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Qupath 24bit images #21

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merged 2 commits into from
Aug 15, 2024
Merged

Qupath 24bit images #21

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16b13fc
Fixed qupath inference
JLrumberger Aug 15, 2024
6e7d4f0
Got rid of a few print statements
JLrumberger Aug 15, 2024
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10 changes: 7 additions & 3 deletions src/nimbus_inference/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -120,6 +120,9 @@ def handle_qupath_segmentation_map(instance_mask: np.array):
logging.warning("QuPath RGB segmentation map detected. Converting to instance map by")
logging.warning("combining the RGB channels into a single channel via the following formula:")
logging.warning("label = RED*256**2 + GREEN * 256 + BLUE")
# move channel axis to last if not already
if instance_mask.shape.index(3) == 0:
instance_mask = np.moveaxis(instance_mask, 0, -1)
instance_mask_handled = instance_mask[..., 0] * 256**2 + instance_mask[..., 1] * 256 \
+ instance_mask[..., 2]
instance_mask_handled = instance_mask_handled.round(0).astype(np.uint64)
Expand Down Expand Up @@ -263,10 +266,11 @@ def get_segmentation(self, fov: str):
fov_path = self.fov_paths[idx]
instance_path = self.segmentation_naming_convention(fov_path)
if isinstance(instance_path, str):
instance_mask = np.squeeze(io.imread(instance_path))
instance_mask = io.imread(instance_path)
else:
instance_mask = np.squeeze(instance_path)
if len(instance_mask.shape) == 3 and instance_mask.shape[-1] == 3:
instance_mask = instance_path
instance_mask = np.squeeze(instance_mask)
if len(instance_mask.shape) == 3:
instance_mask = handle_qupath_segmentation_map(instance_mask)
instance_mask = instance_mask.astype(np.uint32)
return instance_mask
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