def extract_faces(self,
id_faces_to_extract,
return_index=False,
name=None):
"""
Extracts a new mesh from a selection of faces ids
Parameters
----------
id_faces_to_extract : ndarray
Indices of faces that have to be extracted
return_index: bool, optional
Flag to output old indices
name: string, optional
Name for the new mesh
Returns
-------
Mesh
A new Mesh instance composed of the extracted faces
"""
nv = self.nb_vertices
# Determination of the vertices to keep
vertices_mask = np.zeros(nv, dtype=bool)
vertices_mask[self._faces[id_faces_to_extract].flatten()] = True
id_v = np.arange(nv)[vertices_mask]
# Building up the vertex array
v_extracted = self._vertices[id_v]
new_id__v = np.arange(nv)
new_id__v[id_v] = np.arange(len(id_v))
faces_extracted = self._faces[id_faces_to_extract]
faces_extracted = new_id__v[faces_extracted.flatten()].reshape(
(len(id_faces_to_extract), 4))
extracted_mesh = Mesh(v_extracted, faces_extracted)
for prop in self.__internals__:
if prop[:4] == "face":
extracted_mesh.__internals__[prop] = self.__internals__[prop][
id_faces_to_extract]
if name is None:
if self.name is not None and self.name.startswith(
"mesh_extracted_from_"):
extracted_mesh.name = self.name
else:
extracted_mesh.name = f"mesh_extracted_from_{self.name}"
else:
extracted_mesh.name = name
if return_index:
return extracted_mesh, id_v
else:
return extracted_mesh
def _read_nemoh_parameters(self, pyHDB, cal_file, test=True):
"""Reads the Nemoh parameters from the Nemoh.cal file
Parameters
----------
pyHDB : object
pyHDB object for storing the hydrodynamic database.
cal_file : str
Path (relative or absolute) to the Nemoh.cal file
test : bool, optional
If True (default), it will test against consistency between frequencies taken for BEM computations and
meshe's discretization
"""
if not os.path.exists(cal_file):
raise IOError("File %s not found" % cal_file)
with open(cal_file, 'r') as f:
# Getting root directory of the Nemoh computation project
abspath = os.path.abspath(cal_file)
dirname = os.path.dirname(abspath)
self.dirname = dirname
def skip_line():
f.readline()
# Environment parameters
skip_line()
skip_line() # Rho_water.
skip_line() # Grav.
skip_line() # Depth
skip_line() # xreff and yreff.
# Number of bodies
skip_line()
skip_line() # nb_bodies.
for ibody in range(pyHDB.nb_bodies):
skip_line()
meshfile = str(f.readline().split()[0])
abs_meshfile = os.path.join(dirname, meshfile)
# Instantiating mesh object
vertices, faces = load_MAR(abs_meshfile)
mesh = Mesh(vertices, faces)
nb_vertices, nb_faces = list(map(int, f.readline().split()[:2]))
# Verification of mesh information consistency
assert nb_vertices == mesh.nb_vertices
assert nb_faces == mesh.nb_faces
# De-symmetrizing meshes
with open(abs_meshfile, 'r') as fmesh:
_, isym = fmesh.readline().split()
if int(isym) == 1: # Mesh is symmetric
mesh.symmetrize(Plane([0, 1, 0]))
mesh.name, _ = os.path.splitext(meshfile)
# Instantiating BodyDB.
body = body_db.BodyDB(ibody, pyHDB.nb_bodies, pyHDB.nb_wave_freq, pyHDB.nb_wave_dir , mesh)
# RADIATION.
nb_dof = int(f.readline().split()[0])
for idof in range(nb_dof):
dof = f.readline().split()[:7]
motion_type = int(dof[0])
direction = list(map(float, dof[1:4]))
point = list(map(float, dof[4:]))
# Center of gravity.
body.position = point
if motion_type == 1: # Translation.
if(direction[0] == 1):
body.Motion_mask[0] = 1
elif(direction[1] == 1):
body.Motion_mask[1] = 1
elif(direction[2] == 1):
body.Motion_mask[2] = 1
else:
"The linear motion direction must be a unit vector ex, ey or ez. Generalized modes are not taken into account."
exit()
elif motion_type == 2: # Rotation.
if (direction[0] == 1):
body.Motion_mask[3] = 1
elif (direction[1] == 1):
body.Motion_mask[4] = 1
elif (direction[2] == 1):
body.Motion_mask[5] = 1
else:
"The angular motion direction must be a unit vector ex, ey or ez. Generalized modes are not taken into account."
exit()
else:
raise UnknownMotionMode(motion_type, abspath)
# INTEGRATION.
nb_force = int(f.readline().split()[0])
for iforce in range(nb_force):
force = f.readline().split()[:7]
force_type = int(force[0])
direction = list(map(float, force[1:4]))
point = list(map(float, force[4:]))
if force_type == 1: # Pure force
if (direction[0] == 1):
body.Force_mask[0] = 1
elif (direction[1] == 1):
body.Force_mask[1] = 1
elif (direction[2] == 1):
body.Force_mask[2] = 1
else:
"The force direction must be a unit vector ex, ey or ez. Generalized modes are not taken into account."
exit()
elif force_type == 2:
if (direction[0] == 1):
body.Force_mask[3] = 1
body.point[0,:] = point
elif (direction[1] == 1):
body.Force_mask[4] = 1
body.point[1, :] = point
elif (direction[2] == 1):
body.Force_mask[5] = 1
body.point[2, :] = point
else:
"The angular motion direction must be a unit vector ex, ey or ez. Generalized modes are not taken into account."
exit()
else:
raise UnknownForceMode(force_type, abspath)
# Skipping additional lines.
nb_add_line = int(f.readline().split()[0])
for i_add_line in range(nb_add_line):
skip_line()
# Add body to pyHDB.
pyHDB.append(body)
# Reading discretization.
skip_line()
# Getting frequency discretization.
skip_line()
# Getting wave directions discretization.
skip_line()
# Getting post-processing information
skip_line()
# Impulse response function
data = f.readline().split()[:3]
# has_irf = bool(int(data[0]))
# if has_irf:
# self.dt_irf, self.tf_irf = map(float, data[1:])
# TODO: si ok lire -> remettre en place si besoin...
# Show pressure
skip_line()
# self.has_pressure = bool(int(f.readline().split()[0])) # Enlever le skip_line() ci-dessus si décommenté.
# Kochin functions.
data = f.readline().split()[:3]
pyHDB.has_kochin = bool(float(data[0]))
if pyHDB.has_kochin:
pyHDB.nb_angle_kochin = int(data[0])
pyHDB.min_angle_kochin, pyHDB.max_angle_kochin = list(map(float, data[1:]))
pyHDB.set_wave_directions_Kochin()
# # TODO: si ok, lire -> remettre en place si besoin...
# # Free surface elevation
# data = f.readline().split()[:4]
# has_fs_elevation = bool(int(data[0]))
# if has_fs_elevation:
# self.nx_fs, self.ny_fs = map(int, data[:2])
# self.xlim_fs, self.ylim_fs = map(float, data[2:])
if test:
self.test_mesh_frequency_consistency(pyHDB)