lib_msh.Mesh(final)
warped.tris = warped.tris[warped.tris[:,-1] != 2]
warped.tets = np.array([])
os.path.join(args.templates, d + ".mesh"))
return args, templates
if __name__ == "__main__":
#Get the templates and arguments
args, templates = init()
NAME = "reconstruction"
# 1 - If needed, convert the .obj or .stl objects to .mesh
for i, f in enumerate(args.input):
if f.endswith(".obj") or f.endswith(".stl"):
lib_exe.execute(
lib_exe.python_cmd("convert.py") + "-i %s -o %s" %
(f, f.replace(f[-3:], "mesh")))
args.input[i] = f.replace(f[-3:], "mesh")
# 2 - If needed, merge everything together
if len(args.input) > 1:
lib_exe.execute(
lib_exe.python_cmd("merge.py") + "-i %s -o %s" %
(" ".join(args.input), NAME + ".mesh"))
else:
shutil.copyfile(args.input[0], NAME + ".mesh")
# 3 - Transform to an object between 0.1 and 0.9
mesh = lib_msh.Mesh(NAME + ".mesh")
S = 0.8 / np.max(mesh.dims)
C = mesh.center
parser.add_argument("-d", "--icotris", type=int, help="Icosphere triangles reference", required=True)
parser.add_argument("-e", "--icotets", type=int, help="Icosphere tetrahedra reference", required=True)
parser.add_argument("-b", "--fixtris", type=int, help="Fixed triangles reference", required=True)
args = parser.parse_args(sys.argv[1:])
#checks
args.template = os.path.abspath(args.template)
args.signed = os.path.abspath(args.signed)
args.output = os.path.abspath(args.output)
# dref: Fixed surface inside the template (number + ref)
# elref: Elements inside the fixed surface
# bref: Follower elements
shutil.copyfile(args.template, "template.mesh")
cmd = lib_exe.morphing + " %s %s -nit %d -dref 1 %d -elref 1 %d -bref 1 %d > /dev/null 2>&1" % (args.signed, "template.mesh", args.iterations, args.icotris, args.icotets, args.fixtris)
lib_exe.execute(cmd)
#Clean the mesh
mesh = lib_msh.Mesh(args.signed[:-5] + ".1.mesh")
mesh.readSol( args.signed[:-5] + ".1.depl.sol")
mesh.tets = np.array([])
mesh.tris = mesh.tris[mesh.tris[:,-1]!=10]
mesh.discardUnused()
mesh.write(args.output)
mesh.writeSol(args.output.replace("mesh", "sol"))
#Remove the temporary files
os.remove(args.signed[:-5] + ".1.mesh")
os.remove(args.signed[:-5] + ".1.depl.sol")
help="Hausdorff distance",
default=0.01)
parser.add_argument("-r",
"--reference",
type=int,
help="New surface reference",
default=0)
parser.add_argument("-l",
"--levelset",
type=float,
help="Levelset value",
default=0)
args = parser.parse_args(sys.argv[1:])
#checks
args.input = os.path.abspath(args.input)
args.output = os.path.abspath(args.output)
lib_exe.execute(lib_exe.mmg3d + "%s -ls %f -hausd %f -o tmp.mesh" %
(args.input, args.levelset, args.distance))
mesh = lib_msh.Mesh("tmp.mesh")
mesh.tets = np.array([])
mesh.tris = mesh.tris[mesh.tris[:, -1] == 10]
mesh.discardUnused()
mesh.tris[:, -1] = args.reference
mesh.write(args.output)
os.remove("tmp.mesh")
os.remove("tmp.sol")
lib_exe.execute( lib_exe.mmg3d + "box.1.mesh -hausd %f -hmax %f > /dev/null 2>&1" % (hausd, hausd) )
def signedDistance(f, box=None, parallel=False):
if box is not None:
adapt_box_to(f, box)
else:
create_box(f)
ncpus = mp.cpu_count() if parallel else 1
lib_exe.execute( lib_exe.mshdist + "-ncpu " + str(ncpus) + " -noscale box.1.o.mesh " + f + " > /dev/null 2>&1")
if os.path.exists("box.mesh"): os.remove("box.mesh")
if os.path.exists("box.1.mesh"): os.remove("box.1.mesh")
if __name__ == "__main__":
#arguments
parser = argparse.ArgumentParser(description="Computes the signed distance to a .mesh file")
parser.add_argument("-i", "--input", type=str, help="Input mesh", required=True)
parser.add_argument("-o", "--output", type=str, help="Output mesh", required=True)
parser.add_argument("-v", "--volume", type=str, help="Volume mesh to adapt")
parser.add_argument("-p", action="store_true", help="Run in parallel", default=False)
args = parser.parse_args(sys.argv[1:])
#checks
args.input = os.path.abspath(args.input)
args.output = os.path.abspath(args.output)
args.volume = os.path.abspath(args.volume) if args.volume is not None else None
signedDistance(args.input, box=args.volume, parallel=args.p)
lib_exe.execute("mv box.1.o.mesh " + args.output)
lib_exe.execute("mv box.1.o.sol " + args.output.replace(".mesh",".sol"))
#Merge the meshes and run tetgen
exterior, interior = lib_msh.Mesh(args.exterior), lib_msh.Mesh(
args.interior)
#exterior.tris = exterior.tris[exterior.tris[:,-1]!=2]
exterior.tris[:, -1] = 2
exterior.discardUnused()
interior.tris[:, -1] = 1
interior.fondre(exterior)
interior.write("mask.mesh")
if intersects("mask.mesh"):
print("mask is self-intersecting")
sys.exit(3)
#Run tetgen
lib_exe.execute(lib_exe.tetgen + "-pgaANEFY mask.mesh")
for f in os.listdir("."):
if 'mask' in f and ".mesh" not in f and ".py" not in f:
os.remove(f)
lib_exe.execute(
lib_exe.mmg3d +
"-nosurf -nr -hgrad 1.75 mask.1.mesh -out mask.1.o.mesh"
) #Because the number of triangles is not good, therefore tetrahedra re not read!!
os.remove("mask.1.o.sol")
os.remove("mask.mesh")
os.remove("mask.1.mesh")
#Remove the inside of the mask
mesh = lib_msh.Mesh("mask.1.o.mesh")
ext_point_ind = np.argmin(mesh.verts[:, :3], axis=0)[0]
sys.exit()
if not os.path.splitext(args.output)[1] == ".mesh":
print("Output file must be in the .mesh format")
sys.exit()
if args.interiorIsovalue < args.exteriorIsovalue:
print("The inner shell must be closer than the outer shell")
sys.exit()
if args.interiorIsovalue < 5 or args.exteriorIsovalue < 5:
print("The shell must be closer than maxDim/5")
sys.exit()
args.input = os.path.abspath(args.input)
args.output = os.path.abspath(args.output)
#Carve the input mesh
lib_exe.execute(
lib_exe.python_cmd("carve.py") + "-i %s -o %s -r %d" %
(args.input, args.output.replace(".mesh", ".carved.mesh"), 31))
#Create a box and mesh it to compute the signed distance on
mesh = lib_msh.Mesh(args.input)
c = np.max(mesh.dims) / 8
cube = lib_msh.Mesh(cube=[
mesh.xmin - c, mesh.xmax + c, mesh.ymin - c, mesh.ymax + c, mesh.zmin -
c, mesh.zmax + c
])
cube.write("box.mesh")
lib_exe.execute(lib_exe.tetgen + "-pgANEF %s" % ("box.mesh"))
lib_exe.execute(
lib_exe.mmg3d + "%s -hausd %f -hmax %f" %
("box.1.mesh", np.max(mesh.dims) / 50, np.max(mesh.dims) / 25))