# Installing and using Python wrapped Remote Module
**URL:** https://discourse.itk.org/t/installing-and-using-python-wrapped-remote-module/2104
**Category:** Beginner Questions
**Tags:** python
**Created:** [July 29, 2019, 1:46pm UTC](https://discourse.itk.org/t/installing-and-using-python-wrapped-remote-module/2104 "2019-07-29T13:46:29Z")
**Posts on this page:** 14
**Page:** 1
### Author:  [@laqua-stack](https://discourse.itk.org/u/laqua-stack)
#### Post date: [July 29, 2019, 1:46pm UTC](https://discourse.itk.org/t/installing-and-using-python-wrapped-remote-module/2104/1 "2019-07-29T13:46:29Z")
Hi all,
I tried to build ITK Strain Image Filter [https://github.com/KitwareMedical/ITKStrain](https://github.com/KitwareMedical/ITKStrain) and to install it.
I used a conda virtual env with Python 3.6 and ITK 5.0.0.post1 from pypy in the environment, a self-build local ITK 5.0.1 and skbuild using Win 10 x64.
I did “python setup.py install” and it finished without errors. Actually if I “conda list” in the env, there is a package called itk-strain 0.1.0. But I did not manage to import the module to python.
I tried:
“from itk import StrainImageFilter” --\> module ‘itk’ has no attribute ‘StrainImageFilter’
“import itk-strain” --\> syntax-error
“import itk\_strain” --\> no module itk\_strain
Actually, I am not aware how the module is finally named.
I did not finde a module in “help(‘modules’)”, neither did I find a submodule in “dir(‘itk’)”
Is there a specific way to find the correct naming convention of a remote module, wrapped for python? Do I need change something in cmake to enable Python wrapping before I build ITK on my System?
I appreciate any answers and hints.
Kind Regards
---
### Author:  [@laqua-stack](https://discourse.itk.org/u/laqua-stack)
#### Post date: [July 29, 2019, 10:26pm UTC](https://discourse.itk.org/t/installing-and-using-python-wrapped-remote-module/2104/2 "2019-07-29T22:26:34Z")
I tried building ITK with wrapping enabled again and I put WrapITK.pth in sitepackages of a the conda-env I am using, added a path variable to build\lib\release and build\bin\release (Now, I do feel a little bit stupid for posting the question above, though 🙂 ) and now I can import StrainPython and have StrainPython.itkStrainImageFilterIVD22DD available. But I ran in the next issue. GetImageFromArray from ITKExtras does not work anymore as it did in ITK from PyPy…
> ## In [19]: deformationField = itk.GetImageFromArray(test.astype(‘float32’), is\_vector=True)
>
> AttributeError Traceback (most recent call last)
> in
> ----\> 1 deformationField = itk.GetImageFromArray(test.astype(‘float32’), is\_vector=True)
>
> C:\build\Wrapping\Generators\Python\Release\itkExtras.py in GetImageFromArray(arr, is\_vector)
> 295 “”“Get an ITK image from a Python array.
> 296 “””
> → 297 return \_GetImageFromArray(arr, “GetImageFromArray”, is\_vector)
> 298
> 299 image\_from\_array = GetImageFromArray
>
> C:\build\Wrapping\Generators\Python\Release\itkExtras.py in \_GetImageFromArray(arr, function, is\_vector)
> 272 raise ImportError(‘Numpy not available.’)
> 273 import itk
> → 274 PixelType = \_get\_itk\_pixelid(arr)
> 275 if is\_vector:
> 276 Dimension = arr.ndim - 1
>
> C:\build\Wrapping\Generators\Python\Release\itkExtras.py in \_get\_itk\_pixelid(numpy\_array\_type)
> 225 numpy.float32:itk.F,
> 226 numpy.float64:itk.D,
> → 227 numpy.complex64:itk.complex[itk.F],
> 228 numpy.complex128:itk.complex[itk.D]
> 229 }
>
> C:\build\Wrapping\Generators\Python\Release\itkLazy.py in **getattribute** (self, attr)
> 44 module = self.\_\_belong\_lazy\_attributes[attr]
> 45 namespace = {}
> —\> 46 itkBase.LoadModule(module, namespace)
> 47 for k, v in namespace.items():
> 48 setattr(self, k, v)
>
> C:\build\Wrapping\Generators\Python\Release\itkBase.py in LoadModule(name, namespace)
> 61 else:
> 62 swig = namespace.setdefault(‘swig’, imp.new\_module(‘swig’))
> —\> 63 swig. **dict**.update(this\_module.swig. **dict** )
> 64
> 65 # don’t worry about overwriting the symbols in namespace – any
>
> AttributeError: module ‘ITKCommon’ has no attribute ‘swig’
Any suggestions? I am definitly missing somethin, sorry.
---
### Author:  [@laqua-stack](https://discourse.itk.org/u/laqua-stack)
#### Post date: [July 31, 2019, 9:13am UTC](https://discourse.itk.org/t/installing-and-using-python-wrapped-remote-module/2104/3 "2019-07-31T09:13:18Z")
Okay, i tried back and forth, even rebuild itk with python wrapping. And I experienced a rather strange behavior, I cannot explain.
It depends on the order, how itk, and for example StrainPython (applies also to other modules) is imported and what happens inbetween.
I did:
> import itk
> itk.Image # for testing
> #… (some other stuff)
> import StrainPython
And everything works fine.
But if i do nothing inbetween the imports and use any itk function/class the problem in the post above is raised:
> “UnboundLocalError: local variable ‘module’ referenced before assignment”
> in ITKBase.py
To all who might have similar problems:
Try executing any itk class like itk.Image between your imports. This seems to solve the
> “AttributeError: module ‘ITKCommon’ has no attribute ‘swig’”
> and
> “UnboundLocalError: local variable ‘module’ referenced before assignment”
errors, even though I do not understand why.
---
### Author:  [@dzenanz](https://discourse.itk.org/u/dzenanz)
#### Post date: [July 31, 2019, 1:07pm UTC](https://discourse.itk.org/t/installing-and-using-python-wrapped-remote-module/2104/4 "2019-07-31T13:07:19Z")
Perhaps lazy loading has something to do with it? @matt.mccormick
---
### Author:  [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)
#### Post date: [July 31, 2019, 3:17pm UTC](https://discourse.itk.org/t/installing-and-using-python-wrapped-remote-module/2104/5 "2019-07-31T15:17:13Z")
Welcome to the ITK community @laqua-stack!
First, well done building the Python package. 👏
To make it easier, I have uploaded [binary `itk-strain` Python packages to PyPI](https://pypi.org/project/itk-strain/). Please try installing it in a new conda virtual environment with:
```auto
pip install itk-strain
```
> Is there a specific way to find the correct naming convention of a remote module, wrapped for python?
To find out the content of the package, we can do the following:
```auto
from itk import Strain
dir(Strain)
```
which results in:
```auto
['ImageToImageFilter',
'StrainImageFilter',
'_LazyITKModule__belong_lazy_attributes',
' __doc__',
' __loader__',
' __name__',
' __package__',
' __spec__',
'image_to_image_filter',
'lazy_attributes',
'loaded_lazy_modules',
'strain_image_filter']
```
We know that the module is named `Strain` by the [argument to `itk_wrap_module`](https://github.com/KitwareMedical/ITKStrain/blob/master/wrapping/CMakeLists.txt#L1).
`StrainImageFilter` is the ITK class that can be used for [streaming pipelines](https://github.com/KitwareMedical/2019-03-13-KRSCourseInBiomedicalImageAnalysisAndVisualization/blob/master/2_Image_Filtering.ipynb).
`strain_image_filter` provides a [functional, Pythonic interface to the filter](https://discourse.itk.org/t/itk-5-0-beta-1-pythonic-interface/1271).
> Any suggestions? I am definitly missing somethin, sorry.
You are doing excellent 🙂 – I think there is a bug in the wrapping that causes the confusing error. I will follow-up…
---
### Author:  [@laqua-stack](https://discourse.itk.org/u/laqua-stack)
#### Post date: [July 31, 2019, 3:40pm UTC](https://discourse.itk.org/t/installing-and-using-python-wrapped-remote-module/2104/6 "2019-07-31T15:40:46Z")
Thanks for all the nice words and the help 😊.
itk-strain on pypy? Awesome!!! Thank you so much.
I will definitly try this. Is there a concern if a wrapped ITK is already build on the computer? Do i just need to rename WrapITK.pth to .bak in site-packages to make the custom build not interfere with it?
I think it was (ofcourse :-)) a mistake to import StrainPython module in addition to itk, since itk.StrainImageFilter is already there after importing itk. Now I imported itk only. That way it is also possible to use the Filter without specifying the used type like I did before in StrainPython.itkStrainImageFilterIVD22DD.New().
I think the errors I reported came from importing ITK modules (like StrainPython) in addtion to itk.
Again thank you so much.
---
### Author:  [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)
#### Post date: [July 31, 2019, 3:53pm UTC](https://discourse.itk.org/t/installing-and-using-python-wrapped-remote-module/2104/7 "2019-07-31T15:53:10Z")
> [@laqua-stack](#):
>
> WrapITK.pth to .bak in site-packages to make the custom build not interfere with it?
Yes, that will work. A new conda env or virtualenv will work, too.
> [@laqua-stack](#):
>
> I think it was (ofcourse :-)) a mistake to import StrainPython module in addition to itk, since itk.StrainImageFilter is already there after importing itk. Now I imported itk only. That way it is also possible to use the Filter without specifying the used type like I did before in StrainPython.itkStrainImageFilterIVD22DD.New().
Yes, either approach can work. `from itk import Strain` can be helpful to just inspect the contents of the `Strain` module. In most use cases,
```auto
import itk
displacement = itk.imread('mydisplacement.mha')
strain = itk.strain_image_filter(displacement)
```
etc., is convenient.
---
### Author:  [@laqua-stack](https://discourse.itk.org/u/laqua-stack)
#### Post date: [July 31, 2019, 4:10pm UTC](https://discourse.itk.org/t/installing-and-using-python-wrapped-remote-module/2104/8 "2019-07-31T16:10:06Z")
Thanks Matt and Dzenan!
I got it working now 😄
You will get an update regarding pip’s itk-strain today or tomorrow.
---
### Author:  [@laqua-stack](https://discourse.itk.org/u/laqua-stack)
#### Post date: [July 31, 2019, 5:03pm UTC](https://discourse.itk.org/t/installing-and-using-python-wrapped-remote-module/2104/9 "2019-07-31T17:03:09Z")
I tested pip install itk-strain in an conda env, without errors.
However, I am struggling with compatibility between numpy and PyPI’s itk:
> import itk
> import numpy as np
>
> #VectorType=itk.Vector[itk.D,2]
> VectorType=itk.Vector[itk.F,2]
> VectorImageType=itk.Image[VectorType,2]
> SSRTType=itk.Image[itk.SymmetricSecondRankTensor[itk.D,2],2]
>
> nparr=np.ascontiguousarray(np.moveaxis(np.indices((256,256),dtype=‘float32’),0,-1))
> #DisplacementField=itk.GetImageFromArray(nparr,is\_vector=True)
> DisplacementField=itk.PyBuffer[VectorImageType].GetImageFromArray(nparr,is\_vector=True)
>
> testFilter= itk.StrainImageFilter[VectorImageType].New(DisplacementField)
> testFilter.SetInput(DisplacementField)
> testFilter.SetStrainForm(testFilter.GREENLAGRANGIAN)
> testFilter.Update()
> StrainTensorField=itk.PyBuffer[SSRTType].GetArrayFromImage(testFilter.GetOutput())
Only itk.ImageVF22 is supported by PyBuffer in this build and
StrainImageFilter expects itk.ImageVD22 as input.
And VectorCastImageFilter is not available in the PyPI’s itk build.
But I think if I had Images to read in with ITK’s functionality without the Numpy Bridge, it would work fine 😉
For me it works fine with my self-build ITK.
Would it be possible(/not too much work) to wrap VectorCastImageFilter or rewrap PyBuffer for ‘double’ with VectorImage? I did not test ImageAdaptor yet.
---
### Author:  [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)
#### Post date: [August 1, 2019, 10:29pm UTC](https://discourse.itk.org/t/installing-and-using-python-wrapped-remote-module/2104/10 "2019-08-01T22:29:37Z")
> Would it be possible(/not too much work) to wrap VectorCastImageFilter or rewrap PyBuffer for ‘double’ with VectorImage?
Yes, good idea! In ITK 5, we can just use `CastImageFilter` instead of `VectorCastImageFilter`. I created these issues to track this:
>
>
> See:
>
> https://discourse.itk.org/t/installing-and-using-python-wrapped-remote…-module/2104/9
>
>
> Wrap \`CastImageFilter\` to convert to and from vector pixel types like \`Vector\`, …\`CovariantVector\`, etc. and \`VectorImage\`.
>
> See:
>
> https://discourse.itk.org/t/installing-and-using-python-wrapped-remote-module/2104/9
In the meantime, a possible workaround is to write / read from file.
---
### Author:  [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)
#### Post date: [August 1, 2019, 10:30pm UTC](https://discourse.itk.org/t/installing-and-using-python-wrapped-remote-module/2104/11 "2019-08-01T22:30:39Z")
Also, a new version of the `itk-strain` package has been uploaded to PyPI; upgrade with:
```auto
pip install --upgrade itk-strain
```
---
### Author:  [@laqua-stack](https://discourse.itk.org/u/laqua-stack)
#### Post date: [August 8, 2019, 4:10pm UTC](https://discourse.itk.org/t/installing-and-using-python-wrapped-remote-module/2104/12 "2019-08-08T16:10:25Z")
Thank you Matt. I appreciate the new itk-strain version.
Unfortunately I experienced a new problem with the self-build ITK. Since it is closely related to the one I described above, I reply it just here.
When I use the self-build itk in Python 3.6 conda env, everything works fine.
But if I attempt to use the same build in Python 3.7 with WrapITK.pth and PATH and PYTHONPATH set to ITKbuild/lib/Release and ITKbuild/bin/Release it throws the following error. Seems like the lazy loader does not look in the lib/Release folder, where \_ITKPyBasePython.pyd is located.
> import itk
>
> itk.Image
> Traceback (most recent call last):
>
> File “”, line 1, in
> itk.Image
>
> File “C:\build\Wrapping\Generators\Python\Release\itkLazy.py”, line 46, in **getattribute**
> itkBase.LoadModule(module, namespace)
>
> File “C:\build\Wrapping\Generators\Python\Release\itkBase.py”, line 118, in LoadModule
> LoadModule(dep, namespace)
>
> File “C:\build\Wrapping\Generators\Python\Release\itkBase.py”, line 128, in LoadModule
> module = loader.load(swigModuleName)
>
> File “C:\build\Wrapping\Generators\Python\Release\itkBase.py”, line 253, in load
> return importlib.import\_module(name)
>
> File “C:\Users\Fabian\Anaconda3\envs\PythonCPU\lib\importlib\__init_\_.py”, line 127, in import\_module
> return \_bootstrap.\_gcd\_import(name[level:], package, level)
>
> File “”, line 1006, in \_gcd\_import
>
> File “”, line 983, in \_find\_and\_load
>
> File “”, line 967, in \_find\_and\_load\_unlocked
>
> File “”, line 677, in \_load\_unlocked
>
> File “”, line 728, in exec\_module
>
> File “”, line 219, in \_call\_with\_frames\_removed
>
> File “C:\build\lib\ITKPyBasePython.py”, line 32, in
> \_ITKPyBasePython = swig\_import\_helper()
>
> File “C:\build\lib\ITKPyBasePython.py”, line 24, in swig\_import\_helper
> import \_ITKPyBasePython
>
> ImportError: DLL load failed: Das angegebene Modul wurde nicht gefunden.
Even though i do not understand the link, but: Do I need to have an extra ITK build (with different referenced Python in CMAKE)?
Thanks in advance. I will try with PyPI’s ITK in the meantime and report.
---
### Author:  [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)
#### Post date: [August 9, 2019, 3:38am UTC](https://discourse.itk.org/t/installing-and-using-python-wrapped-remote-module/2104/13 "2019-08-09T03:38:52Z")
> [@laqua-stack](#):
>
> When I use the self-build itk in Python 3.6 conda env, everything works fine.
> But if I attempt to use the same build in Python 3.7
Are ITK’s CMake configuration variables, `PYTHON_INCLUDE_DIR` and `PYTHON_LIBRARY` consistent with the runtime version? Building for conda Python 3.6 and running Python 3.7, for example, is not expected to work.
---
### Author:  [@laqua-stack](https://discourse.itk.org/u/laqua-stack)
#### Post date: [August 9, 2019, 7:56pm UTC](https://discourse.itk.org/t/installing-and-using-python-wrapped-remote-module/2104/14 "2019-08-09T19:56:40Z")
I did not build ITK with PYTHON\_INCLUDE\_DIR set to python 3.7 executable yet.
I am going to try this tonight.
I wasn’t aware of the need.
Thank you!