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🐛 Fix AffineWSITransformer.read_rect() #670

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merged 7 commits into from
Jul 31, 2023
Merged

🐛 Fix AffineWSITransformer.read_rect() #670

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2ac58e0
- Fix read_rect to make it work with 'mpp' and 'power' units
ruqayya Jul 31, 2023
e3949c2
- Update jupyter notebook for reading transformed patches using 'powe…
ruqayya Jul 31, 2023
9ea8356
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 31, 2023
af67944
- Rename variable 'level_location' as '_level_location' since it is u…
ruqayya Jul 31, 2023
2005c6a
Merge remote-tracking branch 'origin/fix-bug-AffineWSITransformer' in…
ruqayya Jul 31, 2023
55e3d8f
- Colab downloaded file
ruqayya Jul 31, 2023
053bf61
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 31, 2023
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246 changes: 93 additions & 153 deletions examples/10-wsi-registration.ipynb → examples/10_wsi_registration.ipynb
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40 changes: 25 additions & 15 deletions tiatoolbox/tools/registration/wsi_registration.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1506,6 +1506,7 @@ def get_patch_dimensions(
y = np.array(list(itertools.chain.from_iterable(y)))

points = np.array([x, y]).transpose()
transform = transform * [[1, 1, 0], [1, 1, 0], [1, 1, 1]] # remove translation
transform_points = self.transform_points(points, transform)

width = np.max(transform_points[:, 0]) - np.min(transform_points[:, 0]) + 1
Expand Down Expand Up @@ -1616,9 +1617,9 @@ def read_rect(
"""
(
read_level,
_,
_,
_post_read_scale,
_level_location,
level_size,
post_read_scale,
_baseline_read_size,
) = self.wsi_reader.find_read_rect_params(
location=location,
Expand All @@ -1628,19 +1629,28 @@ def read_rect(
)
transformed_location, max_size = self.get_transformed_location(
location,
size,
level_size,
read_level,
)
patch = self.wsi_reader.read_rect(
transformed_location,
max_size,
resolution=resolution,
units=units,
)

# Read at optimal level and corrected read size
patch = self.wsi_reader.read_region(transformed_location, read_level, max_size)
patch = np.array(patch)

# Apply transformation
transformed_patch = self.transform_patch(patch, max_size)

start_row = int(max_size[1] / 2) - int(size[1] / 2)
end_row = int(max_size[1] / 2) + int(size[1] / 2)
start_col = int(max_size[0] / 2) - int(size[0] / 2)
end_col = int(max_size[0] / 2) + int(size[0] / 2)
return transformed_patch[start_row:end_row, start_col:end_col, :]
# Crop to get rid of black borders due to rotation
start_row = int(max_size[1] / 2) - int(level_size[1] / 2)
end_row = int(max_size[1] / 2) + int(level_size[1] / 2)
start_col = int(max_size[0] / 2) - int(level_size[0] / 2)
end_col = int(max_size[0] / 2) + int(level_size[0] / 2)
transformed_patch = transformed_patch[start_row:end_row, start_col:end_col, :]

# Resize to desired size
return imresize(
img=transformed_patch,
scale_factor=post_read_scale,
output_size=size,
interpolation="optimise",
)
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