Revert "Merge branch 'main' into verify-norm"

This reverts commit 1e09cb0, reversing changes made to be32576.
constantinpape · Jul 16, 2024 · 7f2ec8e · 7f2ec8e
1 parent 1e09cb0
commit 7f2ec8e
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Showing 52 changed files with 120 additions and 2,458 deletions.
diff --git a/experiments/unet-segmentation/dsb/train_boundaries.py b/experiments/unet-segmentation/dsb/train_boundaries.py
@@ -9,16 +9,11 @@ def train_boundaries(args):
 
     patch_shape = (1, 256, 256)
     train_loader = get_dsb_loader(
-        args.input, patch_shape=patch_shape, split="train",
+        args.input, patch_shape, split="train",
         download=True, boundaries=True, batch_size=args.batch_size
     )
-
-    # Uncomment this for checking the loader.
-    # from torch_em.util.debug import check_loader
-    # check_loader(train_loader, 4)
-
     val_loader = get_dsb_loader(
-        args.input, patch_shape=patch_shape, split="test",
+        args.input, patch_shape, split="test",
         boundaries=True, batch_size=args.batch_size
     )
     loss = torch_em.loss.DiceLoss()

diff --git a/scripts/datasets/medical/check_papila.py → scripts/datasets/check_papila.py b/scripts/datasets/medical/check_papila.py → scripts/datasets/check_papila.py
@@ -2,7 +2,7 @@
 from torch_em.data.datasets.medical import get_papila_loader
 
 
-ROOT = "/scratch/share/cidas/cca/data/papila"
+ROOT = "/media/anwai/ANWAI/data/papila"
 
 
 def check_papila():
@@ -16,7 +16,7 @@ def check_papila():
         download=True,
     )
 
-    check_loader(loader, 8, plt=True, save_path="./papila.png")
+    check_loader(loader, 8)
 
 
 if __name__ == "__main__":

diff --git a/scripts/datasets/medical/check_siim_acr.py → scripts/datasets/check_siim_acr.py b/scripts/datasets/medical/check_siim_acr.py → scripts/datasets/check_siim_acr.py
@@ -3,7 +3,7 @@
 from torch_em.data.datasets.medical import get_siim_acr_loader
 
 
-ROOT = "/scratch/share/cidas/cca/data/siim_acr"
+ROOT = "/media/anwai/ANWAI/data/siim_acr"
 
 
 def check_siim_acr():
@@ -13,10 +13,10 @@ def check_siim_acr():
         patch_shape=(512, 512),
         batch_size=2,
         download=True,
-        resize_inputs=True,
+        resize_inputs=False,
         sampler=MinInstanceSampler()
     )
-    check_loader(loader, 8, plt=True, save_path="./siim_acr.png")
+    check_loader(loader, 8)
 
 
 if __name__ == "__main__":

diff --git a/scripts/datasets/medical/check_acdc.py b/scripts/datasets/medical/check_acdc.py
diff --git a/scripts/datasets/medical/check_amos.py b/scripts/datasets/medical/check_amos.py
diff --git a/scripts/datasets/medical/check_cbis_ddsm.py b/scripts/datasets/medical/check_cbis_ddsm.py
diff --git a/scripts/datasets/medical/check_cholecseg8k.py b/scripts/datasets/medical/check_cholecseg8k.py
diff --git a/scripts/datasets/medical/check_covid19_seg.py b/scripts/datasets/medical/check_covid19_seg.py
diff --git a/scripts/datasets/medical/check_dca1.py b/scripts/datasets/medical/check_dca1.py
diff --git a/scripts/datasets/medical/check_duke_liver.py b/scripts/datasets/medical/check_duke_liver.py
diff --git a/scripts/datasets/medical/check_han_seg.py b/scripts/datasets/medical/check_han_seg.py
diff --git a/scripts/datasets/medical/check_isic.py b/scripts/datasets/medical/check_isic.py
diff --git a/scripts/datasets/medical/check_m2caiseg.py b/scripts/datasets/medical/check_m2caiseg.py
diff --git a/scripts/datasets/medical/check_oimhs.py b/scripts/datasets/medical/check_oimhs.py
@@ -2,20 +2,19 @@
 from torch_em.data.datasets.medical import get_oimhs_loader
 
 
-ROOT = "/scratch/share/cidas/cca/data/oimhs"
+ROOT = "/media/anwai/ANWAI/data/oimhs"
 
 
 def check_oimhs():
     loader = get_oimhs_loader(
         path=ROOT,
         patch_shape=(512, 512),
         batch_size=2,
-        split="test",
         download=False,
         resize_inputs=True,
     )
 
-    check_loader(loader, 8, plt=True, save_path="./oimhs.png")
+    check_loader(loader, 8)
 
 
 if __name__ == "__main__":

diff --git a/scripts/datasets/medical/check_osic_pulmofib.py b/scripts/datasets/medical/check_osic_pulmofib.py
@@ -11,11 +11,28 @@ def check_osic_pulmofib():
         patch_shape=(1, 512, 512),
         batch_size=2,
         resize_inputs=False,
-        download=True,
+        download=False,
     )
 
     check_loader(loader, 8)
 
 
+def visualize_data():
+    import os
+    from glob import glob
+
+    import nrrd
+    import napari
+
+    all_volume_paths = sorted(glob(os.path.join(ROOT, "nrrd_heart", "*", "*")))
+    for vol_path in all_volume_paths:
+        vol, header = nrrd.read(vol_path)
+
+        v = napari.Viewer()
+        v.add_image(vol.transpose(2, 0, 1))
+        napari.run()
+
+
 if __name__ == "__main__":
+    # visualize_data()
     check_osic_pulmofib()
diff --git a/scripts/datasets/medical/check_piccolo.py b/scripts/datasets/medical/check_piccolo.py
diff --git a/scripts/datasets/medical/check_sega.py b/scripts/datasets/medical/check_sega.py
@@ -9,9 +9,11 @@
 def check_sega():
     loader = get_sega_loader(
         path=ROOT,
-        patch_shape=(32, 512, 512),
+        patch_shape=(1, 512, 512),
         batch_size=2,
+        ndim=2,
         data_choice="KiTS",
+        resize_inputs=True,
         download=True,
         sampler=MinInstanceSampler(),
     )

diff --git a/scripts/datasets/medical/check_spider.py b/scripts/datasets/medical/check_spider.py