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WIP: ENH nd array itk base serialize 4 dask #1928

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ZhiyLiu wants to merge 5 commits into from
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WIP: ENH nd array itk base serialize 4 dask #1928

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7e0eed8
WIP: serialize NDArrayITKBase
sudomakeinstall May 8, 2020
8ddda78
Merge branch 'WIP_ENH_NDArrayITKBase_Serialize_4_dask' of https://git…
Jul 21, 2020
6e20253
ENH: Serialize/Deserialize NDArrayITKBase
Jul 28, 2020
d52833a
ENH: Serialize/Deserialize NDArrayITKBase
Jul 28, 2020
75830d0
Merge branch 'WIP_ENH_NDArrayITKBase_Serialize_4_dask' of https://git…
Jul 28, 2020
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10 changes: 10 additions & 0 deletions Modules/Bridge/NumPy/wrapping/PyBuffer.i.init
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,16 @@ try:
if obj is None: return
self.itk_base = getattr(obj, 'itk_base', None)

def __reduce_ex__(self, protocol):
np_copy = np.array(self, copy=True)
return type(self)._reconstruct, (np_copy,), None

@classmethod
def _reconstruct(cls, obj):
with memoryview(obj) as m:
obj = m.obj
if type(obj) is np.ndarray:
return cls(obj, itk_base=None)
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@thewtex thewtex Jul 28, 2020

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Based on the discussion here:

The above two methods should be replaced with something like:

def __reduce__(self):
    np_copy = np.array(self, copy=True)
    pickled_state = super(NDArrayITKBase, np_copy).__reduce__()
    return pickled_state

except ImportError:
HAVE_NUMPY = False

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29 changes: 29 additions & 0 deletions Modules/Bridge/NumPy/wrapping/test/itkPyBufferTest.py
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Expand Up @@ -29,6 +29,35 @@ class TestNumpyITKMemoryviewInterface(unittest.TestCase):
def setUp(self):
pass

def test_NDArrayITKBase_pickle(self):
"""
Test the serialization of itk.NDArrayITKBase
"""
Dimension = 3
ScalarImageType = itk.Image[itk.UC, Dimension]
RegionType = itk.ImageRegion[Dimension]

region = RegionType()
region.SetSize(0, 6);
region.SetSize(1, 6);
region.SetSize(2, 6);

scalarImage = ScalarImageType.New()
scalarImage.SetRegions(region);
scalarImage.Allocate(True);
scalarImage.SetPixel([0, 0, 0], 5)
scalarImage.SetPixel([0, 0, 1], 3)
scalarImage.SetPixel([5, 5, 5], 8)
ndarray_itk_base = itk.array_view_from_image(scalarImage)

import pickle

## test serialization of itk ndarrary itk base
pickled = pickle.dumps(ndarray_itk_base)
reloaded = pickle.loads(pickled)
equal = (reloaded == ndarray_itk_base).all()
assert equal, 'Different results before and after pickle'

def test_NumPyBridge_itkScalarImage(self):
"Try to convert all pixel types to NumPy array view"

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