chore: minor changes for pr

MIC-DKFZ · Apr 28, 2024 · 3b9a770 · 3b9a770
1 parent a6b2b47
commit 3b9a770
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Showing 4 changed files with 9 additions and 19 deletions.
diff --git a/...ataset_conversion/Dataset042_BraTS2018.py → .../dataset_conversion/Dataset042_BraTS18.py b/...ataset_conversion/Dataset042_BraTS2018.py → .../dataset_conversion/Dataset042_BraTS18.py
@@ -1,6 +1,5 @@
 import multiprocessing
 import shutil
-from multiprocessing import Pool
 
 import SimpleITK as sitk
 import numpy as np
@@ -47,7 +46,8 @@ def load_convert_labels_back_to_BraTS(filename, input_folder, output_folder):
     sitk.WriteImage(d, join(output_folder, filename))
 
 
-def convert_folder_with_preds_back_to_BraTS_labeling_convention(input_folder: str, output_folder: str, num_processes: int = 12):
+def convert_folder_with_preds_back_to_BraTS_labeling_convention(input_folder: str, output_folder: str,
+                                                                num_processes: int = 12):
     """
     reads all prediction files (nifti) in the input folder, converts the labels back to BraTS convention and saves the
     """
@@ -58,7 +58,7 @@ def convert_folder_with_preds_back_to_BraTS_labeling_convention(input_folder: st
 
 
 if __name__ == '__main__':
-    brats_data_dir = '/home/stud/strasser/archive/brats2018/MICCAI_BraTS_2018_Data_Training'
+    brats_data_dir = ...
 
     task_id = 42
     task_name = "BraTS2018"
@@ -100,7 +100,7 @@ def convert_folder_with_preds_back_to_BraTS_labeling_convention(input_folder: st
                               'background': 0,
                               'whole tumor': (1, 2, 3),
                               'tumor core': (2, 3),
-                              'enhancing tumor': (3, )
+                              'enhancing tumor': (3,)
                           },
                           num_training_cases=(len(case_ids_lgg) + len(case_ids_hgg)),
                           file_ending='.nii',

diff --git a/nnunetv2/dataset_conversion/Dataset043_BraTS19.py b/nnunetv2/dataset_conversion/Dataset043_BraTS19.py
@@ -1,6 +1,5 @@
 import multiprocessing
 import shutil
-from multiprocessing import Pool
 
 import SimpleITK as sitk
 import numpy as np
@@ -47,7 +46,8 @@ def load_convert_labels_back_to_BraTS(filename, input_folder, output_folder):
     sitk.WriteImage(d, join(output_folder, filename))
 
 
-def convert_folder_with_preds_back_to_BraTS_labeling_convention(input_folder: str, output_folder: str, num_processes: int = 12):
+def convert_folder_with_preds_back_to_BraTS_labeling_convention(input_folder: str, output_folder: str,
+                                                                num_processes: int = 12):
     """
     reads all prediction files (nifti) in the input folder, converts the labels back to BraTS convention and saves the
     """
@@ -58,7 +58,7 @@ def convert_folder_with_preds_back_to_BraTS_labeling_convention(input_folder: st
 
 
 if __name__ == '__main__':
-    brats_data_dir = '/home/stud/strasser/archive/brats2019/MICCAI_BraTS_2019_Data_Training'
+    brats_data_dir = ...
 
     task_id = 43
     task_name = "BraTS2019"
@@ -100,7 +100,7 @@ def convert_folder_with_preds_back_to_BraTS_labeling_convention(input_folder: st
                               'background': 0,
                               'whole tumor': (1, 2, 3),
                               'tumor core': (2, 3),
-                              'enhancing tumor': (3, )
+                              'enhancing tumor': (3,)
                           },
                           num_training_cases=(len(case_ids_hgg) + len(case_ids_lgg)),
                           file_ending='.nii',

diff --git a/nnunetv2/dataset_conversion/Dataset137_BraTS21.py b/nnunetv2/dataset_conversion/Dataset137_BraTS21.py
@@ -57,7 +57,7 @@ def convert_folder_with_preds_back_to_BraTS_labeling_convention(input_folder: st
 
 
 if __name__ == '__main__':
-    brats_data_dir = '/home/stud/strasser/data/raw_downloaded_data'
+    brats_data_dir = '/home/isensee/drives/E132-Rohdaten/BraTS_2021/training'
 
     task_id = 137
     task_name = "BraTS2021"

diff --git a/train.sh b/train.sh