Accessing SlicerElastix from within python module

Support
1

I am trying to use SlicerElastix module from my module as a cli call. However, all these fails

slicer.cli.run(module=slicer.modules.slicerelastix, None,
                                parameters, wait_for_completion=True, update_display=False)
>>> module 'modules' has no attribute 'slicerelastix'

slicer.cli.run(module=slicer.modules.elastix, None,
                                parameters, wait_for_completion=True, update_display=False)
>>> module 'modules' has no attribute 'elastix'

any way to call elastix registration from the module? I have the module installed and running.

2

After I install SlicerElastix, the second way you tried allows me to access the module:

>>> slicer.modules.elastix
qSlicerScriptedLoadableModule (qSlicerScriptedLoadableModule at: 0x0000026B63E3A8F0)

But then I got a different error when trying to run the module with an existing parameter node:

>>> slicer.cli.run(slicer.modules.elastix, paramNode)
Traceback (most recent call last):
  File "<console>", line 1, in <module>
  File "C:\Program Files\Slicer 4.11.0-2019-06-11\bin\Python\slicer\cli.py", line 78, in run
    logic.SetDeleteTemporaryFiles(1 if delete_temporary_files else 0)
AttributeError: 'SlicerBaseLogicPython.vtkSlicerScriptedLoadableMod' object has no attribute 'SetDeleteTemporaryFiles'

SetDeleteTemporaryFiles is a function in vtkSlicerCLIModuleLogic, so it is strange that the ‘logic’ variable in cli.py is a vtkSlicerScriptedLoadableModuleNode instance. Not sure how it can happen.

(Note: I used an old nightly, so it may be different on a newer one)

3

I have figure out a way to invoke it as

slicer.cli.run(module=slicer.util.getModule("Elastix"), parameters=parameters, 
                                    wait_for_completion=True, update_display=False)

not the usual way but it get invoked, now the parameter set is a bit awkward and the results I got are not the ones from the module itself (The outputTransformNode is not updated at all)

The error I am getting is

>>>'SlicerBaseLogicPython.vtkSlicerScriptedLoadableMod' object has no attribute 'CreateNodeInScene'
4

You cannot call SlicerElastix as a CLI module because it is not a CLI module but a (Python) loadable module. At the time I’ve added this module, Python CLI option was not available and I would not switch, because loadable module allows creating a more user-friendly GUI.

You can use Sequence registration module as an example of using Elastix from another module.

1 Like
5

I didn’t even bother checking :slight_smile: Right, if it’s not a CLI then it cannot be called like that.

6

OK, made it as

        try:
            import Elastix
            elastixLogic = Elastix.ElastixLogic()
            parameterFilenames = elastixLogic.getRegistrationPresets()[0][Elastix.RegistrationPresets_ParameterFilenames]
            useelastix = True
        except Exception as e:
            print(e)
            useelastix = False

and then

                    elastixLogic.registerVolumes(
                                densRnode['node'], densnode['node'],
                                parameterFilenames = parameterFilenames,
                                outputTransformNode = transformNode
                                )

now it is running as the GUI, Thanks so much!!!

3 Likes
7

Hi Andras,
Is it possible to use elastix as clil module from another module. if not what are the other options.

Thank you

Regards,
Saima Safdar

8

See an example how Elastix is used by another module here: https://github.com/moselhy/SlicerSequenceRegistration/blob/master/SequenceRegistration/SequenceRegistration.py

1 Like