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🩹 Fix save_tiles #752

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Merged
merged 4 commits into from
Dec 15, 2023
Merged

🩹 Fix save_tiles #752

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c250caa
fix tile save
measty Dec 8, 2023
cd54040
fix scaling
measty Dec 10, 2023
6b0d7c2
Merge branch 'develop' into fix-save-tiles
shaneahmed Dec 12, 2023
934faff
Merge branch 'develop' into fix-save-tiles
shaneahmed Dec 15, 2023
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27 changes: 18 additions & 9 deletions tiatoolbox/wsicore/wsireader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -989,11 +989,17 @@ def _find_tile_params(
raise ValueError(
msg,
)
scale_levels_available = [
np.log2(np.round(x, 3)) for x in self.info.level_downsamples
]
try:
level = np.log2(rescale)
if not level.is_integer():
level_scale = np.log2(rescale)
if not level_scale.is_integer():
raise ValueError # noqa: TRY301
level = np.int_(level)
level_scale = np.int_(level_scale)
if level_scale not in scale_levels_available:
raise IndexError # noqa: TRY301
level = scale_levels_available.index(level_scale)
slide_dimension = self.info.level_dimensions[level]
rescale = 1
# Raise index error if desired pyramid level not embedded
Expand Down Expand Up @@ -1549,7 +1555,10 @@ def save_tiles(

# convert to baseline reference frame
bounds = start_w, start_h, end_w, end_h
baseline_bounds = tuple(bound * (2**level) for bound in bounds)
baseline_bounds = tuple(
bound * int(np.round(self.info.level_downsamples[level], 3))
for bound in bounds
)
# Read image region
im = self.read_bounds(baseline_bounds, level)

Expand All @@ -1567,7 +1576,7 @@ def save_tiles(

# Rescale to the correct objective value
if rescale != 1:
im = utils.transforms.imresize(img=im, scale_factor=rescale)
im = utils.transforms.imresize(img=im, scale_factor=(1 / rescale))

img_save_name = (
"_".join(
Expand All @@ -1587,10 +1596,10 @@ def save_tiles(
[
iter_tot,
img_save_name,
start_w,
end_w,
start_h,
end_h,
int(start_w / rescale),
int(end_w / rescale),
int(start_h / rescale),
int(end_h / rescale),
im.shape[0],
im.shape[1],
],
Expand Down