Merge pull request #99 from yupidevs/develop

Remove PyQt5 dependency and minor improvements

docs/source/GS/FAQ.rst

@@ -0,0 +1,86 @@
+Frequently Asked Questions
+==========================
+
+1. Why are plots not showing up? (Qt core dumped error)
+-------------------------------------------------------
+
+If you get an error similar to this::
+
+   QObject::moveToThread: Current thread (0x5632706342d0) is not the object's thread (0x5632
+   706194c0).
+   Cannot move to target thread (0x5632706342d0)
+   
+   qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "/home/USERNAME/.local/lib/p
+   ython/site-packages/cv2/qt/plugins" even though it was found.
+   This application failed to start because no Qt platform plugin could be initialized. Rein
+   stalling the application may fix this problem.
+   
+   Available platform plugins are: xcb, eglfs, linuxfb, minimal, minimalegl, offscreen, vnc,
+    wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, webgl.
+   
+   [1]    1498499 IOT instruction (core dumped)  python example.py
+
+it's proably because you have **PyQt5** and **opencv-python** packages
+installed in the same python enviroment. This is due to a known incompatibility
+between **PyQt5** and **opencv-python** in Linux systems. 
+
+Solutions
++++++++++
+
+Removing **PyQt5**
+******************
+
+If you don't need **PyQt5** in the current enviroment (globally by default) you
+can remove it by simply running:
+
+.. code-block:: bash
+   
+    $ pip uninstall PyQt5
+
+Runing **yupi** in a separated virtual enviroment
+*************************************************
+
+If you don't want to remove **PyQt5** globally, you can create a separated
+enviroment with **yupi**. This can be achieved in an easy way by using the
+`venv` tool provided by python. You can visit `here
+<https://docs.python.org/3/library/venv.html#module-venv>`_ the section
+dedicated to this tool in the Python Docs which contains a guide for the
+enviroment creation and activation.
+
+Once the enviroment is created and activated you can install **yupi** (and all
+the dependencies you might need) using the `pip` command.
+
+.. code-block:: bash
+
+    $ pip install yupi
+
+.. note::
+
+    The last solutions assume that **PyQt5** is not required for your project.
+    If **PyQt5** is one of your project dependencies the next solution shows
+    a way to use it along with **yupi**.
+
+Install opencv from a linux repository
+**************************************
+
+If **PyQt5** is also needed along with **yupi** a known solution is to install
+**opencv** from a linux repository. First you need to remove the current
+**opencv** instalation with `pip`:
+
+.. code-block:: bash
+
+   $ pip uninstall opencv-python
+
+Then install **opencv** from a linux repository using your current package
+manager. For example, if you are using `apt` (for Debian/Ubuntu based systems)
+you can install it by running:
+
+.. code-block:: bash
+
+   $ sudo apt install python3-opencv
+
+.. note::
+
+    The name of the package may vary. For example, in Arch repositories
+    it is called **python-opencv**.
+

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 = '0.9.1'
+release = '0.9.2'
 
 
 # -- General configuration ---------------------------------------------------

docs/source/index.rst

@@ -17,6 +17,7 @@ Standing for Yet Underused Path Instruments, **yupi** is a set of tools designed
    Getting Support <GS/Support>
    GS/Contributing
    GS/About
+   GS/FAQ
 
 .. toctree::
    :maxdepth: 2

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "yupi"
-version = "0.9.1"
+version = "0.9.2"
 description = "A package for tracking and analysing objects trajectories"
 authors = [
     "Gustavo Viera-López <gvieralopez@gmail.com>",
@@ -17,7 +17,6 @@ opencv-python = ">=4.4.0"
 numpy = ">=1.16.5"
 nudged = ">=0.3.1"
 matplotlib = ">=3.2.0"
-PyQt5 = "^5.15.3"
 
 [tool.poetry.dev-dependencies]
 pytest = "^6.2.2"

yupi/__init__.py

@@ -24,4 +24,4 @@
     'WindowType',
 ]
 
-__version__ = '0.9.1'
+__version__ = '0.9.2'

yupi/graphics/_trajs_plots.py

@@ -1,15 +1,22 @@
 import itertools
 import logging
 import matplotlib.pyplot as plt
-from typing import List, Union
+from typing import List, Union, Optional
 from yupi import Trajectory
 from yupi.graphics._style import YUPI_COLORS, LINE
 
 
-
-def plot_2D(trajs: Union[List[Trajectory], Trajectory], line_style: str = LINE,
-            title: str = None, legend: bool = True, show: bool = True,
-            connected: bool = False, units: str = 'm', color = None, **kwargs):
+def plot_2D(
+    trajs: Union[List[Trajectory], Trajectory],
+    line_style: str = LINE,
+    title: Optional[str] = None,
+    legend: bool = True,
+    show: bool = True,
+    connected: bool = False,
+    units: str = "m",
+    color=None,
+    **kwargs,
+):
     """
     Plot all the points of trajectories from ``trajs`` in a 2D plane.
 
@@ -47,14 +54,14 @@ def plot_2D(trajs: Union[List[Trajectory], Trajectory], line_style: str = LINE,
     if isinstance(trajs, Trajectory):
         trajs = [trajs]
 
-    units = '' if units is None else f' [{units}]'
+    units = "" if units is None else f" [{units}]"
 
     cycle = itertools.cycle(YUPI_COLORS)
     colors = [cycle.__next__() for _ in trajs]
 
     if color is not None:
         if isinstance(color, (str, tuple)):
-            kwargs['color'] = color
+            kwargs["color"] = color
         elif isinstance(color, list):
             colors = color
 
@@ -63,7 +70,7 @@ def plot_2D(trajs: Union[List[Trajectory], Trajectory], line_style: str = LINE,
         min_len = min(lengths)
         max_len = max(lengths)
         if min_len != max_len:
-            logging.warning('Not all the trajectories have the same length.')
+            logging.warning("Not all the trajectories have the same length.")
         for i in range(min_len):
             traj_points = [t[i] for t in trajs]
             traj_points.append(traj_points[0])
@@ -72,46 +79,69 @@ def plot_2D(trajs: Union[List[Trajectory], Trajectory], line_style: str = LINE,
                 ys = [tp1.r[1], tp2.r[1]]
                 plt.plot(xs, ys, color=(0.2, 0.2, 0.2), linewidth=0.5)
 
-    for i, t in enumerate(trajs):
+    for i, traj in enumerate(trajs):
 
-        if t.dim != 2:
-            logging.warning(f'Using plot_2D with a trajectory of {t.dim} '
-                            f' dimensions. Trajectory No. {i} with id'
-                            f' {t.traj_id})')
+        if traj.dim != 2:
+            logging.warning(
+                f"Using plot_2D with a trajectory of {traj.dim} "
+                f" dimensions. Trajectory No. {i} with id"
+                f" {traj.traj_id})"
+            )
 
         # Plotting
-        x, y = t.r.x, t.r.y
+        x, y = traj.r.x, traj.r.y
         if colors is not None:
             if i < len(colors):
-                kwargs['color'] = colors[i]
+                kwargs["color"] = colors[i]
             else:
-                kwargs.pop('color')
+                kwargs.pop("color")
         traj_plot = plt.plot(x, y, line_style, **kwargs)
         color = traj_plot[-1].get_color()
-        plt.plot(x[0], y[0], 'o', mfc='white', zorder=2,
-                 label=f'{t.traj_id} initial position', color=color)
-        plt.plot(x[-1], y[-1], 'o', mfc='white', zorder=2, color=color)
-        plt.plot(x[-1], y[-1], 'o', alpha=.5,
-                 label=f'{t.traj_id} final position', color=color)
+        traj_id = traj.traj_id if traj.traj_id is not None else f"traj {i}"
+        plt.plot(
+            x[0],
+            y[0],
+            "o",
+            mfc="white",
+            zorder=2,
+            label=f"{traj_id} initial position",
+            color=color,
+        )
+        plt.plot(x[-1], y[-1], "o", mfc="white", zorder=2, color=color)
+        plt.plot(
+            x[-1],
+            y[-1],
+            "o",
+            alpha=0.5,
+            label=f"{traj_id} final position",
+            color=color,
+        )
 
         if legend:
             plt.legend()
 
         plt.title(title)
-        plt.tick_params(direction='in')
-        plt.axis('equal')
+        plt.tick_params(direction="in")
+        plt.axis("equal")
         plt.grid(True)
-        plt.xlabel(f'x{units}')
-        plt.ylabel(f'y{units}')
+        plt.xlabel(f"x{units}")
+        plt.ylabel(f"y{units}")
 
     if show:
         plt.show()
 
 
-
-def plot_3D(trajs: Union[List[Trajectory], Trajectory], line_style: str = LINE,
-            title: str = None, legend: bool = True, show: bool = True,
-            connected: bool = False, units: str = 'm', color = None, **kwargs):
+def plot_3D(
+    trajs: Union[List[Trajectory], Trajectory],
+    line_style: str = LINE,
+    title: Optional[str] = None,
+    legend: bool = True,
+    show: bool = True,
+    connected: bool = False,
+    units: str = "m",
+    color=None,
+    **kwargs,
+):
     """
     Plot all the points of trajectories from ``trajs`` in a 3D space.
 
@@ -149,26 +179,25 @@ def plot_3D(trajs: Union[List[Trajectory], Trajectory], line_style: str = LINE,
     if isinstance(trajs, Trajectory):
         trajs = [trajs]
 
-    units = '' if units is None else f' [{units}]'
+    units = "" if units is None else f" [{units}]"
 
     cycle = itertools.cycle(YUPI_COLORS)
     colors = [cycle.__next__() for _ in trajs]
 
     if color is not None:
         if isinstance(color, (str, tuple)):
-            kwargs['color'] = color
+            kwargs["color"] = color
         elif isinstance(color, list):
             colors = color
 
-
-    ax = plt.axes(projection='3d')
+    ax = plt.axes(projection="3d")
 
     if connected:
         lengths = list(map(len, trajs))
         min_len = min(lengths)
         max_len = max(lengths)
         if min_len != max_len:
-            logging.warning('Not all the trajectories have the same length.')
+            logging.warning("Not all the trajectories have the same length.")
         for i in range(min_len):
             traj_points = [t[i] for t in trajs]
             traj_points.append(traj_points[0])
@@ -178,40 +207,57 @@ def plot_3D(trajs: Union[List[Trajectory], Trajectory], line_style: str = LINE,
                 zs = [tp1.r[2], tp2.r[2]]
                 ax.plot(xs, ys, zs, color=(0.2, 0.2, 0.2), linewidth=0.5)
 
-    for i, t in enumerate(trajs):
+    for i, traj in enumerate(trajs):
 
-        if t.dim != 3:
-            logging.warning(f'Using plot_3D with a trajectory of {t.dim} '
-                            f' dimensions. Trajectory No. {i} with id'
-                            f' {t.traj_id})')
+        if traj.dim != 3:
+            logging.warning(
+                f"Using plot_3D with a trajectory of {traj.dim} "
+                f" dimensions. Trajectory No. {i} with id"
+                f" {traj.traj_id})"
+            )
 
         # Plotting
-        x, y, z = t.r.x, t.r.y, t.r.z
+        x, y, z = traj.r.x, traj.r.y, traj.r.z
 
         if colors is not None:
             if i < len(colors):
-                kwargs['color'] = colors[i]
+                kwargs["color"] = colors[i]
             else:
-                kwargs.pop('color')
+                kwargs.pop("color")
         traj_plot = ax.plot(x, y, z, line_style, **kwargs)
         color = traj_plot[-1].get_color()
-
-        ax.plot(x[0], y[0], z[0], 'o', mfc='white',
-                 label=f'{t.traj_id} initial position', color=color)
-
-        ax.plot(x[-1], y[-1], z[-1], 'o', mfc='white', color=color)
-        ax.plot(x[-1], y[-1], z[-1], 'o', alpha=.5,
-                 label=f'{t.traj_id} final position', color=color)
+        traj_id = traj.traj_id if traj.traj_id is not None else f"traj {i}"
+
+        ax.plot(
+            x[0],
+            y[0],
+            z[0],
+            "o",
+            mfc="white",
+            label=f"{traj_id} initial position",
+            color=color,
+        )
+
+        ax.plot(x[-1], y[-1], z[-1], "o", mfc="white", color=color)
+        ax.plot(
+            x[-1],
+            y[-1],
+            z[-1],
+            "o",
+            alpha=0.5,
+            label=f"{traj_id} final position",
+            color=color,
+        )
 
         if legend:
             plt.legend()
 
         plt.title(title)
-        plt.tick_params(direction='in')
+        plt.tick_params(direction="in")
         plt.grid(True)
-        ax.set_xlabel(f'x{units}')
-        ax.set_ylabel(f'y{units}')
-        ax.set_zlabel(f'z{units}')
+        ax.set_xlabel(f"x{units}")
+        ax.set_ylabel(f"y{units}")
+        ax.set_zlabel(f"z{units}")
 
     if show:
         plt.show()