def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkImageIslandRemoval2D(), 'Processing.',
('vtkImageData',), ('vtkImageData',),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(self,
module_manager,
vtk.vtkImageIslandRemoval2D(),
'Processing.', ('vtkImageData', ),
('vtkImageData', ),
replaceDoc=True,
inputFunctions=None,
outputFunctions=None)
def VTKIslandRemoval(x,isval,repval,area,numret=0):
if type(x) == np.ndarray: i = NumToVTKImage(x)
else: i = x
d = vtk.vtkImageIslandRemoval2D()
d.SetIslandValue(isval)
d.SetReplaceValue(repval)
d.SetAreaThreshold(area)
d.SquareNeighborhoodOn()
d.SetInputData(i)
o = d.GetOutput()
d.Update()
if numret: return VTKImageToNum(o)
else: return o
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# A script to test the island removal filter.
# first the image is thresholded, then small islands are removed.
# Image pipeline
reader = vtk.vtkPNGReader()
reader.SetFileName("" + str(VTK_DATA_ROOT) + "/Data/fullhead15.png")
thresh = vtk.vtkImageThreshold()
thresh.SetInputConnection(reader.GetOutputPort())
thresh.ThresholdByUpper(2000.0)
thresh.SetInValue(255)
thresh.SetOutValue(0)
thresh.ReleaseDataFlagOff()
island = vtk.vtkImageIslandRemoval2D()
island.SetInputConnection(thresh.GetOutputPort())
island.SetIslandValue(255)
island.SetReplaceValue(128)
island.SetAreaThreshold(100)
island.SquareNeighborhoodOn()
viewer = vtk.vtkImageViewer()
viewer.SetInputConnection(island.GetOutputPort())
viewer.SetColorWindow(255)
viewer.SetColorLevel(127.5)
#viewer DebugOn
viewer.Render()
# --- end of script --
def RemoveCoronalIslands(self, ImageData, IslandSizeThreshold):
IslandRemovalFilter = vtk.vtkImageIslandRemoval2D()
IslandRemovalFilter.SetAreaThreshold(int(IslandSizeThreshold))
IslandRemovalFilter.SetSquareNeighborhood(8)
IslandRemovalFilter.SetIslandValue(1)
IslandRemovalFilter.SetReplaceValue(0)
# Go through each coronal slice of ImageData, storing slices with islands removed
CoronalSliceImages = []
Extent = ImageData.GetExtent()
#print "DEBUG - Island remover instantiated"
for A in range(
Extent[2], Extent[3]
): # Take projetion alond A-P line, posterior to anterior direction
CurrentSliceImageData = vtk.vtkImageData()
CurrentSliceImageData.SetExtent(ImageData.GetExtent()[0:2] +
(0, 1) + ImageData.GetExtent()[4:])
CurrentSliceImageData.SetSpacing(ImageData.GetSpacing())
CurrentSliceImageData.AllocateScalars(ImageData.GetScalarType(), 1)
for S in range(Extent[4],
Extent[5]): # For each row of the labelmap
for R in range(Extent[0],
Extent[1]): # For each column of the label-map
CurrentValue = ImageData.GetScalarComponentAsFloat(
R, A, S, 0)
CurrentSliceImageData.SetScalarComponentFromFloat(
R, 0, S, 0, CurrentValue)
#print "DEBUG - Image data instantiated"
IslandRemovalFilter.SetInputData(CurrentSliceImageData)
IslandRemovalFilter.Update()
#print "DEBUG - Filter ouput updated"
IslandsRemovedSliceImage = IslandRemovalFilter.GetOutput()
CoronalSliceImages.append(IslandsRemovedSliceImage)
#print "DEBUG - All slices' islands removed"
# Merge all slices into one FilteredImageData
ProcessedImageData = vtk.vtkImageData()
ProcessedImageData.SetExtent(ImageData.GetExtent())
ProcessedImageData.SetSpacing(ImageData.GetSpacing())
ProcessedImageData.AllocateScalars(ImageData.GetScalarType(), 1)
for i, A in enumerate(range(Extent[2], Extent[3])):
for S in range(Extent[4],
Extent[5]): # For each row of the labelmap
for R in range(Extent[0],
Extent[1]): # For each column of the label-map
CurrentVoxelLabelValue = CoronalSliceImages[
i].GetScalarComponentAsFloat(R, 0, S, 0)
ProcessedImageData.SetScalarComponentFromFloat(
R, A, S, 0, CurrentVoxelLabelValue)
#print "DEBUG - Image data with islands removed created"
LabelMapIslandsRemoved = slicer.vtkMRMLLabelMapVolumeNode()
LabelMapIslandsRemoved.SetSpacing(ImageData.GetSpacing())
LabelMapIslandsRemoved.SetOrigin(ImageData.GetOrigin())
LabelMapIslandsRemoved.SetAndObserveImageData(ProcessedImageData)
#print "DEBUG - Image data copied to labelmap"
return LabelMapIslandsRemoved
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# A script to test the island removal filter.
# first the image is thresholded, then small islands are removed.
# Image pipeline
reader = vtk.vtkPNGReader()
reader.SetFileName("" + str(VTK_DATA_ROOT) + "/Data/fullhead15.png")
thresh = vtk.vtkImageThreshold()
thresh.SetInputConnection(reader.GetOutputPort())
thresh.ThresholdByUpper(2000.0)
thresh.SetInValue(255)
thresh.SetOutValue(0)
thresh.ReleaseDataFlagOff()
island = vtk.vtkImageIslandRemoval2D()
island.SetInputConnection(thresh.GetOutputPort())
island.SetIslandValue(255)
island.SetReplaceValue(128)
island.SetAreaThreshold(100)
island.SquareNeighborhoodOn()
viewer = vtk.vtkImageViewer()
viewer.SetInputConnection(island.GetOutputPort())
viewer.SetColorWindow(255)
viewer.SetColorLevel(127.5)
#viewer DebugOn
viewer.Render()
# --- end of script --
def create_frog_actor(frog_fn, frog_tissue_fn, tissue, flying_edges, decimate, lut):
# Get the tissue parameters
pixel_size = tissue['PIXEL_SIZE']
columns = tissue['COLUMNS']
rows = tissue['ROWS']
voi = tissue['VOI']
spacing = float(tissue['SPACING'])
start_slice = float(tissue['START_SLICE'])
data_spacing = [pixel_size, pixel_size, spacing]
data_origin = [-(columns / 2.0) * pixel_size, -(rows / 2.0) * pixel_size, start_slice * spacing]
#
# adjust y bounds for PNM coordinate system
#
tmp = voi[2]
voi[2] = rows - voi[3] - 1
voi[3] = rows - tmp - 1
if tissue['NAME'] == 'skin':
fn = frog_fn
else:
fn = frog_tissue_fn
reader = vtk.vtkMetaImageReader()
reader.SetFileName(str(fn))
reader.SetDataSpacing(data_spacing)
reader.SetDataOrigin(data_origin)
reader.SetDataExtent(voi)
reader.Update()
last_connection = reader
if not tissue['NAME'] == 'skin':
if tissue['ISLAND_REPLACE'] >= 0:
island_remover = vtk.vtkImageIslandRemoval2D()
island_remover.SetAreaThreshold(tissue['ISLAND_AREA'])
island_remover.SetIslandValue(tissue['ISLAND_REPLACE'])
island_remover.SetReplaceValue(tissue['TISSUE'])
island_remover.SetInput(last_connection.GetOutput())
island_remover.Update()
last_connection = island_remover
select_tissue = vtk.vtkImageThreshold()
select_tissue.ThresholdBetween(tissue['TISSUE'], tissue['TISSUE'])
select_tissue.SetInValue(255)
select_tissue.SetOutValue(0)
select_tissue.SetInputConnection(last_connection.GetOutputPort())
last_connection = select_tissue
shrinker = vtk.vtkImageShrink3D()
shrinker.SetInputConnection(last_connection.GetOutputPort())
shrinker.SetShrinkFactors(tissue['SAMPLE_RATE'])
shrinker.AveragingOn()
last_connection = shrinker
if not all(v == 0 for v in tissue['GAUSSIAN_STANDARD_DEVIATION']):
gaussian = vtk.vtkImageGaussianSmooth()
gaussian.SetStandardDeviation(*tissue['GAUSSIAN_STANDARD_DEVIATION'])
gaussian.SetRadiusFactors(*tissue['GAUSSIAN_RADIUS_FACTORS'])
gaussian.SetInputConnection(shrinker.GetOutputPort())
last_connection = gaussian
# Time the isocontouring.
ict = collections.defaultdict()
iso_value = tissue['VALUE']
if flying_edges:
iso_surface = vtk.vtkFlyingEdges3D()
iso_surface.SetInputConnection(last_connection.GetOutputPort())
iso_surface.ComputeScalarsOff()
iso_surface.ComputeGradientsOff()
iso_surface.ComputeNormalsOff()
iso_surface.SetValue(0, iso_value)
timer = vtk.vtkExecutionTimer()
timer.SetFilter(iso_surface)
iso_surface.Update()
ict['Flying Edges'] = timer.GetElapsedWallClockTime()
else:
iso_surface = vtk.vtkMarchingCubes()
iso_surface.SetInputConnection(last_connection.GetOutputPort())
iso_surface.ComputeScalarsOff()
iso_surface.ComputeGradientsOff()
iso_surface.ComputeNormalsOff()
iso_surface.SetValue(0, iso_value)
timer = vtk.vtkExecutionTimer()
timer.SetFilter(iso_surface)
iso_surface.Update()
ict['Marching Cubes'] = timer.GetElapsedWallClockTime()
so = SliceOrder()
# transform = so.get(tissue['SLICE_ORDER'])
# Match Frog.py
transform = so.get('hfap')
transform.Scale(1, -1, 1)
tf = vtk.vtkTransformPolyDataFilter()
tf.SetTransform(transform)
tf.SetInputConnection(iso_surface.GetOutputPort())
last_connection = tf
if decimate:
decimator = vtk.vtkDecimatePro()
decimator.SetInputConnection(last_connection.GetOutputPort())
decimator.SetFeatureAngle(tissue['DECIMATE_ANGLE'])
decimator.MaximumIterations = tissue['DECIMATE_ITERATIONS']
decimator.PreserveTopologyOn()
decimator.SetErrorIsAbsolute(1)
decimator.SetAbsoluteError(tissue['DECIMATE_ERROR'])
decimator.SetTargetReduction(tissue['DECIMATE_REDUCTION'])
last_connection = decimator
smoother = vtk.vtkWindowedSincPolyDataFilter()
smoother.SetInputConnection(last_connection.GetOutputPort())
smoother.SetNumberOfIterations(tissue['SMOOTH_ITERATIONS'])
smoother.BoundarySmoothingOff()
smoother.FeatureEdgeSmoothingOff()
smoother.SetFeatureAngle(tissue['SMOOTH_ANGLE'])
smoother.SetPassBand(tissue['SMOOTH_FACTOR'])
smoother.NonManifoldSmoothingOn()
smoother.NormalizeCoordinatesOff()
smoother.Update()
normals = vtk.vtkPolyDataNormals()
normals.SetInputConnection(smoother.GetOutputPort())
normals.SetFeatureAngle(tissue['FEATURE_ANGLE'])
stripper = vtk.vtkStripper()
stripper.SetInputConnection(normals.GetOutputPort())
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(stripper.GetOutputPort())
# Create iso-surface
contour = vtk.vtkContourFilter()
contour.SetInputConnection(reader.GetOutputPort())
contour.SetValue(0, iso_value)
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetOpacity(tissue['OPACITY'])
actor.GetProperty().SetDiffuseColor(lut.GetTableValue(tissue['TISSUE'])[:3])
actor.GetProperty().SetSpecular(0.5)
actor.GetProperty().SetSpecularPower(10)
return ict, actor
