Question

我正在尝试使用ITK的GeodesicActiveContourLevelSetImageFilter分割图像中的对象。我的代码与https://itk.org/ITKExamples/src/Segmentation/LevelSets/SegmentWithGeodesicActiveContourLevelSet/Documentation.html中的示例几乎相同，但出现以下错误：

RuntimeError: c:\p\ipp\standalone-build\itk-source\modules\core\common\include\itkImageToImageFilter.hxx:241:
itk::ERROR: GeodesicActiveContourLevelSetImageFilter(000002189D4F4460): 
Inputs do not occupy the same physical space! 
InputImage Direction: -1.0000000e+00 0.0000000e+00 0.0000000e+00
0.0000000e+00 -1.0000000e+00 0.0000000e+00
0.0000000e+00 0.0000000e+00 -1.0000000e+00, 
InputImageInitialImage Direction: 1.0000000e+00 0.0000000e+00 0.0000000e+00
0.0000000e+00 1.0000000e+00 0.0000000e+00
0.0000000e+00 0.0000000e+00 1.0000000e+00

Tolerance: 1.0000000e-06

似乎（NifTi）图像的方向在CurvatureAnisotropicDiffusionImageFilter之后发生了变化-由于某些原因，我认为它在此阶段已镜像。该错误是在“ writer.Update（）”处触发的（请参阅下面的代码）。

这是我第一次在ITK工作，感谢您的帮助。

initialDistance = 0.0
sigma = 0.5
alpha = -0.3
beta = 2.0
propagationScaling = 10.0
numberOfIterations = 400
seedValue = -initialDistance

Dimension = 3
InputPixelType = itk.F
OutputPixelType = itk.UC
InputImageType = itk.Image[InputPixelType, Dimension]
OutputImageType = itk.Image[OutputPixelType, Dimension]

ReaderType = itk.ImageFileReader[InputImageType]
WriterType = itk.ImageFileWriter[OutputImageType]

reader = ReaderType.New()
reader.SetFileName(inputFileName)

SmoothingFilterType = itk.CurvatureAnisotropicDiffusionImageFilter[InputImageType, InputImageType]
smoothing = SmoothingFilterType.New()
smoothing.SetTimeStep(0.0625)
smoothing.SetNumberOfIterations(5)
smoothing.SetConductanceParameter(1.5)
smoothing.SetInput(reader.GetOutput())

GradientFilterType = itk.GradientMagnitudeRecursiveGaussianImageFilter[InputImageType, InputImageType]
gradientMagnitude = GradientFilterType.New()
gradientMagnitude.SetSigma(sigma)
gradientMagnitude.SetInput(smoothing.GetOutput())

SigmoidFilterType = itk.SigmoidImageFilter[InputImageType, InputImageType]
sigmoid = SigmoidFilterType.New()
sigmoid.SetOutputMinimum(0.0)
sigmoid.SetOutputMaximum(1.0)
sigmoid.SetAlpha(alpha)
sigmoid.SetBeta(beta)
sigmoid.SetInput(gradientMagnitude.GetOutput())

FastMarchingFilterType = itk.FastMarchingImageFilter[InputImageType, InputImageType]
fastMarching = FastMarchingFilterType.New()

GeoActiveContourFilterType = itk.GeodesicActiveContourLevelSetImageFilter[InputImageType, InputImageType, InputPixelType]
geodesicActiveContour = GeoActiveContourFilterType.New()
geodesicActiveContour.SetPropagationScaling(propagationScaling)
geodesicActiveContour.SetCurvatureScaling(1.0)
geodesicActiveContour.SetAdvectionScaling(1.0)
geodesicActiveContour.SetMaximumRMSError(0.02)
geodesicActiveContour.SetNumberOfIterations(numberOfIterations)
geodesicActiveContour.SetInput(fastMarching.GetOutput())  
geodesicActiveContour.SetFeatureImage(sigmoid.GetOutput())

ThresholdingFilterType = itk.BinaryThresholdImageFilter[InputImageType, OutputImageType]
thresholder = ThresholdingFilterType.New()
thresholder.SetLowerThreshold(-1000.0)
thresholder.SetUpperThreshold(0.0)
thresholder.SetOutsideValue(itk.NumericTraits[OutputPixelType].min())
thresholder.SetInsideValue(itk.NumericTraits[OutputPixelType].max())
thresholder.SetInput(geodesicActiveContour.GetOutput())

seeds = itk.VectorContainer[itk.UI, itk.LevelSetNode[InputPixelType, Dimension]].New()
seeds.Initialize()
for i in range(len(seedsCoords[0])): # seedCoords are supplied from another func in the form of ([x coordinates], [y coordinates], [z coordinates])
    seedPosition = itk.Index[Dimension]()
    seedPosition[0] = int(seedsCoords[0][i])
    seedPosition[1] = int(seedsCoords[1][i])
    seedPosition[2] = int(seedsCoords[2][i])

    node = itk.LevelSetNode[InputPixelType, Dimension]()
    node.SetValue(seedValue)
    node.SetIndex(seedPosition)
    seeds.InsertElement(0, node)

fastMarching.SetTrialPoints(seeds)
fastMarching.SetSpeedConstant(1.0)

CastFilterType = itk.RescaleIntensityImageFilter[InputImageType, OutputImageType]

caster1 = CastFilterType.New()
caster2 = CastFilterType.New()
caster3 = CastFilterType.New()
caster4 = CastFilterType.New()
#
writer1 = WriterType.New()
writer2 = WriterType.New()
writer3 = WriterType.New()
writer4 = WriterType.New()

caster1.SetInput(smoothing.GetOutput())
writer1.SetInput(caster1.GetOutput())
writer1.SetFileName("GeodesicActiveContourImageFilterOutput1.png")
caster1.SetOutputMinimum(itk.NumericTraits[OutputPixelType].min())
caster1.SetOutputMaximum(itk.NumericTraits[OutputPixelType].max())
writer1.Update()

caster2.SetInput(gradientMagnitude.GetOutput())
writer2.SetInput(caster2.GetOutput())
writer2.SetFileName("GeodesicActiveContourImageFilterOutput2.png")
caster2.SetOutputMinimum(itk.NumericTraits[OutputPixelType].min())
caster2.SetOutputMaximum(itk.NumericTraits[OutputPixelType].max())
writer2.Update()

caster3.SetInput(sigmoid.GetOutput())
writer3.SetInput(caster3.GetOutput())
writer3.SetFileName("GeodesicActiveContourImageFilterOutput3.png")
caster3.SetOutputMinimum(itk.NumericTraits[OutputPixelType].min())
caster3.SetOutputMaximum(itk.NumericTraits[OutputPixelType].max())
writer3.Update()

caster4.SetInput(fastMarching.GetOutput())
writer4.SetInput(caster4.GetOutput())
writer4.SetFileName("GeodesicActiveContourImageFilterOutput4.png")
caster4.SetOutputMinimum(itk.NumericTraits[OutputPixelType].min())
caster4.SetOutputMaximum(itk.NumericTraits[OutputPixelType].max())
fastMarching.SetOutputSize(reader.GetOutput().GetBufferedRegion().GetSize())

writer = WriterType.New()
writer.SetFileName(outputFileName)
writer.SetInput(thresholder.GetOutput())
writer.Update()  # triggers the error

print(
    "Max. no. iterations: " +
    str(geodesicActiveContour.GetNumberOfIterations()) + "\n")
print(
    "Max. RMS error: " +
    str(geodesicActiveContour.GetMaximumRMSError()) + "\n")
print(
    "No. elpased iterations: " +
    str(geodesicActiveContour.GetElapsedIterations()) + "\n")
print("RMS change: " + str(geodesicActiveContour.GetRMSChange()) + "\n")

writer4.Update()

InternalWriterType = itk.ImageFileWriter[InputImageType]

mapWriter = InternalWriterType.New()
mapWriter.SetInput(fastMarching.GetOutput())
mapWriter.SetFileName("GeodesicActiveContourImageFilterOutput4.mha")
mapWriter.Update()

speedWriter = InternalWriterType.New()
speedWriter.SetInput(sigmoid.GetOutput())
speedWriter.SetFileName("GeodesicActiveContourImageFilterOutput3.mha")
speedWriter.Update()

gradientWriter = InternalWriterType.New()
gradientWriter.SetInput(gradientMagnitude.GetOutput())
gradientWriter.SetFileName("GeodesicActiveContourImageFilterOutput2.mha")
gradientWriter.Update()

Answer 1

您正在使用哪个版本的ITK？您是否尝试过最新的稳定版本（4.13.1）或最新的发行版？

未修改的示例是否会出现问题？如果不是这样，比较差异应该可以找到解决方案。

如果这些都不能解决问题，您可以共享输入图像吗？或者更好的是，显示了问题的输入图像裁剪了吗？

“ itk :: ERROR：GeodesicActiveContourLevelSetImageFilter（000002189D4F4460）：输入不占用相同的物理空间！”

1 个答案: