Merge remote-tracking branch 'tawald/master'

Author: FabianIsensee

nnunetv2/training/dataloading/utils.py

@@ -1,13 +1,92 @@
+from __future__ import annotations
 import multiprocessing
 import os
 from multiprocessing import Pool
 from typing import List
+from pathlib import Path
+from warnings import warn
 
 import numpy as np
 from batchgenerators.utilities.file_and_folder_operations import isfile, subfiles
 from nnunetv2.configuration import default_num_processes
 
 
+def find_broken_image_and_labels(
+    path_to_data_dir: str | Path,
+) -> tuple[set[str], set[str]]:
+    """
+    Iterates through all numpys and tries to read them once to see if a ValueError is raised.
+    If so, the case id is added to the respective set and returned for potential fixing.
+
+    :path_to_data_dir: Path/str to the preprocessed directory containing the npys and npzs.
+    :returns: Tuple of a set containing the case ids of the broken npy images and a set of the case ids of broken npy segmentations. 
+    """
+    content = os.listdir(path_to_data_dir)
+    unique_ids = [c[:-4] for c in content if c.endswith(".npz")]
+    failed_data_ids = set()
+    failed_seg_ids = set()
+    for unique_id in unique_ids:
+        # Try reading data
+        try:
+            np.load(path_to_data_dir / (unique_id + ".npy"), "r")
+        except ValueError:
+            failed_data_ids.add(unique_id)
+        # Try reading seg
+        try:
+            np.load(path_to_data_dir / (unique_id + "_seg.npy"), "r")
+        except ValueError:
+            failed_seg_ids.add(unique_id)
+
+    return failed_data_ids, failed_seg_ids
+
+
+def try_fix_broken_npy(path_do_data_dir: Path, case_ids: set[str], fix_image: bool):
+    """ 
+    Receives broken case ids and tries to fix them by re-extracting the npz file (up to 5 times).
+
+    :param case_ids: Set of case ids that are broken.
+    :param path_do_data_dir: Path to the preprocessed directory containing the npys and npzs.
+    :raises ValueError: If the npy file could not be unpacked after 5 tries. --
+    """
+    for case_id in case_ids:
+        for i in range(5):
+            try:
+                key = "data" if fix_image else "seg"
+                suffix = ".npy" if fix_image else "_seg.npy"
+                read_npz = np.load(path_do_data_dir / (case_id + ".npz"), "r")[key]
+                np.save(path_do_data_dir / (case_id + suffix), read_npz)
+                # Try loading the just saved image.
+                np.load(path_do_data_dir / (case_id + suffix), "r")
+                break
+            except ValueError:
+                if i == 4:
+                    raise ValueError(
+                        f"Could not unpack {case_id + suffix} after 5 tries!"
+                    )
+                continue
+
+def verify_or_stratify_npys(path_to_data_dir: str | Path) -> None:
+    """
+    This re-reads the npy files after unpacking. Should there be a loading issue with any, it will try to unpack this file again and overwrites the existing.
+    If the new file does not get saved correctly 5 times, it will raise an error with the file name to the user. Does the same for images and segmentations.
+    :param path_to_data_dir: Path to the preprocessed directory containing the npys and npzs.
+    :raises ValueError: If the npy file could not be unpacked after 5 tries. --
+      Otherwise an obscured error will be raised later during training (depending when the broken file is sampled)
+    """
+    path_to_data_dir = Path(path_to_data_dir)
+    # Check for broken image and segmentation npys
+    failed_data_ids, failed_seg_ids = find_broken_image_and_labels(path_to_data_dir)
+
+    if len(failed_data_ids) != 0 or len(failed_seg_ids) != 0:
+        warn(
+            f"Found {len(failed_data_ids)} faulty data npys and {len(failed_seg_ids)}!\n"
+            + f"Faulty images: {failed_data_ids}; Faulty segmentations: {failed_seg_ids})\n"
+            + "Trying to fix them now."
+        )
+        # Try to fix the broken npys by reextracting the npz. If that fails, raise error
+        try_fix_broken_npy(path_to_data_dir, failed_data_ids, fix_image=True)
+        try_fix_broken_npy(path_to_data_dir, failed_seg_ids, fix_image=False)
+
 def _convert_to_npy(npz_file: str, unpack_segmentation: bool = True, overwrite_existing: bool = False) -> None:
     try:
         a = np.load(npz_file)  # inexpensive, no compression is done here. This just reads metadata
@@ -34,6 +113,7 @@ def unpack_dataset(folder: str, unpack_segmentation: bool = True, overwrite_exis
                                        [unpack_segmentation] * len(npz_files),
                                        [overwrite_existing] * len(npz_files))
                   )
+    verify_or_stratify_npys(folder)
 
 
 def get_case_identifiers(folder: str) -> List[str]: