Add sinuosity + travel dist

navipy/trajectories/__init__.py

@@ -640,9 +640,57 @@ class Trajectory(pd.DataFrame):
                                    'dalpha_2']] = rot.squeeze()
         return velocity
 
+    def traveled_distance(self):
+        """ Calculate the travel distance
+
+        Note that Nans are linearly interpolated
+        """
+        # We remove nans between section
+        # and then calculate the velocity
+        # it is equivalent to interpolate between non-nan blocks
+        subtraj = self.location.dropna().reset_index().drop('index',
+                                                            axis=1, level=0)
+        if subtraj.dropna().shape[0] < 2:
+            print('Trajectory has less than 2 non nans points')
+            return np.nan
+        velocity = subtraj.diff()  # only location is of relevance
+        speed = np.sqrt(velocity.x**2 + velocity.y**2 + velocity.z**2)
+        travel_dist = np.sum(speed)
+        return travel_dist
+
+    def sinuosity(self, shortest_dist=None):
+        """ Calculate the sinosity
+        Sinusity is defined as:
+              Travelled distance
+           S=--------------------
+               Shortest distance
+
+        Note that Nans are linearly interpolated
+
+        :param shortest_dist: Assign shortest distance (default\
+ None the shortest distance is equal to the bee line between \
+first and last no-nan point.
+        """
+        travel_dist = self.traveled_distance()
+        if shortest_dist is None:
+            # we need to calculate the shortest distance
+            # assuming the direct line
+            firstpoint = self.location.dropna().iloc[0, :]
+            lastpoint = self.location.dropna().iloc[-1, :]
+            shortest_dist = lastpoint-firstpoint
+            shortest_dist = np.sqrt(
+                shortest_dist.x**2 + shortest_dist.y**2 + shortest_dist.z**2)
+        # sanity check
+        # the travelled distance can not be shorter than the shortest distance
+        if shortest_dist > travel_dist:
+            msg = "Travel distance is shorter than the shortest distance"
+            msg += "\n {}>{}".format(shortest_dist, travel_dist)
+            raise NameError(msg)
+        return travel_dist/shortest_dist
     # --------------------------------------------
     # ---------------- FILTER --------------------
     # --------------------------------------------
+
     def filtfilt(self, order, cutoff, padlen=None):
         """
         Filter the trajectory with order and cutoff by

navipy/trajectories/test_trajectory.py

@@ -53,6 +53,40 @@ class TestTrajectoryTransform(unittest.TestCase):
     def test_velocity(self):
         pass
 
+    def test_traveldist(self):
+        indeces = np.linspace(0, 2*np.pi, 1000)
+        radius = 5
+        mytraj = Trajectory(indeces=indeces, rotconv='zyx')
+        mytraj.x = indeces
+        mytraj.y = radius*np.cos(indeces)
+        mytraj.z = 0
+        # The length of a cos from 0 to 2pi
+        # is equal to perimeter of the circle
+        # 2*pi*r
+        travel_dist_theo = 2*np.pi*radius
+        travel_dist = mytraj.traveled_distance()
+        np.testing.assert_almost_equal(travel_dist, travel_dist_theo)
+        # Test with nans
+        mytraj.loc[[15, 50, 90], :] = np.nan
+        travel_dist = mytraj.traveled_distance()
+        np.testing.assert_almost_equal(travel_dist, travel_dist_theo)
+
+    def test_sinuosity(self):
+        indeces = np.linspace(0, 2*np.pi, 1000)
+        radius = 5
+        mytraj = Trajectory(indeces=indeces, rotconv='zyx')
+        mytraj.x = indeces
+        mytraj.y = radius*np.cos(indeces)
+        mytraj.z = 0
+        # The length of a cos from 0 to 2pi
+        # is equal to perimeter of the circle
+        # 2*pi*r
+        # the sinuosity will be equal to the radius
+        # because dist from start to end is 2*pi
+        sinuosity_theo = radius
+        sinuosity = mytraj.sinuosity()
+        np.testing.assert_almost_equal(sinuosity, sinuosity_theo)
+
 
 if __name__ == '__main__':
     unittest.main()