Skip to content

Navigation Menu

Sign in
Appearance settings

Search code, repositories, users, issues, pull requests...

Provide feedback

We read every piece of feedback, and take your input very seriously.

Saved searches

Use saved searches to filter your results more quickly

Appearance settings

Commit 75c44e0

Browse filesBrowse files
authored
fix: handle metadata loading and shape calculation in transforms (#1990)
Fixes # . handle metadata loading and shape calculation in transforms ### Description - Add image_only=False and ensure_channel_first=True to LoadImaged transform to properly load metadata - Fix shape mismatch in PreprocessAnisotropic.calculate_new_shape by handling 4D input shapes - Addresses KeyError: 'image_meta_dict' and ValueError: operands could not be broadcast together Note: The metadata loading issue might be related to MONAI version differences. Current version: 1.4.0 ### Checks - [x] Avoid including large-size files in the PR. - [x] Clean up long text outputs from code cells in the notebook. - [x] For security purposes, please check the contents and remove any sensitive info such as user names and private key. --------- Signed-off-by: Tristan Kirscher <85068746+Kirscher@users.noreply.github.com>
1 parent 211cfd8 commit 75c44e0
Copy full SHA for 75c44e0

File tree

Expand file treeCollapse file tree

1 file changed

+4
-2
lines changed
Filter options
Expand file treeCollapse file tree

1 file changed

+4
-2
lines changed

‎modules/dynunet_pipeline/transforms.py

Copy file name to clipboardExpand all lines: modules/dynunet_pipeline/transforms.py
+4-2Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -40,9 +40,9 @@ def get_task_transforms(mode, task_id, pos_sample_num, neg_sample_num, num_sampl
4040
keys = ["image", "label"]
4141
else:
4242
keys = ["image"]
43-
43+
# 1. loading
4444
load_transforms = [
45-
LoadImaged(keys=keys),
45+
LoadImaged(keys=keys, image_only=False),
4646
EnsureChannelFirstd(keys=keys),
4747
]
4848
# 2. sampling
@@ -284,6 +284,8 @@ def __init__(
284284

285285
def calculate_new_shape(self, spacing, shape):
286286
spacing_ratio = np.array(spacing) / np.array(self.target_spacing)
287+
if len(shape) == 4: # If shape includes channel dimension
288+
shape = shape[1:]
287289
new_shape = (spacing_ratio * np.array(shape)).astype(int).tolist()
288290
return new_shape
289291

0 commit comments

Comments
0 (0)
Morty Proxy This is a proxified and sanitized view of the page, visit original site.