Dependency propblem:

[olegl]

Hello.

I seem to have a problem running ITKElastix both with my own registration script and with itkElastixRegistrationMethodTest.py from master.

$ python3 itkElastixRegistrationMethodTest.py global_0001.png global_0002.png  test.png
Traceback (most recent call last):
  File "itkElastixRegistrationMethodTest.py", line 61, in <module>
    registered, transform = itk.elastix_registration_method(fixed, moving)
  File "/home/lobacheo/.local/lib/python3.7/site-packages/itkLazy.py", line 52, in __getattribute__
    itkBase.LoadModule(module, namespace)
  File "/home/lobacheo/.local/lib/python3.7/site-packages/itkBase.py", line 82, in LoadModule
    LoadModule(dep, namespace)
  File "/home/lobacheo/.local/lib/python3.7/site-packages/itkBase.py", line 78, in LoadModule
    data = module_data[name]
KeyError: 'ITKSmoothing'

I have Python bindings to ITK from the latest pip.

$ pip3 install --upgrade --user pip
Requirement already up-to-date: pip in /home/lobacheo/.local/lib/python3.7/site-packages (20.0.2)
$ pip3 list | grep itk | awk '{print $1}' | xargs pip3 install --user --upgrade

$ pip3 list | grep itk
itk                          5.1rc1.post1       
itk-anisotropicdiffusionlbr  1.0.2              
itk-core                     5.1rc1.post1       
itk-elastix                  0.5.1              
itk-elastix-opencl           0.5.1              
itk-filtering                5.1rc1.post1       
itk-io                       5.1rc1.post1       
itk-meshtopolydata           0.5.1              
itk-numerics                 5.1rc1.post1       
itk-registration             5.1rc1.post1       
itk-segmentation             5.1rc1.post1       
itkwidgets                   0.25.2             

$ uname -a
Linux iana1 4.19.0-6-amd64 #1 SMP Debian 4.19.67-2+deb10u1 (2019-09-20) x86_64 GNU/Linux
$ cat /etc/debian_version 
10.2
$ python3 --version
Python 3.7.3

python -v dump is attached: py-v_dump.txt.

I can provide the images at the request, but it lloks to be as the poblem is not the input. It is also not the file format. It is around the parameter file object, as far as I can see.

Best,
Oleg

[thewtex]

itk-anisotropicdiffusionlbr 1.0.2

itk-meshtopolydata 0.5.1

In a fresh virtualenv without these packages, does the error still occur?

python3 -m pip install --upgrade pip
python3 -m pip install --upgrade --pre itk-elastix itk

[olegl]

I uninstalled anisotropicdiffusionlbr and meshtopolydata. Error persits. I upgraded pip and itk (but it was already at the most recent version). Error persists.

$ python3 -m pip install --upgrade --user pip
Requirement already up-to-date: pip in /home/lobacheo/.local/lib/python3.7/site-packages (20.0.2)
$ python3 -m pip install --upgrade --user --pre itk-elastix itk
Requirement already up-to-date: itk-elastix in /home/lobacheo/.local/lib/python3.7/site-packages (0.5.1)
Requirement already up-to-date: itk in /home/lobacheo/.local/lib/python3.7/site-packages (5.1rc1.post1)
Requirement already satisfied, skipping upgrade: itk-filtering==5.1rc1.post1 in /home/lobacheo/.local/lib/python3.7/site-packages (from itk) (5.1rc1.post1)
Requirement already satisfied, skipping upgrade: itk-registration==5.1rc1.post1 in /home/lobacheo/.local/lib/python3.7/site-packages (from itk) (5.1rc1.post1)
Requirement already satisfied, skipping upgrade: itk-core==5.1rc1.post1 in /home/lobacheo/.local/lib/python3.7/site-packages (from itk) (5.1rc1.post1)
Requirement already satisfied, skipping upgrade: numpy in /home/lobacheo/.local/lib/python3.7/site-packages (from itk) (1.17.4)
Requirement already satisfied, skipping upgrade: itk-segmentation==5.1rc1.post1 in /home/lobacheo/.local/lib/python3.7/site-packages (from itk) (5.1rc1.post1)
Requirement already satisfied, skipping upgrade: itk-numerics==5.1rc1.post1 in /home/lobacheo/.local/lib/python3.7/site-packages (from itk) (5.1rc1.post1)
Requirement already satisfied, skipping upgrade: itk-io==5.1rc1.post1 in /home/lobacheo/.local/lib/python3.7/site-packages (from itk) (5.1rc1.post1)
$ python3 itkElastixRegistrationMethodTest.py input_0001.png input_0002.png  test.png
Traceback (most recent call last):
  File "itkElastixRegistrationMethodTest.py", line 61, in <module>
    registered, transform = itk.elastix_registration_method(fixed, moving)
  File "/home/lobacheo/.local/lib/python3.7/site-packages/itkLazy.py", line 52, in __getattribute__
    itkBase.LoadModule(module, namespace)
  File "/home/lobacheo/.local/lib/python3.7/site-packages/itkBase.py", line 82, in LoadModule
    LoadModule(dep, namespace)
  File "/home/lobacheo/.local/lib/python3.7/site-packages/itkBase.py", line 78, in LoadModule
    data = module_data[name]
KeyError: 'ITKSmoothing'
$ pip3 list | grep itk
itk                          5.1rc1.post1       
itk-core                     5.1rc1.post1       
itk-elastix                  0.5.1              
itk-elastix-opencl           0.5.1              
itk-filtering                5.1rc1.post1       
itk-io                       5.1rc1.post1       
itk-numerics                 5.1rc1.post1       
itk-registration             5.1rc1.post1       
itk-segmentation             5.1rc1.post1       
itkwidgets                   0.25.2 

[olegl]

A fresh virtualenv seems to bring me further. The current error is gone. Thank you!

I still get:

(test) $ python3 ../itkElastixRegistrationMethodTest.py ../input_0001.png ../input_0002.png  test.png
Traceback (most recent call last):
  File "../itkElastixRegistrationMethodTest.py", line 61, in <module>
    registered, transform = itk.elastix_registration_method(fixed, moving)
TypeError: cannot unpack non-iterable itkImageF2 object

I am investigating futher.

[olegl]

Okay, it works.

One caveat, as expected from above: in https://github.com/InsightSoftwareConsortium/ITKElastix/blob/master/wrapping/test/itkElastixRegistrationMethodTest.py in else branch (line 60): we are not getting a transform back. So, there is no tuple. And also no transform defined for the later output.

[thewtex]

registered, transform = itk.elastix_registration_method(fixed, moving)

This is a difference in the API of master versus the released Python package.

Thank you for your patience.

This will be cleaned up with the ITK 5.1.0 release.