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Improve performance for NormalizeIntensity #6887

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merged 2 commits into from
Aug 18, 2023
Merged

Improve performance for NormalizeIntensity #6887

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ddce39f
improve performance for NormalizeIntensity
john-zielke-snkeos Aug 18, 2023
82b46b8
Merge branch 'dev' into feature/improve-intensity-normalize-performance
wyli Aug 18, 2023
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26 changes: 15 additions & 11 deletions monai/transforms/intensity/array.py
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Original file line number Diff line number Diff line change
Expand Up @@ -839,29 +839,33 @@ def _normalize(self, img: NdarrayOrTensor, sub=None, div=None) -> NdarrayOrTenso

if self.nonzero:
slices = img != 0
masked_img = img[slices]
if not slices.any():
return img
else:
if isinstance(img, np.ndarray):
slices = np.ones_like(img, dtype=bool)
else:
slices = torch.ones_like(img, dtype=torch.bool)
if not slices.any():
return img
slices = None
masked_img = img

_sub = sub if sub is not None else self._mean(img[slices])
_sub = sub if sub is not None else self._mean(masked_img)
if isinstance(_sub, (torch.Tensor, np.ndarray)):
_sub, *_ = convert_to_dst_type(_sub, img)
_sub = _sub[slices]
if slices is not None:
_sub = _sub[slices]

_div = div if div is not None else self._std(img[slices])
_div = div if div is not None else self._std(masked_img)
if np.isscalar(_div):
if _div == 0.0:
_div = 1.0
elif isinstance(_div, (torch.Tensor, np.ndarray)):
_div, *_ = convert_to_dst_type(_div, img)
_div = _div[slices]
if slices is not None:
_div = _div[slices]
_div[_div == 0.0] = 1.0

img[slices] = (img[slices] - _sub) / _div
if slices is not None:
img[slices] = (masked_img - _sub) / _div
else:
img = (img - _sub) / _div
return img

def __call__(self, img: NdarrayOrTensor) -> NdarrayOrTensor:
Expand Down