prevents weighting index outside the atlas

DeepSlice/coord_post_processing/angle_methods.py

@@ -111,6 +111,7 @@ def propagate_angles(df, method, species):
     DV_angle, ML_angle = get_mean_angle(
         DV_angle_list, ML_angle_list, method, depths, species
     )
+    print(f"DV angle: {DV_angle}\nML angle: {ML_angle}")
     # adjust the angles for each section in the dataset
     df = set_angles(df, DV_angle, ML_angle)
     return df

DeepSlice/coord_post_processing/plane_alignment_functions/plane_alignment.py

@@ -99,6 +99,8 @@ def rotation_around_axis(axis, angle):
 def make_gaussian_weights(size):
     x = np.linspace(-np.pi, np.pi, size)
     weights = np.exp(-(x ** 2) / 2) / np.sqrt(2 * np.pi)
+    weights[weights>size-1] = size-1
+    weights[weights<0] = 0
     return weights
 
 

DeepSlice/main.py

@@ -24,10 +24,11 @@ def __init__(self, species):
 
     def predict(
         self,
-        image_directory: str,
+        image_directory: str = None,
         ensemble: bool = None,
         section_numbers: bool = True,
         legacy_section_numbers=False,
+        image_list = None
     ):
         """predicts the atlas position for a folder full of histological brain sections