Merge pull request #95 from yupidevs/develop

Upgrade velocity estimation methods

docs/source/conf.py

@@ -28,7 +28,7 @@
 author = 'Gustavo Viera-López, Alfredo Reyes, Jorge Morgado, Ernesto Altshuler'
 
 # The full version, including alpha/beta/rc tags
-release = '0.8.7'
+release = '0.8.8'
 
 
 # -- General configuration ---------------------------------------------------

docs/source/examples/example3.rst

@@ -167,7 +167,7 @@ The temporal evolution of the efficiency can be plotted by:
 .. code-block:: python
 
    import matplotlib.pyplot as plt
-   plt.plot(wheel.t[1:], eff)
+   plt.plot(wheel.t, eff)
    plt.xlabel('time [s]')
    plt.ylabel('efficiency')
    plt.show()

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "yupi"
-version = "0.8.7"
+version = "0.8.8"
 description = "A package for tracking and analysing objects trajectories"
 authors = [
     "Gustavo Viera-López <[email protected]>",

tests/test_stats/test_stats.py

@@ -1,6 +1,6 @@
 import numpy as np
 import pytest
-from yupi import Trajectory, VelMethod
+from yupi import Trajectory, VelocityMethod, WindowType
 from yupi.stats import *
 
 APPROX_REL_TOLERANCE = 1e-10
@@ -9,19 +9,39 @@
 @pytest.fixture
 def traj():
     points = [[0, 0], [1, 0], [1, 1], [2, 1]]
-    return Trajectory(points=points, vel_est={"method": VelMethod.FORWARD})
+    return Trajectory(
+        points=points,
+        vel_est={
+            "method": VelocityMethod.LINEAR_DIFF,
+            "window_type": WindowType.FORWARD,
+        },
+    )
 
 
 @pytest.fixture
 def traj1():
     x = [0, 8, 5, 11]
-    return Trajectory(x, dt=2, vel_est={"method": VelMethod.FORWARD})
+    return Trajectory(
+        x=x,
+        dt=2,
+        vel_est={
+            "method": VelocityMethod.LINEAR_DIFF,
+            "window_type": WindowType.FORWARD,
+        },
+    )
 
 
 @pytest.fixture
 def traj2():
     x = [0, 8.5, 4.9, 10.5]
-    return Trajectory(x, dt=2, vel_est={"method": VelMethod.FORWARD})
+    return Trajectory(
+        x=x,
+        dt=2,
+        vel_est={
+            "method": VelocityMethod.LINEAR_DIFF,
+            "window_type": WindowType.FORWARD,
+        },
+    )
 
 
 def test_turning_angles(traj):
@@ -75,7 +95,7 @@ def test_psd(traj1):
     psd_o = psd([traj1], lag=lag, omega=True)
     assert psd_o[0] == pytest.approx([8.5, 6.5])
     assert psd_o[1] == pytest.approx([0, 0])
-    assert psd_o[2] == pytest.approx([-9.8696044,  0.])
+    assert psd_o[2] == pytest.approx([-9.8696044, 0.0])
 
 
 def test_checkers():

tests/test_trajectory/test_creation.py

@@ -1,5 +1,5 @@
 import pytest
-from yupi import Trajectory, VelMethod, VelPadding
+from yupi import Trajectory, VelocityMethod, WindowType
 
 APPROX_REL_TOLERANCE = 1e-10
 
@@ -88,45 +88,33 @@ def test_creation_general():
 def test_velocity_estimation_methods():
     x = [1, 2, 4, 8, 16]
 
-    Trajectory.global_vel_method(VelMethod.FORWARD)
+    Trajectory.global_vel_method(VelocityMethod.LINEAR_DIFF, WindowType.FORWARD)
     traj = Trajectory(x=x)
 
     assert traj.v == pytest.approx([1, 2, 4, 8, 8], rel=APPROX_REL_TOLERANCE)
 
-    Trajectory.global_vel_method(VelMethod.CENTERED)
-    traj.set_vel_method(VelMethod.BACKWARD)
+    Trajectory.global_vel_method(VelocityMethod.LINEAR_DIFF)
+    traj.set_vel_method(VelocityMethod.LINEAR_DIFF, WindowType.BACKWARD)
 
     assert traj.v == pytest.approx([1, 1, 2, 4, 8], rel=APPROX_REL_TOLERANCE)
 
     traj = Trajectory(x=x)
 
     assert traj.v == pytest.approx([3 / 2, 3 / 2, 3, 6, 6], rel=APPROX_REL_TOLERANCE)
 
-    traj = Trajectory(x=x, vel_est={"method": VelMethod.FORWARD, "h": 2})
+    vel_est = {
+        "method": VelocityMethod.FORNBERG_DIFF,
+        "window_type": WindowType.CENTRAL,
+        "accuracy": 2,
+    }
 
-    assert traj.v == pytest.approx([3 / 2, 3, 6, 6, 6], rel=APPROX_REL_TOLERANCE)
+    traj = Trajectory(x=x, vel_est=vel_est)
 
-    traj = Trajectory(
-        x=x,
-        vel_est={
-            "method": VelMethod.BACKWARD,
-            "h": 2,
-            "padding": VelPadding.VALUE,
-            "padding_val": 0,
-        },
-    )
-
-    assert traj.v == pytest.approx([0, 0, 3 / 2, 3, 6], rel=APPROX_REL_TOLERANCE)
-
-    traj.set_vel_method(VelMethod.CENTERED, h=2)
-
-    assert traj.v == pytest.approx(
-        [15 / 4, 15 / 4, 15 / 4, 15 / 4, 15 / 4], rel=APPROX_REL_TOLERANCE
-    )
+    vel_est["accuracy"] = 3
 
     with pytest.raises(ValueError):
-        traj.set_vel_method(VelMethod.CENTERED, h=0)
+        traj.set_vel_method(**vel_est)
 
-    with pytest.raises(ValueError):
-        traj.set_vel_method(VelMethod.CENTERED, h=8)
+    vel_est["accuracy"] = 2
 
+    traj = Trajectory(x=x, y=[i**2 for i in x], vel_est=vel_est)

tests/test_trajectory/test_operations.py

@@ -1,10 +1,11 @@
 import numpy as np
-from pytest import approx, fixture
 import pytest
-from yupi import Trajectory, VelMethod
+from pytest import approx, fixture
+from yupi import Trajectory, WindowType
 
 APPROX_REL_TOLERANCE = 1e-12
 
+
 @fixture
 def points():
     return np.array([[1, 2], [4, 3], [4, 1], [6, 8], [5, 7]], dtype=float)
@@ -32,7 +33,7 @@ def timed_traj(points, angles, time):
 
 @fixture
 def simple_traj():
-    return Trajectory(x=[0,1], y=[0,1])
+    return Trajectory(x=[0, 1], y=[0, 1], vel_est={"window_type": WindowType.FORWARD})
 
 
 def test_length(points, traj):
@@ -59,9 +60,10 @@ def test_iteration(points, angles, traj):
         t = time[i]
 
         assert point == approx(tp.r, APPROX_REL_TOLERANCE)  # Position
-        assert t == approx(tp.t, APPROX_REL_TOLERANCE)      # Time
+        assert t == approx(tp.t, APPROX_REL_TOLERANCE)  # Time
         assert ang == approx(tp.ang, APPROX_REL_TOLERANCE)  # Angle
 
+
 def test_rotation(simple_traj):
     # 45 degrees
     ang = np.pi / 4
@@ -70,12 +72,14 @@ def test_rotation(simple_traj):
     # [1, 1] -> [0, sqrt(2)]
     simple_traj.rotate2d(ang)
 
-    assert simple_traj.r[0] == approx([0,0], APPROX_REL_TOLERANCE)
-    assert simple_traj.r[1] == approx([0,np.sqrt(2)], APPROX_REL_TOLERANCE)
+    assert simple_traj.r[0] == approx([0, 0], APPROX_REL_TOLERANCE)
+    assert simple_traj.r[1] == approx([0, np.sqrt(2)], APPROX_REL_TOLERANCE)
 
 
 def test_rotation_3d():
-    traj = Trajectory(x=[0,1], y=[0,0], z=[0,0])
+    traj = Trajectory(
+        x=[0, 1], y=[0, 0], z=[0, 0], vel_est={"window_type": WindowType.FORWARD}
+    )
 
     traj.rotate3d(-np.pi / 2, [0, 0, 3])
 
@@ -114,7 +118,7 @@ def test_traj_addition(points, traj):
 
 def test_wrong_addition(traj):
     with pytest.raises(TypeError):
-        traj += 'wrong'
+        traj += "wrong"
 
 
 def test_constant_substraction(points, traj):
@@ -144,7 +148,7 @@ def test_traj_substraction(points, traj):
 
 def test_wrong_substraction(traj):
     with pytest.raises(TypeError):
-        traj -= 'wrong'
+        traj -= "wrong"
 
 
 def test_constant_multiplication(points, traj):
@@ -157,7 +161,7 @@ def test_constant_multiplication(points, traj):
 
 def test_wrong_multiplication(traj):
     with pytest.raises(TypeError):
-        traj *= 'wrong'
+        traj *= "wrong"
     with pytest.raises(TypeError):
         traj *= [1, 2]
 
@@ -205,5 +209,3 @@ def test_slicing(traj, timed_traj):
     # Test dt
     assert slice_5.dt == approx(traj.dt * 2, APPROX_REL_TOLERANCE)
     assert slice_6.dt == approx(traj.dt * 2, APPROX_REL_TOLERANCE)
-
-

yupi/__init__.py

@@ -7,7 +7,7 @@
 from yupi.features import Features
 from yupi.trajectory import Trajectory, TrajectoryPoint
 from yupi.vector import Vector
-from yupi._vel_estimators import VelMethod, VelPadding
+from yupi._vel_estimators import VelocityMethod, WindowType
 
 logging.basicConfig(
     level=logging.INFO,
@@ -20,8 +20,8 @@
     'TrajectoryPoint',
     'Features',
     'Vector',
-    'VelMethod',
-    'VelPadding'
+    'VelocityMethod',
+    'WindowType',
 ]
 
-__version__ = '0.8.7'
+__version__ = '0.8.8'