Merge pull request #93 from yupidevs/develop

Example issues

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 = '0.8.5'
+release = '0.8.6'
 
 
 # -- General configuration ---------------------------------------------------

docs/source/examples/example1.rst

@@ -48,13 +48,6 @@ Import all the dependencies:
       plot_velocity_hist
    )
 
-Fix the random generator seed to make results reproducible:
-
-.. code-block:: python
-
-   np.random.seed(0)
-
-
 .. _Definition of parameters 1:
 
 2. Definition of parameters
@@ -113,7 +106,7 @@ we just need to instantiate the class and generate the Trajectories:
 
 .. code-block:: python
 
-   lg = LangevinGenerator(tt, dim, N, dt, tau, sigma)
+   lg = LangevinGenerator(tt, dim, N, dt, tau, sigma, seed=0)
    trajs = lg.generate()
 
 
@@ -132,7 +125,7 @@ Plot spacial trajectories
 
 .. code-block:: python
 
-   ax1 = plt.subplot(231)
+   plt.subplot(231)
    plot_2D(trajs[:5], legend=False, show=False)
 
 Plot velocity histogram
@@ -149,7 +142,7 @@ Plot turning angles
 
    theta = turning_angles_ensemble(trajs)
    ax3 = plt.subplot(233, projection='polar')
-   plot_angles_hist(theta, bins=60, show=False)
+   plot_angles_hist(theta, bins=60, ax=ax3, show=False)
 
 
 Plot Velocity autocorrelation function
@@ -158,7 +151,7 @@ Plot Velocity autocorrelation function
 
    lag_vacf = 50
    vacf, _ = vacf(trajs, time_avg=True, lag=lag_vacf)
-   ax6 = plt.subplot(234)
+   plt.subplot(234)
    plot_vacf(vacf, dt, lag_vacf, show=False)
 
 
@@ -168,17 +161,17 @@ Plot Mean Square Displacement
 
    lag_msd = 30
    msd, msd_std = msd(trajs, time_avg=True, lag=lag_msd)
-   ax4 = plt.subplot(235)
+   plt.subplot(235)
    plot_msd(msd, msd_std, dt, lag=lag_msd, show=False)
 
 Plot Kurtosis
 
 .. code-block:: python
 
-   kurtosis = kurtosis(trajs, time_avg=False, lag=30)
+   kurt, _ = kurtosis(trajs, time_avg=False, lag=30)
    kurt_ref = kurtosis_reference(trajs)
-   ax5 = plt.subplot(236)
-   plot_kurtosis(kurtosis, kurtosis_ref=kurt_ref, dt=dt, show=False)
+   plt.subplot(236)
+   plot_kurtosis(kurt, kurtosis_ref=kurt_ref, dt=dt, show=False)
 
 
 Generate plot

docs/source/examples/example4.rst

@@ -114,8 +114,8 @@ effect of gravity:
 
 .. code-block:: python
 
-   tl[0].rotate(- pi / 2)
-   tl[1].rotate(- pi / 2)
+   tl[0].rotate2d(- pi / 2)
+   tl[1].rotate2d(- pi / 2)
 
 
 Next, we update the coordinate system to place it at the initial position of

docs/source/examples/example6.rst

@@ -37,13 +37,6 @@ Import all the dependencies:
    from yupi.graphics import plot_hists
    from yupi.generators import DiffDiffGenerator
 
-Fix the random generator seed to make results reproducible:
-
-.. code-block:: python
-
-   np.random.seed(0)
-
-
 .. _Definition of parameters 6:
 
 2. Definition of parameters
@@ -69,7 +62,7 @@ we just need to instantiate the class and generate the Trajectories:
 
 .. code-block:: python
 
-   dd = DiffDiffGenerator(T, N=N, dt=dt)
+   dd = DiffDiffGenerator(T, N=N, dt=dt, seed=0)
    trajs = dd.generate()
 
 

docs/source/tutorials/operations.rst

@@ -46,7 +46,7 @@ Rotation can be made using the :py:func:`~yupi.Trajectory.rotate` method:
 .. code-block:: python
 
     traj_2 = Trajectory(points=[[0,0], [1,0]])
-    traj_2.rotate(-np.pi / 2)   # traj_2 points: [[0,0], [0,1]]
+    traj_2.rotate2d(-np.pi / 2)   # traj_2 points: [[0,0], [0,1]]
 
 
 Indexing and slicing

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "yupi"
-version = "0.8.5"
+version = "0.8.6"
 description = "A package for tracking and analysing objects trajectories"
 authors = [
     "Gustavo Viera-López <gvieralopez@gmail.com>",

tests/test_trajectory/test_operations.py

@@ -67,7 +67,7 @@ def test_rotation(simple_traj):
 
     # [0, 0] -> [0,       0]
     # [1, 1] -> [0, sqrt(2)]
-    simple_traj.rotate(ang)
+    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)
@@ -76,12 +76,12 @@ def test_rotation(simple_traj):
 def test_rotation_3d():
     traj = Trajectory(x=[0,1], y=[0,0], z=[0,0])
 
-    traj.rotate3d([0, 0, 3], -np.pi / 2)
+    traj.rotate3d(-np.pi / 2, [0, 0, 3])
 
     assert traj.r[0] == approx([0, 0, 0], APPROX_REL_TOLERANCE)
     assert traj.r[1] == approx([0, 1, 0], APPROX_REL_TOLERANCE)
 
-    traj.rotate3d([1, 0, 0], np.pi)
+    traj.rotate3d(np.pi, [1, 0, 0])
 
     assert traj.r[1] == approx([0, -1, 0], APPROX_REL_TOLERANCE)
 

yupi/__init__.py

@@ -21,4 +21,4 @@
     'Vector'
 ]
 
-__version__ = '0.8.5'
+__version__ = '0.8.6'

yupi/graphics/_stats_plots.py

@@ -135,7 +135,9 @@ def plot_angles_hist(ang, bins, show: bool = True, ax=None, **kwargs):
     """
 
     if ax is None:
-        ax = plt.gca(projection="polar")
+        ax = plt.axes(projection="polar")
+    elif ax.name != "polar":
+        raise ValueError("The axes must be polar")
     default_kwargs = {"color": LIGHT_BLUE, "ec": (0, 0, 0, 0.6), "density": True}
     default_kwargs.update(kwargs)
     plt.hist(ang, bins, **default_kwargs)

yupi/graphics/_trajs_plots.py

@@ -161,7 +161,7 @@ def plot_3D(trajs: Union[List[Trajectory], Trajectory], line_style: str = LINE,
             colors = color
 
 
-    ax = plt.gca(projection='3d')
+    ax = plt.axes(projection='3d')
 
     if connected:
         lengths = list(map(len, trajs))

yupi/trajectory.py

@@ -362,7 +362,7 @@ def add_polar_offset(self, radius: float, angle: float) -> None:
         y = rad * np.sin(ang)
         self.r = Vector.create([x,y]).T
 
-    def rotate(self, angle: float):
+    def rotate2d(self, angle: float):
         """
         Rotates the trajectory around the center coordinates [0,0]
 
@@ -373,7 +373,7 @@ def rotate(self, angle: float):
         """
         self.add_polar_offset(0, angle)
 
-    def rotate3d(self, vector: Union[list, np.ndarray], angle: float):
+    def rotate3d(self, angle: float, vector: Union[list, np.ndarray]):
         """
         Rotates the trajectory around a given vector.