Feature/ignored dicoms in config

config.yml

@@ -14,4 +14,16 @@ wahab_labels_dir: "1Felix and Rich make models/Training dataset Tiffs/Training s
 
 # Where random stuff from the scripts should go, relative to the root of the repository
 script_output: "script_output/"
-boring_script_output: "script_output/boring_stuff/"
+boring_script_output: "script_output/boring_stuff/"
+
+# Bad Dicoms
+# These ones are in multiple training sets
+duplicate_ids:
+ - 39
+# These ones are broken for various reasons
+broken_ids:
+ - 92
+ - 90
+ - 69
+ - 36
+ - 166

fishjaw/model/model.py

@@ -5,7 +5,6 @@
 
 import os
 import pickle
-from math import sqrt
 from dataclasses import dataclass
 from typing import Type, Any
 

fishjaw/util/files.py

@@ -178,3 +178,19 @@ def boring_script_out_dir() -> pathlib.Path:
     if not retval.is_dir():
         retval.mkdir()
     return retval
+
+
+def broken_dicoms() -> set[int]:
+    """
+    Get the IDs of the broken DICOMs
+
+    """
+    return set(util.config()["broken_ids"])
+
+
+def duplicate_dicoms() -> set[int]:
+    """
+    Get the IDs of the broken DICOMs
+
+    """
+    return set(util.config()["duplicate_ids"])

scripts/arch_summary.py

@@ -7,9 +7,9 @@
 
 import torch
 from prettytable import PrettyTable
+from monai.networks.nets import attentionunet
 
 from fishjaw.model import model, data
-from monai.networks.nets import attentionunet
 
 
 def count_parameters(net: torch.nn.Module) -> None:

scripts/create_dicoms.py

@@ -282,19 +282,12 @@ def main():
     """
     config = util.userconf()
 
-    # Some might be duplicated between the different sets; we only want
-    # the whole jaws in this case
-    duplicates = {39}
-
-    # I might know some are broken - this is usually because the label and
-    # Wahab's TIFF are different shapes. Maybe the 3D tiffs are broken?
-    broken = {92, 90, 69, 36, 166}
-
     create_set_1(config)
-    create_set_2(config, ignore=broken)
+    create_set_2(config, ignore=files.broken_dicoms())
 
-    # Ignore the duplicates here
-    create_set_3(config, ignore=duplicates | broken)
+    # Some might be duplicated between the different sets; we only want
+    # the whole jaws in this case
+    create_set_3(config, ignore=files.broken_dicoms() | files.duplicate_dicoms())
 
 
 if __name__ == "__main__":