TypeError when using WriteParameterFile

[tfunck]

Hi,

I've come across the following error when trying to use WriteParameterFile. Below is a toy example that reproduces this problem on my system.

import SimpleITK as sitk
import numpy as np

f = sitk.ElastixImageFilter()

fixedImage = sitk.GetImageFromArray(np.array([[0, 0, 1, 0, 0 ],[0, 0, 1, 0, 0],[1, 1, 1, 1, 1],[0, 0, 1, 0, 0 ],[0, 0, 1, 0, 0] ]))
movingImage = sitk.GetImageFromArray(np.array([[1, 0, 0, 0, 1 ],[0, 1, 0, 1, 0],[0, 0, 1, 0, 0],[0, 1, 0, 1, 0 ],[1, 0, 0, 0, 1] ]))

elastixImageFilter = sitk.ElastixImageFilter()
elastixImageFilter.SetFixedImage(fixedImage)
elastixImageFilter.SetMovingImage(movingImage)
elastixImageFilter.SetParameterMap(sitk.GetDefaultParameterMap("rigid"))
elastixImageFilter.Execute()

transformParameterMap = elastixImageFilter.GetTransformParameterMap()

elastixImageFilter.WriteParameterFile( transformParameterMap, "test_transform.txt" )

Here is the error that I get:

Traceback (most recent call last):
File "example.py", line 17, in
elastixImageFilter.WriteParameterFile( transformParameterMap, "test_transform.txt" )
File "/usr/local/lib/python3.6/dist-packages/SimpleITK-1.0.1rc1.dev345+g9dfa8-py3.6-linux-x86_64.egg/SimpleITK/SimpleITK.py", line 10127, in WriteParameterFile
return _SimpleITK.ElastixImageFilter_WriteParameterFile(self, parameterMap, filename)
TypeError: in method 'ElastixImageFilter_WriteParameterFile', argument 2 of type 'std::map< std::string,std::vector< std::string,std::allocator< std::string > >,std::less< std::string >,std::allocator< std::pair< std::string const,std::vector< std::string,std::allocator< std::string > > > > > const'

Not sure if it's relevant, but I'm using Ubuntu 17.10 and SWIG 3.0.

[tfunck]

I found my mistake. The argument that is causing the error is not the output filename for WriteParameterFile, but the parameter map itself. It didn't occur to me that WriteParameter also passes "self" as an argument and therefore that "argument 2" refers to the "parameterMap" and not the "filename" argument.

In the toy example I posted above, the solution is simply to use the first element of the structure returned by GetTransformParameterMap:

transformParameterMap = elastixImageFilter.GetTransformParameterMap()[0]

Apologies if this was something obvious, but it wasn't to me and so maybe this information will be useful to someone else in the future.