--- a
+++ b/init.py
@@ -0,0 +1,58 @@
+import argparse
+import os
+
+
+class Options():
+
+    """This class defines options used during both training and test time."""
+
+    def __init__(self):
+        """Reset the class; indicates the class hasn't been initailized"""
+        self.initialized = False
+
+    def initialize(self, parser):
+
+        # basic parameters
+        parser.add_argument('--images_folder', type=str, default='./Data_folder/images')
+        parser.add_argument('--labels_folder', type=str, default='./Data_folder/labels')
+        parser.add_argument('--increase_factor_data',  default=1, help='Increase data number per epoch')
+        parser.add_argument('--preload', type=str, default=None)
+        parser.add_argument('--gpu_ids', type=str, default='2,3', help='gpu ids: e.g. 0  0,1,2, 0,2. use -1 for CPU')
+        parser.add_argument('--workers', default=8, type=int, help='number of data loading workers')
+
+        # dataset parameters
+        parser.add_argument('--network', default='unetr', help='nnunet, unetr')
+        parser.add_argument('--patch_size', default=(256, 256, 16), help='Size of the patches extracted from the image')
+        parser.add_argument('--spacing', default=[0.7, 0.7, 3], help='Original Resolution')
+        parser.add_argument('--resolution', default=None, help='New Resolution, if you want to resample the data in training. I suggest to resample in organize_folder_structure.py, otherwise in train resampling is slower')
+        parser.add_argument('--batch_size', type=int, default=4, help='batch size, depends on your machine')
+        parser.add_argument('--in_channels', default=1, type=int, help='Channels of the input')
+        parser.add_argument('--out_channels', default=1, type=int, help='Channels of the output')
+
+        # training parameters
+        parser.add_argument('--epochs', default=1000, help='Number of epochs')
+        parser.add_argument('--lr', default=0.01, help='Learning rate')
+        parser.add_argument('--benchmark', default=True)
+        
+        # Inference
+        # This is just a trick to make the predict script working, do not touch it now for the training.
+        parser.add_argument('--result', default=None, help='Keep this empty and go to predict_single_image script')
+        parser.add_argument('--weights', default=None, help='Keep this empty and go to predict_single_image script')
+
+        self.initialized = True
+        return parser
+
+    def parse(self):
+        if not self.initialized:
+            parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+            parser = self.initialize(parser)
+        opt = parser.parse_args()
+        # set gpu ids
+        if opt.gpu_ids != '-1':
+            os.environ["CUDA_VISIBLE_DEVICES"] = opt.gpu_ids
+        return opt
+
+
+
+
+