Refactor medical imaging datasets for experiments (#406)

Refactor medical imaging datasets for experiments

scripts/datasets/medical/check_cbis_ddsm.py

@@ -1,23 +1,30 @@
+import os
+import sys
+
 from torch_em.data import MinInstanceSampler
 from torch_em.util.debug import check_loader
 from torch_em.data.datasets.medical import get_cbis_ddsm_loader
 
 
-ROOT = "/media/anwai/ANWAI/data/cbis_ddsm"
+sys.path.append("..")
 
 
 def check_cbis_ddsm():
+    from util import ROOT
+
     loader = get_cbis_ddsm_loader(
-        path=ROOT,
+        path=os.path.join(ROOT, "cbis_ddsm"),
         patch_shape=(512, 512),
         batch_size=2,
-        split="Train",
+        split="Val",
         task=None,
         tumour_type=None,
         resize_inputs=True,
-        sampler=MinInstanceSampler()
+        sampler=MinInstanceSampler(),
+        download=True,
     )
-    check_loader(loader, 8)
+
+    check_loader(loader, 8, plt=True, save_path="./cbis_ddsm.png")
 
 
 if __name__ == "__main__":

scripts/datasets/medical/check_curvas.py

@@ -16,6 +16,7 @@ def check_curvas():
         path=os.path.join(ROOT, "curvas"),
         patch_shape=(1, 512, 512),
         batch_size=2,
+        split="val",
         ndim=2,
         rater="1",
         resize_inputs=False,

scripts/datasets/medical/check_dca1.py

@@ -1,20 +1,26 @@
+import os
+import sys
+
 from torch_em.util.debug import check_loader
 from torch_em.data.datasets.medical import get_dca1_loader
 
 
-ROOT = "/media/anwai/ANWAI/data/dca1"
+sys.path.append("..")
 
 
 def check_dca1():
+    from util import ROOT
+
     loader = get_dca1_loader(
-        path=ROOT,
+        path=os.path.join(ROOT, "dca1"),
         patch_shape=(512, 512),
-        batch_size=2,
+        batch_size=1,
         split="test",
         resize_inputs=True,
-        download=False,
+        download=True,
     )
-    check_loader(loader, 8)
+
+    check_loader(loader, 8, plt=True, save_path="./dca1.png")
 
 
 if __name__ == "__main__":

scripts/datasets/medical/check_drive.py

@@ -1,20 +1,26 @@
+import os
+import sys
+
 from torch_em.util.debug import check_loader
 from torch_em.data.datasets.medical import get_drive_loader
 
 
-ROOT = "/media/anwai/ANWAI/data/drive"
+sys.path.append("..")
 
 
 def check_drive():
+    from util import ROOT
+
     loader = get_drive_loader(
-        path=ROOT,
-        patch_shape=(256, 256),
-        batch_size=2,
+        path=os.path.join(ROOT, "drive"),
+        patch_shape=(512, 512),
+        split="train",
+        batch_size=1,
         resize_inputs=True,
         download=True,
     )
 
-    check_loader(loader, 8)
+    check_loader(loader, 8, plt=True, save_path="./drive.png")
 
 
 if __name__ == "__main__":

scripts/datasets/medical/check_duke_liver.py

@@ -1,22 +1,25 @@
+import os
+import sys
+
 from torch_em.util.debug import check_loader
 from torch_em.data.datasets.medical import get_duke_liver_loader
 
 
-ROOT = "/media/anwai/ANWAI/data/duke_liver"
+sys.path.append("..")
 
 
 def check_duke_liver():
-    from micro_sam.training import identity
+    from util import ROOT
+
     loader = get_duke_liver_loader(
-        path=ROOT,
+        path=os.path.join(ROOT, "duke_liver"),
         patch_shape=(32, 512, 512),
         batch_size=2,
         split="train",
         download=False,
-        raw_transform=identity,
-
     )
-    check_loader(loader, 8)
+
+    check_loader(loader, 8, plt=True, save_path="./duke_liver.png")
 
 
 if __name__ == "__main__":

scripts/datasets/medical/check_isic.py

@@ -1,14 +1,19 @@
+import os
+import sys
+
 from torch_em.util.debug import check_loader
 from torch_em.data.datasets.medical import get_isic_loader
 
 
-ROOT = "/scratch/share/cidas/cca/data/isic"
+sys.path.append("..")
 
 
 def check_isic():
+    from util import ROOT
+
     loader = get_isic_loader(
-        path=ROOT,
-        patch_shape=(700, 700),
+        path=os.path.join(ROOT, "isic"),
+        patch_shape=(512, 512),
         batch_size=2,
         split="test",
         download=True,

scripts/datasets/medical/check_lgg_mri.py

@@ -13,11 +13,15 @@ def check_lgg_mri():
 
     loader = get_lgg_mri_loader(
         path=os.path.join(ROOT, "lgg_mri"),
-        patch_shape=(8, 512, 512),
+        patch_shape=(4, 512, 512),
+        ndim=3,
+        split="train",
         batch_size=1,
+        resize_inputs=True,
+        channels="flair",
         download=True,
     )
-    check_loader(loader, 8)
+    check_loader(loader, 8, plt=True, save_path="./lgg_mri.png")
 
 
 if __name__ == "__main__":

scripts/datasets/medical/check_micro_usp.py

@@ -1,14 +1,19 @@
+import os
+import sys
+
 from torch_em.data import MinInstanceSampler
 from torch_em.util.debug import check_loader
 from torch_em.data.datasets.medical import get_micro_usp_loader
 
 
-ROOT = "/media/anwai/ANWAI/data/micro-usp"
+sys.path.append("..")
 
 
 def check_micro_usp():
+    from util import ROOT
+
     loader = get_micro_usp_loader(
-        path=ROOT,
+        path=os.path.join(ROOT, "micro_usp"),
         patch_shape=(1, 512, 512),
         batch_size=2,
         split="train",
@@ -17,7 +22,7 @@ def check_micro_usp():
         sampler=MinInstanceSampler(),
     )
 
-    check_loader(loader, 8)
+    check_loader(loader, 8, plt=True, save_path="./micro_usp.png")
 
 
 if __name__ == "__main__":

scripts/datasets/medical/check_montgomery.py

@@ -1,20 +1,25 @@
+import os
+import sys
+
 from torch_em.util.debug import check_loader
 from torch_em.data.datasets.medical import get_montgomery_loader
 
 
-ROOT = "/media/anwai/ANWAI/data/montgomery"
+sys.path.append("..")
 
 
 def check_montgomery():
+    from util import ROOT
+
     loader = get_montgomery_loader(
-        path=ROOT,
+        path=os.path.join(ROOT, "montgomery"),
         patch_shape=(512, 512),
         batch_size=2,
         resize_inputs=True,
         download=True,
     )
 
-    check_loader(loader, 8)
+    check_loader(loader, 8, plt=True, save_path="./montgomery.png")
 
 
 if __name__ == "__main__":

scripts/datasets/medical/check_oasis.py

@@ -14,10 +14,14 @@ def check_oasis():
     loader = get_oasis_loader(
         path=os.path.join(ROOT, "oasis"),
         patch_shape=(8, 512, 512),
+        split="train",
         batch_size=1,
+        label_annotations="4",
+        resize_inputs=True,
         download=True,
     )
-    check_loader(loader, 8)
+
+    check_loader(loader, 8, plt=True, save_path="./oasis.png")
 
 
 if __name__ == "__main__":

scripts/datasets/medical/check_oimhs.py

@@ -1,17 +1,22 @@
+import os
+import sys
+
 from torch_em.util.debug import check_loader
-from torch_em.data.datasets.medical import get_oimhs_loader
+from torch_em.data.datasets import get_oimhs_loader
 
 
-ROOT = "/scratch/share/cidas/cca/data/oimhs"
+sys.path.append("..")
 
 
 def check_oimhs():
+    from util import ROOT
+
     loader = get_oimhs_loader(
-        path=ROOT,
+        path=os.path.join(ROOT, "oimhs"),
         patch_shape=(512, 512),
         batch_size=2,
         split="test",
-        download=False,
+        download=True,
         resize_inputs=True,
     )
 

scripts/datasets/medical/check_osic_pulmofib.py

@@ -1,21 +1,27 @@
+import os
+import sys
+
 from torch_em.util.debug import check_loader
 from torch_em.data.datasets.medical import get_osic_pulmofib_loader
 
 
-ROOT = "/media/anwai/ANWAI/data/osic_pulmofib"
+sys.path.append("..")
 
 
 def check_osic_pulmofib():
+    from util import ROOT
+
     loader = get_osic_pulmofib_loader(
-        path=ROOT,
-        patch_shape=(4, 256, 256),
+        path=os.path.join(ROOT, "osic_pulmofib"),
+        patch_shape=(4, 512, 512),
         ndim=3,
         batch_size=2,
+        split="train",
         resize_inputs=True,
         download=True,
     )
 
-    check_loader(loader, 8)
+    check_loader(loader, 8, plt=True, save_path="./osic_pulmofib.png")
 
 
 if __name__ == "__main__":

scripts/datasets/medical/check_piccolo.py

@@ -1,19 +1,25 @@
+import os
+import sys
+
 from torch_em.util.debug import check_loader
 from torch_em.data.datasets.medical import get_piccolo_loader
 
 
-ROOT = "/media/anwai/ANWAI/data/piccolo"
+sys.path.append("..")
 
 
 def check_piccolo():
+    from util import ROOT
+
     loader = get_piccolo_loader(
-        path=ROOT,
+        path=os.path.join(ROOT, "piccolo"),
         patch_shape=(512, 512),
-        batch_size=2,
+        batch_size=1,
         split="train",
         resize_inputs=True,
     )
-    check_loader(loader, 8)
+
+    check_loader(loader, 8, plt=True, save_path="./piccolo.png")
 
 
 if __name__ == "__main__":

scripts/datasets/medical/check_sega.py

@@ -1,22 +1,27 @@
+import os
+import sys
+
 from torch_em.data import MinInstanceSampler
 from torch_em.util.debug import check_loader
 from torch_em.data.datasets.medical import get_sega_loader
 
 
-ROOT = "/media/anwai/ANWAI/data/sega"
+sys.path.append("..")
 
 
 def check_sega():
+    from util import ROOT
+
     loader = get_sega_loader(
-        path=ROOT,
+        path=os.path.join(ROOT, "sega"),
         patch_shape=(32, 512, 512),
         batch_size=2,
         data_choice="KiTS",
         download=True,
         sampler=MinInstanceSampler(),
     )
 
-    check_loader(loader, 8)
+    check_loader(loader, 8, plt=True, save_path="./sega.png")
 
 
 if __name__ == "__main__":

scripts/datasets/medical/check_segthy.py

@@ -15,10 +15,12 @@ def check_segthy():
         path=os.path.join(ROOT, "segthy"),
         patch_shape=(1, 512, 512),
         batch_size=1,
-        source="MRI",
+        split="train",
+        source="US",
         ndim=2,
         download=True,
     )
+
     check_loader(loader, 8, plt=True, save_path="./test.png")