add background_max5

extraction/core/functions/defaults.py

@@ -30,6 +30,7 @@ def exparams_from_meta(meta: Union[dict, PosixPath, str], extras=["ph"]):
         "mean",
         "median",
         "imBackground",
+        "background_max5",
         "max2p5pc",
         "max2p5pc_med",
         "max5px",

extraction/core/functions/trap.py

@@ -4,13 +4,26 @@ import numpy as np
 
 
 def imBackground(cell_masks, trap_image):
-    '''
+    """
     :param cell_masks: (numpy 3d array) cells' segmentation mask
     :param trap_image: the image for the trap in which the cell is (all
     channels)
-    '''
+    """
     if not len(cell_masks):
         cell_masks = np.zeros_like(trap_image)
 
     background = ~cell_masks.sum(axis=2).astype(bool)
-    return (np.median(trap_image[np.where(background)]))
+    return np.median(trap_image[np.where(background)])
+
+
+def background_max5(cell_masks, trap_image):
+    """
+    :param cell_masks: (numpy 3d array) cells' segmentation mask
+    :param trap_image: the image for the trap in which the cell is (all
+    channels)
+    """
+    if not len(cell_masks):
+        cell_masks = np.zeros_like(trap_image)
+
+    background = ~cell_masks.sum(axis=2).astype(bool)
+    return np.mean(np.sort(trap_image[np.where(background)])[-5:])