Merge branch 'main' into pre-commit-ci-update-config

Author: ericspod

DAE/Pretrain_full_contrast/models/simmim_advanced.py

@@ -1218,7 +1218,7 @@ def __init__(
             kernel_size=3,
             upsample_kernel_size=2,
             norm_name=norm_name,
-            stride=1
+            stride=1,
             # res_block=True,
         )
 

SkullRec/cranialDefects.py

@@ -16,9 +16,9 @@ def generate_hole_implants(data, cube_dim):
     z = int(z_ * (3 / 4))
     cube_masking = np.zeros(shape=(cube_dim, cube_dim, z_ - z))
     print(cube_masking.shape)
-    full_masking[
-        x - int(cube_dim / 2) : x + int(cube_dim / 2), y - int(cube_dim / 2) : y + int(cube_dim / 2), z:z_
-    ] = cube_masking
+    full_masking[x - int(cube_dim / 2) : x + int(cube_dim / 2), y - int(cube_dim / 2) : y + int(cube_dim / 2), z:z_] = (
+        cube_masking
+    )
     return full_masking
 
 

SwinMM/WORD/models/cross_attention.py

@@ -1,4 +1,5 @@
 """TransFusion from TransFusion: Multi-view Divergent Fusion for Medical Image Segmentation with Transformers."""
+
 import copy
 import math
 from typing import Sequence, Union

SwinMM/WORD/models/swin_unetr.py

@@ -1,4 +1,5 @@
 """SwinUNETR with cross attention."""
+
 from typing import MutableMapping, Sequence, Tuple, Union
 
 import torch
@@ -118,11 +119,13 @@ def group_matcher(self, coarse=False):
         """Layer counting helper, used by timm."""
         return dict(
             stem=r"^swinViT\.absolute_pos_embed|patch_embed",  # stem and embed
-            blocks=r"^swinViT\.layers(\d+)\.0"
-            if coarse
-            else [
-                (r"^swinViT\.layers(\d+)\.0.downsample", (0,)),
-                (r"^swinViT\.layers(\d+)\.0\.\w+\.(\d+)", None),
-                (r"^swinViT\.norm", (99999,)),
-            ],
+            blocks=(
+                r"^swinViT\.layers(\d+)\.0"
+                if coarse
+                else [
+                    (r"^swinViT\.layers(\d+)\.0.downsample", (0,)),
+                    (r"^swinViT\.layers(\d+)\.0\.\w+\.(\d+)", None),
+                    (r"^swinViT\.norm", (99999,)),
+                ]
+            ),
         )

auto3dseg/algorithm_templates/segresnet/configs/hyper_parameters.yaml

@@ -34,6 +34,8 @@ log_output_file: null
 cache_class_indices: null
 early_stopping_fraction: 0.001
 determ: false
+orientation_ras: true
+crop_foreground: true
 
 learning_rate: 2.0e-4
 batch_size: '@num_images_per_batch'