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aux_functions.py
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import vtk
import math
import numpy as np
from vtk.util.numpy_support import numpy_to_vtk, vtk_to_numpy
import os
import sys
from scipy import sparse
import scipy.sparse.linalg as linalg_sp
from scipy.sparse import vstack, hstack, coo_matrix, csc_matrix
import csv
import seedselector
def seed_interactor(surface):
"""Interactor for seed selection. Needs VMTK"""
computer = seedselector.vmtkPickPointSeedSelector()
computer.SetSurface(surface)
computer.Execute()
return computer.GetSourceSeedIds()
def select_RA_seeds(surface, seeds_filename):
nseeds = 3
labels = [0, 1, 2]
if not os.path.exists(seeds_filename):
print('Select 3 seeds in this order: \n 1. Appendage extreme \n 2. Superior Vena Cava (SVC) \n 3. Inferior Vena Cava (IVC)')
seeds = seed_interactor(surface)
if not seeds.GetNumberOfIds() == nseeds:
print('You should select exactly', nseeds, ' seeds. Try again!')
seeds = seed_interactor(surface)
# create the mesh with seeds
newpoints = vtk.vtkPoints()
newvertices = vtk.vtkCellArray()
labels_array = vtk.vtkDoubleArray()
labels_array.SetName('seed_label')
for s in range(seeds.GetNumberOfIds()):
label = labels[s]
point = surface.GetPoint(seeds.GetId(s))
pid = newpoints.InsertNextPoint(point)
labels_array.InsertNextValue(label)
# Create the topology of the point (a vertex)
newvertices.InsertNextCell(1)
newvertices.InsertCellPoint(pid)
pointspd = vtk.vtkPolyData()
pointspd.SetPoints(newpoints)
pointspd.SetVerts(newvertices)
pointspd.GetPointData().AddArray(labels_array)
writevtk(pointspd, seeds_filename)
def mark_filled_holes(m_open, surface):
"""Add scalar array with value = 1 in the points corresponding to the filled holes"""
array_labels = np.zeros(surface.GetNumberOfPoints())
locator = vtk.vtkPointLocator()
locator.SetDataSet(m_open)
locator.BuildLocator()
for p in range(surface.GetNumberOfPoints()):
point = surface.GetPoint(p)
closestpoint_id = locator.FindClosestPoint(point)
dist = euclideandistance(point, m_open.GetPoint(closestpoint_id))
if dist > 0.05: # empirical
array_labels[p] = 1
newarray = numpy_to_vtk(array_labels)
newarray.SetName("hole")
surface.GetPointData().AddArray(newarray)
return surface
def identify_RA_contours(edges, seeds):
"""Given RA edges (hole contours) and manual seeds, separate and identify the different contours: TV (biggest), SVC and IVC"""
c0 = pointthreshold(edges, 'RegionId', 0, 0)
c1 = pointthreshold(edges, 'RegionId', 1, 1)
c2 = pointthreshold(edges, 'RegionId', 2, 2)
if c0.GetNumberOfPoints() > c1.GetNumberOfPoints() and c0.GetNumberOfPoints() > c2.GetNumberOfPoints():
tv_cont = c0
dist1 = euclideandistance(c1.GetPoint(0), seeds.GetPoint(1)) # distance from 2 other conts to SVC
dist2 = euclideandistance(c2.GetPoint(0), seeds.GetPoint(1))
if dist1 < dist2:
svc_cont = c1
ivc_cont = c2
else:
svc_cont = c2
ivc_cont = c1
if c1.GetNumberOfPoints() > c0.GetNumberOfPoints() and c1.GetNumberOfPoints() > c2.GetNumberOfPoints():
tv_cont = c1
dist1 = euclideandistance(c0.GetPoint(0), seeds.GetPoint(1)) # distance from 2 other conts to SVC
dist2 = euclideandistance(c2.GetPoint(0), seeds.GetPoint(1))
if dist1 < dist2:
svc_cont = c0
ivc_cont = c2
else:
svc_cont = c2
ivc_cont = c0
if c2.GetNumberOfPoints() > c0.GetNumberOfPoints() and c2.GetNumberOfPoints() > c1.GetNumberOfPoints():
tv_cont = c2
dist1 = euclideandistance(c0.GetPoint(0), seeds.GetPoint(1)) # distance from 2 other conts to SVC
dist2 = euclideandistance(c1.GetPoint(0), seeds.GetPoint(1))
if dist1 < dist2:
svc_cont = c0
ivc_cont = c1
else:
svc_cont = c1
ivc_cont = c0
return tv_cont, svc_cont, ivc_cont
def identify_ordered_RA_contours_in_to_be_flat_mesh(locator_open, tv_cont, svc_cont, ivc_cont):
"""Given to_be_flat_mesh and separated countours get the ordered list of ids corresponding to contours in the to_be_flat mesh"""
# get ordered contour
tv_conts = get_ordered_cont_ids_based_on_distance(tv_cont)
svc_conts = get_ordered_cont_ids_based_on_distance(svc_cont)
ivc_conts = get_ordered_cont_ids_based_on_distance(ivc_cont)
# get corresponding ordered contours in the to-be-flat mesh
tv_cont_ids = np.zeros(tv_conts.size)
svc_cont_ids = np.zeros(svc_conts.size)
ivc_cont_ids = np.zeros(ivc_conts.size)
for i in range(tv_cont_ids.shape[0]):
p = tv_cont.GetPoint(tv_conts[i])
tv_cont_ids[i] = int(locator_open.FindClosestPoint(p))
for i in range(svc_cont_ids.shape[0]):
p = svc_cont.GetPoint(svc_conts[i])
svc_cont_ids[i] = int(locator_open.FindClosestPoint(p))
for i in range(ivc_cont_ids.shape[0]):
p = ivc_cont.GetPoint(ivc_conts[i])
ivc_cont_ids[i] = int(locator_open.FindClosestPoint(p))
return tv_cont_ids, svc_cont_ids, ivc_cont_ids
def project_paths_to_open_mesh(m_open, locator_open, path0, path1, path2):
"""Given to_be_flat mesh, corresponding locator and computed dividing paths,
project paths to the to_be_flat mesh.
They will be used to identify boundary/dividing paths intersecting points"""
s0_ids = np.array([])
for i in range(path0.GetNumberOfPoints()): # these paths are already ordered
p = path0.GetPoint(i)
p_id = locator_open.FindClosestPoint(p)
if euclideandistance(m_open.GetPoint(p_id), p) < 0.01: # if close enough, append
s0_ids = np.append(s0_ids, p_id)
s1_ids = np.array([])
for i in range(path1.GetNumberOfPoints()):
p = path1.GetPoint(i)
p_id = locator_open.FindClosestPoint(p)
if euclideandistance(m_open.GetPoint(p_id), p) < 0.01:
s1_ids = np.append(s1_ids, p_id)
s2_ids = np.array([])
for i in range(path2.GetNumberOfPoints()):
p = path2.GetPoint(i)
p_id = locator_open.FindClosestPoint(p)
if euclideandistance(m_open.GetPoint(p_id), p) < 0.01:
s2_ids = np.append(s2_ids, p_id)
return s0_ids, s1_ids, s2_ids
def create_dividing_paths(surface, id_tv0, id_tv1, id_svc, id_ivc, args):
path0 = find_create_path(surface, id_tv0, id_svc)
path1 = find_create_path(surface, id_svc, id_ivc)
path2 = find_create_path(surface, id_ivc, id_tv1)
writevtk(path0, os.path.join(args.meshfile[0:len(args.meshfile) - 4] + 'path0.vtk'))
writevtk(path1, os.path.join(args.meshfile[0:len(args.meshfile) - 4] + 'path1.vtk'))
writevtk(path2, os.path.join(args.meshfile[0:len(args.meshfile) - 4] + 'path2.vtk'))
return path0, path1, path2
def find_tv_extremes(contour, seeds, locator):
"""Identify TV extremes, i.e. intersections with paths connecting to SVC and IVC"""
# find closest point in TV contour to IVC and SVC seeds
locator_tv = vtk.vtkPointLocator()
locator_tv.SetDataSet(contour)
locator_tv.BuildLocator()
id_0 = locator_tv.FindClosestPoint(seeds.GetPoint(1))
id_1 = locator_tv.FindClosestPoint(seeds.GetPoint(2))
# in surface
id_tv0 = locator.FindClosestPoint(contour.GetPoint(id_0))
id_tv1 = locator.FindClosestPoint(contour.GetPoint(id_1))
return id_tv0, id_tv1
def reorder_tv(surface, locator_open, tv_cont_ids, id_tv0, id_tv1, args):
"""order tv_cont_ids to start in TV1 (connection with IVC)"""
final_tv1 = int(locator_open.FindClosestPoint(surface.GetPoint(id_tv1)))
final_tv0 = int(locator_open.FindClosestPoint(surface.GetPoint(id_tv0)))
reordered_tv_cont = np.append(tv_cont_ids[int(np.where(tv_cont_ids == final_tv1)[0]): tv_cont_ids.shape[0]],
tv_cont_ids[0: int(np.where(tv_cont_ids == final_tv1)[0])]).astype(int)
if args.flip == True:
aux = np.zeros(reordered_tv_cont.size)
for i in range(reordered_tv_cont.size):
aux[reordered_tv_cont.size - 1 - i] = reordered_tv_cont[i]
# mantain the first point (after the flip is the last one)
reordered_tv_cont = np.append(aux[aux.size - 1], aux[0:aux.size - 1]).astype(int)
return reordered_tv_cont
def reorder_ivc(ivc_cont_ids, s2_ids, args):
"""order ivc_cont_ids to start in the last point of s2_ids (intersection of path2 and IVC contour)"""
ivc0 = s2_ids[s2_ids.shape[0] - 1]
reordered_ivc_cont = np.append(ivc_cont_ids[int(np.where(ivc_cont_ids == ivc0)[0]): ivc_cont_ids.shape[0]],
ivc_cont_ids[0: int(np.where(ivc_cont_ids == ivc0)[0])]).astype(int)
if args.flip == False:
aux = np.zeros(reordered_ivc_cont.size)
for i in range(reordered_ivc_cont.size):
aux[reordered_ivc_cont.size - 1 - i] = reordered_ivc_cont[i]
# mantain the v1l as the first one (after the flip is the last one)
reordered_ivc_cont = np.append(aux[aux.size - 1], aux[0:aux.size - 1]).astype(int)
return reordered_ivc_cont
def reorder_svc(svc_cont_ids, s1_ids, args):
# reorder to start in intersection of path1 and SVC contour
last_s1 = int(s1_ids[s1_ids.shape[0] - 1])
reordered_svc_cont = np.append(svc_cont_ids[int(np.where(svc_cont_ids == last_s1)[0]): svc_cont_ids.shape[0]],
svc_cont_ids[0: int(np.where(svc_cont_ids == last_s1)[0])]).astype(int)
if args.flip == False:
aux = np.zeros(reordered_svc_cont.size)
for i in range(reordered_svc_cont.size):
aux[reordered_svc_cont.size - 1 - i] = reordered_svc_cont[i]
# mantain the v1l as the first one (after the flip is the last one)
reordered_svc_cont = np.append(aux[aux.size - 1], aux[0:aux.size - 1]).astype(int)
return reordered_svc_cont
### Input/Output ###
def readvtk(filename):
"""Read VTK file"""
reader = vtk.vtkPolyDataReader()
reader.SetFileName(filename)
reader.Update()
return reader.GetOutput()
def readvtp(filename):
"""Read VTP file"""
reader = vtk.vtkXMLPolyDataReader()
reader.SetFileName(filename)
reader.Update()
return reader.GetOutput()
def writevtk(surface, filename, type='ascii'):
"""Write binary or ascii VTK file"""
writer = vtk.vtkPolyDataWriter()
writer.SetInputData(surface)
writer.SetFileName(filename)
if type == 'ascii':
writer.SetFileTypeToASCII()
elif type == 'binary':
writer.SetFileTypeToBinary()
writer.Write()
def writevtp(surface, filename):
"""Write VTP file"""
writer = vtk.vtkXMLPolyDataWriter()
writer.SetInputData(surface)
writer.SetFileName(filename)
# writer.SetDataModeToBinary()
writer.Write()
### Math ###
def euclideandistance(point1, point2):
return math.sqrt((point1[0] - point2[0])**2 + (point1[1] - point2[1])**2 + (point1[2] - point2[2])**2)
def normvector(v):
return math.sqrt(dot(v, v))
def angle(v1, v2):
return math.acos(dot(v1, v2) / (normvector(v1) * normvector(v2)))
def acumvectors(point1, point2):
return [point1[0] + point2[0], point1[1] + point2[1], point1[2] + point2[2]]
def subtractvectors(point1, point2):
return [point1[0] - point2[0], point1[1] - point2[1], point1[2] - point2[2]]
def dividevector(point, n):
nr = float(n)
return [point[0]/nr, point[1]/nr, point[2]/nr]
def multiplyvector(point, n):
nr = float(n)
return [nr*point[0], nr*point[1], nr*point[2]]
def sumvectors(vect1, scalar, vect2):
return [vect1[0] + scalar*vect2[0], vect1[1] + scalar*vect2[1], vect1[2] + scalar*vect2[2]]
def cross(v1, v2):
return [v1[1]*v2[2] - v1[2]*v2[1], v1[2]*v2[0] - v1[0]*v2[2], v1[0]*v2[1] - v1[1]*v2[0]]
def dot(v1, v2):
return sum((a*b) for a, b in zip(v1, v2))
def normalizevector(v):
norm = normvector(v)
return [v[0] / norm, v[1] / norm, v[2] / norm]
### Mesh processing ###
def cleanpolydata(polydata):
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInputData(polydata)
cleaner.Update()
return cleaner.GetOutput()
def fillholes(polydata, size):
"""Fill mesh holes smaller than 'size' """
filler = vtk.vtkFillHolesFilter()
filler.SetInputData(polydata)
filler.SetHoleSize(size)
filler.Update()
return filler.GetOutput()
def pointthreshold(polydata, arrayname, start=0, end=1, alloff=0):
""" Clip polydata according to given thresholds in scalar array"""
threshold = vtk.vtkThreshold()
if (vtk.vtkVersion.GetVTKMajorVersion() >= 9):
threshold.SetLowerThreshold(start)
threshold.SetUpperThreshold(end)
else:
threshold.ThresholdBetween(start, end)
threshold.SetInputData(polydata)
threshold.SetInputArrayToProcess(0, 0, 0, vtk.vtkDataObject.FIELD_ASSOCIATION_POINTS, arrayname)
if (alloff):
threshold.AllScalarsOff()
threshold.Update()
surfer = vtk.vtkDataSetSurfaceFilter()
surfer.SetInputData(threshold.GetOutput())
surfer.Update()
return surfer.GetOutput()
def cellthreshold(polydata, arrayname, start=0, end=1):
threshold = vtk.vtkThreshold()
threshold.SetInputData(polydata)
threshold.SetInputArrayToProcess(0, 0, 0, vtk.vtkDataObject.FIELD_ASSOCIATION_CELLS, arrayname)
if (vtk.vtkVersion.GetVTKMajorVersion() >= 9):
threshold.SetLowerThreshold(start)
threshold.SetUpperThreshold(end)
else:
threshold.ThresholdBetween(start, end)
threshold.Update()
surfer = vtk.vtkDataSetSurfaceFilter()
surfer.SetInputConnection(threshold.GetOutputPort())
surfer.Update()
return surfer.GetOutput()
def roundpointarray(polydata, name):
"""Round values in point array"""
# get original array
array = polydata.GetPointData().GetArray(name)
# round labels
for i in range(polydata.GetNumberOfPoints()):
value = array.GetValue(i)
array.SetValue(i, round(value))
return polydata
def planeclip(surface, point, normal, insideout=1):
"""Clip surface using plane given by point and normal"""
clipplane = vtk.vtkPlane()
clipplane.SetOrigin(point)
clipplane.SetNormal(normal)
clipper = vtk.vtkClipPolyData()
clipper.SetInputData(surface)
clipper.SetClipFunction(clipplane)
if insideout == 1:
# print 'insideout ON'
clipper.InsideOutOn()
else:
# print 'insideout OFF'
clipper.InsideOutOff()
clipper.Update()
return clipper.GetOutput()
def cutdataset(dataset, point, normal):
"""Similar to planeclip but using vtkCutter instead of vtkClipPolyData"""
cutplane = vtk.vtkPlane()
cutplane.SetOrigin(point)
cutplane.SetNormal(normal)
cutter = vtk.vtkCutter()
cutter.SetInputData(dataset)
cutter.SetCutFunction(cutplane)
cutter.Update()
return cutter.GetOutput()
def pointset_centreofmass(polydata):
centre = [0, 0, 0]
for i in range(polydata.GetNumberOfPoints()):
point = [polydata.GetPoints().GetPoint(i)[0],
polydata.GetPoints().GetPoint(i)[1],
polydata.GetPoints().GetPoint(i)[2]]
centre = acumvectors(centre,point)
return dividevector(centre, polydata.GetNumberOfPoints())
def seeds_to_csv(seedsfile, arrayname, labels, outfile):
"""Read seeds from VTP file, write coordinates in csv"""
# f = open(outfile, 'wb')
f = open(outfile, 'w')
allseeds = readvtp(seedsfile)
for l in labels:
currentseeds = pointthreshold(allseeds, arrayname, l, l, 0)
# currentpoint = currentseeds.GetPoint(0) # only 1
currentpoint = pointset_centreofmass(currentseeds)
line = str(currentpoint[0]) + ',' + str(currentpoint[1]) + ',' + str(currentpoint[2]) + '\n'
# line = currentpoint[0] + b',' + currentpoint[1] + b',' + currentpoint[2] + b'\n'
f.write(line)
f.close()
def point2vertexglyph(point):
"""Create glyph from points to visualise them"""
points = vtk.vtkPoints()
points.InsertNextPoint(point[0], point[1], point[2])
poly = vtk.vtkPolyData()
poly.SetPoints(points)
glyph = vtk.vtkVertexGlyphFilter()
glyph.SetInputConnection(poly.GetProducerPort())
glyph.Update()
return glyph.GetOutput()
def generateglyph(polyIn, scalefactor=2):
vertexGlyphFilter = vtk.vtkGlyph3D()
sphereSource = vtk.vtkSphereSource()
vertexGlyphFilter.SetSourceData(sphereSource.GetOutput())
vertexGlyphFilter.SetInputData(polyIn)
vertexGlyphFilter.SetColorModeToColorByScalar()
vertexGlyphFilter.SetSourceConnection(sphereSource.GetOutputPort())
vertexGlyphFilter.ScalingOn()
vertexGlyphFilter.SetScaleFactor(scalefactor)
vertexGlyphFilter.Update()
return vertexGlyphFilter.GetOutput()
def linesource(p1, p2):
"""Create vtkLine from coordinates of 2 points"""
source = vtk.vtkLineSource()
source.SetPoint1(p1[0], p1[1], p1[2])
source.SetPoint2(p2[0], p2[1], p2[2])
return source.GetOutput()
def append(polydata1, polydata2):
"""Define new polydata appending polydata1 and polydata2"""
appender = vtk.vtkAppendPolyData()
appender.AddInput(polydata1)
appender.AddInput(polydata2)
appender.Update()
return appender.GetOutput()
def extractcells(polydata, idlist):
"""Extract cells from polydata whose cellid is in idlist."""
cellids = vtk.vtkIdList() # specify cellids
cellids.Initialize()
for i in idlist:
cellids.InsertNextId(i)
extract = vtk.vtkExtractCells() # extract cells with specified cellids
extract.SetInputData(polydata)
extract.AddCellList(cellids)
extraction = extract.GetOutput()
geometry = vtk.vtkGeometryFilter() # unstructured grid to polydata
geometry.SetInputData(extraction)
geometry.Update()
return geometry.GetOutput()
def extractboundaryedge(polydata):
edge = vtk.vtkFeatureEdges()
edge.SetInputData(polydata)
edge.FeatureEdgesOff()
edge.NonManifoldEdgesOff()
edge.Update()
return edge.GetOutput()
def extractlargestregion(polydata):
"""Keep only biggest region"""
surfer = vtk.vtkDataSetSurfaceFilter()
surfer.SetInputData(polydata)
surfer.Update()
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInputData(surfer.GetOutput())
cleaner.Update()
connect = vtk.vtkPolyDataConnectivityFilter()
connect.SetInputData(cleaner.GetOutput())
connect.SetExtractionModeToLargestRegion()
connect.Update()
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInputData(connect.GetOutput())
cleaner.Update()
return cleaner.GetOutput()
def countregions(polydata):
"""Count number of connected components/regions"""
# preventive measures: clean before connectivity filter to avoid artificial regionIds
surfer = vtk.vtkDataSetSurfaceFilter()
surfer.SetInputData(polydata)
surfer.Update()
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInputData(surfer.GetOutput())
cleaner.Update()
connect = vtk.vtkPolyDataConnectivityFilter()
connect.SetInputData(cleaner.GetOutput())
connect.Update()
return connect.GetNumberOfExtractedRegions()
def extractclosestpointregion(polydata, point=[0, 0, 0]):
# NOTE: preventive measures: clean before connectivity filter
# to avoid artificial regionIds
# It slices the surface down the middle
surfer = vtk.vtkDataSetSurfaceFilter()
surfer.SetInputData(polydata)
surfer.Update()
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInputData(surfer.GetOutput())
cleaner.Update()
connect = vtk.vtkPolyDataConnectivityFilter()
connect.SetInputData(cleaner.GetOutput())
connect.SetExtractionModeToClosestPointRegion()
connect.SetClosestPoint(point)
connect.Update()
return connect.GetOutput()
def extractconnectedregion(polydata, regionid):
"""Extract connected region with label = regionid """
surfer = vtk.vtkDataSetSurfaceFilter()
surfer.SetInputData(polydata)
surfer.Update()
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInputData(surfer.GetOutput())
cleaner.Update()
connect = vtk.vtkPolyDataConnectivityFilter()
connect.SetInputData(cleaner.GetOutput())
connect.SetExtractionModeToAllRegions()
connect.ColorRegionsOn()
connect.Update()
surface = pointthreshold(connect.GetOutput(), 'RegionId', float(regionid), float(regionid))
return surface
def get_connected_edges(polydata):
"""Extract all connected regions"""
connect = vtk.vtkPolyDataConnectivityFilter()
connect.SetInputData(polydata)
connect.SetExtractionModeToAllRegions()
connect.ColorRegionsOn()
connect.Update()
return connect
def find_create_path(mesh, p1, p2):
"""Get shortest path (using Dijkstra algorithm) between p1 and p2 on the mesh. Returns a polydata"""
dijkstra = vtk.vtkDijkstraGraphGeodesicPath()
# (VTK 9.1 and later...) The Dijkistra interpolator will not accept cells that aren't triangles
if (vtk.vtkVersion.GetVTKMajorVersion() >= 9):
triangleFilter = vtk.vtkTriangleFilter()
triangleFilter.SetInputData(mesh)
triangleFilter.Update()
pd = triangleFilter.GetOutput()
dijkstra.SetInputData(pd)
else:
dijkstra.SetInputData(mesh)
dijkstra.SetStartVertex(p1)
dijkstra.SetEndVertex(p2)
dijkstra.Update()
return dijkstra.GetOutput()
def compute_geodesic_distance(mesh, id_p1, id_p2):
"""Compute geodesic distance from point id_p1 to id_p2 on surface 'mesh'
It first computes the path across the edges and then the corresponding distance adding up point to point distances)"""
path = find_create_path(mesh, id_p1, id_p2)
total_dist = 0
n = path.GetNumberOfPoints()
for i in range(n-1): # Ids are ordered in the new polydata, from 0 to npoints_in_path
p0 = path.GetPoint(i)
p1 = path.GetPoint(i+1)
dist = math.sqrt(math.pow(p0[0]-p1[0], 2) + math.pow(p0[1]-p1[1], 2) + math.pow(p0[2]-p1[2], 2) )
total_dist = total_dist + dist
return total_dist, path
def transfer_array(ref, target, arrayname, targetarrayname):
"""Transfer scalar array using closest point approximation"""
locator = vtk.vtkPointLocator()
locator.SetDataSet(ref)
locator.BuildLocator()
refarray = ref.GetPointData().GetArray(arrayname) # get array from reference
numberofpoints = target.GetNumberOfPoints()
newarray = vtk.vtkDoubleArray()
newarray.SetName(targetarrayname)
newarray.SetNumberOfTuples(numberofpoints)
target.GetPointData().AddArray(newarray)
# go through each point of target surface, determine closest point on surface, copy value
for i in range(target.GetNumberOfPoints()):
point = target.GetPoint(i)
closestpoint_id = locator.FindClosestPoint(point)
value = refarray.GetValue(closestpoint_id)
newarray.SetValue(i, value)
return target
def transfer_all_scalar_arrays(m1, m2):
""" Transfer all scalar arrays from m1 to m2"""
for i in range(m1.GetPointData().GetNumberOfArrays()):
print('Transferring scalar array: {}'.format(m1.GetPointData().GetArray(i).GetName()))
transfer_array(m1, m2, m1.GetPointData().GetArray(i).GetName(), m1.GetPointData().GetArray(i).GetName())
def transfer_all_scalar_arrays_by_point_id(m1, m2):
""" Transfer all scalar arrays from m1 to m2 by point id"""
for i in range(m1.GetPointData().GetNumberOfArrays()):
print('Transferring scalar array: {}'.format(m1.GetPointData().GetArray(i).GetName()))
m2.GetPointData().AddArray(m1.GetPointData().GetArray(i))
def get_ordered_cont_ids_based_on_distance(mesh):
""" Given a contour, get the ordered list of Ids (not ordered by default).
Open the mesh duplicating the point with id = 0. Compute distance transform of point 0
and get a ordered list of points (starting in 0) """
m = vtk.vtkMath()
m.RandomSeed(0)
# copy the original mesh point by point
points = vtk.vtkPoints()
polys = vtk.vtkCellArray()
cover = vtk.vtkPolyData()
nver = mesh.GetNumberOfPoints()
points.SetNumberOfPoints(nver+1)
new_pid = nver # id of the duplicated point
added = False
for j in range(mesh.GetNumberOfCells()):
# get the 2 point ids
ptids = mesh.GetCell(j).GetPointIds()
cell = mesh.GetCell(j)
if (ptids.GetNumberOfIds() != 2):
# print "Non contour mesh (lines)"
break
# read the 2 involved points
pid0 = ptids.GetId(0)
pid1 = ptids.GetId(1)
p0 = mesh.GetPoint(ptids.GetId(0)) # returns coordinates
p1 = mesh.GetPoint(ptids.GetId(1))
if pid0 == 0:
if added == False:
# Duplicate point 0. Add gaussian noise to the original point
new_p = [p0[0] + m.Gaussian(0.0, 0.0005), p0[1] + m.Gaussian(0.0, 0.0005), p0[2] + m.Gaussian(0.0, 0.0005)]
points.SetPoint(new_pid, new_p)
points.SetPoint(pid1, p1)
polys.InsertNextCell(2)
polys.InsertCellPoint(pid1)
polys.InsertCellPoint(new_pid)
added = True
else: # act normal
points.SetPoint(ptids.GetId(0), p0)
points.SetPoint(ptids.GetId(1), p1)
polys.InsertNextCell(2)
polys.InsertCellPoint(cell.GetPointId(0))
polys.InsertCellPoint(cell.GetPointId(1))
elif pid1 == 0:
if added == False:
new_p = [p1[0] + m.Gaussian(0.0, 0.0005), p1[1] + m.Gaussian(0.0, 0.0005), p1[2] + m.Gaussian(0.0, 0.0005)]
points.SetPoint(new_pid, new_p)
points.SetPoint(pid0, p0)
polys.InsertNextCell(2)
polys.InsertCellPoint(pid0)
polys.InsertCellPoint(new_pid)
added = True
else: # act normal
points.SetPoint(ptids.GetId(0), p0)
points.SetPoint(ptids.GetId(1), p1)
polys.InsertNextCell(2)
polys.InsertCellPoint(cell.GetPointId(0))
polys.InsertCellPoint(cell.GetPointId(1))
else:
points.SetPoint(ptids.GetId(0), p0)
points.SetPoint(ptids.GetId(1), p1)
polys.InsertNextCell(2)
polys.InsertCellPoint(cell.GetPointId(0))
polys.InsertCellPoint(cell.GetPointId(1))
if added == False:
print('Warning: I have not added any point, list of indexes may not be correct.')
cover.SetPoints(points)
if (vtk.vtkVersion.GetVTKMajorVersion() >= 9):
cover.SetLines(polys)
else:
cover.SetPolys(polys)
cover.Update()
# compute distance from point with id 0 to all the rest
npoints = cover.GetNumberOfPoints()
dists = np.zeros(npoints)
for i in range(npoints):
[dists[i], poly] = compute_geodesic_distance(cover, int(0), i)
list_ = np.argsort(dists).astype(int)
return list_[0:len(list_)-1] # skip last one, duplicated
def define_pv_segments_proportions(t_v5, t_v6, t_v7, alpha):
"""define number of points of each pv hole segment to ensure appropriate distribution"""
props = np.zeros([4, 3])
props[0, 0] = np.divide(1.0, 4.0) # proportion of the total number of points of the pv contour according to the proportion of circle
props[0, 1] = np.divide(1.0, 4.0) + t_v5 * np.divide(1.0, 2.0*np.pi)
props[0, 2] = 1.0 - props[0, 0] - props[0, 1]
# print('Proportions sum up:', props[0, 0]+props[0, 1]+props[0, 2])
props[1, 0] = np.divide(t_v6, 2.0*np.pi) - np.divide(1.0, 2.0)
props[1, 2] = np.divide(1.0, 4.0) # s3
props[1, 1] = 1.0 - props[1, 0] - props[1, 2] # s2
# print('Proportions sum up:', props[1, 0]+props[1, 1]+props[1, 2])
props[2, 0] = np.divide(1.0, 4.0)
props[2, 1] = np.divide(t_v7, 2.0*np.pi) - props[2, 0]
props[2, 2] = 1.0 - props[2, 0] - props[2, 1]
# print('Proportions sum up:', props[1, 0]+props[1, 1]+props[1, 2])
props[3, 0] = np.divide(1.0, 4.0) # a bit more if the LAA is displaced to the left
props[3, 1] = np.divide(1.0, 2.0) # a bit less if the LAA is displaced to the left
# props[3, 0] = np.divide(1.0, 4.0) + alpha * np.divide(1.0, 2.0*np.pi) # a bit more if the LAA is displaced to the left
# props[3, 1] = np.divide(1.0, 2.0) - alpha * np.divide(1.0, 2.0*np.pi) # a bit less if the LAA is displaced to the left
props[3, 2] = np.divide(1.0, 4.0)
return props
def define_disk_template(rdisk, rhole_rspv, rhole_ripv, rhole_lipv, rhole_lspv, rhole_laa, xhole_center, yhole_center,
laa_hole_center_x, laa_hole_center_y, t_v5, t_v6, t_v7, t_v8):
"""Define target positions in the disk template, return coordinates (x,y) corresponding to:
v1r, v1d, v1l, v2u, v2r, v2l, v3u, v3r, v3l, v4r, v4u, v4d, vlaad, vlaau, p5, p6, p7, p8 """
coordinates = np.zeros([2, 18])
complete_circumf_t = np.linspace(0, 2 * np.pi, 1000, endpoint=False)
rspv_hole_x = np.cos(complete_circumf_t) * rhole_rspv + xhole_center[0]
rspv_hole_y = np.sin(complete_circumf_t) * rhole_rspv + yhole_center[0]
ripv_hole_x = np.cos(complete_circumf_t) * rhole_ripv + xhole_center[1]
ripv_hole_y = np.sin(complete_circumf_t) * rhole_ripv + yhole_center[1]
lipv_hole_x = np.cos(complete_circumf_t) * rhole_lipv + xhole_center[2]
lipv_hole_y = np.sin(complete_circumf_t) * rhole_lipv + yhole_center[2]
lspv_hole_x = np.cos(complete_circumf_t) * rhole_lspv + xhole_center[3]
lspv_hole_y = np.sin(complete_circumf_t) * rhole_lspv + yhole_center[3]
laa_hole_x = np.cos(complete_circumf_t) * rhole_laa + laa_hole_center_x
laa_hole_y = np.sin(complete_circumf_t) * rhole_laa + laa_hole_center_y
# define (x,y) positions where I put v5, v6, v7 and v8
coordinates[0, 14] = np.cos(t_v5) * rdisk # p5_x
coordinates[1, 14] = np.sin(t_v5) * rdisk # p5_y
coordinates[0, 15] = np.cos(t_v6) * rdisk # p6_x
coordinates[1, 15] = np.sin(t_v6) * rdisk # p6_y
coordinates[0, 16] = np.cos(t_v7) * rdisk # p7_x
coordinates[1, 16] = np.sin(t_v7) * rdisk # p7_y
coordinates[0, 17] = np.cos(t_v8) * rdisk # p8_x
coordinates[1, 17] = np.sin(t_v8) * rdisk # p8_y
# define target points corresponding to the pv holes
# RSPV (right (in the line connecting to MV; left (horizontal line), down, vertical line))
coordinates[0, 0] = rspv_hole_x[
np.abs(complete_circumf_t - t_v5).argmin()] # v1r_x, x in rspv circumf where angle is pi/4
coordinates[1, 0] = rspv_hole_y[np.abs(complete_circumf_t - t_v5).argmin()]
coordinates[0, 1] = rspv_hole_x[np.abs(complete_circumf_t - (3 * np.pi / 2)).argmin()]
coordinates[1, 1] = rspv_hole_y[np.abs(complete_circumf_t - (3 * np.pi / 2)).argmin()]
coordinates[0, 2] = rspv_hole_x[(np.abs(complete_circumf_t - np.pi)).argmin()]
coordinates[1, 2] = rspv_hole_y[(np.abs(complete_circumf_t - np.pi)).argmin()]
# RIPV
coordinates[0, 3] = ripv_hole_x[np.abs(complete_circumf_t - (np.pi / 2)).argmin()] # x in ripv circumf UP
coordinates[1, 3] = ripv_hole_y[np.abs(complete_circumf_t - (np.pi / 2)).argmin()]
coordinates[0, 4] = ripv_hole_x[np.abs(complete_circumf_t - t_v6).argmin()]
coordinates[1, 4] = ripv_hole_y[np.abs(complete_circumf_t - t_v6).argmin()]
coordinates[0, 5] = ripv_hole_x[np.abs(complete_circumf_t - (np.pi)).argmin()]
coordinates[1, 5] = ripv_hole_y[np.abs(complete_circumf_t - (np.pi)).argmin()]
# LIPV
coordinates[0, 6] = lipv_hole_x[np.abs(complete_circumf_t - (np.pi / 2)).argmin()]
coordinates[1, 6] = lipv_hole_y[np.abs(complete_circumf_t - (np.pi / 2)).argmin()]
coordinates[0, 7] = lipv_hole_x[complete_circumf_t.argmin()] # angle = 0
coordinates[1, 7] = lipv_hole_y[complete_circumf_t.argmin()]
coordinates[0, 8] = lipv_hole_x[np.abs(complete_circumf_t - t_v7).argmin()]
coordinates[1, 8] = lipv_hole_y[np.abs(complete_circumf_t - t_v7).argmin()]
# LSPV
coordinates[0, 9] = lspv_hole_x[complete_circumf_t.argmin()] # angle = 0
coordinates[1, 9] = lspv_hole_y[complete_circumf_t.argmin()]
coordinates[0, 10] = lspv_hole_x[np.abs(complete_circumf_t - (np.pi / 2)).argmin()]
coordinates[1, 10] = lspv_hole_y[np.abs(complete_circumf_t - (np.pi / 2)).argmin()]
coordinates[0, 11] = lspv_hole_x[np.abs(complete_circumf_t - (3 * np.pi / 2)).argmin()]
coordinates[1, 11] = lspv_hole_y[np.abs(complete_circumf_t - (3 * np.pi / 2)).argmin()]
# LAA
coordinates[0, 12] = laa_hole_x[np.abs(complete_circumf_t - (3 * np.pi / 2)).argmin()]
coordinates[1, 12] = laa_hole_y[np.abs(complete_circumf_t - (3 * np.pi / 2)).argmin()]
coordinates[0, 13] = laa_hole_x[np.abs(complete_circumf_t - t_v8).argmin()] # angle = pi/2 + pi/8
coordinates[1, 13] = laa_hole_y[np.abs(complete_circumf_t - t_v8).argmin()]
return coordinates
def get_coords(c):
"""Given all coordinates in a matrix, identify and return them separately"""
return c[0,0], c[1,0], c[0,1], c[1,1], c[0,2], c[1,2], c[0,3], c[1,3], c[0,4], c[1,4], c[0,5], c[1,5], c[0,6], c[1,6], c[0,7], c[1,7], c[0,8], c[1,8], c[0,9], c[1,9], c[0,10], c[1,10], c[0,11], c[1,11], c[0,12], c[1,12], c[0,13], c[1,13], c[0,14], c[1,14], c[0,15], c[1,15], c[0,16], c[1,16], c[0,17], c[1,17]
def extract_LA_contours(m_open, filename, save=False):
"""Given LA with clipped PVs, LAA and MV identify and classify all 5 contours using 'autolables' array.
Save contours if save=True"""
edges = extractboundaryedge(m_open)
conn = get_connected_edges(edges)
poly_edges = conn.GetOutput()
if save==True:
writevtk(poly_edges, filename[0:len(filename) - 4] + '_detected_edges.vtk')
print('Detected {} regions'.format(conn.GetNumberOfExtractedRegions()))
if conn.GetNumberOfExtractedRegions() != 6:
print(
'WARNING: the number of contours detected is not the expected. The classification of contours may be wrong')
for i in range(6):
print('Detecting region index: {}'.format(i))
c = pointthreshold(poly_edges, 'RegionId', i, i)
autolabels = vtk_to_numpy(c.GetPointData().GetArray('autolabels'))
counts = np.bincount(autolabels.astype(int))
mostcommon = np.argmax(counts)
if mostcommon == 36: # use the most repeated label since some of they are 36 (body). Can be 36 more common in the other regions?
print('Detected MV')
if save == True:
writevtk(c, filename[0:len(filename) - 4] + '_cont_mv.vtk')
cont_mv = c
if mostcommon == 37:
print('Detected LAA')
if save == True:
writevtk(c, filename[0:len(filename) - 4] + '_cont_laa.vtk')
cont_laa = c
if mostcommon == 76:
print('Detected RSPV')
if save == True:
writevtk(c, filename[0:len(filename) - 4] + '_cont_rspv.vtk')
cont_rspv = c
if mostcommon == 77:
print('Detected RIPV')
if save == True:
writevtk(c, filename[0:len(filename) - 4] + '_cont_ripv.vtk')
cont_ripv = c
if mostcommon == 78:
print('Detected LSPV')
if save == True:
writevtk(c, filename[0:len(filename) - 4] + '_cont_lspv.vtk')
cont_lspv = c
if mostcommon == 79:
print('Detected LIPV')
if save == True:
writevtk(c, filename[0:len(filename) - 4] + '_cont_lipv.vtk')
cont_lipv = c
return cont_rspv, cont_ripv, cont_lipv, cont_lspv, cont_mv, cont_laa
def build_locators(mesh, m_open, cont_rspv, cont_ripv, cont_lipv, cont_lspv, cont_laa):
"""Build different locators to find corresponding points between different meshes (open/closed, open/contours, etc)"""
locator = vtk.vtkPointLocator()
locator.SetDataSet(mesh) # clipped + CLOSED - where the seeds are marked
locator.BuildLocator()
locator_open = vtk.vtkPointLocator()
locator_open.SetDataSet(m_open)
locator_open.BuildLocator()
locator_rspv = vtk.vtkPointLocator()
locator_rspv.SetDataSet(cont_rspv)
locator_rspv.BuildLocator()
locator_ripv = vtk.vtkPointLocator()
locator_ripv.SetDataSet(cont_ripv)
locator_ripv.BuildLocator()
locator_lipv = vtk.vtkPointLocator()
locator_lipv.SetDataSet(cont_lipv)
locator_lipv.BuildLocator()
locator_lspv = vtk.vtkPointLocator()
locator_lspv.SetDataSet(cont_lspv)
locator_lspv.BuildLocator()
locator_laa = vtk.vtkPointLocator()
locator_laa.SetDataSet(cont_laa)
locator_laa.BuildLocator()
return locator, locator_open, locator_rspv, locator_ripv, locator_lipv, locator_lspv, locator_laa
def read_paths(filename, npaths):
"""read the paths (lines) defined in the 3D mesh using 3_divide_LA.py"""
for i in range(npaths):
if os.path.isfile(filename[0:len(filename)-4]+'path'+ str(i+1) +'.vtk')==False:
sys.exit('ERROR: dividing line path' + str(i+1) + ' not found. Run 3_divide_LA.py')
else:
if i == 0:
path1 = readvtk(filename[0:len(filename) - 4] + 'path' + str(i + 1) + '.vtk')
elif i == 1:
path2 = readvtk(filename[0:len(filename) - 4] + 'path' + str(i + 1) + '.vtk')
elif i == 2:
path3 = readvtk(filename[0:len(filename) - 4] + 'path' + str(i + 1) + '.vtk')
elif i == 3:
path4 = readvtk(filename[0:len(filename) - 4] + 'path' + str(i + 1) + '.vtk')
elif i == 4:
path5 = readvtk(filename[0:len(filename) - 4] + 'path' + str(i + 1) + '.vtk')
elif i == 5:
path6 = readvtk(filename[0:len(filename) - 4] + 'path' + str(i + 1) + '.vtk')
elif i == 6:
path7 = readvtk(filename[0:len(filename) - 4] + 'path' + str(i + 1) + '.vtk')
# read laa related paths: line from lspv to laa and from laa to mv
if os.path.isfile(filename[0:len(filename)-4] + 'path_laa1.vtk')==False:
sys.exit('ERROR: dividing line path_laa1 not found. Run 3_divide_LA.py')
else:
path_laa1 = readvtk(filename[0:len(filename)-4] + 'path_laa1.vtk')
if os.path.isfile(filename[0:len(filename)-4] + 'path_laa2.vtk')==False:
sys.exit('ERROR: dividing line path_laa2 not found. Run 3_divide_LA.py')
else:
path_laa2 = readvtk(filename[0:len(filename)-4] + 'path_laa2.vtk')
if os.path.isfile(filename[0:len(filename)-4] + 'path_laa3.vtk')==False:
sys.exit('ERROR: dividing line path_laa3 not found. Run 3_divide_LA.py')
else:
path_laa3 = readvtk(filename[0:len(filename)-4] + 'path_laa3.vtk')
return path1, path2, path3, path4, path5, path6, path7, path_laa1, path_laa2, path_laa3
def get_mv_contour_ids(cont_mv, locator_open):
"""Obtain ids of the MV contour"""
edge_cont_ids = get_ordered_cont_ids_based_on_distance(cont_mv)
mv_cont_ids = np.zeros(edge_cont_ids.size)
for i in range(mv_cont_ids.shape[0]):
p = cont_mv.GetPoint(edge_cont_ids[i])
mv_cont_ids[i] = locator_open.FindClosestPoint(p)
return mv_cont_ids
def identify_segments_extremes(path1, path2, path3, path4, path5, path6, path7, path_laa1, path_laa2, path_laa3,
locator_open, locator_rspv, locator_ripv, locator_lipv, locator_lspv, locator_laa,
cont_rspv, cont_ripv, cont_lipv, cont_lspv, cont_laa,
v5, v6, v7, v8):
"""Identify ids in the to_be_flat mesh corresponding to the segment extremes: v1d, v1r, ect."""
# start with segments of PVs because they will modify the rest of segments (we try to have uniform number of points in the 3 segments of the veins)
# first identify ALL pv segments extremes (v1d, v2u etc.)
# s1 - Find ids corresponding to v1d and v2u as intersection of rspv (ripv) contour and path1
dists1 = np.zeros(path1.GetNumberOfPoints())
dists2 = np.zeros(path1.GetNumberOfPoints())
for i in range(path1.GetNumberOfPoints()):
p = path1.GetPoint(i)
dists1[i] = euclideandistance(p, cont_rspv.GetPoint(locator_rspv.FindClosestPoint(p)))
dists2[i] = euclideandistance(p, cont_ripv.GetPoint(locator_ripv.FindClosestPoint(p)))
v1d_in_path1 = np.argmin(dists1)
v2u_in_path1 = np.argmin(dists2)
v1d = locator_open.FindClosestPoint(path1.GetPoint(v1d_in_path1))
v2u = locator_open.FindClosestPoint(path1.GetPoint(v2u_in_path1))
# s2 - Find 2l and v3r
dists1 = np.zeros(path2.GetNumberOfPoints())
dists2 = np.zeros(path2.GetNumberOfPoints())
for i in range(path2.GetNumberOfPoints()):
p = path2.GetPoint(i)
dists1[i] = euclideandistance(p, cont_ripv.GetPoint(locator_ripv.FindClosestPoint(p)))
dists2[i] = euclideandistance(p, cont_lipv.GetPoint(locator_lipv.FindClosestPoint(p)))
v2l_in_path2 = np.argmin(dists1)
v3r_in_path2 = np.argmin(dists2)
v2l = locator_open.FindClosestPoint(path2.GetPoint(v2l_in_path2))
v3r = locator_open.FindClosestPoint(path2.GetPoint(v3r_in_path2))
# s3 - Find v3u and v4d
dists1 = np.zeros(path3.GetNumberOfPoints())
dists2 = np.zeros(path3.GetNumberOfPoints())
for i in range(path3.GetNumberOfPoints()):
p = path3.GetPoint(i)
dists1[i] = euclideandistance(p, cont_lipv.GetPoint(locator_lipv.FindClosestPoint(p)))
dists2[i] = euclideandistance(p, cont_lspv.GetPoint(locator_lspv.FindClosestPoint(p)))
v3u_in_path3 = np.argmin(dists1)
v4d_in_path3 = np.argmin(dists2)
v3u = locator_open.FindClosestPoint(path3.GetPoint(v3u_in_path3))
v4d = locator_open.FindClosestPoint(path3.GetPoint(v4d_in_path3))
# s4 - Find v4r and v1l
dists1 = np.zeros(path4.GetNumberOfPoints())
dists2 = np.zeros(path4.GetNumberOfPoints())
for i in range(path4.GetNumberOfPoints()):
p = path4.GetPoint(i)
dists1[i] = euclideandistance(p, cont_lspv.GetPoint(locator_lspv.FindClosestPoint(p)))
dists2[i] = euclideandistance(p, cont_rspv.GetPoint(locator_rspv.FindClosestPoint(p)))
v4r_in_path4 = np.argmin(dists1)
v1l_in_path4 = np.argmin(dists2)
v4r = locator_open.FindClosestPoint(path4.GetPoint(v4r_in_path4))
v1l = locator_open.FindClosestPoint(path4.GetPoint(v1l_in_path4))
# find ids in the MV
id_v5 = locator_open.FindClosestPoint(v5)
id_v6 = locator_open.FindClosestPoint(v6)
id_v7 = locator_open.FindClosestPoint(v7)
id_v8 = locator_open.FindClosestPoint(v8)
# Next 4 segments: s5, s6, s7, s8 : FROM pvs (v1r,v2r,v3l,v4l) TO points in the MV
dists1 = np.zeros(path5.GetNumberOfPoints())
for i in range(path5.GetNumberOfPoints()):
p = path5.GetPoint(i)
dists1[i] = euclideandistance(p, cont_rspv.GetPoint(locator_rspv.FindClosestPoint(p)))
v1r_in_path5 = np.argmin(dists1)
v1r = locator_open.FindClosestPoint(path5.GetPoint(v1r_in_path5))