Add Annes Lobecke sample experiment for didactiv purposes

navipy/models/Hafner_2000.py → navipy/models/hafner_2000.py

 from navipy import Brain
-from navipy.processing.pcode import apcv
+from navipy.processing.pcode import apcv, skyline
 import pandas as pd
-import numpy as np
 # 0) Define a class heriting from Brain
 
 
+def processing(scene, viewing_directions, channel):
+    """ Return the average skyline vector by doing
+
+    * inverse of distance (i.e. distance -> nearness)
+    * summing along elevation (i.e. estimate of skyline)
+    * vector summing of skyline vector
+
+    Average place cell vector on the skyline
+    refer as skyline vector:
+    * Müller et al. 2018
+    * Basten and Mallot 2010
+    refer as COMANV in :
+    * Hafter 2000,
+    * Bertrand 2015
+    center of mass of average nearness vector
+    """
+    # Invert distance to nearness
+    scene[..., 3, :] = 1/scene[..., 3, :]
+    # Calculate the skyline
+    scene = skyline(scene)
+
+    comanv = apcv(scene, viewing_directions)
+    return comanv[..., channel, :]
+
+
+def comparing(current, memory):
+    """ Calculate homing vector
+
+    homing vector  = current vector - memory vector
+    """
+
+
 class ASVBrain(Brain):
     def __init__(self,
                  memory,
@@ -15,19 +46,13 @@ class ASVBrain(Brain):
         self.channel = channel
         self.memory = memory
 
-    def asv(self):
-        if self.channel > 3:
-            return apcv(1/self.vision.scene,
-                        self.vision.viewing_directions)[..., 3, :]
-        else:
-            return apcv(self.vision.scene,
-                        self.vision.viewing_directions)[..., self.channel, :]
-
     def velocity(self):
         index = self.posorient.index
         convention = index.levels[0][-1]
-        homing_vector = self.memory - self.asv()
-        homing_vector = np.squeeze(homing_vector)
+        current = processing(self.vision.scene,
+                             self.vision.viewing_directions,
+                             self.channel)
+        homing_vector = comparing(current, self.memory)
         indeces = [('location', 'dx'), ('location', 'dy'),
                    ('location', 'dz'), (convention, 'dalpha_0'),
                    (convention, 'dalpha_1'), (convention, 'dalpha_2')]