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"""
The module is used to extact centerlines from a surface mesh.
"""
import os
from pathlib import Path
import numpy as np
import logging
from .manage import get_logger_name
import vtk
from vtk.util.numpy_support import vtk_to_numpy as v2n
from .utils import SurfaceFileFormats, read_surface, read_polydata
[docs]class Centerlines(object):
"""
The Centerlines class is used to encapsulate centerline calculations.
"""
def __init__(self):
self.inlet_face_name = None
self.inlet_center = None
self.outlet_centers = None
self.outlet_face_names = None
self.geometry = None
self.cap_ids = None
self.logger = logging.getLogger(get_logger_name())
[docs] def read(self, params, file_name):
"""
Read centerlines from a .vtp file.
"""
self.geometry = read_polydata(file_name)
[docs] def get_inlet_outlet_centers(self, params):
"""
Get the centers of the inlet and outlet surface geometry.
Surface inlet and outlet faces are identifed by their file name.
"""
surf_mesh_dir = Path(params.boundary_surfaces_dir)
inlet_file_name = params.inlet_face_input_file
self.outlet_face_names = []
self.outlet_centers = []
for face_file in surf_mesh_dir.iterdir():
file_name = face_file.name
self.logger.debug("Surface file name: %s" % file_name)
file_suffix = face_file.suffix.lower()[1:]
if file_suffix not in SurfaceFileFormats or file_name.lower().startswith('wall'):
continue
if file_name == inlet_file_name:
inlet_path = str(face_file.absolute())
self.logger.info("Inlet file: %s" % inlet_path)
polydata = read_surface(inlet_path, file_suffix)
self.inlet_center = get_polydata_centroid(polydata)
self.inlet_face_name = face_file.stem
else:
outlet_path = str(face_file.absolute())
self.outlet_face_names.append(face_file.stem)
self.logger.info("Outlet: %s" % file_name)
polydata = read_surface(outlet_path, file_suffix)
# Use extend because vmtk expects a list of floats.
self.outlet_centers.extend(get_polydata_centroid(polydata))
if not self.inlet_face_name:
raise RuntimeError("No inlet face found in the boundary surface directory '%s'" % params.boundary_surfaces_dir)
# get surface points closest to cap centers
cp = ClosestPoints(read_surface(params.surface_model))
caps = np.vstack((self.inlet_center, np.array(self.outlet_centers).reshape(-1, 3)))
self.cap_ids = cp.search(caps)
self.logger.info("Number of outlet faces: %d" % len(self.outlet_centers))
[docs] def write_outlet_face_names(self, params):
"""
Write outlet face names
"""
file_name = os.path.join(params.output_directory, params.CENTERLINES_OUTLET_FILE_NAME)
self.logger.info("Write outlet face names to: %s" % file_name)
with open(file_name, "w") as fp:
for name in self.outlet_face_names:
fp.write(name+"\n")
[docs]def get_polydata_centroid(poly_data):
"""
Calculate the centroid of polydata
"""
return np.mean(v2n(poly_data.GetPoints().GetData()), axis=0).tolist()
[docs]def sv_centerlines(p):
"""
Call SimVascular centerline generation
"""
try:
import sv
except ImportError:
raise ImportError('Run with sv --python -- this_script.py')
# create a modeler
kernel = sv.modeling.Kernel.POLYDATA
modeler = sv.modeling.Modeler(kernel)
# read surface mesh
model = modeler.read(p['surf_in'])
model_polydata = model.get_polydata()
# generate centerline
# todo: try use_face_ids
centerlines_polydata = sv.vmtk.centerlines(model_polydata, [p['caps'][0]], p['caps'][1:], use_face_ids=False)
# write centerline to file
writer = vtk.vtkXMLPolyDataWriter()
writer.SetFileName(p['cent_out'])
writer.SetInputData(centerlines_polydata)
writer.Update()
writer.Write()
[docs]class ClosestPoints:
"""
Find closest points within a geometry
"""
def __init__(self, inp):
dataset = vtk.vtkPolyData()
dataset.SetPoints(inp.GetPoints())
locator = vtk.vtkPointLocator()
locator.Initialize()
locator.SetDataSet(dataset)
locator.BuildLocator()
self.locator = locator
[docs] def search(self, points):
"""
Get ids of points in geometry closest to input points
Args:
points: list of points to be searched
Returns:
Id list
"""
ids = []
for p in points:
ids += [self.locator.FindClosestPoint(p)]
return ids