a100 and liam suggested change

BiomedSciAI · May 16, 2023 · 21eebe8 · 21eebe8
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commit 21eebe8
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diff --git a/fuse_examples/imaging/segmentation/picai/runner.py b/fuse_examples/imaging/segmentation/picai/runner.py
@@ -234,7 +234,6 @@ def run_train(paths: NDict, train: NDict) -> None:
         accelerator=train["trainer"]["accelerator"],
         devices=train["trainer"]["devices"],
         num_sanity_val_steps=-1,
-        auto_select_gpus=True,
     )
 
     # train from scratch

diff --git a/fuseimg/datasets/picai.py b/fuseimg/datasets/picai.py
@@ -156,6 +156,7 @@ def static_pipeline(
                     OpLoadPICAISegmentation(data_dir, seg_dir),
                     dict(key_in="data.input.img_path", key_out="data.gt.seg", gt="data.gt.classification"),
                 ),
+                (OpRepeat(OpLambda(partial(np.transpose, axes=[2,0,1])), kwargs_per_step_to_add=repeat_images_with_seg), dict()),
                 (
                     OpRepeat(
                         (