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Modify vmtksurfaceendclipper to clip based on centerline information #200

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Merged
rlizzo merged 3 commits into from
Jan 10, 2018
Merged

Modify vmtksurfaceendclipper to clip based on centerline information #200

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b9683cb
Merge issues fixed
kayarre Oct 18, 2017
c53c6ef
missed a small merge conflict
kayarre Oct 18, 2017
50f5d7d
updated documentation and minor formatting tweaks
rlizzo Jan 10, 2018
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94 changes: 76 additions & 18 deletions vmtkScripts/vmtksurfaceendclipper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,8 @@
## Note: this class was contributed by
## Simone Manini
## Orobix Srl
## And adapted and modified by
## Kurt Sansom

from __future__ import absolute_import #NEEDS TO STAY AS TOP LEVEL MODULE FOR Py2-3 COMPATIBILITY
import vtk
Expand All @@ -32,6 +34,7 @@ class vmtkSeedSelector(object):
def __init__(self):
self._Surface = None
self._SeedIds = None
self._MainBodySeedIds = vtk.vtkIdList()
self._SourceSeedIds = vtk.vtkIdList()
self._TargetSeedIds = vtk.vtkIdList()
self.PrintError = None
Expand All @@ -42,9 +45,13 @@ def __init__(self):

def SetSurface(self,surface):
self._Surface = surface

def GetSurface(self):
return self._Surface

def GetMainBodySeedIds(self):
return self._MainBodySeedIds

def GetSourceSeedIds(self):
return self._SourceSeedIds

Expand All @@ -63,6 +70,7 @@ def __init__(self):
self.vmtkRenderer = None
self.OwnRenderer = 0
self.Script = None
self.SetOutlets = 0

def UndoCallback(self, obj):
self.InitializeSeeds()
Expand Down Expand Up @@ -105,6 +113,7 @@ def Execute(self):
self.PrintError('vmtkPickPointSeedSelector Error: Surface not set.')
return

self._MainBodySeedIds.Initialize()
self._SourceSeedIds.Initialize()
self._TargetSeedIds.Initialize()

Expand Down Expand Up @@ -148,16 +157,29 @@ def Execute(self):
self.InitializeSeeds()
self.vmtkRenderer.Render()
any = self.PickedSeedIds.GetNumberOfIds()
self._SourceSeedIds.DeepCopy(self.PickedSeedIds)
self._MainBodySeedIds.DeepCopy(self.PickedSeedIds)

self.InputInfo('Please position the mouse and press space to add points at clip locations, \'u\' to undo\n')
if( self.SetOutlets ):
self.InputInfo('Please position the mouse and press space to add point on vessel wall near each Inlet location, \'u\' to undo\n')
else:
self.InputInfo('Please position the mouse and press space to add points at clip locations, \'u\' to undo\n')

any = 0
while any == 0:
self.InitializeSeeds()
self.vmtkRenderer.Render()
any = self.PickedSeedIds.GetNumberOfIds()
self._TargetSeedIds.DeepCopy(self.PickedSeedIds)
self._SourceSeedIds.DeepCopy(self.PickedSeedIds)

if(self.SetOutlets):
self.InputInfo('Please position the mouse and press space to add point on vessel wall near each Outlet location, \'u\' to undo\n')

any = 0
while any == 0:
self.InitializeSeeds()
self.vmtkRenderer.Render()
any = self.PickedSeedIds.GetNumberOfIds()
self._TargetSeedIds.DeepCopy(self.PickedSeedIds)

if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
Expand All @@ -169,6 +191,10 @@ def __init__(self):

pypes.pypeScript.__init__(self)

self.Centerlines = None
self.CenterlineNormals = 0
self.FrenetTangentArrayName = 'FrenetTangent'

self.Surface = None
self.vmtkRenderer = None
self.OwnRenderer = 0
Expand All @@ -181,9 +207,16 @@ def __init__(self):
self.CleanOutput = 1

self.SetScriptName('vmtksurfaceendclipper')
self.SetScriptDoc('interactively clip a tubular surface with normals estimated at seed locations')
self.SetScriptDoc('interactively clip a tubular surface with normals estimated at seed locations. It is \
recomended that the option to clip based on centerlines normals is enabled to increase \
the accuracy of the clipping. If desired, a centerline containing the Frenet Tangent Array \
must be fed in along with the surface. This is generated by passing a centerline through the \
vmtkcenterlinegeometry script.')
self.SetInputMembers([
['Surface','i','vtkPolyData',1,'','the input surface','vmtksurfacereader'],
['CenterlineNormals','centerlinenormal','bool',1,'','toggle using centerline tangent for normal estimation'],
['Centerlines','centerlines','vtkPolyData',1,'','the input centerlines','vmtksurfacereader'],
['FrenetTangentArrayName','frenettangentarray','str',1,'','name of the array where centerline tangent vectors of the Frenet reference system are stored'],
['vmtkRenderer','renderer','vmtkRenderer',1,'','external renderer']
])
self.SetOutputMembers([
Expand All @@ -195,6 +228,9 @@ def Execute(self):
if self.Surface == None:
self.PrintError('Error: no Surface.')

if (self.CenterlineNormals) and (self.Centerlines == None):
self.PrintError('Error: No input centerlines.')

if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
Expand All @@ -204,6 +240,8 @@ def Execute(self):
self.SeedSelector.vmtkRenderer = self.vmtkRenderer
self.SeedSelector.Script = self

if (self.CenterlineNormals):
self.SeedSelector.SetOutlets = 1
self.SeedSelector.SetSurface(self.Surface)
self.SeedSelector.InputInfo = self.InputInfo
self.SeedSelector.InputText = self.InputText
Expand All @@ -212,11 +250,11 @@ def Execute(self):
self.SeedSelector.PrintLog = self.PrintLog
self.SeedSelector.Execute()

mainBodySeedIds = self.SeedSelector.GetSourceSeedIds()
mainBodySeedIds = self.SeedSelector.GetMainBodySeedIds()
mainBodySeedId = mainBodySeedIds.GetId(0)
mainBodyPoint = self.Surface.GetPoint(mainBodySeedId)

clipSeedIds = self.SeedSelector.GetTargetSeedIds()
clipSeedIds = self.SeedSelector.GetSourceSeedIds()

surfaceCleaner = vtk.vtkCleanPolyData()
surfaceCleaner.SetInputData(self.Surface)
Expand All @@ -230,25 +268,45 @@ def Execute(self):

clippedSurface = surfaceTriangulator.GetOutput()

n_seeds = clipSeedIds.GetNumberOfIds() # get the number of inlets
if (self.CenterlineNormals):
targetSeedIds = self.SeedSelector.GetTargetSeedIds()
for i in range(targetSeedIds.GetNumberOfIds()):
clipSeedIds.InsertNextId(targetSeedIds.GetId(i))
locator_ctr = vtk.vtkPointLocator()
locator_ctr.SetDataSet(self.Centerlines)
locator_ctr.BuildLocator()

for i in range(clipSeedIds.GetNumberOfIds()):

seedId = clipSeedIds.GetId(i)

locator = vtk.vtkPointLocator()
locator.SetDataSet(clippedSurface)
locator.BuildLocator()

seedPoint = self.Surface.GetPoint(seedId)
seedPointId = locator.FindClosestPoint(seedPoint)

planeEstimator = vtkvmtk.vtkvmtkPolyDataNormalPlaneEstimator()
planeEstimator.SetInputData(clippedSurface)
planeEstimator.SetOriginPointId(seedPointId)
planeEstimator.Update()
# the frenet tangent must be inverted as it is directed outwards
# the seam filter requires an inward facing normal
if (self.CenterlineNormals):
centerlinePointId = locator_ctr.FindClosestPoint(seedPoint)
origin = self.Centerlines.GetPoint(centerlinePointId)
normal = self.Centerlines.GetPointData().GetArray(self.FrenetTangentArrayName).GetTuple(centerlinePointId)
if( i >= n_seeds ):
# invert outward facing normals
normal = tuple( -p for p in normal)
else:
locator = vtk.vtkPointLocator()
locator.SetDataSet(clippedSurface)
locator.BuildLocator()
seedPointId = locator.FindClosestPoint(seedPoint)

planeEstimator = vtkvmtk.vtkvmtkPolyDataNormalPlaneEstimator()
planeEstimator.SetInputData(clippedSurface)
planeEstimator.SetOriginPointId(seedPointId)
planeEstimator.Update()
origin = planeEstimator.GetOrigin()
normal = planeEstimator.GetNormal()

plane = vtk.vtkPlane()
plane.SetOrigin(planeEstimator.GetOrigin())
plane.SetNormal(planeEstimator.GetNormal())
plane.SetOrigin(origin)
plane.SetNormal(normal)

seamFilter = vtkvmtk.vtkvmtkTopologicalSeamFilter()
seamFilter.SetInputData(clippedSurface)
Expand Down