ITKReader does not read NRRD05 images with 'measurement frame' field

[adamaji]

Describe the bug
ITKReader throws an error when reading NRRD05 images with the "measurement frame" field. Here's part of the traceback:

~/workspace/envs/sono-env/lib/python3.6/site-packages/monai/data/image_reader.py in _get_meta_dict(self, img)
    220             if key.startswith("ITK_original_"):
    221                 continue
--> 222             meta_dict[key] = img_meta_dict[key]
    223         meta_dict["origin"] = np.asarray(img.GetOrigin())
    224         meta_dict["spacing"] = np.asarray(img.GetSpacing())

~/workspace/envs/sono-env/lib/python3.6/site-packages/itk/ITKCommonBasePython.py in __getitem__(self, key)
    887         import itk
    888         obj = self.Get(key)
--> 889         return itk.down_cast(obj).GetMetaDataObjectValue()
    890     def __len__(self):
    891         return self.GetKeys().size()

~/workspace/envs/sono-env/lib/python3.6/site-packages/itkExtras.py in down_cast(obj)
   1198         raise RuntimeError(
   1199             "Can't downcast to a specialization of %s" %
-> 1200             className)
   1201     else:
   1202         return t.cast(obj)

RuntimeError: Can't downcast to a specialization of MetaDataObject

To Reproduce
Run

import numpy as np
import SimpleITK as sitk
from monai.data import ITKReader
from monai.transforms import LoadImage

fn = "tmp.seg.nrrd"
data = np.zeros((3,3,3))
im = sitk.GetImageFromArray(data)
im.SetMetaData("NRRD_measurement frame", "(1,0,0) (0,1,0) (0,0,1)")
sitk.WriteImage(im, fn)

LoadImage(reader=ITKReader())(fn)

Commenting out the SetMetaData line runs fine.

Expected behavior
ITKReader reads NRRD005 files.

Environment

================================
Printing MONAI config...
================================
MONAI version: 0.4.0
Numpy version: 1.17.4
Pytorch version: 1.6.0.dev20200528+cu101
MONAI flags: HAS_EXT = False, USE_COMPILED = False
MONAI rev id: 0563a4467fa602feca92d91c7f47261868d171a1

Optional dependencies:
Pytorch Ignite version: 0.4.2
Nibabel version: 3.2.1
scikit-image version: 0.17.2
Pillow version: 6.2.1
Tensorboard version: 2.4.0
gdown version: 3.12.2
TorchVision version: 0.7.0.dev20200528+cu101
ITK version: 5.1.2
tqdm version: 4.54.1
lmdb version: NOT INSTALLED or UNKNOWN VERSION.
psutil version: NOT INSTALLED or UNKNOWN VERSION.

Additional context
Is ignoring the measurement frame field like this here an acceptable fix? adamaji@13cbe07 If so, I can issue the PR.

[Nic-Ma]

Hi @thewtex ,

Could you please help take a look at this issue and give a solution?

Thanks in advance.

[Nic-Ma]

Hi @thewtex @aylward ,

Could you please help check this issue and provide some solution or guide?

Thanks in advance.

[thewtex]

@Nic-Ma looking into the issue, I cannot reproduce it on MONAI master,

In [1]: import numpy as np
   ...: import SimpleITK as sitk
   ...: from monai.data import ITKReader
   ...: from monai.transforms import LoadImage
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-1-7f860b729d04> in <module>
      1 import numpy as np
      2 import SimpleITK as sitk
----> 3 from monai.data import ITKReader
      4 from monai.transforms import LoadImage

ImportError: cannot import name 'ITKReader' from 'monai.data' (/home/matt/src/MONAI/monai/data/__init__.py)

any pointers to how this has been refactored?

[Nic-Ma]

Can you import any other MONAI modules?
Thanks.

[thewtex]

I can:

import monai
import monai.data

but

from monai.transforms import LoadImage`

fails similarly.

I installed with:

pip install -e .

Is this not expected to work? Is there a better way? Thanks, @Nic-Ma

[rijobro]

@thewtex Not sure where your error is coming from, but we might end up going down a rabbit hole trying to fix it.

From the installation instructions, maybe you could simply try one of the other methods? Github options 1 or 2 might be good, depending on whether you plan on modifying the source code or not.

[wyli]

yes perhaps run pip uninstall monai and/or python -m pip uninstall monai before installation, and double check print(monai.__file__)

[thewtex]

@rijobro @wyli thanks for the pointers. After starting from a clean conda environment, I ran into the same issue with BUILD_MONAI=1 python setup.py develop. But, I did a git pull, and I think I must have landed on an unlucky commit. It is working now 🔓 🍀. Thanks again!

[thewtex]

This is addressed in InsightSoftwareConsortium/ITK#2270, and will be available in a few weeks with the release of itk 5.2rc2.

[adamaji]

Thanks for looking into this @thewtex !