def get_neighbors_around_minima(f, polyData, rd):
points = np.array(polyData.GetPoints().GetData())
gaussian = get_curvature_gaussian(rd)
Mean = get_curvature_mean(rd)
normals = get_normals(rd)
T_Tree = vtk.vtkKdTreePointLocator()
T_Tree.SetDataSet(polyData)
T_Tree.BuildLocator()
neighbours = []
neighbours.append([
points[f][0], points[f][1], points[f][2], 0, gaussian[f], Mean[f],
normals[f][0], normals[f][1], normals[f][2]
])
f = [points[f][0], points[f][1], points[f][2]]
result = vtk.vtkIdList()
num_of_neighbors = 200
T_Tree.FindClosestNPoints(num_of_neighbors, f, result)
for i in range(0, result.GetNumberOfIds()):
point_ind = result.GetId(i)
closestPoint = [0.0, 0.0, 0.0]
T_Tree.GetDataSet().GetPoint(point_ind, closestPoint)
distance = float(
math.sqrt(vtk.vtkMath.Distance2BetweenPoints(closestPoint, f)))
neighbours.append([
closestPoint[0], closestPoint[1], closestPoint[2], distance,
gaussian[point_ind], Mean[point_ind], normals[point_ind][0],
normals[point_ind][1], normals[point_ind][2]
])
y = np.array([np.array(xi) for xi in neighbours])
return np.array(neighbours)
def transfer_mesh_scalars_get_weighted_average_n_closest(
new_mesh, old_mesh, n=3):
kDTree = vtk.vtkKdTreePointLocator()
kDTree.SetDataSet(old_mesh)
kDTree.BuildLocator()
new_scalars = np.zeros(new_mesh.GetNumberOfPoints())
scalars_old_mesh = np.copy(
vtk_to_numpy(old_mesh.GetPointData().GetScalars()))
for new_mesh_pt_idx in range(new_mesh.GetNumberOfPoints()):
point = new_mesh.GetPoint(new_mesh_pt_idx)
closest_ids = vtk.vtkIdList()
kDTree.FindClosestNPoints(n, point, closest_ids)
list_scalars = []
distance_weighting = []
for closest_pts_idx in range(closest_ids.GetNumberOfIds()):
pt_idx = closest_ids.GetId(closest_pts_idx)
_point = old_mesh.GetPoint(pt_idx)
list_scalars.append(scalars_old_mesh[pt_idx])
distance_weighting.append(1 / np.sqrt(
np.sum(np.square(np.asarray(point) - np.asarray(_point)))))
total_distance = np.sum(distance_weighting)
normalized_value = np.sum(
np.asarray(list_scalars) *
np.asarray(distance_weighting)) / total_distance
new_scalars[new_mesh_pt_idx] = normalized_value
return new_scalars
def build_kd_tree(mesh):
"""
This function..
:param mesh:
:return:
"""
kd_tree = vtk.vtkKdTreePointLocator()
kd_tree.SetDataSet(mesh)
kd_tree.BuildLocator()
return kd_tree
def locator(filename):
vtk_reader = vtk.vtkXMLUnstructuredGridReader()
vtk_reader.SetFileName(filename)
vtk_reader.Update()
grid = vtk_reader.GetOutput()
kdtree = vtk.vtkKdTreePointLocator()
kdtree.SetDataSet(grid)
kdtree.BuildLocator()
time = numpy_support.vtk_to_numpy(grid.GetPointData().GetScalars())
return kdtree, time
def build_kd_tree(mesh):
"""
This function..
:param mesh:
:return:
"""
kd_tree = vtk.vtkKdTreePointLocator()
kd_tree.SetDataSet(mesh)
kd_tree.BuildLocator()
return kd_tree
def find_closest_point(vtk_obj, point=(0., 0., 0.)):
pointTree = vtk.vtkKdTreePointLocator()
pointTree.SetDataSet(vtk_obj)
pointTree.BuildLocator()
radius = None
if radius is None:
vtkId = pointTree.FindClosestPoint(point)
pcoord = vtk_obj.GetPoint(vtkId)
return vtkId, pcoord
def find_point_correspondence(mesh, points):
"""
Find the point IDs of the points on a VTK PolyData
Args:
mesh: the PolyData to find IDs on
points: vtk Points
Returns
IdList: list containing the IDs
"""
IdList = [None] * points.GetNumberOfPoints()
locator = vtk.vtkKdTreePointLocator()
locator.SetDataSet(mesh)
locator.BuildLocator()
for i in range(len(IdList)):
newPt = points.GetPoint(i)
IdList[i] = locator.FindClosestPoint(newPt)
return IdList
def keyPressEvent(self,obj,event):
key = self.parent.GetKeySym()
if key == 'Tab':
if self.ActiveSelection == 0:
self.ActiveSelection = 1
self.textActor.SetInput("Current selection: max point (green)")
print("To locate max point")
self.parent.GetRenderWindow().Render()
else:
self.ActiveSelection = 0
self.textActor.SetInput("Current selection: min point (red)")
print("To locate min point")
self.parent.GetRenderWindow().Render()
if key == "space":
self.parent.GetPicker().Pick(self.parent.GetEventPosition()[0],
self.parent.GetEventPosition()[1],
0, # always zero.
self.parent.GetRenderWindow().GetRenderers().GetFirstRenderer())
picked = self.parent.GetPicker().GetPickPosition();
# Create kd tree
kDTree = vtk.vtkKdTreePointLocator()
kDTree.SetDataSet(self.centerline)
kDTree.BuildLocator()
# Find the closest points to picked point
iD = kDTree.FindClosestPoint(picked)
# Get the coordinates of the closest point
closestPoint = kDTree.GetDataSet().GetPoint(iD)
if self.ActiveSelection == 0:
self.minSphereSource.SetCenter(closestPoint)
else:
self.maxSphereSource.SetCenter(closestPoint)
self.parent.GetRenderWindow().Render()
if key == "Return":
# Close the window
self.parent.GetRenderWindow().Finalize()
# Stop the interactor
self.parent.TerminateApp()
return
def FindNewLandmarks(vtkPoints, meanSurfaceFilename, dirOutput):
newLandmarks = vtk.vtkPoints()
reader = vtk.vtkPolyDataReader()
reader.SetFileName(meanSurfaceFilename)
reader.Update()
meanSurface = reader.GetOutput()
print(meanSurface.GetBounds())
kdTree = vtk.vtkKdTreePointLocator()
kdTree.SetDataSet(meanSurface)
kdTree.BuildLocator()
for index in range(vtkPoints.GetNumberOfPoints()):
point = [0, 0, 0]
closestPoint = [0, 0, 0]
vtkPoints.GetPoint(index, point)
print(point)
idx = kdTree.FindClosestPoint(point)
kdTree.GetDataSet().GetPoint(idx, closestPoint)
print(closestPoint)
newLandmarks.InsertNextPoint(closestPoint)
filename = meanSurfaceFilename[:-4] + '.txt'
WriteLandmarkFile(newLandmarks, filename)
def translesional_result(centerline_file, wall_file,vtk_file_list, output_dir,minPoint=(0,0,0), prox_dist=5, dist_dist=5):
# read centerline
centerlineReader = vtk.vtkXMLPolyDataReader()
centerlineReader.SetFileName(centerline_file)
centerlineReader.Update()
centerline = centerlineReader.GetOutput()
# read vessel wall
wallReader = vtk.vtkSTLReader()
wallReader.SetFileName(wall_file)
wallReader.Update()
# read vtk files
vtk_files = []
centerlines = []
if not os.path.exists(output_dir):
os.makedirs(output_dir)
if not os.path.exists(os.path.join(output_dir,"centerlines")):
os.makedirs(os.path.join(output_dir,"centerlines"))
# average filter
averageFilter = vtk.vtkTemporalStatistics()
for file_name in vtk_file_list:
reader = vtk.vtkUnstructuredGridReader()
reader.SetFileName(file_name)
reader.Update()
geomFilter = vtk.vtkGeometryFilter()
geomFilter.SetInputData(reader.GetOutput())
geomFilter.Update()
# scale up the CFD result
transform = vtk.vtkTransform()
transform.Scale(1000,1000,1000)
transformFilter = vtk.vtkTransformPolyDataFilter()
transformFilter.SetInputData(geomFilter.GetOutput())
transformFilter.SetTransform(transform)
transformFilter.Update()
vtk_files.append(transformFilter.GetOutput())
interpolator = vtk.vtkPointInterpolator()
interpolator.SetSourceData(transformFilter.GetOutput())
interpolator.SetInputData(centerline)
interpolator.Update()
# convert to desired unit
# get the first element pressure
try:
first_point_pressure = interpolator.GetOutput().GetPointData().GetArray("p").GetValue(0)
except:
first_point_pressure = 120
converter = vtk.vtkArrayCalculator()
converter.SetInputData(interpolator.GetOutput())
converter.AddScalarArrayName("p")
converter.SetFunction("120 + (p - {}) * 921 * 0.0075".format(first_point_pressure)) # 921 = mu/nu = density of blood, 0.0075 converts from Pascal to mmHg, offset 120mmHg at ica
converter.SetResultArrayName("p(mmHg)")
converter.Update()
converter2 = vtk.vtkArrayCalculator()
converter2.SetInputData(converter.GetOutput())
converter2.AddVectorArrayName("wallShearStress")
converter2.SetFunction("wallShearStress * 921") # 921 = mu/nu = density of blood, 0.0075 converts from Pascal to mmHg, http://aboutcfd.blogspot.com/2017/05/wallshearstress-in-openfoam.html
converter2.SetResultArrayName("wallShearStress(Pa)")
converter2.Update()
# output the probe centerline
centerline_output_path = os.path.join(
os.path.dirname(centerline_file),
output_dir,
"centerlines",
"centerline_probe_{}.vtp".format(os.path.split(file_name)[1].split("_")[1].split(".")[0])
)
centerlines.append(converter2.GetOutput())
averageFilter.SetInputData(converter2.GetOutput())
averageFilter.Update()
centerline = averageFilter.GetOutput()
# extract lesion section
# get the abscissas of min radius point
# Create kd tree
kDTree = vtk.vtkKdTreePointLocator()
kDTree.SetDataSet(centerline)
kDTree.BuildLocator()
minIdx = kDTree.FindClosestPoint(minPoint)
minPoint_absc = centerline.GetPointData().GetArray("Abscissas_average").GetTuple(minIdx)[0]
thresholdFilter = vtk.vtkThreshold()
thresholdFilter.ThresholdBetween(minPoint_absc-prox_dist,minPoint_absc+dist_dist)
thresholdFilter.SetInputData(centerline)
thresholdFilter.SetAllScalars(0) # important !!!
thresholdFilter.SetInputArrayToProcess(0, 0, 0, vtk.vtkDataObject.FIELD_ASSOCIATION_POINTS,"Abscissas_average");
thresholdFilter.Update()
# to vtkpolydata
geometryFilter = vtk.vtkGeometryFilter()
geometryFilter.SetInputData(thresholdFilter.GetOutput())
geometryFilter.Update()
# get closest line
connectFilter = vtk.vtkConnectivityFilter()
connectFilter.SetExtractionModeToClosestPointRegion()
connectFilter.SetClosestPoint(minPoint)
connectFilter.SetInputData(geometryFilter.GetOutput())
connectFilter.Update()
# compute result values
abscissas = vtk_to_numpy(thresholdFilter.GetOutput().GetPointData().GetArray("Abscissas_average"))
abscissas_unique, index = np.unique(sorted(abscissas), axis=0, return_index=True)
pressure = vtk_to_numpy(thresholdFilter.GetOutput().GetPointData().GetArray("p(mmHg)_average"))
pressure = [x for _, x in sorted(zip(abscissas,pressure))]
pressure = [pressure[x] for x in index]
pressure_gradient = np.diff(pressure)/np.diff(abscissas_unique)
velocity = vtk_to_numpy(thresholdFilter.GetOutput().GetPointData().GetArray("U_average"))
velocity = [math.sqrt(value[0]**2 + value[1]**2 +value[2]**2 ) for value in velocity]
velocity = [x for _, x in sorted(zip(abscissas,velocity))]
velocity = [velocity[x] for x in index]
velocity_gradient = np.diff(velocity)/np.diff(abscissas_unique)
vorticity = vtk_to_numpy(thresholdFilter.GetOutput().GetPointData().GetArray("vorticity_average"))
vorticity = [math.sqrt(value[0]**2 + value[1]**2 +value[2]**2 ) for value in vorticity]
vorticity = [x for _, x in sorted(zip(abscissas,vorticity))]
vorticity = [vorticity[x] for x in index]
vorticity_gradient = np.diff(vorticity)/np.diff(abscissas_unique)
wss = vtk_to_numpy(thresholdFilter.GetOutput().GetPointData().GetArray("wallShearStress(Pa)_average"))
wss = [math.sqrt(value[0]**2 + value[1]**2 +value[2]**2 ) for value in wss]
wss = [wss[x] for x in index]
wss = [x for _, x in sorted(zip(abscissas,wss))]
wss_gradient = np.diff(wss)/np.diff(abscissas_unique)
epsilon = 0.00001
p_ratio = np.mean(pressure[-4:-1])/(np.mean(pressure[0:3])+epsilon)
u_ratio = np.mean(velocity[-4:-1])/(np.mean(velocity[0:3])+epsilon)
w_ratio = np.mean(vorticity[-4:-1])/(np.mean(vorticity[0:3])+epsilon)
wss_ratio = np.mean(wss[-4:-1])/(np.mean(wss[0:3])+epsilon)
dp_ratio = np.mean(pressure_gradient[-4:-1])/(np.mean(pressure_gradient[0:3])+epsilon)
du_ratio = np.mean(velocity_gradient[-4:-1])/(np.mean(velocity_gradient[0:3])+epsilon)
dw_ratio = np.mean(vorticity_gradient[-4:-1])/(np.mean(vorticity_gradient[0:3])+epsilon)
dwss_ratio = np.mean(wss_gradient[-4:-1])/(np.mean(wss_gradient[0:3])+epsilon)
return_value = {
'translesion peak presssure(mmHg)': np.mean(heapq.nlargest(1, pressure)),
'translesion presssure ratio': p_ratio,
'translesion peak pressure gradient(mmHgmm^-1)': np.mean(heapq.nlargest(1, pressure_gradient)),
'translesion pressure gradient ratio': dp_ratio,
'translesion peak velocity(ms^-1)': np.mean(heapq.nlargest(1, velocity)),
'translesion velocity ratio': u_ratio,
'translesion velocity gradient ratio': du_ratio,
'translesion peak velocity gradient(ms^-1mm^-1)': np.mean(heapq.nlargest(1, velocity_gradient)),
'translesion peak vorticity(ms^-1)': np.mean(heapq.nlargest(1, vorticity)),
'translesion vorticity ratio': w_ratio,
'translesion vorticity gradient ratio': dw_ratio,
'translesion peak vorticity gradient(Pamm^-1)':np.mean(heapq.nlargest(1, vorticity_gradient)),
'translesion peak wss(Pa)': np.mean(heapq.nlargest(1, wss)),
'translesion peak wss gradient(Pamm^-1)': np.mean(heapq.nlargest(1, wss_gradient)),
'translesion wss ratio': wss_ratio,
'translesion wss gradient ratio': dwss_ratio,
}
return return_value
def probe_min_max_point(centerline_filename, surface_filename, minPoint=(0,0,0), maxPoint=(0,0,0),probe=True):
centerlineReader = vtk.vtkXMLPolyDataReader()
centerlineReader.SetFileName(centerline_filename)
centerlineReader.Update()
centerline = centerlineReader.GetOutput()
centerline.GetCellData().SetScalars(centerline.GetCellData().GetArray(2));
centerline.GetPointData().SetScalars(centerline.GetPointData().GetArray("Radius"));
surfaceReader = vtk.vtkSTLReader()
surfaceReader.SetFileName(surface_filename)
surfaceReader.Update()
surface = surfaceReader.GetOutput()
lut = vtk.vtkLookupTable()
# lut.SetNumberOfTableValues(3);
lut.Build()
# Fill in a few known colors, the rest will be generated if needed
# lut.SetTableValue(0, 1.0000, 0 , 0, 1);
# lut.SetTableValue(1, 0.0000, 1.0000, 0.0000, 1);
# lut.SetTableValue(2, 0.0000, 0.0000, 1.0000, 1);
centerlineMapper = vtk.vtkPolyDataMapper()
centerlineMapper.SetInputData(centerline)
centerlineMapper.SetScalarRange(0, centerline.GetPointData().GetScalars().GetMaxNorm());
centerlineMapper.SetLookupTable(lut);
centerlineMapper.SetScalarModeToUsePointData()
surfaceMapper = vtk.vtkPolyDataMapper()
surfaceMapper.SetInputData(surface)
scalarBar = vtk.vtkScalarBarActor()
scalarBar.SetLookupTable(centerlineMapper.GetLookupTable());
scalarBar.SetTitle("Radius");
scalarBar.SetNumberOfLabels(4);
scalarBar.SetWidth(0.08)
scalarBar.SetHeight(0.6)
scalarBar.SetPosition(0.9,0.1)
# auto find the smallest radius point
radius = centerline.GetPointData().GetArray("Radius")
# build kd tree to locate the nearest point
# Create kd tree
kDTree = vtk.vtkKdTreePointLocator()
kDTree.SetDataSet(centerline)
kDTree.BuildLocator()
minSource = vtk.vtkSphereSource()
if minPoint == (0,0,0):
minIdx = vtkArrayMin(radius)
closestPoint = centerline.GetPoint(minIdx)
else:
# Find the closest point to the picked point
iD = kDTree.FindClosestPoint(minPoint)
# Get the id of the closest point
closestPoint = kDTree.GetDataSet().GetPoint(iD)
minSource.SetCenter(closestPoint)
minSource.SetRadius(0.3);
minMapper = vtk.vtkPolyDataMapper()
minMapper.SetInputConnection(minSource.GetOutputPort());
minActor = vtk.vtkActor()
minActor.SetMapper(minMapper);
minActor.GetProperty().SetColor((1.0,0.0,0.0))
maxSource = vtk.vtkSphereSource()
if maxPoint == (0,0,0):
maxIdx = vtkArrayMin(radius)
closestPoint = centerline.GetPoint(maxIdx)
else:
# Find the closest point to the picked point
iD = kDTree.FindClosestPoint(maxPoint)
# Get the id of the closest point
closestPoint = kDTree.GetDataSet().GetPoint(iD)
maxSource.SetCenter(closestPoint)
maxSource.SetRadius(0.3);
maxMapper = vtk.vtkPolyDataMapper()
maxMapper.SetInputConnection(maxSource.GetOutputPort());
maxActor = vtk.vtkActor()
maxActor.SetMapper(maxMapper);
maxActor.GetProperty().SetColor((0.0,1.0,0.0))
centerlineActor = vtk.vtkActor()
centerlineActor.SetMapper(centerlineMapper)
surfaceActor = vtk.vtkActor()
surfaceActor.SetMapper(surfaceMapper)
surfaceActor.GetProperty().SetOpacity(0.3)
# text actor
usageTextActor = vtk.vtkTextActor()
usageTextActor.GetPositionCoordinate().SetCoordinateSystemToNormalizedViewport()
usageTextActor.GetPosition2Coordinate().SetCoordinateSystemToNormalizedViewport()
usageTextActor.SetPosition([0.001, 0.05])
usageTextActor.SetInput("Tab: Switch max/min point\nSpace: Locate max/min point\nEnter/Close Window: Process")
currentSelectionTextActor = vtk.vtkTextActor()
currentSelectionTextActor.GetPositionCoordinate().SetCoordinateSystemToNormalizedViewport()
currentSelectionTextActor.GetPosition2Coordinate().SetCoordinateSystemToNormalizedViewport()
currentSelectionTextActor.SetPosition([0.25, 0.1])
currentSelectionTextActor.SetInput("Current selection: min point (red)")
if probe:
renderer = vtk.vtkRenderer()
renderer.AddActor(centerlineActor)
renderer.AddActor(surfaceActor)
renderer.AddActor(minActor)
renderer.AddActor(maxActor)
renderer.AddActor2D(scalarBar)
renderer.AddActor(usageTextActor)
renderer.AddActor(currentSelectionTextActor)
renderWindow = vtk.vtkRenderWindow()
renderWindow.AddRenderer(renderer)
renderWindowInteractor = vtk.vtkRenderWindowInteractor()
renderWindowInteractor.SetRenderWindow(renderWindow)
mystyle = MyInteractorStyle(renderWindowInteractor)
mystyle.SetMaxSphereSource(maxSource)
mystyle.SetMinSphereSource(minSource)
mystyle.SetCenterline(centerline)
mystyle.SetSelectionTextActor(currentSelectionTextActor)
renderWindowInteractor.SetInteractorStyle(mystyle)
renderWindow.SetSize(1024,780); #(width, height)
renderWindow.Render()
renderWindowInteractor.Start()
minPoint = minSource.GetCenter()
maxPoint = maxSource.GetCenter()
# compute degree of stenosis
minIdx = kDTree.FindClosestPoint(minPoint)
minRadius = centerline.GetPointData().GetArray("Radius").GetTuple(minIdx)[0]
maxIdx = kDTree.FindClosestPoint(maxPoint)
maxRadius = centerline.GetPointData().GetArray("Radius").GetTuple(maxIdx)[0]
DoS = (1-minRadius/maxRadius)*100
tqdm.write("min radius = {:.2f}\nmax radius = {:.2f} mm\nDegree of stenosis = {:.2f} %".format(minRadius,maxRadius,DoS))
return DoS, minPoint, maxPoint
def moving_variance_matrix(centerline,fields, windows, minPoint=(0,0,0), bifurcationPoint=(0,0,0), result_path="", dev_result_path=""):
# create input array from centerline
thresholdFilter = vtk.vtkThreshold()
thresholdFilter.SetInputData(centerline)
thresholdFilter.SetInputArrayToProcess(0, 0, 0, vtk.vtkDataObject.FIELD_ASSOCIATION_CELLS, "CenterlineIds_average")
thresholdFilter.Update()
fig, axs = plt.subplots(len(fields),1)
fig.suptitle("CFD Moving Variance")
fig.set_size_inches(10,8)
fig2, axs2 = plt.subplots(len(fields),1)
fig2.suptitle("CFD Derivative Moving Variance")
fig2.set_size_inches(10,8)
# build kd tree to locate the nearest point
# Create kd tree
kDTree = vtk.vtkKdTreePointLocator()
kDTree.SetDataSet(centerline)
kDTree.BuildLocator()
# get the abscissas of bifurcation point
if bifurcationPoint != (0,0,0):
iD = kDTree.FindClosestPoint(bifurcationPoint)
# Get the id of the closest point
bifPointAbscissas = kDTree.GetDataSet().GetPointData().GetArray("Abscissas_average").GetTuple(iD)[0] - \
vtk_to_numpy(thresholdFilter.GetOutput().GetPointData().GetArray("Abscissas_average"))[0]
# get the abscissas of min point
if minPoint != (0,0,0):
iD = kDTree.FindClosestPoint(minPoint)
# Get the id of the closest point
minPointAbscissas = kDTree.GetDataSet().GetPointData().GetArray("Abscissas_average").GetTuple(iD)[0] - \
vtk_to_numpy(thresholdFilter.GetOutput().GetPointData().GetArray("Abscissas_average"))[0]
col_name = ["branch","window"] + fields
pmv_df = pd.DataFrame(columns=col_name)
col_name_dy = ["branch","window"] + [y+"_dev" for y in fields]
pmv_dy_df = pd.DataFrame(columns=col_name_dy)
for lineId in range(int(centerline.GetCellData().GetArray("CenterlineIds_average").GetMaxNorm())):
a_x = []
a_y = []
a_dy = []
thresholdFilter.ThresholdBetween(lineId,lineId)
thresholdFilter.Update()
# need at least 3 points to perform interpolation
if thresholdFilter.GetOutput().GetNumberOfPoints() < 4:
continue
for i in range(len(fields)):
x = vtk_to_numpy(thresholdFilter.GetOutput().GetPointData().GetArray("Abscissas_average"))
x = [(value - x[0]) for value in x]
y = vtk_to_numpy(thresholdFilter.GetOutput().GetPointData().GetArray(fields[i]))
if len(y.shape) > 1:
if y.shape[1] == 3:
y = [math.sqrt(value[0]**2 + value[1]**2 +value[2]**2 ) for value in y]
order = np.argsort(x)
xs = np.array(x)[order]
ys = np.array(y)[order]
unique, index = np.unique(xs, axis=-1, return_index=True)
xs = xs[index]
ys = ys[index]
f = interp1d(xs,ys,kind="cubic")
xnew = np.linspace(0, np.amax(x), num=50, endpoint=True)
ynew = f(xnew)
dy = np.gradient(ynew, xnew)
a_x.append(xnew)
a_y.append(ynew)
a_dy.append(dy)
a_x = np.array(a_x)
a_y = np.array(a_y)
a_dy = np.array(a_dy)
for window in windows:
mv = np.var(rolling_window(a_y, window) , axis=-1)
mv_dy = np.var(rolling_window(a_dy, window) , axis=-1)
pmv = np.amax(mv,axis=-1)
pmv = np.concatenate(([lineId,window],pmv))
pmv_df.loc[len(pmv_df)] = pmv
pmv_dy = np.amax(mv_dy,axis=-1)
pmv_dy = np.concatenate(([lineId,window],pmv_dy))
pmv_dy_df.loc[len(pmv_dy_df)] = pmv_dy
for i in range(len(fields)):
# plot moving variance
if len(fields) == 1:
ax = axs
ax2 = axs2
else:
ax = axs[i]
ax2 = axs2[i]
ax.plot(a_x[i,:],mv[i,:])
ax2.plot(a_x[i,:],mv_dy[i,:])
if fields[i] == "Radius_average":
ylabel = "Radius (mm)"
ymin = 0
ymax = 0.5
elif fields[i] == "U_average":
ylabel = "Velocity (ms^-1)"
ymin = 0
ymax = 0.5
elif fields[i] == "p(mmHg)_average":
ylabel = "Pressure (mmHg)"
ymin = 0
ymax = 1e3
elif fields[i] == "vorticity_average":
ylabel = "Vorticity (s^-1)"
ymin = 0
ymax = 1e7
elif fields[i] == "Curvature_average":
ylabel = "Curvature"
ymin = 0
ymax = 1e0
elif fields[i] == "Torsion_average":
ylabel = "Torsion"
ymin = 0
ymax = 1e9
if bifurcationPoint !=(0,0,0):
ax.axvline(x=bifPointAbscissas,ymin=0,ymax=1,linestyle="--",color='m')
ax2.axvline(x=bifPointAbscissas,ymin=0,ymax=1,linestyle="--",color='m')
if minPoint !=(0,0,0):
ax.axvline(x=minPointAbscissas,ymin=0,ymax=1,linestyle="--",color='c')
ax2.axvline(x=minPointAbscissas,ymin=0,ymax=1,linestyle="--",color='c')
ax.set_ylabel(ylabel)
ax2.set_ylabel(ylabel)
if i == (len(fields)-1):
ax.set_xlabel("Abscissas (mm)")
ax2.set_xlabel("Abscissas (mm)")
else:
ax.set_xticklabels([])
ax2.set_xticklabels([])
ax.set_xlim(x[0],x[-1])
ax.set_ylim(ymin,ymax)
ax2.set_xlim(x[0],x[-1])
ax2.set_ylim(ymin,ymax)
# save the plot
fig.savefig(result_path,dpi=100)
fig.clf()
fig2.savefig(dev_result_path,dpi=100)
fig2.clf()
plt.close("all")
pmv_df = pmv_df.groupby(['window']).max()
pmv_df = pmv_df.drop(columns=['branch'])
pmv_dy_df = pmv_dy_df.groupby(['window']).max()
pmv_dy_df = pmv_dy_df.drop(columns=['branch'])
return pmv_df, pmv_dy_df
def plot_centerline_result(centerline, array_names, result_path, dev_result_path ,minPoint=(0,0,0),bifurcationPoint=(0,0,0)):
thresholdFilter = vtk.vtkThreshold()
thresholdFilter.ThresholdBetween(1,9999)
thresholdFilter.SetInputData(centerline)
thresholdFilter.SetInputArrayToProcess(0, 0, 0, vtk.vtkDataObject.FIELD_ASSOCIATION_CELLS, "CenterlineIds_average")
thresholdFilter.Update()
x = vtk_to_numpy(thresholdFilter.GetOutput().GetPointData().GetArray("Abscissas_average"))
x = [(value - x[0]) for value in x]
kDTree = vtk.vtkKdTreePointLocator()
kDTree.SetDataSet(centerline)
kDTree.BuildLocator()
# get the abscissas of bifurcation point
if bifurcationPoint != (0,0,0):
iD = kDTree.FindClosestPoint(bifurcationPoint)
# Get the id of the closest point
bifPointAbscissas = kDTree.GetDataSet().GetPointData().GetArray("Abscissas_average").GetTuple(iD)[0] - \
vtk_to_numpy(thresholdFilter.GetOutput().GetPointData().GetArray("Abscissas_average"))[0]
# get the abscissas of min point
if minPoint != (0,0,0):
iD = kDTree.FindClosestPoint(minPoint)
# Get the id of the closest point
minPointAbscissas = kDTree.GetDataSet().GetPointData().GetArray("Abscissas_average").GetTuple(iD)[0] - \
vtk_to_numpy(thresholdFilter.GetOutput().GetPointData().GetArray("Abscissas_average"))[0]
fig, axs = plt.subplots(len(array_names),1)
fig.suptitle("CFD result")
fig.set_size_inches(10,8)
fig2, axs2 = plt.subplots(len(array_names),1)
fig2.suptitle("CFD result derivatives")
fig2.set_size_inches(10,8)
fit_dict= {}
for i in range(len(array_names)):
popt_list = []
for lineId in range(int(centerline.GetCellData().GetArray("CenterlineIds_average").GetMaxNorm())):
thresholdFilter.ThresholdBetween(lineId,lineId)
thresholdFilter.Update()
x = vtk_to_numpy(thresholdFilter.GetOutput().GetPointData().GetArray("Abscissas_average"))
x = [(value - x[0]) for value in x]
if len(x) < 3:
continue
y = vtk_to_numpy(thresholdFilter.GetOutput().GetPointData().GetArray(array_names[i]))
if len(y.shape) > 1:
if y.shape[1] == 3:
y = [math.sqrt(value[0]**2 + value[1]**2 +value[2]**2 ) for value in y]
if len(array_names) == 1:
ax = axs
ax2 = axs2
else:
ax = axs[i]
ax2 = axs2[i]
order = np.argsort(x)
xs = np.array(x)[order]
ys = np.array(y)[order]
unique, index = np.unique(xs, axis=-1, return_index=True)
xs = xs[index]
ys = ys[index]
f = interp1d(xs,ys,kind="cubic")
xs = np.linspace(0, np.amax(x), num=200, endpoint=True)
ys = f(xs)
dys = np.gradient(ys, xs)
ax.plot(xs,ys)
ax2.plot(xs,dys)
# curve fitting on specific values
if array_names[i] == "Radius_average" or array_names[i] == "U_average" or array_names[i] == "p(mmHg)_average":
try:
popt, pcov = curve_fit(fit_func, xs, dys, p0=[50,0.1,-50])
yfit = fit_func(xs, *popt)
ax2.plot(xs, fit_func(xs, *popt), 'k-.',label='fit: a=%5.3f, b=%5.3f, c=%5.3f' % tuple(popt))
except RuntimeError:
popt = [0,0,0]
popt_list.append(popt)
if array_names[i] == "Radius_average":
ylabel = "Radius (mm)"
ymin=0
ymax = 5
ymin2=-5
ymax2 = 5
elif array_names[i] == "U_average":
ylabel = "Velocity (ms^-1)"
ymin=0
ymax = 3
ymin2=-3
ymax2 = 3
elif array_names[i] == "p(mmHg)_average":
ylabel = "Pressure (mmHg)"
ymin=0
ymax = 180
ymin2=-180
ymax2 = 180
elif array_names[i] == "vorticity_average":
ylabel = "Vorticity (s^-1)"
ymin=0
ymax = 4000
ymin2=-4000
ymax2 = 4000
elif array_names[i] == "Curvature_average":
ylabel = "Curvature"
ymin = -1.5
ymax = 1.5
ymin2 = -1.5
ymax2 = 1.5
elif array_names[i] == "Torsion_average":
ylabel = "Torsion"
ymin = -100000
ymax = 100000
ymin2 = -100000
ymax2 = 100000
if bifurcationPoint !=(0,0,0):
ax.axvline(x=bifPointAbscissas,ymin=ymin,ymax=ymax,linestyle ="--",color='m')
ax2.axvline(x=bifPointAbscissas,ymin=ymin,ymax=ymax,linestyle ="--",color='m')
if minPoint !=(0,0,0):
ax.axvline(x=minPointAbscissas,ymin=ymin,ymax=ymax,linestyle ="--",color='c')
ax2.axvline(x=minPointAbscissas,ymin=ymin,ymax=ymax,linestyle ="--",color='c')
ax.set_ylabel(ylabel)
ax2.set_ylabel(ylabel)
if i == (len(array_names)-1):
ax.set_xlabel("Abscissas (mm)")
ax2.set_xlabel("Abscissas (mm)")
else:
ax.set_xticklabels([])
ax2.set_xticklabels([])
x = vtk_to_numpy(centerline.GetPointData().GetArray("Abscissas_average"))
ax.set_xlim(x[0],x[-1])
ax.set_ylim(ymin,ymax)
ax2.set_xlim(x[0],x[-1])
ax2.set_ylim(ymin2,ymax2)
# max of popt[0]
if len(popt_list) > 0:
fit_dict.update({array_names[i]: np.abs(np.amax(np.array(popt_list),axis=0)[0])})
# save the plot
fig.savefig(result_path,dpi=100)
fig.clf()
fig2.savefig(dev_result_path,dpi=100)
fig2.clf()
plt.close("all")
return fit_dict
def vtu_To_hf3inp_inc_MV_matIDs_Producer(inputfilename, surfaceMesh, outputfilename):
# ======================================================================
# Define matIDs --------------------------------------------------------
ID_UP = 21 # preliminary result, which gets overwritten by ID_ANT and ID_POST.
ID_DOWN = 20
ID_ANT = 17
ID_POST = 18
# ======================================================================
# get system arguments -------------------------------------------------
valve3dFilename_ = inputfilename
valve2dFilename_ = surfaceMesh
outputFilename_ = outputfilename
print " "
print "==========================================================================================="
print "=== Execute Python script to produce HiFlow3 inp file (incl. matIDs) for MVR-Simulation ==="
print "==========================================================================================="
print " "
# ======================================================================
# read in files: -------------------------------------------------------
# read in 3d valve
# NOTE: ensure that the precedent meshing algorithm (CGAL or similar)
# produces consistent/good results w.r.t. the 'normal glyphs'.
vtureader = vtk.vtkXMLUnstructuredGridReader()
vtureader.SetFileName(valve3dFilename_)
vtureader.Update()
valve3d_ = vtureader.GetOutput()
# get surface mesh of valve3d_
geometryFilter = vtk.vtkGeometryFilter()
if vtk.vtkVersion().GetVTKMajorVersion() >= 6:
geometryFilter.SetInputData(valve3d_)
else:
geometryFilter.SetInput(valve3d_)
geometryFilter.Update()
valve3dSurface_ = geometryFilter.GetOutput()
# compute normals of surface mesh
normalsSurface_ = vtk.vtkPolyDataNormals()
if vtk.vtkVersion().GetVTKMajorVersion() >= 6:
normalsSurface_.SetInputData(valve3dSurface_)
else:
normalsSurface_.SetInput(valve3dSurface_)
normalsSurface_.SplittingOn()
normalsSurface_.ConsistencyOn() # such that on a surface the normals are oriented either 'all' outward OR 'all' inward.
normalsSurface_.AutoOrientNormalsOn() # such that normals point outward or inward.
normalsSurface_.ComputePointNormalsOff() # adapt here. On/Off.
normalsSurface_.ComputeCellNormalsOn() # adapt here.
normalsSurface_.FlipNormalsOff()
normalsSurface_.NonManifoldTraversalOn()
normalsSurface_.Update()
# get cell normals
normalsSurfaceRetrieved_ = normalsSurface_.GetOutput().GetCellData().GetNormals() # adapt here.
# read in 2d valve -----------------------------------------------------
vtpreader = vtk.vtkXMLPolyDataReader()
vtpreader.SetFileName(valve2dFilename_)
vtpreader.Update()
valve2d_ = vtpreader.GetOutput()
# compute normals of valve2d_
normalsValve2d_ = vtk.vtkPolyDataNormals()
if vtk.vtkVersion().GetVTKMajorVersion() >= 6:
normalsValve2d_.SetInputData(valve2d_)
else:
normalsValve2d_.SetInput(valve2d_)
normalsValve2d_.SplittingOn()
normalsValve2d_.ConsistencyOn()
normalsValve2d_.ComputePointNormalsOff() # adapt here.
normalsValve2d_.ComputeCellNormalsOn()
normalsValve2d_.FlipNormalsOff()
normalsValve2d_.NonManifoldTraversalOn()
normalsValve2d_.Update()
# get cell normals
normalsValve2dRetrieved_ = normalsValve2d_.GetOutput().GetCellData().GetNormals() # adapt here.
print "Reading 3D and 2D-annotated input files: DONE."
# ======================================================================
# initialize cell locator for closest cell search ----------------------
# (using vtk methods, that find the closest point in a grid for an arbitrary point in R^3)
cellLocator = vtk.vtkCellLocator()
cellLocator.SetDataSet(valve2d_)
cellLocator.BuildLocator()
# ======================================================================
# allocate memory for cell_udlr_list_ (up-down-left-right) -------------
cell_udlr_list_ = [0 for i in range(valve3dSurface_.GetNumberOfCells())]
# ======================================================================
# iterate over the cells of the surface and compare normals ------------
for i in range(valve3dSurface_.GetNumberOfCells()):
# get cellId of closest point
iD = valve3dSurface_.GetCell(i).GetPointId(0) # NOTE: only one (test)point (0) of respective cell
testPoint = valve3dSurface_.GetPoint(iD)
closestPoint = np.zeros(3)
closestPointDist2 = vtk.mutable(0)
cellId = vtk.mutable(0)
subId = vtk.mutable(0)
cellLocator.FindClosestPoint(testPoint, closestPoint, cellId, subId, closestPointDist2)
normalSurf_ = np.zeros(3)
normalsSurfaceRetrieved_.GetTuple(i, normalSurf_)
normalV2d_ = np.zeros(3)
normalsValve2dRetrieved_.GetTuple(cellId, normalV2d_)
# set cell_udlr_list_ entry to (preliminary) "1", if cell is on upper side of leaflet
if np.dot(normalSurf_, normalV2d_) > 0.0:
cell_udlr_list_[i] = 1 # NOTE: "cell_udlr_list_[i] = 1" means "cell on upside".
# ======================================================================
# iterate over cells on the upper side of the leaflet surface, and set ids for left/right ------------------
kDTree = vtk.vtkKdTreePointLocator()
kDTree.SetDataSet(valve2d_)
kDTree.BuildLocator()
VertexIDs_ = valve2d_.GetPointData().GetArray('VertexIDs')
# allocate memory for upCellList_ (indicating if cell is on left/right side)
upCellList_ = [i for i in range(valve3dSurface_.GetNumberOfCells()) if cell_udlr_list_[i]]
for i in upCellList_:
iD = valve3dSurface_.GetCell(i).GetPointId(0)
testPoint = valve3dSurface_.GetPoint(iD)
result_ = vtk.vtkIdList()
counter = 1
cond_ = True
while cond_:
kDTree.FindClosestNPoints(counter, testPoint, result_)
for j in range(result_.GetNumberOfIds()):
iD2 = result_.GetId(j)
if int(VertexIDs_.GetTuple1(iD2)) == ID_ANT:
cond_ = False
cell_udlr_list_[i] = 2 # NOTE: "cell_udlr_list_[i] = 2" means "cell on ANT upside".
if int(VertexIDs_.GetTuple1(iD2)) == ID_POST:
cond_ = False
cell_udlr_list_[i] = 3 # NOTE: "cell_udlr_list_[i] = 3" means "cell on POST upside".
counter += 1
print "Computing hf3-inp MV matID information: DONE."
# ======================================================================
# write results to inp file --------------------------------------------
f = open(outputFilename_, 'w')
# write first line
s = str(valve3d_.GetNumberOfPoints()) + ' ' + str(valve3dSurface_.GetNumberOfCells()+valve3d_.GetNumberOfCells()) + ' 0 0 0\n'
f.write(s)
# write point coordinates
for i in range(valve3d_.GetNumberOfPoints()):
pt = valve3d_.GetPoint(i)
s = str(i) + ' ' + str(pt[0]) + ' ' + str(pt[1]) + ' ' + str(pt[2]) + '\n'
f.write(s)
# write connectivity information of triangles
# integer, material id, vertex point ids
for i in range(valve3dSurface_.GetNumberOfCells()):
cell = valve3dSurface_.GetCell(i)
iDs = cell.GetPointIds()
if cell_udlr_list_[i] == 2: # NOTE: "cell_udlr_list_[i] = 2" means "cell on ANT upside".
matId = ID_ANT
elif cell_udlr_list_[i] == 3: # NOTE: "cell_udlr_list_[i] = 3" means "cell on POST upside".
matId = ID_POST
else: # NOTE: "cell_udlr_list_[i] = 0" means "cell on downside".
matId = ID_DOWN
s = str(0) + ' ' + str(matId) + ' tri ' + str(iDs.GetId(0)) + ' ' + str(iDs.GetId(1)) + ' ' + str(iDs.GetId(2)) + '\n'
f.write(s)
# write connectivity information of tetrahedrons
# integer, material id, vertex point ids
for i in range(valve3d_.GetNumberOfCells()):
cell = valve3d_.GetCell(i)
iDs = cell.GetPointIds()
matId = 10
s = str(0) + ' ' + str(matId) + ' tet ' + str(iDs.GetId(0)) + ' ' + str(iDs.GetId(1)) + ' ' + str(iDs.GetId(2)) + ' ' + str(iDs.GetId(3)) + '\n'
f.write(s)
# close stream
f.close()
# ======================================================================
print "Writing HiFlow3 inp output file (incl. MV matIDs): DONE."
print "========================================================"
print " "
def create_kdtree(self, polydata=None):
tree = vtk.vtkKdTreePointLocator()
tree.SetDataSet(polydata)
tree.BuildLocator()
return tree
cN = [0.0, 0.0, 0.0]
p = [0.0, 0.0, 0.0]
size_points = normFilter.GetOutput().GetNumberOfPoints()
pointNormalsArray = vtk.vtkDoubleArray()
pointNormalsArray.SetNumberOfComponents(3)
pointNormalsArray.SetNumberOfTuples(10000000)
pts_Inner = vtk.vtkPoints()
for i in range(0, size_points):
normFilter.GetOutput().GetPoint(i, p)
pointNormalsRetrieved.GetTuple(i, cN)
pts_Inner.InsertNextPoint(p)
pointNormalsArray.SetTuple(i, cN)
kdTree = vtk.vtkKdTreePointLocator()
kdTree.SetDataSet(epicardial_wall)
kdTree.BuildLocator()
ps = [0.0, 0.0, 0.0]
pt = [0.0, 0.0, 0.0]
x = [0.0, 0.0, 0.0]
distmat = []
pts_Intersect = vtk.vtkPoints()
size_pts = endocardial_wall.GetNumberOfPoints()
for i in range(0, size_pts):
pts_Inner.GetPoint(i, ps)
iD = kdTree.FindClosestPoint(ps)
def __init__(self, pts):
ds = vtk.vtkPolyData()
ds.SetPoints(pts)
self.locator = vtk.vtkKdTreePointLocator()
self.locator.SetDataSet(ds)
self.locator.BuildLocator()
def GetSemiUniDistnaceGrid(
self, m_holePerSlice, m_numberOfSlice, m_errorTolerance=1, m_startPadding=0, m_endPadding=0, m_bufferDeg=40
):
"""
Obtain a set of coordinates roughly equal to a projection of periodic square grid vertex on the arm
surface. The gird also can arbitrarily has a buffer zone where no holes are drilled.
:param m_holePerSlice: [int] Desired number of holes per slice
:param m_numberOfSlice: [int] Desired number of slices
:param m_errorTolerance: [float] The maximum allowed deviation of hole coordinate from idea grid
:param m_startPadding: [int] Starting side padding where no holes will be drilled
:param m_endPadding: [int] Ending side padding where no holes will be drilled
:param m_bufferDeg: [float] Angle between planes where buffers zones are in between. Default to 40
:return: [list] List of hole coordinates
"""
vtkmath = vtk.vtkMath()
if not self._centerLine._IS_READ_FLAG:
self._centerLine.Read()
if self._bufferAngle != None:
m_bufferDeg = self._bufferAngle
m_totalDistance = 0
for i in xrange(
1 + int(m_startPadding / 0.3), self._centerLine._data.GetNumberOfPoints() - int(m_endPadding / 0.3)
):
m_totalDistance += self._centerLine.GetDistance(i, i - 1)
# Shrink the distance a bit before deviding it so that all intervals will lie in the padded segment
m_sliceSpacing = (m_totalDistance) * 0.98 / (m_numberOfSlice)
m_intervalIndexes = self._centerLine.GetEqualDistanceIntervalsIndex(
m_sliceSpacing, m_startPadding, m_endPadding
)
self._centerLineIntervals = m_intervalIndexes
m_tangents = []
for k in xrange(len(m_intervalIndexes)):
m_tmp = self._centerLine.GetNormalizedTangent(m_intervalIndexes[k], range=12, step=3)
m_tangents.append(m_tmp)
m_average = [sum([m_tangents[i][j] for i in xrange(3)]) / float(len(m_tangents)) for j in xrange(3)]
m_openingList = []
m_holeList = []
m_alphaNormal = None
m_masterPt = self._centerLine.GetPoint(m_intervalIndexes[0])
# Define cast opening zone and start drilling zone
if m_bufferDeg != None and self._openingMarker != None:
m_kdtree = vtk.vtkKdTreePointLocator()
m_kdtree.SetDataSet(self._centerLine._data)
m_kdtree.BuildLocator()
m_closestCenterlinePointId = m_kdtree.FindClosestPoint(self._openingMarker)
m_closestCenterlinePoint = self._centerLine.GetPoint(m_closestCenterlinePointId)
m_masterPt = m_closestCenterlinePoint
# Drill along intervals
for i in xrange(len(m_intervalIndexes)):
l_sliceCenter = self._centerLine.GetPoint(m_intervalIndexes[i])
l_slice = self.SliceSurface(l_sliceCenter, m_average)
if i == 0:
# Define the starting vector for all slice
# l_ringAlphaPt = l_slice.GetPoint(i)
l_ringAlphaVect = [self._openingMarker[j] - m_masterPt[j] for j in xrange(3)]
m_alphaNormal = [0, 0, 0]
vtkmath.Cross(m_average, l_ringAlphaVect, m_alphaNormal)
m_alphaNormalMag = sum([m_alphaNormal[i] for i in xrange(3)])
m_alphaNormal = [m_alphaNormal[i] / m_alphaNormalMag for i in xrange(3)]
# Define an initial accuracy which relax if no suitable points is found, affects calculation speed
m_loopAccuracy = 0.25
m_ringSliceAlphaVect = None
while m_ringSliceAlphaVect == None:
for j in xrange(l_slice.GetNumberOfPoints()):
l_ringSliceAlphaVect = [l_slice.GetPoint(j)[k] - l_sliceCenter[k] for k in xrange(3)]
# l_ringSliceMasterVect = [l_slice.GetPoint(j)[k] - m_masterPt[k] for k in xrange(3)]
if (
math.fabs(vtkmath.Dot(l_ringSliceAlphaVect, m_alphaNormal)) < m_loopAccuracy
and vtkmath.Dot(l_ringSliceAlphaVect, l_ringAlphaVect) > 0
):
m_ringSliceAlphaVect = l_ringSliceAlphaVect
break
m_loopAccuracy *= 2
if m_loopAccuracy >= 10:
raise ValueError("Slice Alpha Vector search reaches maximum tolerance")
break
l_uniformSectionDegree = (360.0 - m_bufferDeg) / m_holePerSlice
l_sectionDegree = (360.0 - m_bufferDeg) / m_holePerSlice
l_loopbreak = 0
m_openingList.append(
[l_ringSliceAlphaVect[k] + l_sliceCenter[k] for k in xrange(3)]
) # Include first vector
l_holeList = []
while len(l_holeList) < m_holePerSlice - 1:
if len(l_holeList) == 0:
l_sectionDegree += m_bufferDeg / 2
for j in xrange(l_slice.GetNumberOfPoints()):
l_p1 = [0.0, 0.0, 0.0]
l_ringVect = [l_slice.GetPoint(j)[k] - l_sliceCenter[k] for k in xrange(3)]
vtkmath.Cross(l_ringSliceAlphaVect, l_ringVect, l_p1)
l_p2 = vtkmath.Dot(l_p1, m_average)
l_angleBetweenRunningAndInitialVector = vtkmath.AngleBetweenVectors(
l_ringSliceAlphaVect, l_ringVect
)
if (
l_angleBetweenRunningAndInitialVector
> vtkmath.RadiansFromDegrees(l_sectionDegree - m_errorTolerance / 2)
and l_angleBetweenRunningAndInitialVector
< vtkmath.RadiansFromDegrees(l_sectionDegree + m_errorTolerance / 2.0)
and l_p2 > 0
):
l_ringSliceAlphaVect = l_ringVect
l_holeList.append([l_ringVect[k] + l_sliceCenter[k] for k in xrange(3)])
l_sectionDegree += l_uniformSectionDegree - vtkmath.DegreesFromRadians(
l_angleBetweenRunningAndInitialVector
)
break
if l_loopbreak == m_holePerSlice:
raise RuntimeError("Current error tolerence setting is to low to produce anything.")
l_loopbreak += 1
m_holeList.extend(l_holeList)
self._openingList = m_openingList
return m_holeList
def addCSVFile(self,fname,mode='folded',csvDelimiter=None):
self.setCaption(r' File:'+str(fname))
pts=np.loadtxt(fname,csvDelimiter)
points = vtk.vtkPoints()
r,t,z = rec2cyl(pts[:,0],pts[:,1],pts[:,2])
im_g=getGeomImperfection(r,z,np.mean(r))
if pts.shape[1] == 4:
useThickImp=True
else:
useThickImp=False
if useThickImp:
im_t=pts[:,3]
else:
im_t=np.zeros(pts.shape[0])
rid=r-im_g
if mode == 'unfolded':
tt=t*r.mean()
rr=im_g*self.scalingFactor
for i in range(0,pts.shape[0]):
points.InsertPoint(i,tt[i],z[i],rr[i] )
else:
xx,yy,zz=cyl2rec(rid+im_g*self.scalingFactor,t,z)
for i in range(0,pts.shape[0]):
points.InsertPoint(i,xx[i],yy[i],zz[i] )
polydata = vtk.vtkPolyData()
polydata.SetPoints(points)
polydata.Update()
if useThickImp:
imps=im_t
else:
imps=im_g
# imps=vtk.vtkFloatArray()
# if useThickImp:
# for i in range(0,polydata.GetNumberOfPoints()):
# imps.InsertNextValue(im_t[i])
# else:
# imps.InsertNextValue(im_g[i])
# polydata.GetPointData().SetScalars(imps);
#
surf =vtk.vtkSurfaceReconstructionFilter()
surf.SetInput(polydata)
surf.SetNeighborhoodSize(self.nbSize)
surf.SetSampleSpacing(self.sampleSpacing)
contourFilter = vtk.vtkContourFilter()
contourFilter.SetInputConnection(surf.GetOutputPort())
reverse = vtk.vtkReverseSense()
reverse.SetInputConnection(contourFilter.GetOutputPort())
reverse.ReverseCellsOn()
reverse.ReverseNormalsOn()
reverse.Update()
outputPolyData=reverse.GetOutput()
newSurf = self.transform_back( points, reverse.GetOutput());
pts2=np.zeros((newSurf.GetNumberOfPoints(),3))
for i in range(0,newSurf.GetNumberOfPoints()):
pts2[i,:]=newSurf.GetPoint(i)
r2,t2,z2 = rec2cyl(pts2[:,0],pts2[:,1],pts2[:,2])
kDTree = vtk.vtkKdTreePointLocator()
kDTree.SetDataSet(polydata)
kDTree.BuildLocator()
colors=vtk.vtkFloatArray()
for i in range(0,len(pts2)):
kid=kDTree.FindClosestPoint(pts2[i])
colors.InsertNextValue(imps[kid])
# if mode == 'folded':
# im2=getGeomImperfection(r2,z2,np.mean(r2))/self.scalingFactor
#
# if mode == 'unfolded':
# im2=pts2[:,2]/self.scalingFactor
#
# colors=vtk.vtkFloatArray()
# for i in range(0,newSurf.GetNumberOfPoints()):
# colors.InsertNextValue(im2[i])
newSurf.GetPointData().SetScalars(colors);
self.scalarRange=colors.GetRange()
self.lut=vtk.vtkLookupTable()
self.lut.SetNumberOfTableValues(100)
self.lut.SetTableRange(self.scalarRange)
self.lut.SetHueRange(0.667, 0.0)
self.lut.Build()
self.resP=newSurf.GetProducerPort()
self.colors=colors
self.outputs.append(newSurf)
mapper = vtk.vtkPolyDataMapper();
mapper.SetLookupTable(self.lut)
mapper.InterpolateScalarsBeforeMappingOn()
mapper.SetInputConnection(newSurf.GetProducerPort())
mapper.SetScalarModeToUsePointData()
mapper.ScalarVisibilityOn();
mapper.SetScalarRange(colors.GetRange())
surfaceActor = vtk.vtkActor();
surfaceActor.SetMapper(mapper);
self.boundBox=newSurf.GetBounds()
self.ren.AddActor(surfaceActor);
def BCdata_for_Hf3Sim_Producer(inputfilename, surfaceMesh, ringFilename, outputfilename):
# ======================================================================
# define number of given annulus point IDs -----------------------------
# (see notation/representation of Annuloplasty Rings by DKFZ and corresponding addInfo)
numberOfAnnulusPtIDs_ = 16
# get system arguments -------------------------------------------------
valve3dFilename_ = inputfilename
valve2dFilename_ = surfaceMesh
ringFilename_ = ringFilename
outputFilename_ = outputfilename
print " "
print "====================================================================================="
print "=== Execute Python script to produce BCdata for the HiFlow3-based MVR-Simulation ==="
print "====================================================================================="
print " "
# ======================================================================
# read in files: -------------------------------------------------------
# read in 3d valve
vtureader = vtk.vtkXMLUnstructuredGridReader()
vtureader.SetFileName(valve3dFilename_)
vtureader.Update()
valve3d_ = vtureader.GetOutput()
# get surface mesh of valve3d_
geometryFilter = vtk.vtkGeometryFilter()
if vtk.vtkVersion().GetVTKMajorVersion() >= 6:
geometryFilter.SetInputData(valve3d_)
else:
geometryFilter.SetInput(valve3d_)
geometryFilter.Update()
valve3dSurface_ = geometryFilter.GetOutput()
# read in 2d valve
vtpreader = vtk.vtkXMLPolyDataReader()
vtpreader.SetFileName(valve2dFilename_)
vtpreader.Update()
valve2d_ = vtpreader.GetOutput()
# read in ring
vtpreader = vtk.vtkXMLPolyDataReader()
vtpreader.SetFileName(ringFilename_)
vtpreader.Update()
ring_ = vtpreader.GetOutput()
# get vertex ids of valve2d_ and ring_ ---------------------------------
valve2dVertexIds_ = valve2d_.GetPointData().GetArray('VertexIDs')
ringVertexIds_ = ring_.GetPointData().GetArray('VertexIDs')
print "Reading input files: DONE."
# ======================================================================
# init. tree for closest point search ----------------------------------
kDTree = vtk.vtkKdTreePointLocator()
kDTree.SetDataSet(valve3dSurface_)
kDTree.BuildLocator()
# ======================================================================
# arrays for storage of coordinates of annulus points (and interpolated points) on the MV surface and on the ring -----------------
ringPoints_ = np.zeros((2*numberOfAnnulusPtIDs_,3))
valvePoints_ = np.zeros((2*numberOfAnnulusPtIDs_,3))
# Store coordiantes in arrays ---------------------------------------------------------------------------
# NOTE: Alternatively, instead of a loop over all points and looking for their IDs,
# one could also loop over the array of vertexIDs and get the pointID.
# find coordinates of points of ring_
for i in range(ring_.GetNumberOfPoints()):
if 0 <= int(ringVertexIds_.GetTuple1(i)) and int(ringVertexIds_.GetTuple1(i)) < numberOfAnnulusPtIDs_:
ringPoints_[int(ringVertexIds_.GetTuple1(i))] = np.array(ring_.GetPoint(i))
# find coordinates of points of valve2d_
for i in range(valve2d_.GetNumberOfPoints()):
if 0 <= int(valve2dVertexIds_.GetTuple1(i)) and int(valve2dVertexIds_.GetTuple1(i)) < numberOfAnnulusPtIDs_:
valvePoints_[int(valve2dVertexIds_.GetTuple1(i))] = np.array(valve2d_.GetPoint(i))
# find closest points to points stored in valvePoints_ on valve3dSurface_ and store (i.e. overwrite) them in valvePoints_
for i in range(numberOfAnnulusPtIDs_):
iD = kDTree.FindClosestPoint(valvePoints_[i])
kDTree.GetDataSet().GetPoint(iD, valvePoints_[i])
# ======================================================================
# add additional boundary conditions by linear interpolation -------------------------------------------
# NOTE: this requires the IDs to be ordered and going around annulus once!!!
for i in range(numberOfAnnulusPtIDs_):
valvePoints_[numberOfAnnulusPtIDs_+i] = 0.5 * (valvePoints_[i]+valvePoints_[(i+1)%numberOfAnnulusPtIDs_])
ringPoints_[numberOfAnnulusPtIDs_+i] = 0.5 * (ringPoints_[i]+ringPoints_[(i+1)%numberOfAnnulusPtIDs_])
# ======================================================================
# Compute displacements ------------------------------------------------
displacement_ = ringPoints_ - valvePoints_
# ======================================================================
# convert arrays to strings --------------------------------------------
valvePointString_ = ""
displacementString_ = ""
for i in range(2*numberOfAnnulusPtIDs_):
for j in range(3):
valvePointString_ += str(valvePoints_[i][j])
displacementString_ += str(displacement_[i][j])
if j == 2:
if i < 2*numberOfAnnulusPtIDs_-1:
valvePointString_ += ";"
displacementString_ += ";"
else:
valvePointString_ += ","
displacementString_ += ","
print "Computing BC data: DONE."
# ======================================================================
# Write BC data to XML file --------------------------------------------
# build a tree structure
root = ET.Element("Param")
BCData = ET.SubElement(root, "BCData")
DisplacementConstraintsBCs = ET.SubElement(BCData, "DisplacementConstraintsBCs")
numberOfDPoints = ET.SubElement(DisplacementConstraintsBCs, "NumberOfDisplacedDirichletPoints")
numberOfDPoints.text = str(2*numberOfAnnulusPtIDs_)
dDPoints = ET.SubElement(DisplacementConstraintsBCs, "dDPoints")
dDPoints.text = valvePointString_
dDisplacements = ET.SubElement(DisplacementConstraintsBCs, "dDisplacements")
dDisplacements.text = displacementString_
# wrap it in an ElementTree instance, and save as XML
tree = ET.ElementTree(root)
tree.write(outputFilename_)
# ======================================================================
print "Writing mvrSimBCdata.xml output file: DONE."
print "==========================================="
print " "
def execute(working_dir):
# convert vtk to stl
reader = vtk.vtkGenericDataObjectReader()
reader.SetFileName(os.path.join(working_dir, "surface.vtk"))
reader.Update()
surface = reader.GetOutput()
writer = vtk.vtkSTLWriter()
writer.SetFileName(os.path.join(working_dir, "surface.stl"))
writer.SetInputData(surface)
writer.Update()
# compute centerline
command = binary_path + " " + \
os.path.join(working_dir,"surface.stl") + " " + \
os.path.join(working_dir,"surface_capped.stl") + " " + \
os.path.join(working_dir,"centerline.vtp")
# os.system(command)
# crop equal distance from the defected zone
# load defected zone coordinate
defected_point = open(os.path.join(working_dir, "defected_point.fcsv"),
"r").readlines()[3]
defected_point = defected_point.split(",")[1:4]
defected_point = [float(i) for i in defected_point]
# load the centerline file
reader = vtk.vtkXMLPolyDataReader()
reader.SetFileName(os.path.join(working_dir, "centerline.vtp"))
reader.Update()
centerline = reader.GetOutput()
kdTree = vtk.vtkKdTreePointLocator()
kdTree.SetDataSet(centerline)
iD = kdTree.FindClosestPoint(defected_point)
end_id = centerline.GetNumberOfPoints() - 1
defected_point_absc = centerline.GetPointData().GetArray(
"Abscissas").GetComponent(iD, 0)
# find the start point
start_id = 0
start_point_absc = 0
start_point = [0, 0, 0]
start_point_tangent = [1, 0, 0]
start_point_normal = [0, 1, 0]
start_point_binormal = [0, 0, 1]
for i in range(centerline.GetNumberOfPoints() - 1):
if defected_point_absc - centerline.GetPointData().GetArray(
"Abscissas").GetComponent(i, 0) < dist_from_defect:
break
else:
start_id = i
start_point_absc = centerline.GetPointData().GetArray(
"Abscissas").GetComponent(i, 0)
start_point = list(centerline.GetPoints().GetPoint(i))
start_point_tangent = list(centerline.GetPointData().GetArray(
"FrenetTangent").GetTuple(i))
start_point_normal = list(
centerline.GetPointData().GetArray("FrenetNormal").GetTuple(i))
start_point_binormal = list(centerline.GetPointData().GetArray(
"FrenetBinormal").GetTuple(i))
print(start_id, start_point, start_point_tangent, start_point_normal,
start_point_binormal)
clipBoxes = []
clipPlanes = []
surface, clipBox, clipPlane = clip_polydata_by_box(surface, start_point,
start_point_tangent,
start_point_normal,
start_point_binormal)
centerline, _, _ = clip_polydata_by_box(centerline, start_point,
start_point_tangent,
start_point_normal,
start_point_binormal)
clipBoxes.append(clipBox)
clipPlanes.append(clipPlane)
# find end points
# split the polydata by centerline id
splitter = vtk.vtkThreshold()
splitter.SetInputData(centerline)
splitted_centerlines = []
for i in range(
int(centerline.GetCellData().GetArray("CenterlineIds").GetRange()
[1]) + 1):
splitter.ThresholdBetween(i, i)
splitter.SetInputArrayToProcess(
0, 0, 0, vtk.vtkDataObject.FIELD_ASSOCIATION_CELLS,
"CenterlineIds")
splitter.Update()
splitted_centerline = vtk.vtkPolyData()
splitted_centerline.DeepCopy(splitter.GetOutput())
splitted_centerlines.append(splitted_centerline)
end_ids = []
end_points = []
end_points_tangent = []
end_points_normal = []
end_points_binormal = []
for splitted_centerline in splitted_centerlines:
end_id = splitted_centerline.GetNumberOfPoints() - 1
end_point_absc = splitted_centerline.GetPointData().GetArray(
"Abscissas").GetComponent(
splitted_centerline.GetNumberOfPoints() - 1, 0)
end_point = list(splitted_centerline.GetPoints().GetPoint(
splitted_centerline.GetNumberOfPoints() - 1))
end_point_tangent = list(splitted_centerline.GetPointData().GetArray(
"FrenetTangent").GetTuple(splitted_centerline.GetNumberOfPoints() -
1))
end_point_normal = list(splitted_centerline.GetPointData().GetArray(
"FrenetNormal").GetTuple(splitted_centerline.GetNumberOfPoints() -
1))
end_point_binormal = list(
splitted_centerline.GetPointData().GetArray("FrenetBinormal").
GetTuple(splitted_centerline.GetNumberOfPoints() - 1))
for i in range(splitted_centerline.GetNumberOfPoints()):
if splitted_centerline.GetPointData().GetArray(
"Abscissas").GetComponent(
i, 0) - start_point_absc > 2 * dist_from_defect:
end_ids.append(end_id)
end_points.append(end_point)
end_points_tangent.append(end_point_tangent)
end_points_normal.append(end_point_normal)
end_points_binormal.append(end_point_binormal)
break
else:
end_id = i
end_point_absc = splitted_centerline.GetPointData().GetArray(
"Abscissas").GetComponent(i, 0)
end_point = list(splitted_centerline.GetPoints().GetPoint(i))
end_point_tangent = list(
splitted_centerline.GetPointData().GetArray(
"FrenetTangent").GetTuple(i))
end_point_normal = list(
splitted_centerline.GetPointData().GetArray(
"FrenetNormal").GetTuple(i))
end_point_binormal = list(
splitted_centerline.GetPointData().GetArray(
"FrenetBinormal").GetTuple(i))
if i == splitted_centerline.GetNumberOfPoints() - 1:
end_ids.append(end_id)
end_points.append(end_point)
end_points_tangent.append(end_point_tangent)
end_points_normal.append(end_point_normal)
end_points_binormal.append(end_point_binormal)
for i in range(len(end_ids)):
print(end_ids[i], end_points[i], end_points_tangent[i],
end_points_normal[i], end_points_binormal[i])
surface, clipBox, clipPlane = clip_polydata_by_box(
surface, end_points[i], end_points_tangent[i],
end_points_normal[i], end_points_binormal[i])
centerline, _, _ = clip_polydata_by_box(centerline, end_points[i],
end_points_tangent[i],
end_points_normal[i],
end_points_binormal[i])
clipBoxes.append(clipBox)
clipPlanes.append(clipPlane)
# connected component calculation on surface and centerline
connectedFilter = vtk.vtkConnectivityFilter()
# connectedFilter.SetExtractionModeToAllRegions()
# connectedFilter.ColorRegionsOn()
connectedFilter.SetExtractionModeToClosestPointRegion()
connectedFilter.SetClosestPoint(defected_point)
connectedFilter.SetInputData(surface)
connectedFilter.Update()
surface.DeepCopy(connectedFilter.GetOutput())
# output
vtpWriter = vtk.vtkXMLPolyDataWriter()
vtpWriter.SetFileName(os.path.join(working_dir, "surface_clipped.vtp"))
vtpWriter.SetInputData(surface)
vtpWriter.Update()
connectedFilter.SetInputData(centerline)
connectedFilter.Update()
centerline.DeepCopy(connectedFilter.GetOutput())
vtpWriter.SetFileName(os.path.join(working_dir, "centerline_clipped.vtp"))
vtpWriter.SetInputData(centerline)
vtpWriter.Update()
for i in range(len(clipBoxes)):
writer.SetFileName(
os.path.join(working_dir, "clip_box_" + str(i) + ".stl"))
writer.SetInputData(clipBoxes[i])
writer.Update()
writer.SetFileName(
os.path.join(working_dir, "clip_plane_" + str(i) + ".stl"))
writer.SetInputData(clipPlanes[i])
writer.Update()
def _run_interface(self, runtime):
labelmap = sitk.ReadImage(self.inputs.labels_file)
uncleanwm = readPolyData(self.inputs.wm_file)
uncleangm = readPolyData(self.inputs.gm_file)
if isdefined(self.inputs.atlas_info):
atlas_dict = parse_labels_xml(self.inputs.atlas_info)
# Clean the data
cleanwm = vtk.vtkCleanPolyData()
cleanwm.SetInputData(uncleanwm)
cleangm = vtk.vtkCleanPolyData()
cleangm.SetInputData(uncleangm)
cleanwm.Update()
cleangm.Update()
wmsurf = cleanwm.GetOutput()
gmsurf = cleangm.GetOutput()
# setup KdTrees for each surface
# this will help in finding the closest points
kdTreewm = vtk.vtkKdTreePointLocator()
kdTreewm.SetDataSet(wmsurf)
kdTreewm.BuildLocator()
kdTreegm = vtk.vtkKdTreePointLocator()
kdTreegm.SetDataSet(gmsurf)
kdTreegm.BuildLocator()
measurements = dict()
wmPD = wmsurf.GetPointData()
wmPoints = wmsurf.GetPoints()
wmCount = wmPD.GetNumberOfTuples()
for i in range(0, wmCount):
wmP = wmPoints.GetPoint(i)
# Find the closest point to the gray matter surface point
gmIndex = kdTreegm.FindClosestPoint(wmP)
gmP = kdTreegm.GetDataSet().GetPoint(gmIndex)
# Get the gray matter label from the label map
gmlabel = vtkPoint_to_label(gmP, labelmap)
if gmlabel != 0:
label = str(gmlabel)
else:
# if the gray matter label is not defined try the wm label
wmlabel = vtkPoint_to_label(wmP, labelmap)
if wmlabel != 0:
label = str(wmlabel)
else:
# label is not known
label = 'UNKNOWN'
# compute the distance
# distance from wm point to gm point
dst1 = distance.euclidean(wmP, gmP)
wmIndex = kdTreewm.FindClosestPoint(gmP)
wmP2 = kdTreegm.GetDataSet().GetPoint(wmIndex)
# distnace from gm to closest wm point
dst2 = distance.euclidean(gmP, wmP2)
# average the two distances
thickness = (dst1 + dst2) / 2
if not measurements.has_key(label):
# first point in a labeled region
measurements[label] = [thickness]
else:
measurements[label].append(thickness)
mu = ["mean"]
median = ["median"]
std = ["std"]
count = ["points"]
minimum = ["min"]
maximum = ["max"]
labels = ["label"]
for key in measurements.iterkeys():
labels.append(key)
data = np.array(measurements[key])
mu.append(np.mean(data))
median.append(np.median(data))
std.append(np.std(data))
count.append(len(data))
minimum.append(np.min(data))
maximum.append(np.max(data))
out_csv = self._list_outputs()['out_file']
with open(out_csv, 'w') as CSV_file:
writer = csv.writer(CSV_file)
writer.writerows([labels, mu, std, count, minimum, maximum])
return runtime
polyData = iter.GetCurrentDataObject()
if not polyData.IsA("vtkPolyData"):
print "ERROR: unexpected input (not vtkPolyData)"
exit(1)
nc = polyData.GetNumberOfCells()
print "boundary",boundary_id,":",nc
for i in range(nc):
cell = polyData.GetCell(i)
midpoint = get_midpoint(cell)
boundary_mid_points.InsertNextPoint(midpoint)
boundary_id_array.InsertNextValue(boundary_id)
boundary_id += 1
iter.GoToNextItem()
num_boundaries = boundary_id
loc = vtk.vtkKdTreePointLocator()
boundary_dataset = vtk.vtkPolyData()
boundary_dataset.SetPoints(boundary_mid_points)
loc.SetDataSet(boundary_dataset)
loc.BuildLocator()
# map from boundaries to a list of tuples containing point ids and the cell id
boundary_faces = []
for i in range(num_boundaries):
boundary_faces.append([])
internal_faces = []
volume.BuildLinks()
nc = volume.GetNumberOfCells()
def build_kd_tree(mesh):
kd_tree = vtk.vtkKdTreePointLocator()
kd_tree.SetDataSet(mesh)
kd_tree.BuildLocator()
return kd_tree
def normalizeVessels(case_dir,
dist_from_bif_inlet=35,
dist_from_bif_outlet=35):
# phases = ["baseline","baseline-post","12months","followup"]
phases = ["baseline"]
centerlines = {}
surfaces = {}
for phase in phases:
if not os.path.exists(os.path.join(case_dir, phase, "centerline.vtp")):
continue
# load the centerline file
reader = vtk.vtkXMLPolyDataReader()
reader.SetFileName(os.path.join(case_dir, phase, "centerline.vtp"))
reader.Update()
centerline = reader.GetOutput()
centerlines.update({phase: centerline})
# load surface files
if not os.path.exists(os.path.join(case_dir, phase, "surface.stl")):
continue
# reader = vtk.vtkGenericDataObjectReader()
reader = vtk.vtkSTLReader()
reader.SetFileName(os.path.join(case_dir, phase, "surface.stl"))
reader.Update()
surface = reader.GetOutput()
surfaces.update({phase: surface})
# get the bifurcation point from baseline data
# split the polydata by centerline id
splitter = vtk.vtkThreshold()
splitter.SetInputData(centerlines["baseline"])
splitter.ThresholdBetween(0, 0)
splitter.SetInputArrayToProcess(0, 0, 0,
vtk.vtkDataObject.FIELD_ASSOCIATION_CELLS,
"GroupIds")
splitter.Update()
mainBranch = splitter.GetOutput()
maxAbsc = 0
maxAbscId = 0
for i in range(mainBranch.GetNumberOfPoints()):
absc = mainBranch.GetPointData().GetArray("Abscissas").GetComponent(
i, 0)
if absc > maxAbsc:
maxAbsc = absc
maxAbscId = i
bifPoint = mainBranch.GetPoint(maxAbscId)
bifPoint_list = {}
bifPoint_absc_list = {}
bifPoint_id_list = {}
endPoint1_absc_list = {}
endPoint1_id_list = {}
endPoint2_absc_list = {}
endPoint2_id_list = {}
for key, centerline in centerlines.items():
kdTree = vtk.vtkKdTreePointLocator()
kdTree.SetDataSet(centerline)
iD = kdTree.FindClosestPoint(bifPoint)
bifPoint_absc_list.update({
key:
centerline.GetPointData().GetArray("Abscissas").GetComponent(
iD, 0)
})
bifPoint_id_list.update({key: iD})
splitter = vtk.vtkThreshold()
splitter.SetInputData(centerline)
splitter.SetInputArrayToProcess(
0, 0, 0, vtk.vtkDataObject.FIELD_ASSOCIATION_CELLS, "GroupIds")
splitter.ThresholdBetween(2, 2)
splitter.Update()
ACA = splitter.GetOutput()
endPoint1_absc_list.update({
key:
ACA.GetPointData().GetArray("Abscissas").GetComponent(
ACA.GetNumberOfPoints() - 1, 0) - bifPoint_absc_list[key]
})
endPoint1_id_list.update({key: ACA.GetNumberOfPoints() - 1})
splitter.ThresholdBetween(3, 3)
splitter.Update()
MCA = splitter.GetOutput()
endPoint2_absc_list.update({
key:
ACA.GetPointData().GetArray("Abscissas").GetComponent(
MCA.GetNumberOfPoints() - 1, 0) - bifPoint_absc_list[key]
})
endPoint2_id_list.update({key: ACA.GetNumberOfPoints() - 1})
# append the bifurcation point
bifPoint_list.update({key: bifPoint})
# get the start point coordinate
start_id = 0
start_point_absc = 0
start_point = [0, 0, 0]
start_point_tangent = [1, 0, 0]
start_point_normal = [0, 1, 0]
start_point_binormal = [0, 0, 1]
for i in range(centerlines["baseline"].GetNumberOfPoints()):
if (bifPoint_absc_list["baseline"] - centerlines["baseline"].GetPointData().GetArray("Abscissas").GetComponent(i,0) < min(bifPoint_absc_list.values())) and \
(bifPoint_absc_list["baseline"] - centerlines["baseline"].GetPointData().GetArray("Abscissas").GetComponent(i,0) < dist_from_bif_inlet):
break
else:
start_id = i
start_point_absc = centerlines["baseline"].GetPointData().GetArray(
"Abscissas").GetComponent(i, 0)
start_point = list(centerlines["baseline"].GetPoint(i))
start_point_tangent = list(
centerlines["baseline"].GetPointData().GetArray(
"FrenetTangent").GetTuple(i))
start_point_normal = list(
centerlines["baseline"].GetPointData().GetArray(
"FrenetNormal").GetTuple(i))
start_point_binormal = list(
centerlines["baseline"].GetPointData().GetArray(
"FrenetBinormal").GetTuple(i))
# get the end point coordinates
end_ids = []
end_points = []
end_points_tangent = []
end_points_normal = []
end_points_binormal = []
splitter = vtk.vtkThreshold()
splitter.SetInputData(centerlines["baseline"])
splitter.SetInputArrayToProcess(0, 0, 0,
vtk.vtkDataObject.FIELD_ASSOCIATION_CELLS,
"GroupIds")
groupdIds = [2, 3]
for groupId in groupdIds:
splitter.ThresholdBetween(groupId, groupId)
splitter.Update()
splitted_centerline = splitter.GetOutput()
end_id = splitted_centerline.GetNumberOfPoints() - 1
end_point_absc = splitted_centerline.GetPointData().GetArray(
"Abscissas").GetComponent(
splitted_centerline.GetNumberOfPoints() - 1, 0)
end_point = list(splitted_centerline.GetPoints().GetPoint(
splitted_centerline.GetNumberOfPoints() - 1))
end_point_tangent = list(splitted_centerline.GetPointData().GetArray(
"FrenetTangent").GetTuple(splitted_centerline.GetNumberOfPoints() -
1))
end_point_normal = list(splitted_centerline.GetPointData().GetArray(
"FrenetNormal").GetTuple(splitted_centerline.GetNumberOfPoints() -
1))
end_point_binormal = list(
splitted_centerline.GetPointData().GetArray("FrenetBinormal").
GetTuple(splitted_centerline.GetNumberOfPoints() - 1))
for i in range(splitted_centerline.GetNumberOfPoints()):
if groupId == 2:
endPoint_absc_list = endPoint1_absc_list.values()
else:
endPoint_absc_list = endPoint2_absc_list.values()
if (splitter.GetOutput().GetPointData().GetArray("Abscissas").GetComponent(i,0)-bifPoint_absc_list["baseline"]< min(endPoint_absc_list)) and \
(splitter.GetOutput().GetPointData().GetArray("Abscissas").GetComponent(i,0)-bifPoint_absc_list["baseline"] < dist_from_bif_outlet):
end_id = i
end_point_absc = splitted_centerline.GetPointData().GetArray(
"Abscissas").GetComponent(i, 0)
end_point = list(splitted_centerline.GetPoints().GetPoint(i))
end_point_tangent = list(
splitted_centerline.GetPointData().GetArray(
"FrenetTangent").GetTuple(i))
end_point_normal = list(
splitted_centerline.GetPointData().GetArray(
"FrenetNormal").GetTuple(i))
end_point_binormal = list(
splitted_centerline.GetPointData().GetArray(
"FrenetBinormal").GetTuple(i))
else:
end_ids.append(end_id)
end_points.append(end_point)
end_points_tangent.append(end_point_tangent)
end_points_normal.append(end_point_normal)
end_points_binormal.append(end_point_binormal)
break
if i == splitted_centerline.GetNumberOfPoints() - 1:
end_ids.append(end_id)
end_points.append(end_point)
end_points_tangent.append(end_point_tangent)
end_points_normal.append(end_point_normal)
end_points_binormal.append(end_point_binormal)
# clip the surfaces
clipBoxes = {}
clipPlanes = {}
boundaryCaps = {}
surfaces_clipped = {}
centerlines_clipped = {}
# connected component calculation on surface and centerline
connectedFilter = vtk.vtkConnectivityFilter()
# connectedFilter.SetExtractionModeToAllRegions()
# connectedFilter.ColorRegionsOn()
connectedFilter.SetExtractionModeToClosestPointRegion()
connectedFilter.SetClosestPoint(bifPoint)
key_point_list = {}
for key, surface in surfaces.items():
clipBoxes_ = {}
clipPlanes_ = {}
boundaryCaps_ = {}
key_point_list_ = {}
kdTree = vtk.vtkKdTreePointLocator()
kdTree.SetDataSet(centerlines[key])
iD = kdTree.FindClosestPoint(bifPoint_list[key])
kdTree.Update()
bif_point_ = list(centerlines[key].GetPoint(iD))
bif_point_tangent_ = list(centerlines[key].GetPointData().GetArray(
"FrenetTangent").GetTuple(iD))
bif_point_normal_ = list(centerlines[key].GetPointData().GetArray(
"FrenetNormal").GetTuple(iD))
bif_point_binormal_ = list(centerlines[key].GetPointData().GetArray(
"FrenetBinormal").GetTuple(iD))
bif_point_dict = {
"coordinate": bif_point_,
"tangent": bif_point_tangent_,
"normal": bif_point_normal_,
"binormal": bif_point_binormal_
}
key_point_list_.update({"BifurcationPoint": bif_point_dict})
iD = kdTree.FindClosestPoint(start_point)
kdTree.Update()
start_point_ = list(centerlines[key].GetPoint(iD))
start_point_tangent_ = list(centerlines[key].GetPointData().GetArray(
"FrenetTangent").GetTuple(iD))
start_point_normal_ = list(centerlines[key].GetPointData().GetArray(
"FrenetNormal").GetTuple(iD))
start_point_binormal_ = list(centerlines[key].GetPointData().GetArray(
"FrenetBinormal").GetTuple(iD))
start_point_dict = {
"coordinate": start_point_,
"tangent": start_point_tangent_,
"normal": start_point_normal_,
"binormal": start_point_binormal_
}
key_point_list_.update({"ICA": start_point_dict})
clip_result = clip_polydata_by_box(surface,
start_point_,
start_point_tangent_,
start_point_normal_,
start_point_binormal_,
size=[15, 15, 1],
capping=capping)
# perform lcc everytime after clipping to guarantee clean result
connectedFilter.SetInputData(clip_result["clipped_surface"])
connectedFilter.Update()
surface.DeepCopy(connectedFilter.GetOutput())
clipBoxes_.update({"ICA": clip_result["clip_box"]})
clipPlanes_.update({"ICA": clip_result["clip_plane"]})
connectedFilter_cap = vtk.vtkConnectivityFilter()
connectedFilter_cap.SetExtractionModeToClosestPointRegion()
connectedFilter_cap.SetClosestPoint([
start_point_[i] + start_point_tangent_[i]
for i in range(len(start_point_))
])
connectedFilter_cap.SetInputData(clip_result["boundary_cap"])
connectedFilter_cap.Update()
start_cap = vtk.vtkPolyData()
start_cap.DeepCopy(connectedFilter_cap.GetOutput())
boundaryCaps_.update({"ICA": start_cap})
for i in range(len(end_points)):
if i == 0:
outlet_key = "ACA"
else:
outlet_key = "MCA"
kdTree = vtk.vtkKdTreePointLocator()
kdTree.SetDataSet(centerlines[key])
iD = kdTree.FindClosestPoint(end_points[i])
kdTree.Update()
end_point_ = list(centerlines[key].GetPoint(iD))
end_point_tangent_ = list(centerlines[key].GetPointData().GetArray(
"FrenetTangent").GetTuple(iD))
end_point_normal_ = list(centerlines[key].GetPointData().GetArray(
"FrenetNormal").GetTuple(iD))
end_point_binormal_ = list(
centerlines[key].GetPointData().GetArray(
"FrenetBinormal").GetTuple(iD))
end_point_dict = {
"coordinate": end_point_,
"tangent": end_point_tangent_,
"normal": end_point_normal_,
"binormal": end_point_binormal_
}
key_point_list_.update({outlet_key: start_point_dict})
clip_result = clip_polydata_by_box(surface,
end_point_,
end_point_tangent_,
end_point_normal_,
end_point_binormal_,
size=[10, 10, 1],
capping=capping)
# perform lcc everytime after clipping to guarantee clean result
connectedFilter.SetInputData(clip_result["clipped_surface"])
connectedFilter.Update()
surface.DeepCopy(connectedFilter.GetOutput())
clipBoxes_.update({outlet_key: clip_result["clip_box"]})
clipPlanes_.update({outlet_key: clip_result["clip_plane"]})
connectedFilter_cap = vtk.vtkConnectivityFilter()
connectedFilter_cap.SetExtractionModeToClosestPointRegion()
connectedFilter_cap.SetClosestPoint([
end_point_[i] - end_point_tangent_[i]
for i in range(len(end_point_))
])
connectedFilter_cap.SetInputData(clip_result["boundary_cap"])
connectedFilter_cap.Update()
end_cap = vtk.vtkPolyData()
end_cap.DeepCopy(connectedFilter_cap.GetOutput())
# end_cap = clip_result["boundary_cap"]
boundaryCaps_.update({outlet_key: end_cap})
clipBoxes.update({key: clipBoxes_})
clipPlanes.update({key: clipPlanes_})
boundaryCaps.update({key: boundaryCaps_})
surfaces_clipped.update({key: surface})
key_point_list.update({key: key_point_list_})
for key, centerline in centerlines.items():
kdTree = vtk.vtkKdTreePointLocator()
kdTree.SetDataSet(centerlines[key])
iD = kdTree.FindClosestPoint(start_point)
kdTree.Update()
start_point_ = list(centerlines[key].GetPoint(iD))
start_point_tangent_ = list(centerlines[key].GetPointData().GetArray(
"FrenetTangent").GetTuple(iD))
start_point_normal_ = list(centerlines[key].GetPointData().GetArray(
"FrenetNormal").GetTuple(iD))
start_point_binormal_ = list(centerlines[key].GetPointData().GetArray(
"FrenetBinormal").GetTuple(iD))
clip_result = clip_polydata_by_box(centerline,
start_point_,
start_point_tangent_,
start_point_normal_,
start_point_binormal_,
size=[15, 15, 1])
centerline = clip_result["clipped_surface"]
for i in range(len(end_ids)):
kdTree = vtk.vtkKdTreePointLocator()
kdTree.SetDataSet(centerlines[key])
iD = kdTree.FindClosestPoint(end_points[i])
kdTree.Update()
end_point_ = list(centerlines[key].GetPoint(iD))
end_point_tangent_ = list(centerlines[key].GetPointData().GetArray(
"FrenetTangent").GetTuple(iD))
end_point_normal_ = list(centerlines[key].GetPointData().GetArray(
"FrenetNormal").GetTuple(iD))
end_point_binormal_ = list(
centerlines[key].GetPointData().GetArray(
"FrenetBinormal").GetTuple(iD))
clip_result = clip_polydata_by_box(centerline,
end_point_,
end_point_tangent_,
end_point_normal_,
end_point_binormal_,
size=[10, 10, 1])
centerline = clip_result["clipped_surface"]
connectedFilter.SetInputData(centerline)
connectedFilter.Update()
centerline.DeepCopy(connectedFilter.GetOutput())
centerlines_clipped.update({key: centerline})
# output
vtpWriter = vtk.vtkXMLPolyDataWriter()
for key, value in centerlines_clipped.items():
vtpWriter.SetFileName(
os.path.join(case_dir, key, "centerline_clipped.vtp"))
vtpWriter.SetInputData(value)
vtpWriter.Update()
stlWriter = vtk.vtkSTLWriter()
for key, value in surfaces_clipped.items():
stlWriter.SetFileName(
os.path.join(case_dir, key, "surface_clipped.stl"))
stlWriter.SetInputData(value)
stlWriter.Update()
for key, value in clipBoxes.items():
for key_, value_ in value.items():
stlWriter.SetFileName(
os.path.join(case_dir, key, "clip_box_" + key_ + ".stl"))
stlWriter.SetInputData(value_)
stlWriter.Update()
for key, value in clipPlanes.items():
for key_, value_ in value.items():
stlWriter.SetFileName(
os.path.join(case_dir, key, "clip_plane_" + key_ + ".stl"))
stlWriter.SetInputData(value_)
stlWriter.Update()
for key, value in boundaryCaps.items():
for key_, value_ in value.items():
stlWriter.SetFileName(
os.path.join(case_dir, key, "boundary_cap_" + key_ + ".stl"))
stlWriter.SetInputData(value_)
stlWriter.Update()
inletKeys = ["ICA", "ACA", "MCA"]
if stl_concat:
for phase in phases:
if not os.path.exists(
os.path.join(case_dir, phase, "surface_clipped.stl")):
continue
os.remove(os.path.join(case_dir, phase, "surface_capped.stl"))
# check nan and correct
mesh = trimesh.load_mesh(
os.path.join(case_dir, phase, "surface_clipped.stl"))
mesh.process()
mesh.export(os.path.join(case_dir, phase, "surface_clipped.stl"),
file_type='stl_ascii')
stl_text = open(
os.path.join(case_dir, phase,
"surface_clipped.stl")).read().splitlines(True)
stl_text[0] = "solid vessel\n"
stl_text.append("\n")
fout = open(os.path.join(case_dir, phase, "surface_capped.stl"),
'w')
fout.writelines(stl_text)
for inletKey in inletKeys:
# check nan and correct
mesh = trimesh.load_mesh(
os.path.join(
os.path.join(case_dir, phase,
"boundary_cap_" + inletKey + ".stl")))
mesh.process()
mesh.export(os.path.join(case_dir, phase,
"boundary_cap_" + inletKey + ".stl"),
file_type='stl_ascii')
stl_text = open(
os.path.join(case_dir, phase, "boundary_cap_" + inletKey +
".stl")).read().splitlines(True)
stl_text[0] = "solid " + inletKey + "\n"
stl_text.append("\n")
fout.writelines(stl_text)
fout.close()
# output keypoint as json file
for phase in phases:
if not os.path.exists(os.path.join(case_dir, phase)):
continue
with open(os.path.join(case_dir, phase, "inlets.json"), "w") as fp:
json.dump(key_point_list[phase], fp, indent=4)
