Creation of a bias field augmentation layer. Usage presented in the s…

…egmentation_bfaug application in contrib. The bias field is modelled as a linear combination of polynomial functions, exponentiated and multiplicative to the image to augment.

config/default_segmentation_bf.ini

@@ -0,0 +1,77 @@
+############################ input configuration sections
+[modality1]
+csv_file=
+path_to_search = ./example_volumes/monomodal_parcellation
+filename_contains = T1
+filename_not_contains =
+spatial_window_size = (20, 42, 42)
+interp_order = 3
+pixdim=(1.0, 1.0, 1.0)
+axcodes=(A, R, S)
+
+[label]
+path_to_search = ./example_volumes/monomodal_parcellation
+filename_contains = Label
+filename_not_contains =
+spatial_window_size = (20, 42, 42)
+interp_order = 0
+pixdim=(1.0, 1.0, 1.0)
+axcodes=(A, R, S)
+
+############################## system configuration sections
+[SYSTEM]
+cuda_devices = ""
+num_threads = 2
+num_gpus = 1
+model_dir = ./models/model_monomodal_toy
+
+[NETWORK]
+name = toynet
+activation_function = prelu
+batch_size = 1
+decay = 0.1
+reg_type = L2
+
+# volume level preprocessing
+volume_padding_size = 21
+# histogram normalisation
+histogram_ref_file = ./example_volumes/monomodal_parcellation/standardisation_models.txt
+norm_type = percentile
+cutoff = (0.01, 0.99)
+normalisation = False
+whitening = False
+normalise_foreground_only=True
+foreground_type = otsu_plus
+multimod_foreground_type = and
+
+queue_length = 20
+
+
+[TRAINING]
+sample_per_volume = 32
+rotation_angle =
+scaling_percentage =
+bf_order = 3
+bias_field_range = (-0.5, 0.5)
+random_flipping_axes= 1
+lr = 0.01
+loss_type = Dice
+starting_iter = 0
+save_every_n = 100
+max_iter = 10
+max_checkpoints = 20
+
+[INFERENCE]
+border = (0, 0, 1)
+#inference_iter = 10
+save_seg_dir = ./output/toy
+output_interp_order = 0
+spatial_window_size = (0, 0, 3)
+
+############################ custom configuration sections
+[SEGMENTATION]
+image = modality1
+label = label
+output_prob = False
+num_classes = 160
+label_normalisation = True