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PERF: Check for mask non-zero more efficiently #123

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Merged
Leengit merged 2 commits into from
Mar 27, 2023
Merged

PERF: Check for mask non-zero more efficiently #123

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56f7422
PERF: Check for mask non-zero more efficiently
Mar 27, 2023
d135e90
PERF: Move functionality to new TilesByGridAndMask.check_mask_filenam…
Mar 27, 2023
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19 changes: 11 additions & 8 deletions histomics_stream/configure.py
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Original file line number Diff line number Diff line change
Expand Up @@ -486,11 +486,7 @@ def __init__(self, study, **kwargs):
f' tile_width ({study["tile_width"]}).'
)
if mask_filename != "":
mask_itk = itk.imread(mask_filename) # May throw exception
if mask_itk.GetImageDimension() != 2:
raise ValueError(
f"The mask ({mask_filename}) should be a 2-dimensional image."
)
mask_itk = self.check_mask_filename(mask_filename)
if not (
isinstance(mask_threshold, float)
and mask_threshold >= 0.0
Expand Down Expand Up @@ -587,6 +583,14 @@ def __call__(self, slide):
random.sample(slide["tiles"].items(), self.randomly_select)
)

def check_mask_filename(self, mask_filename):
mask_itk = itk.imread(mask_filename) # May throw exception
if mask_itk.GetImageDimension() != 2:
raise ValueError(
f"The mask ({mask_filename}) should be a 2-dimensional image."
)
return mask_itk

def compute_from_mask(self, top_left):
# Check that the input and output aspect ratios are pretty close
if (
Expand Down Expand Up @@ -614,9 +618,8 @@ def compute_from_mask(self, top_left):
cumulative_mask = np.zeros(
(self.mask_height + 2, self.mask_width + 2), dtype=np.int64
)
nonzero = np.vectorize(lambda x: int(x != 0))
cumulative_mask[1 : self.mask_height + 1, 1 : self.mask_width + 1] = nonzero(
itk.GetArrayViewFromImage(self.mask_itk)
cumulative_mask[1 : self.mask_height + 1, 1 : self.mask_width + 1] = (
itk.GetArrayViewFromImage(self.mask_itk).astype(bool).astype(np.int64)
)
cumulative_mask = np.cumsum(np.cumsum(cumulative_mask, axis=0), axis=1)

Expand Down