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fix: handle metadata loading and shape calculation in transforms #1990

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Merged
ericspod merged 3 commits into from
May 16, 2025
Merged

fix: handle metadata loading and shape calculation in transforms #1990

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d3dad8c
fix: handle metadata loading and shape calculation in transforms
Kirscher May 15, 2025
f8810ad
fix: adress review comments about ensure_channel_first
Kirscher May 16, 2025
1a67cab
fix: DCO issue
Kirscher May 16, 2025
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6 changes: 4 additions & 2 deletions modules/dynunet_pipeline/transforms.py
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Original file line number Diff line number Diff line change
Expand Up @@ -40,9 +40,9 @@ def get_task_transforms(mode, task_id, pos_sample_num, neg_sample_num, num_sampl
keys = ["image", "label"]
else:
keys = ["image"]

# 1. loading
load_transforms = [
LoadImaged(keys=keys),
LoadImaged(keys=keys, image_only=False),
EnsureChannelFirstd(keys=keys),
]
# 2. sampling
Expand Down Expand Up @@ -284,6 +284,8 @@ def __init__(

def calculate_new_shape(self, spacing, shape):
spacing_ratio = np.array(spacing) / np.array(self.target_spacing)
if len(shape) == 4: # If shape includes channel dimension
shape = shape[1:]
new_shape = (spacing_ratio * np.array(shape)).astype(int).tolist()
return new_shape

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