def surfaceclipp_centerline(input_file, output_file):
'''
使用中心线自动的裁剪端口
'''
surface_reader = sr.vmtkSurfaceReader()
surface_reader.InputFileName = input_file
surface_reader.Execute()
centerline = cl.vmtkCenterlines()
centerline.Surface = surface_reader.Surface
centerline.Execute()
endpointextractor = ep.vmtkEndpointExtractor()
endpointextractor.Centerlines = centerline.Centerlines
endpointextractor.Execute()
branchclipper = bc.vmtkBranchClipper()
branchclipper.Surface = surface_reader.Surface
branchclipper.Centerlines = endpointextractor.Centerlines
branchclipper.Execute()
surface_connectivity = sufct.vmtkSurfaceConnectivity()
surface_connectivity.Surface = branchclipper.Surface
surface_connectivity.CleanOutput = 1
surface_connectivity.Execute()
surface_writer = sw.vmtkSurfaceWriter()
surface_writer.Surface = surface_connectivity.Surface
surface_writer.OutputFileName = output_file
surface_writer.Execute()
def make_compare_centerline(centerline, reference_file, tolerance=0.001, method='distance', arrayname=''):
reader = surfacereader.vmtkSurfaceReader()
try:
datadir = os.path.join(
os.path.dirname(
os.path.dirname(
os.path.realpath(__file__))), 'vmtk-test-data', 'centerlinereference')
if not os.path.isdir(datadir): raise ValueError()
except ValueError:
datadir = os.path.join(
os.path.dirname(
os.path.dirname(
os.path.dirname(
os.path.dirname(
os.path.realpath(__file__))))),
'vmtk-test-data', 'centerlinereference')
if not os.path.isdir(datadir):
raise ValueError('the vmtk-test-data repository cannot be found at the same level as vmtk. expected it to be at', datadir)
reader.InputFileName = os.path.join(datadir, reference_file)
reader.Execute()
comp = surfacecompare.vmtkSurfaceCompare()
comp.Surface = centerline
comp.ReferenceSurface = reader.Surface
comp.Method = method
comp.ArrayName = arrayname
comp.Tolerance = tolerance
comp.Execute()
return comp.Result
def make_compare_centerline(centerline,
reference_file,
tolerance=0.001,
method='distance',
arrayname=''):
reader = surfacereader.vmtkSurfaceReader()
try:
datadir = os.path.join(
os.path.dirname(os.path.dirname(os.path.realpath(__file__))),
'vmtk-test-data', 'centerlinereference')
if not os.path.isdir(datadir): raise ValueError()
except ValueError:
datadir = os.path.join(
os.path.dirname(
os.path.dirname(
os.path.dirname(
os.path.dirname(os.path.realpath(__file__))))),
'vmtk-test-data', 'centerlinereference')
if not os.path.isdir(datadir):
raise ValueError(
'the vmtk-test-data repository cannot be found at the same level as vmtk. expected it to be at',
datadir)
reader.InputFileName = os.path.join(datadir, reference_file)
reader.Execute()
comp = surfacecompare.vmtkSurfaceCompare()
comp.Surface = centerline
comp.ReferenceSurface = reader.Surface
comp.Method = method
comp.ArrayName = arrayname
comp.Tolerance = tolerance
comp.Execute()
return comp.Result
def suface_flow_extension(input_file, output_file):
'''
给表面添加流拓展
'''
surface_reader = sr.vmtkSurfaceReader()
surface_reader.InputFileName = input_file
surface_reader.Execute()
centerline = cl.vmtkCenterlines()
centerline.Surface = surface_reader.Surface
centerline.SeedSelectorName = 'openprofiles'
centerline.Execute()
flow_extension = fex.vmtkFlowExtensions()
flow_extension.Surface = surface_reader.Surface
flow_extension.Centerlines = centerline.Centerlines
flow_extension.AdaptiveExtensionLength = 1
flow_extension.ExtensionRatio = 20
flow_extension.CenterlineNormalEstimationDistanceRatio = 1
flow_extension.Interactive = 0
flow_extension.Execute()
surface_writer = sw.vmtkSurfaceWriter()
surface_writer.Surface = flow_extension.Surface
surface_writer.OutputFileName = output_file
surface_writer.Execute()
def aorta_surface_open_ends(input_datadir):
import vmtk.vmtksurfacereader as surfacereader
reader = surfacereader.vmtkSurfaceReader()
reader.InputFileName = os.path.join(input_datadir,
'aorta-surface-open-ends.stl')
reader.Execute()
return reader.Surface
def aorta_surface_two_segments(input_datadir):
import vmtk.vmtksurfacereader as surfacereader
reader = surfacereader.vmtkSurfaceReader()
reader.InputFileName = os.path.join(input_datadir,
'aorta-surface-two-segments.vtp')
reader.Execute()
return reader.Surface
def test_read_stl_surface(input_datadir):
reader = r.vmtkSurfaceReader()
reader.InputFileName = os.path.join(input_datadir, 'fixture.stl')
reader.Execute()
conv = wrap.vmtkSurfaceToNumpy()
conv.Surface = reader.Surface
conv.Execute()
assert sha1(conv.ArrayDict['Points']).hexdigest() == 'a3b3c7608de5a7a9fecf9f7280f9fc65565e7ded'
def test_read_vtp_surface(input_datadir):
reader = r.vmtkSurfaceReader()
reader.InputFileName = os.path.join(input_datadir, 'aorta-surface.vtp')
reader.Execute()
conv = wrap.vmtkSurfaceToNumpy()
conv.Surface = reader.Surface
conv.Execute()
assert sha1(conv.ArrayDict['Points']).hexdigest() == '2d589cf877f713cf805d7be952fa5bdb2f2ef0ee'
def test_read_vtp_surface(input_datadir):
reader = r.vmtkSurfaceReader()
reader.InputFileName = os.path.join(input_datadir, 'aorta-surface.vtp')
reader.Execute()
conv = wrap.vmtkSurfaceToNumpy()
conv.Surface = reader.Surface
conv.Execute()
assert sha1(conv.ArrayDict['Points']).hexdigest() == '2d589cf877f713cf805d7be952fa5bdb2f2ef0ee'
def test_read_stl_surface(input_datadir):
reader = r.vmtkSurfaceReader()
reader.InputFileName = os.path.join(input_datadir, 'fixture.stl')
reader.Execute()
conv = wrap.vmtkSurfaceToNumpy()
conv.Surface = reader.Surface
conv.Execute()
assert sha1(conv.ArrayDict['Points']).hexdigest() == 'a3b3c7608de5a7a9fecf9f7280f9fc65565e7ded'
def surfaceclipp(input_file, out_file):
'''
裁剪表面的端口,交互的方式
'''
surface_reader = sr.vmtkSurfaceReader()
surface_reader.InputFileName = input_file
surface_reader.Execute()
surface_clipper = sc.vmtkSurfaceClipper()
surface_clipper.Surface = surface_reader.Surface
surface_clipper.Execute()
surface_writer = sw.vmtkSurfaceWriter()
surface_writer.Surface = surface_clipper.Surface
surface_writer.OutputFileName = output_file
surface_writer.Execute()
def surface_capper(input_file, output_file):
'''
将网格变得端口封住
'''
reader = sr.vmtkSurfaceReader()
reader.InputFileName = input_file
reader.Execute()
capper = sc.vmtkSurfaceCapper()
capper.Surface = reader.Surface
capper.Execute()
writer = sw.vmtkSurfaceWriter()
writer.OutputFileName = output_file
writer.Surface = capper.Surface
writer.Mode = 'ascii'
writer.Execute()
def surface_smooth():
'''
网格表面的平滑
'''
input_file = 'id2_model.vtp'
output_file = 'id2_mode_sm_laplace.vtp'
surfacereader = sr.vmtkSurfaceReader()
surfacereader.InputFileName = input_file
surfacereader.Execute()
# 没有平滑的网格表面
originsurface_mapper = vtk.vtkPolyDataMapper()
originsurface_mapper.SetInputData(surfacereader.Surface)
originsurface_actor = vtk.vtkActor()
originsurface_actor.SetMapper(originsurface_mapper)
color = [0, 1, 0]
originsurface_actor.GetProperty().SetColor(color)
originsurface_actor.GetProperty().SetOpacity(0.8)
surfacesmooth = ss.vmtkSurfaceSmoothing()
surfacesmooth.Surface = surfacereader.Surface
surfacesmooth.NumberOfIterations = 30
surfacesmooth.PassBand = 1.0
surfacesmooth.RelaxationFactor = 0.01
surfacesmooth.BoundarySmoothing = 1
surfacesmooth.NormalizeCoordinates = 1
surfacesmooth.Method = "laplace" # ["taubin","laplace"]
surfacesmooth.Execute()
renderer = rd.vmtkRenderer()
renderer.Initialize()
renderer.Renderer.AddActor(originsurface_actor)
surface_viewer = sv.vmtkSurfaceViewer()
surface_viewer.vmtkRenderer = renderer
surface_viewer.Surface = surfacesmooth.Surface
surface_viewer.Display = 1
surface_viewer.Color = [1.0, 0, 0]
surface_viewer.ColorMap = "cooltowarm"
surface_viewer.Execute()
surface_writer = sw.vmtkSurfaceWriter()
surface_writer.OutputFileName = output_file
surface_writer.Surface = surfacesmooth.Surface
surface_writer.Execute()
def surfacesubdivision(input_file, output_file):
'''
对网格表面进行细分
'''
surface_reader = sr.vmtkSurfaceReader()
surface_reader.InputFileName = input_file
surface_reader.Execute()
surface_subdivision = ssdv.vmtkSurfaceSubdivision()
surface_subdivision.NumberOfSubdivisions = 1
surface_subdivision.Surface = surface_reader.Surface
surface_subdivision.Method = "butterfly"
surface_subdivision.Execute()
surface_writer = sw.vmtkSurfaceWriter()
surface_writer.OutputFileName = output_file
surface_writer.Surface = surface_subdivision.Surface
surface_writer.Execute()
def centerlines():
'''
显示中心线
'''
input_file = "data\\levelSet\\vessellevelset_0.vtp"
surfacereader = sr.vmtkSurfaceReader()
surfacereader.InputFileName = input_file
surfacereader.Execute()
centerline = cl.vmtkCenterlines()
centerline.Surface = surfacereader.Surface
centerline.Execute()
''' centerline_mapper = vtk.vtkPolyDataMapper()
centerline_mapper.SetInputData(centerline.Centerlines)
centerline_actor = vtk.vtkActor()
centerline_actor.SetMapper(centerline_mapper)
centerline.vmtkRenderer.Renderer.AddActor(centerline_actor)
surface_actor = centerline.vmtkRenderer.Renderer.GetActors().GetLastActor()
surface_actor.GetProperty().SetOpacity(0)
surface_actor.GetProperty().SetColor([0.1, 0.2, 0.5])
centerline.vmtkRenderer.Render()'''
surface_mapper = vtk.vtkPolyDataMapper()
surface_mapper.SetInputData(surfacereader.Surface)
surface_actor = vtk.vtkActor()
surface_actor.SetMapper(surface_mapper)
surface_actor.GetProperty().SetOpacity(0.3)
color = [0.5, 0.6, 0.7]
surface_actor.GetProperty().SetColor(color)
renderer = rd.vmtkRenderer()
renderer.Initialize()
renderer.Renderer.AddActor(surface_actor)
surfaceviewer = sv.vmtkSurfaceViewer()
surfaceviewer.Surface = centerline.Centerlines
# surfaceviwer.Surface = centerline.VoronoiDiagram
surfaceviewer.Color = [0.5, 0.6, 0.7]
surfaceviewer.ColorMap = "rainbow" # "rainbow","blackbody","cooltowarm","grayscale"
surfaceviewer.vmtkRenderer = renderer # centerline中vmtkrenderer在调用结束后，就回收内存了
surfaceviewer.ArrayName = "MaximumInscribedSphereRadius"
surfaceviewer.Execute()
def reference_system(input_datadir):
reader = surfacereader.vmtkSurfaceReader()
reader.InputFileName = os.path.join(input_datadir, 'aorta-centerline-referencesystem.vtp')
reader.Execute()
return reader.Surface
def aorta_surface_reference(input_datadir):
reader = surfacereader.vmtkSurfaceReader()
reader.InputFileName = os.path.join(
input_datadir, 'aorta-surface-connectivity-reference.stl')
reader.Execute()
return reader.Surface
def aorta_surface_reference(input_datadir):
reader = surfacereader.vmtkSurfaceReader()
reader.InputFileName = os.path.join(input_datadir, 'aorta-surface-connectivity-reference.stl')
reader.Execute()
return reader.Surface
def centerline_attribute_branched(input_datadir):
reader = surfacereader.vmtkSurfaceReader()
reader.InputFileName = os.path.join(input_datadir, 'aorta-centerline-attribute-branches.vtp')
reader.Execute()
return reader.Surface
def reference_system(input_datadir):
reader = surfacereader.vmtkSurfaceReader()
reader.InputFileName = os.path.join(
input_datadir, 'aorta-centerline-referencesystem.vtp')
reader.Execute()
return reader.Surface
def aorta_surface_branches(input_datadir):
reader = surfacereader.vmtkSurfaceReader()
reader.InputFileName = os.path.join(input_datadir, 'aorta-surface-branch-split.vtp')
reader.Execute()
return reader.Surface
def aorta_surface_two_segments(input_datadir):
import vmtk.vmtksurfacereader as surfacereader
reader = surfacereader.vmtkSurfaceReader()
reader.InputFileName = os.path.join(input_datadir, 'aorta-surface-two-segments.vtp')
reader.Execute()
return reader.Surface
def aorta_centerline(input_datadir):
reader = surfacereader.vmtkSurfaceReader()
reader.InputFileName = os.path.join(input_datadir, 'aorta-centerline.vtp')
reader.Execute()
return reader.Surface
def aorta_centerline_branches(input_datadir):
reader = surfacereader.vmtkSurfaceReader()
reader.InputFileName = os.path.join(input_datadir,
'aorta-centerline-branches.vtp')
reader.Execute()
return reader.Surface
def aorta_surface_open_ends(input_datadir):
import vmtk.vmtksurfacereader as surfacereader
reader = surfacereader.vmtkSurfaceReader()
reader.InputFileName = os.path.join(input_datadir, 'aorta-surface-open-ends.stl')
reader.Execute()
return reader.Surface
def aorta_surface_branches(input_datadir):
reader = surfacereader.vmtkSurfaceReader()
reader.InputFileName = os.path.join(input_datadir,
'aorta-surface-branch-split.vtp')
reader.Execute()
return reader.Surface
def aorta_surface2(input_datadir):
reader = surfacereader.vmtkSurfaceReader()
reader.InputFileName = os.path.join(input_datadir,
'aorta-surface-segment-2.stl')
reader.Execute()
return reader.Surface
def aorta_surface2(input_datadir):
reader = surfacereader.vmtkSurfaceReader()
reader.InputFileName = os.path.join(input_datadir, 'aorta-surface-segment-2.stl')
reader.Execute()
return reader.Surface
