python - Elastix 3D 注册停止 python 没有任何错误

Question

我想注册 2 个 3D 数据集，这些数据集被读入 numpy 数组，然后提供给 registrate() 函数。当我执行代码时，它会打印以下日志：

安装所有组件。安装组件成功。

ELASTIX 版本：5.0.1 来自 ElastixBase 的命令行选项：
-fMask 未指定，因此未使用固定掩码
-mMask 未指定，因此未使用移动掩码
-out D:\...\test/
-priority 未指定，因此 NORMAL 进程优先级
-未指定线程，因此使用了所有可用线程
TransformBase 中的命令行选项：
-t0 未指定，因此不使用初始转换

读取图像...
读取图像需要 1 毫秒。

之后只是停止并返回到正常的命令行。它没有达到'step2'。

有没有办法回溯哪里出了问题，为什么？

def registrate(vol1, vol2, log_out_path):
    """

    Parameters
    ----------
    vol1: np.array, fixed image
    vol2: np.array, moving image
    log_out_path: str, path to the directory for the logfile

    Returns
    -------
    None
    """

    fixed_img = itk.GetImageFromArray(vol1)
    moving_img = itk.GetImageFromArray(vol2)

    print(type(moving_img))

    parameter_object_ = itk.ParameterObject.New()
    default_euler_ = parameter_object_.GetDefaultParameterMap("rigid", 3)
    parameter_object_.AddParameterMap(default_euler_)
    set_elastix_parameters(parameter_object_, 0, "euler")
    print("step1")
    result_image_, result_transform_parameters_ = itk.elastix_registration_method(fixed_img,  # fixed
                                                                                  moving_img,  # moving
                                                                                  parameter_object=parameter_object_,
                                                                                  log_to_console=True,
                                                                                  output_directory=log_out_path,
                                                                                  log_file_name=r"log.txt",
                                                                                  log_to_file=True,
                                                                                  )

    print("step2")
    deformed_image_ = apply_transformix([result_transform_parameters_], moving_img)
    print("Step3")
    save_volume(itk.GetArrayFromImage(deformed_image_), r"D:\...\deformed",
                     "de", True)
    save_volume(itk.GetArrayFromImage(result_image_),
                     r"D:\...\result_transformed", "re", True)


if __name__ == "__main__":

    moving_img = read_in_volume(r"D:\...\sample1")
    print("moving image read in correctly")
    fixed_img = read_in_volume(r"D:\...\sample2")
    print("fixed image read in correctly")

    registrate(fixed_img, moving_img, r"D:\...\test") 

---

使用的参数如下：

def set_elastix_parameters(parameters, i, transform):
    # Image types
    parameters.SetParameter(i, "UseDirectionCosines", "true")
    # Main components
    parameters.SetParameter(i, "Registration", "MultiResolutionRegistration")
    # parameters.SetParameter(i, "Interpolator", "BSplineInterpolatorFloat") not avalaible for python
    parameters.SetParameter(i, "Interpolator", "LinearInterpolator")
    parameters.SetParameter(i, "ResampleInterpolator", "FinalBSplineInterpolator")
    parameters.SetParameter(i, "Resampler", "DefaultResampler")
    parameters.SetParameter(i, "FixedImageBSplineInterpolationOrder", "1")
    parameters.SetParameter(i, "BSplineInterpolationOrder", "1")
    parameters.SetParameter(i, "FixedImagePyramid", "FixedSmoothingImagePyramid")
    parameters.SetParameter(i, "MovingImagePyramid", "MovingSmoothingImagePyramid")
    parameters.SetParameter(i, "Optimizer", "AdaptiveStochasticGradientDescent")
    parameters.SetParameter(i, "Metric", "AdvancedMattesMutualInformation")
    parameters.SetParameter(i, "FixedInternalImagePixelType", "float")
    parameters.SetParameter(i, "MovingInternalImagePixelType", "float")

    # Transformation
    if transform == "euler":
        parameters.SetParameter(i, "Transform", "EulerTransform")
        parameters.SetParameter(i, "AutomaticTransformInitialization", "true")
    else:
        parameters.SetParameter(i, "Transform", "BSplineTransform")
        parameters.SetParameter(i, "BSplineTransformSplineOrder", "3")
    parameters.SetParameter(i, "FinalGridSpacingInPhysicalUnits", "12")
    parameters.SetParameter(i, "GridSpacingSchedule", ["16", "8", "4", "2", "1"])
    parameters.SetParameter(i, "HowToCombineTransforms", "Compose")
    parameters.SetParameter(i, "UseCyclicTransform", "false")
    # Similarity measure
    parameters.SetParameter(i, "NumberOfHistogramBins", "64")
    parameters.SetParameter(i, "NumberOfFixedHistogramBins", "64")
    parameters.SetParameter(i, "NumberOfMovingHistogramBins", "64")
    parameters.SetParameter(i, "ShowExactMetricValue", "false")
    parameters.SetParameter(i, "CheckNumberOfSamples", "true")
    # Multiresolution
    parameters.SetParameter(i, "NumberOfResolutions", "5")
    parameters.SetParameter(i, "ImagePyramidSchedule",
                            ["16", "16", "8", "8", "8", "4", "4", "4", "2", "2", "2", "2", "1", "1", "1"])
    # Optimizer
    parameters.SetParameter(i, "MaximumNumberOfIterations", "2000")
    parameters.SetParameter(i, "FixedLimitRangeRatio", "0.01")
    parameters.SetParameter(i, "MovingLimitRangeRatio", "0.01")
    parameters.SetParameter(i, "FixedKernelBSplineOrder", "0")
    parameters.SetParameter(i, "MovingKernelBSplineOrder", "3")
    parameters.SetParameter(i, "UseFastAndLowMemoryVersion", "true")
    parameters.SetParameter(i, "UseJacobianPreconditioning", "false")
    parameters.SetParameter(i, "FiniteDifferenceDerivative", "false")
    parameters.SetParameter(i, "SP_A", "20")
    parameters.SetParameter(i, "MaximumNumberOfSamplingAttempts", "0")
    parameters.SetParameter(i, "SigmoidInitialTime", "0")
    parameters.SetParameter(i, "MaxBandCovSize", "192")
    parameters.SetParameter(i, "NumberOfBandStructureSamples", "10")
    parameters.SetParameter(i, "UseAdaptiveStepSizes", "true")
    parameters.SetParameter(i, "AutomaticParameterEstimation", "true")
    parameters.SetParameter(i, "MaximumStepLength", "0.976562")
    parameters.SetParameter(i, "NumberOfGradientMeasurements", "0")
    parameters.SetParameter(i, "NumberOfJacobianMeasurements", "1000")
    parameters.SetParameter(i, "NumberOfSamplesForExactGradient", "100000")
    parameters.SetParameter(i, "SigmoidScaleFactor", "0.1")
    parameters.SetParameter(i, "ASGDParameterEstimationMethod", "Original")
    # Image sampling
    parameters.SetParameter(i, "UseRandomSampleRegion", "false")
    parameters.SetParameter(i, "NumberOfSpatialSamples", "4096")
    parameters.SetParameter(i, "NewSamplesEveryIteration", "true")
    parameters.SetParameter(i, "ImageSampler", "RandomCoordinate")
    # Interpolation and Resampling
    parameters.SetParameter(i, "FinalBSplineInterpolationOrder", "3")
    parameters.SetParameter(i, "DefaultPixelValue", "-1000")
    parameters.SetParameter(i, "WriteResultImage", "true")
    parameters.SetParameter(i, "WriteDVFFromCoeff", "true")
    parameters.SetParameter(i, "ResultImageFormat", "mhd")

标签： pythonitkelastix-itk