From 3b9a7700efb9177cbcd5ddc9fea3056fc9225f3b Mon Sep 17 00:00:00 2001
From: Patrick Strasser <strasserpatrick@outlook.de>
Date: Sun, 28 Apr 2024 20:43:07 +0200
Subject: [PATCH] chore: minor changes for pr

---
 .../{Dataset042_BraTS2018.py => Dataset042_BraTS18.py} |  8 ++++----
 nnunetv2/dataset_conversion/Dataset043_BraTS19.py      |  8 ++++----
 nnunetv2/dataset_conversion/Dataset137_BraTS21.py      |  2 +-
 train.sh                                               | 10 ----------
 4 files changed, 9 insertions(+), 19 deletions(-)
 rename nnunetv2/dataset_conversion/{Dataset042_BraTS2018.py => Dataset042_BraTS18.py} (94%)
 delete mode 100755 train.sh

diff --git a/nnunetv2/dataset_conversion/Dataset042_BraTS2018.py b/nnunetv2/dataset_conversion/Dataset042_BraTS18.py
similarity index 94%
rename from nnunetv2/dataset_conversion/Dataset042_BraTS2018.py
rename to nnunetv2/dataset_conversion/Dataset042_BraTS18.py
index 0fe76bf13..12a2b5022 100644
--- a/nnunetv2/dataset_conversion/Dataset042_BraTS2018.py
+++ b/nnunetv2/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
index b03673708..35a176f00 100644
--- 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
index 74c259b95..b4817d282 100644
--- 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
deleted file mode 100755
index f728c332c..000000000
--- a/train.sh
+++ /dev/null
@@ -1,10 +0,0 @@
-#!/bin/bash
-source ~/env_file
-
-eval "$(conda shell.bash hook)"
-conda activate generic-nnunet
-
-cd /home/stud/strasser/workspace/nnUNet && git checkout dev
-
-echo "starting training with fold $fold"
-nnUNetv2_train 42 3d_fullres  $fold --npz