task conversion

nnunet/dataset_conversion/Task500_Glacier_inference.py

@@ -1,11 +1,94 @@
-from batchgenerators.utilities.file_and_folder_operations import *
 from nnunet.utilities.file_conversions import convert_2d_image_to_nifti
 from nnunet.paths import nnUNet_raw_data, preprocessing_output_dir
 from nnunet.dataset_conversion.utils import generate_dataset_json
 
 import argparse
 
+import os
+import pickle
+import json
+from typing import List
 
+
+def subdirs(folder: str, join: bool = True, prefix: str = None, suffix: str = None, sort: bool = True) -> List[str]:
+    if join:
+        l = os.path.join
+    else:
+        l = lambda x, y: y
+    res = [l(folder, i) for i in os.listdir(folder) if os.path.isdir(os.path.join(folder, i))
+           and (prefix is None or i.startswith(prefix))
+           and (suffix is None or i.endswith(suffix))]
+    if sort:
+        res.sort()
+    return res
+
+
+def subfiles(folder: str, join: bool = True, prefix: str = None, suffix: str = None, sort: bool = True) -> List[str]:
+    if join:
+        l = os.path.join
+    else:
+        l = lambda x, y: y
+    res = [l(folder, i) for i in os.listdir(folder) if os.path.isfile(os.path.join(folder, i))
+           and (prefix is None or i.startswith(prefix))
+           and (suffix is None or i.endswith(suffix))]
+    if sort:
+        res.sort()
+    return res
+
+
+def nifti_files(folder: str, join: bool = True, sort: bool = True) -> List[str]:
+    return subfiles(folder, join=join, sort=sort, suffix='.nii.gz')
+
+
+def maybe_mkdir_p(directory: str) -> None:
+    os.makedirs(directory, exist_ok=True)
+
+
+def load_pickle(file: str, mode: str = 'rb'):
+    with open(file, mode) as f:
+        a = pickle.load(f)
+    return a
+
+
+def write_pickle(obj, file: str, mode: str = 'wb') -> None:
+    with open(file, mode) as f:
+        pickle.dump(obj, f)
+
+
+def load_json(file: str):
+    with open(file, 'r') as f:
+        a = json.load(f)
+    return a
+
+
+def save_json(obj, file: str, indent: int = 4, sort_keys: bool = True) -> None:
+    with open(file, 'w') as f:
+        json.dump(obj, f, sort_keys=sort_keys, indent=indent)
+
+
+def pardir(path: str):
+    return os.path.join(path, os.pardir)
+
+
+def split_path(path: str) -> List[str]:
+    """
+    splits at each separator. This is different from os.path.split which only splits at last separator
+    """
+    return path.split(os.sep)
+
+
+# I'm tired of typing these out
+join = os.path.join
+isdir = os.path.isdir
+isfile = os.path.isfile
+listdir = os.listdir
+makedirs = maybe_mkdir_p
+os_split_path = os.path.split
+
+# I am tired of confusing those
+subfolders = subdirs
+save_pickle = write_pickle
+write_json = save_json
 if __name__ == '__main__':
     parser = argparse.ArgumentParser()
     parser.add_argument("-data_percentage", default=100,