Implement NrrdReader

[kbressem]

Signed-off-by: kbressem kenobressem@gmail.com

Fixes #4238.

Description

This PR proposes the NrrdReader class to correctly read .nrrd and .seg.nrrd files.

Status

Ready for review

Files changes/created

monai/data/image_reader.py --> add NrrdReader and NrrdImage
monai/data/__init__.py --> add NrrdReader to imports
monai/transforms/io/array.py --> add NrrdReader to imports and "nrrdreader" to SUPPORTED_READERS
monai/config/deviceconfig.py --> add pynrrd to get_optional_config_values

tests/test_init_reader.py  --> add test for NrrdReader
tests/min_tests.py  --> exclude tests for NrrdReader
requirements-dev.txt --> add pynrrd

FIles created

tests/test_nrrd_reader.py --> tests for NrrdReader

Types of changes

• Non-breaking change (fix or new feature that would not break existing functionality).
• New tests added to cover the changes.
• Integration tests passed locally by running ./runtests.sh -f -u --net --coverage.
• Quick tests passed locally by running ./runtests.sh --quick --unittests --disttests.
• In-line docstrings updated.
• Documentation updated, tested make html command in the docs/ folder.

[Nic-Ma]

Hi @kbressem ,

Thanks very much for your contribution.
There are several places need to add the optional package, you can search pandas as the reference.

Thanks in advance.

[kbressem]

Hi @Nic-Ma

I've searched for optional_import("pandas"), pandas, 'optional_import("nibabel")', nibabel and nib in all scripts. Then I went through the scripts, to check if adding nrrd as optional import would be usefull.

pandas was imported in:

• monai/data/iterable_dataset.py No image reader is called. I believe nrrd would not be used
• monai/data/utils.py pandas is used to convert tables to dicts. nrrd would not be used
• monai/data/dataset.py No image reader is called. I believe nrrd would not be used
• monai/config/deviceconfig.py I've added nrrd to get_optional_config_values

nibabel was imported in:

• monai/transforms/spatial/dictionary.py nibabel is used in Orientationd only. nrrd would not be used.
• monai/transforms/spatial/array.py nibabel is used in SpatialResample only, nrrd would not be used.
• monai/transforms/io/array.py added nrrd as optional import and "nrrdreader" to SUPPORTED_READERS
• monai/data/image_reader.py obviously added nrrd :)
• monai/data/utils.py nibabel is used to reorient spatial axes. nrrd would not be used
• monai/data/nifti_writer.py nrrd would not be used
• monai/data/image_writer.py Currently there is no NrrdWriter. We are working on one in MONAI-Label and would like to contribute in a future PR.
• monai/utils/module.py adding nrrd here would not make sense
• monai/config/deviceconfig.py I've added nrrd to get_optional_config_values

I did not find any new instance where importing nrrd would be useful. Did I miss something?

[Nic-Ma]

Hi @kbressem ,

Sorry maybe I didn't make it clear.
I mean you need to add new optional import into some project config files, referring to pandas. For example:
https://github.com/Project-MONAI/MONAI/blob/dev/setup.cfg
https://github.com/Project-MONAI/MONAI/blob/dev/docs/requirements.txt
https://github.com/Project-MONAI/MONAI/blob/dev/requirements-dev.txt
https://github.com/Project-MONAI/MONAI/blob/dev/environment-dev.yml
https://github.com/Project-MONAI/MONAI/blob/dev/docs/source/installation.md
https://github.com/Project-MONAI/MONAI/blob/dev/monai/config/deviceconfig.py

Thanks.

[kbressem]

Hi @kbressem ,

Sorry maybe I didn't make it clear. I mean you need to add new optional import into some project config files, referring to pandas. For example: https://github.com/Project-MONAI/MONAI/blob/dev/setup.cfg https://github.com/Project-MONAI/MONAI/blob/dev/docs/requirements.txt https://github.com/Project-MONAI/MONAI/blob/dev/requirements-dev.txt https://github.com/Project-MONAI/MONAI/blob/dev/environment-dev.yml https://github.com/Project-MONAI/MONAI/blob/dev/docs/source/installation.md https://github.com/Project-MONAI/MONAI/blob/dev/monai/config/deviceconfig.py

Thanks.

Thank you for the clarification. I have added pynrrd to all required files.

[wyli]

this looks nice, one additional test that is worth adding is to check the consistency of the writer/reader...

ideally we should have a TestLoadSaveNrrd, structured like this one:

MONAI/tests/test_image_rw.py

Lines 82 to 117 in 812275a

	class TestLoadSavePNG(unittest.TestCase):
	def setUp(self):
	self.test_dir = tempfile.mkdtemp()
	def tearDown(self):
	shutil.rmtree(self.test_dir, ignore_errors=True)
	def png_rw(self, test_data, reader, writer, dtype, resample=True):
	test_data = test_data.astype(dtype)
	ndim = len(test_data.shape) - 1
	for p in TEST_NDARRAYS:
	output_ext = ".png"
	filepath = f"testfile_{ndim}d"
	saver = SaveImage(
	output_dir=self.test_dir, output_ext=output_ext, resample=resample, separate_folder=False, writer=writer
	)
	saver(p(test_data), {"filename_or_obj": f"{filepath}.png", "spatial_shape": (6, 8)})
	saved_path = os.path.join(self.test_dir, filepath + "_trans" + output_ext)
	self.assertTrue(os.path.exists(saved_path))
	loader = LoadImage(reader=reader)
	data, meta = loader(saved_path)
	if meta["original_channel_dim"] == -1:
	_test_data = moveaxis(test_data, 0, -1)
	else:
	_test_data = test_data[0]
	assert_allclose(data, _test_data)
	@parameterized.expand(itertools.product([PILReader, ITKReader], [PILWriter, ITKWriter]))
	def test_2d(self, reader, writer):
	test_data = np.arange(48, dtype=np.uint8).reshape(1, 6, 8)
	self.png_rw(test_data, reader, writer, np.uint8)
	@parameterized.expand(itertools.product([PILReader, ITKReader], ["monai.data.PILWriter", ITKWriter]))
	def test_rgb(self, reader, writer):
	test_data = np.arange(48, dtype=np.uint8).reshape(3, 2, 8)
	self.png_rw(test_data, reader, writer, np.uint8, False)

the goal is to test whether the nrrd file created by monai's ITKWriter is readable by monai's NrrdReader for some basic (non multichannel?)cases.

[kbressem]

the goal is to test whether the nrrd file created by monai's ITKWriter is readable by monai's NrrdReader for some basic (non multichannel?)cases.

I have added a TestLoadSaveNrrd class to test_image_rw.py which tests writing and reading 2d and 3d images. At the moment this only writes using ITKWriter, in the future an NrrdWriter, which is currently developed at MONAILabel might be used: Project-MONAI/MONAILabel#779

[wyli]

/build