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neuronets · Jun 14, 2024 · b5087ec · b5087ec
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diff --git a/nobrainer/ext/SynthSeg/evaluate.py b/nobrainer/ext/SynthSeg/evaluate.py
@@ -16,12 +16,13 @@
 # python imports
 import os
 
-# third-party imports
-from nobrainer.ext.lab2im import edit_volumes, utils
 import numpy as np
 from scipy.ndimage.morphology import distance_transform_edt
 from scipy.stats import wilcoxon
 
+# third-party imports
+from nobrainer.ext.lab2im import edit_volumes, utils
+
 
 def fast_dice(x, y, labels):
     """Fast implementation of Dice scores.

diff --git a/nobrainer/ext/SynthSeg/metrics_model.py b/nobrainer/ext/SynthSeg/metrics_model.py
@@ -13,15 +13,16 @@
 License.
 """
 
-# third-party imports
-from nobrainer.ext.lab2im import layers
 import keras.layers as KL
 from keras.models import Model
 
 # python imports
 import numpy as np
 import tensorflow as tf
 
+# third-party imports
+from nobrainer.ext.lab2im import layers
+
 
 def metrics_model(input_model, label_list, metrics="dice"):
 

diff --git a/nobrainer/ext/SynthSeg/predict.py b/nobrainer/ext/SynthSeg/predict.py
@@ -18,17 +18,18 @@
 # python imports
 import os
 
+import keras.backend as K
+import keras.layers as KL
+from keras.models import Model
+import numpy as np
+import tensorflow as tf
+
 # project imports
 from nobrainer.ext.SynthSeg import evaluate
 
 # third-party imports
 from nobrainer.ext.lab2im import edit_volumes, layers, utils
 from nobrainer.ext.neuron import models as nrn_models
-import keras.backend as K
-import keras.layers as KL
-from keras.models import Model
-import numpy as np
-import tensorflow as tf
 
 
 def predict(

diff --git a/nobrainer/ext/SynthSeg/predict_denoiser.py b/nobrainer/ext/SynthSeg/predict_denoiser.py
@@ -16,17 +16,18 @@
 # python imports
 import os
 
+import keras.layers as KL
+from keras.models import Model
+import numpy as np
+import tensorflow as tf
+
 # project imports
 from nobrainer.ext.SynthSeg import evaluate
 from nobrainer.ext.SynthSeg.predict import postprocess, write_csv
 
 # third-party imports
 from nobrainer.ext.lab2im import edit_volumes, layers, utils
 from nobrainer.ext.neuron import models as nrn_models
-import keras.layers as KL
-from keras.models import Model
-import numpy as np
-import tensorflow as tf
 
 
 def predict(

diff --git a/nobrainer/ext/SynthSeg/predict_group.py b/nobrainer/ext/SynthSeg/predict_group.py
@@ -16,17 +16,18 @@
 # python imports
 import os
 
+import keras.layers as KL
+from keras.models import Model
+import numpy as np
+import tensorflow as tf
+
 # project imports
 from nobrainer.ext.SynthSeg import evaluate
 from nobrainer.ext.SynthSeg.predict import write_csv
 
 # third-party imports
 from nobrainer.ext.lab2im import edit_volumes, layers, utils
 from nobrainer.ext.neuron import models as nrn_models
-import keras.layers as KL
-from keras.models import Model
-import numpy as np
-import tensorflow as tf
 
 
 def predict(

diff --git a/nobrainer/ext/SynthSeg/predict_qc.py b/nobrainer/ext/SynthSeg/predict_qc.py
@@ -16,16 +16,17 @@
 # python imports
 import os
 
+import keras.layers as KL
+from keras.models import Model
+import numpy as np
+import tensorflow as tf
+
 # project imports
 from nobrainer.ext.SynthSeg import evaluate
 
 # third-party imports
 from nobrainer.ext.lab2im import edit_volumes, utils
 from nobrainer.ext.neuron import models as nrn_models
-import keras.layers as KL
-from keras.models import Model
-import numpy as np
-import tensorflow as tf
 
 
 def predict(

diff --git a/nobrainer/ext/SynthSeg/predict_synthseg.py b/nobrainer/ext/SynthSeg/predict_synthseg.py
@@ -18,18 +18,19 @@
 import sys
 import traceback
 
+import keras.backend as K
+import keras.layers as KL
+from keras.models import Model
+import numpy as np
+import tensorflow as tf
+
 # project imports
 from nobrainer.ext.SynthSeg import evaluate
 from nobrainer.ext.SynthSeg.predict import get_flip_indices, write_csv
 
 # third-party imports
 from nobrainer.ext.lab2im import edit_volumes, layers, utils
 from nobrainer.ext.neuron import models as nrn_models
-import keras.backend as K
-import keras.layers as KL
-from keras.models import Model
-import numpy as np
-import tensorflow as tf
 
 
 def predict(

diff --git a/nobrainer/ext/SynthSeg/sample_segmentation_pairs_d.py b/nobrainer/ext/SynthSeg/sample_segmentation_pairs_d.py
@@ -18,16 +18,17 @@
 # python imports
 import os
 
+from keras import models
+import keras.layers as KL
+import numpy as np
+import tensorflow as tf
+
 # third-party imports
 from nobrainer.ext.lab2im import edit_tensors as l2i_et
 from nobrainer.ext.lab2im import edit_volumes
 from nobrainer.ext.lab2im import layers as layers
 from nobrainer.ext.lab2im import utils
 from nobrainer.ext.neuron import models as nrn_models
-from keras import models
-import keras.layers as KL
-import numpy as np
-import tensorflow as tf
 
 
 def sample_segmentation_pairs(

diff --git a/nobrainer/ext/SynthSeg/training.py b/nobrainer/ext/SynthSeg/training.py
@@ -22,20 +22,21 @@
 # python imports
 import os
 
+import keras
+from keras import models
+import keras.callbacks as KC
+from keras.optimizers import Adam
+import numpy as np
+import tensorflow as tf
+
 # project imports
 from nobrainer.ext.SynthSeg import metrics_model as metrics
-from nobrainer.processing.brain_generator import BrainGenerator
 
 # third-party imports
 from nobrainer.ext.lab2im import layers, utils
 from nobrainer.ext.neuron import layers as nrn_layers
 from nobrainer.ext.neuron import models as nrn_models
-import keras
-from keras import models
-import keras.callbacks as KC
-from keras.optimizers import Adam
-import numpy as np
-import tensorflow as tf
+from nobrainer.processing.brain_generator import BrainGenerator
 
 
 def training(

diff --git a/nobrainer/ext/SynthSeg/training_denoiser.py b/nobrainer/ext/SynthSeg/training_denoiser.py
@@ -16,19 +16,20 @@
 # python imports
 import os
 
+from keras import layers as KL
+from keras import models
+import numpy as np
+import tensorflow as tf
+
 # project imports
 from nobrainer.ext.SynthSeg import metrics_model as metrics
-from nobrainer.models.labels_to_image_model import get_shapes
 from nobrainer.ext.SynthSeg.training import train_model
 from nobrainer.ext.SynthSeg.training_supervised import build_model_inputs
 
 # third-party imports
 from nobrainer.ext.lab2im import layers, utils
 from nobrainer.ext.neuron import models as nrn_models
-from keras import layers as KL
-from keras import models
-import numpy as np
-import tensorflow as tf
+from nobrainer.models.labels_to_image_model import get_shapes
 
 
 def training(

diff --git a/nobrainer/ext/SynthSeg/training_group.py b/nobrainer/ext/SynthSeg/training_group.py
@@ -21,21 +21,22 @@
 # python imports
 import os
 
+from keras import models
+import keras.layers as KL
+import numpy as np
+import tensorflow as tf
+
 # project imports
 from nobrainer.ext.SynthSeg import metrics_model as metrics
-from nobrainer.processing.brain_generator import BrainGenerator
-from nobrainer.models.labels_to_image_model import get_shapes
 from nobrainer.ext.SynthSeg.training import train_model
 
 # third-party imports
 from nobrainer.ext.lab2im import edit_tensors as l2i_et
 from nobrainer.ext.lab2im import layers, utils
 from nobrainer.ext.lab2im.edit_volumes import get_ras_axes
 from nobrainer.ext.neuron import models as nrn_models
-from keras import models
-import keras.layers as KL
-import numpy as np
-import tensorflow as tf
+from nobrainer.models.labels_to_image_model import get_shapes
+from nobrainer.processing.brain_generator import BrainGenerator
 
 
 def training(

diff --git a/nobrainer/ext/SynthSeg/training_qc.py b/nobrainer/ext/SynthSeg/training_qc.py
@@ -22,6 +22,15 @@
 # python imports
 import os
 
+import keras
+from keras import models
+import keras.backend as K
+import keras.callbacks as KC
+import keras.layers as KL
+from keras.optimizers import Adam
+import numpy as np
+import tensorflow as tf
+
 # project imports
 from nobrainer.ext.SynthSeg import metrics_model as metrics
 
@@ -31,14 +40,6 @@
 from nobrainer.ext.neuron import layers as nrn_layers
 from nobrainer.ext.neuron import models as nrn_models
 from nobrainer.ext.neuron import utils as nrn_utils
-import keras
-from keras import models
-import keras.backend as K
-import keras.callbacks as KC
-import keras.layers as KL
-from keras.optimizers import Adam
-import numpy as np
-import tensorflow as tf
 
 
 def training(

diff --git a/nobrainer/ext/SynthSeg/training_supervised.py b/nobrainer/ext/SynthSeg/training_supervised.py
@@ -21,21 +21,22 @@
 # python imports
 import os
 
+from keras import models
+import keras.layers as KL
+import numpy as np
+import numpy.random as npr
+import tensorflow as tf
+
 # project imports
 from nobrainer.ext.SynthSeg import metrics_model as metrics
-from nobrainer.models.labels_to_image_model import get_shapes
 from nobrainer.ext.SynthSeg.training import train_model
 
 # third-party imports
 from nobrainer.ext.lab2im import edit_tensors as l2i_et
 from nobrainer.ext.lab2im import layers, utils
 from nobrainer.ext.lab2im.edit_volumes import get_ras_axes
 from nobrainer.ext.neuron import models as nrn_models
-from keras import models
-import keras.layers as KL
-import numpy as np
-import numpy.random as npr
-import tensorflow as tf
+from nobrainer.models.labels_to_image_model import get_shapes
 
 
 def training(

diff --git a/nobrainer/ext/SynthSeg/validate.py b/nobrainer/ext/SynthSeg/validate.py
@@ -19,14 +19,15 @@
 import os
 import re
 
+import matplotlib.pyplot as plt
+import numpy as np
+from tensorflow.python.summary.summary_iterator import summary_iterator
+
 # project imports
 from nobrainer.ext.SynthSeg.predict import predict
 
 # third-party imports
 from nobrainer.ext.lab2im import utils
-import matplotlib.pyplot as plt
-import numpy as np
-from tensorflow.python.summary.summary_iterator import summary_iterator
 
 
 def validate_training(

diff --git a/nobrainer/ext/SynthSeg/validate_qc.py b/nobrainer/ext/SynthSeg/validate_qc.py
@@ -19,14 +19,15 @@
 import os
 import re
 
+import matplotlib.pyplot as plt
+import numpy as np
+from tensorflow.python.summary.summary_iterator import summary_iterator
+
 # project imports
 from nobrainer.ext.SynthSeg.predict_qc import predict
 
 # third-party imports
 from nobrainer.ext.lab2im import utils
-import matplotlib.pyplot as plt
-import numpy as np
-from tensorflow.python.summary.summary_iterator import summary_iterator
 
 
 def validate_training(

diff --git a/nobrainer/processing/brain_generator.py b/nobrainer/processing/brain_generator.py
@@ -16,13 +16,12 @@
 # python imports
 import numpy as np
 
-from nobrainer.models.labels_to_image_model import labels_to_image_model
-
 # project imports
 from nobrainer.ext.SynthSeg.model_inputs import build_model_inputs
 
 # third-party imports
 from nobrainer.ext.lab2im import edit_volumes, utils
+from nobrainer.models.labels_to_image_model import labels_to_image_model
 
 
 class BrainGenerator: