I want to register 2 3D datasets that are read into numpy arrays and then given to the registrate() function. When I execute the code it prints the following log:
Installing all components.
InstallingComponents was successful.
ELASTIX version: 5.0.1
Command line options from ElastixBase:
-fMask unspecified, so no fixed mask used
-mMask unspecified, so no moving mask used
-out D:\...\test/
-priority unspecified, so NORMAL process priority
-threads unspecified, so all available threads are used
Command line options from TransformBase:
-t0 unspecified, so no initial transform used
Reading images...
Reading images took 1 ms.
After that is just stops and goes back to the normal command line. It doesn't reach 'step2'.
Is there a way to backtrack what goes wrong and why?
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")
The parameters used are the folowing:
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")
