sorenchr2011
commented
3 years ago Hi, See how to get the final transformparametermap and how to use transformix to apply it under the section where transformix is mentioned: https://simpleelastix.readthedocs.io/HelloWorld.html
On Thu, Mar 18, 2021 at 2:15 PM binarycai @.***> wrote:
I've registered two images via point based image registration. Trying to transform other images with generated parameter files(“TransformParameters.0.txt TransformParameters.1.txt TransformParameters.2.txt”) but failed.
Codes pasted below: import SimpleITK as sitk
read parameter files
parameter0=sitk.ReadParameterFile("TransformParameters.0.txt") parameter1=sitk.ReadParameterFile("TransformParameters.1.txt") parameter2=sitk.ReadParameterFile("TransformParameters.2.txt")
set parameter maps
myfilter=sitk.ElastixImageFilter() myfilter.SetParameterMap(parameter0) myfilter.AddParameterMap(parameter1) myfilter.AddParameterMap(parameter2)
movingimg=sitk.ReadImage("slicesmarker02.tif") fixedimg=sitk.ReadImage("slicesmarker01.tif") myfilter.SetMovingImage(movingimg) myfilter.SetFixedImage(fixedimg) myfilter.Execute()
What could I do to fix this?
WARNING: The parameter "Registration", requested at entry number 0, does not exist at all. The default value "MultiResolutionRegistration" is used instead. WARNING: The parameter "FixedImagePyramid", requested at entry number 0, does not exist at all. The default value "FixedSmoothingImagePyramid" is used instead. WARNING: The parameter "MovingImagePyramid", requested at entry number 0, does not exist at all. The default value "MovingSmoothingImagePyramid" is used instead. WARNING: The parameter "ImageSampler", requested at entry number 0, does not exist at all. The default value "" is used instead. WARNING: The parameter "Interpolator", requested at entry number 0, does not exist at all. The default value "BSplineInterpolator" is used instead. WARNING: The parameter "Metric", requested at entry number 0, does not exist at all. The default value "" is used instead. ERROR: the following component has not been specified: Metric WARNING: The parameter "Optimizer", requested at entry number 0, does not exist at all. The default value "" is used instead. ERROR: the following component has not been specified: Optimizer ERROR: One or more components could not be created. Traceback (most recent call last): File "D:/MyProjects/Python Projects/pointransform/main.py", line 18, in myfilter.Execute() File "C:\Users\cly\AppData\Local\Programs\Python\Python38\lib\site-packages\simpleitk-2.0.0rc2.dev908+g8244e-py3.8-win-amd64.egg\SimpleITK\SimpleITK.py", line 11130, in Execute return _SimpleITK.ElastixImageFilter_Execute(self) RuntimeError: Exception thrown in SimpleITK ElastixImageFilter_Execute: D:\packes for cmake compiling\SITK\SimpleElastix\Code\Elastix\src\sitkElastixImageFilterImpl.cxx:259: sitk::ERROR: itk::ExceptionObject (00000031DFBEC1F0) Location: "unknown" File: d:\extralibs\sitk\elastix\core\main\elxElastixFilter.hxx Line: 253 Description: itk::ERROR: ElastixFilter(0000018AF89DA770): Internal elastix error: See elastix log (use LogToConsoleOn() or LogToFileOn()).
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binarycai
I've registered two images via point based image registration. Trying to transform other images with generated parameter files(“TransformParameters.0.txt TransformParameters.1.txt TransformParameters.2.txt”) but failed.
Codes pasted below: import SimpleITK as sitk
read parameter files
parameter0=sitk.ReadParameterFile("TransformParameters.0.txt") parameter1=sitk.ReadParameterFile("TransformParameters.1.txt") parameter2=sitk.ReadParameterFile("TransformParameters.2.txt")
set parameter maps
myfilter=sitk.ElastixImageFilter() myfilter.SetParameterMap(parameter0) myfilter.AddParameterMap(parameter1) myfilter.AddParameterMap(parameter2)
movingimg=sitk.ReadImage("slicesmarker02.tif") fixedimg=sitk.ReadImage("slicesmarker01.tif") myfilter.SetMovingImage(movingimg) myfilter.SetFixedImage(fixedimg) myfilter.Execute()
What could I do to fix this?
WARNING: The parameter "Registration", requested at entry number 0, does not exist at all. The default value "MultiResolutionRegistration" is used instead. WARNING: The parameter "FixedImagePyramid", requested at entry number 0, does not exist at all. The default value "FixedSmoothingImagePyramid" is used instead. WARNING: The parameter "MovingImagePyramid", requested at entry number 0, does not exist at all. The default value "MovingSmoothingImagePyramid" is used instead. WARNING: The parameter "ImageSampler", requested at entry number 0, does not exist at all. The default value "" is used instead. WARNING: The parameter "Interpolator", requested at entry number 0, does not exist at all. The default value "BSplineInterpolator" is used instead. WARNING: The parameter "Metric", requested at entry number 0, does not exist at all. The default value "" is used instead. ERROR: the following component has not been specified: Metric WARNING: The parameter "Optimizer", requested at entry number 0, does not exist at all. The default value "" is used instead. ERROR: the following component has not been specified: Optimizer ERROR: One or more components could not be created. Traceback (most recent call last): File "D:/MyProjects/Python Projects/pointransform/main.py", line 18, in
myfilter.Execute()
File "C:\Users\cly\AppData\Local\Programs\Python\Python38\lib\site-packages\simpleitk-2.0.0rc2.dev908+g8244e-py3.8-win-amd64.egg\SimpleITK\SimpleITK.py", line 11130, in Execute
return _SimpleITK.ElastixImageFilter_Execute(self)
RuntimeError: Exception thrown in SimpleITK ElastixImageFilter_Execute: D:\packes for cmake compiling\SITK\SimpleElastix\Code\Elastix\src\sitkElastixImageFilterImpl.cxx:259:
sitk::ERROR:
itk::ExceptionObject (00000031DFBEC1F0)
Location: "unknown"
File: d:\extralibs\sitk\elastix\core\main\elxElastixFilter.hxx
Line: 253
Description: itk::ERROR: ElastixFilter(0000018AF89DA770): Internal elastix error: See elastix log (use LogToConsoleOn() or LogToFileOn()).