Update paper

mrsonandrade · Jul 28, 2023 · 6bc4303 · 6bc4303
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diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@
 [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 [![Documentation Status](https://readthedocs.org/projects/pyswarming/badge/?version=latest)](https://pyswarming.readthedocs.io/en/latest/?badge=latest)
 ![version](https://img.shields.io/badge/version-1.1.2-blue)
-[![Downloads](https://static.pepy.tech/badge/pyswarming)](https://pepy.tech/project/pyswarming)
+[![Downloads](https://static.pepy.tech/personalized-badge/pyswarming?period=total&units=none&left_color=black&right_color=blue&left_text=Downloads)](https://pepy.tech/project/pyswarming)
 
 <img align="left" src="docs/readme_pics/logo.png">
 
@@ -132,7 +132,7 @@ my_swarm.simulate()
 Considering a swarm of robots, they can show different behaviors by using ``pyswarming``. The following codes are simplified implementations, for detailed ones, see the [examples](https://github.com/mrsonandrade/pyswarming/tree/main/examples) folder.
 ```python
 # importing the swarming behaviors
-import pyswarming.behaviors as ps
+import pyswarming.behaviors as pb
 
 # importing numpy to work with arrays
 import numpy as np
@@ -157,7 +157,7 @@ for t in range(15):
     print(robot_position_i)
 
     # update the robot (x, y, z) position
-    robot_position_i += robot_speed_i*ps.target(robot_position_i, target_position)
+    robot_position_i += robot_speed_i*pb.target(robot_position_i, target_position)
 ```
 ![Target](notebooks/pics/Target.gif)
 
@@ -183,7 +183,7 @@ for time_i in range(15):
     for r_ind in range(len(robot_speed)):
         r_i = robot_speed[r_ind]
         r_j = np.delete(robot_speed, np.array([r_ind]), axis=0)
-        robot_speed[r_ind] += robot_speed*ps.aggregation(r_i, r_j)
+        robot_speed[r_ind] += robot_speed*pb.aggregation(r_i, r_j)
 ```
 ![Aggregation](notebooks/pics/Aggregation.gif)
 
@@ -209,7 +209,7 @@ for time_i in range(15):
     for r_ind in range(len(robot_position)):
         r_i = robot_position[r_ind]
         r_j = np.delete(robot_position, np.array([r_ind]), axis=0)
-        robot_position[r_ind] += robot_speed*ps.repulsion(r_i, r_j, 3.0)
+        robot_position[r_ind] += robot_speed*pb.repulsion(r_i, r_j, 3.0)
 ```
 ![Repulsion](notebooks/pics/Repulsion.gif)
 
@@ -234,7 +234,7 @@ for time_i in range(15):
     for r_ind in range(len(robot_position)):
         r_i = robot_position[r_ind]
         r_j = np.delete(robot_position, np.array([r_ind]), axis=0)
-        robot_position[r_ind] += s_i*(ps.aggregation(r_i, r_j) + ps.repulsion(r_i, r_j, 5.0))
+        robot_position[r_ind] += s_i*(pb.aggregation(r_i, r_j) + pb.repulsion(r_i, r_j, 5.0))
 ```
 ![AggregationRepulsion](notebooks/pics/AggregationRepulsion.gif)
 

diff --git a/docs/source/example_notebooks/03_Custom_Animations.ipynb b/docs/source/example_notebooks/03_Custom_Animations.ipynb
@@ -84,14 +84,6 @@
     "HTML(anim.to_jshtml())"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "8a9d181e",
-   "metadata": {},
-   "source": [
-    "[Click here to see the Target output](https://github.com/mrsonandrade/pyswarming/tree/main/Examples/pics/Target.gif)"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "35bcb062",
@@ -176,14 +168,6 @@
     "HTML(anim.to_jshtml())"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "05d60513",
-   "metadata": {},
-   "source": [
-    "[Click here to see the Aggregation output](https://github.com/mrsonandrade/pyswarming/tree/main/Examples/pics/Aggregation.gif)"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "0d6c573c",
@@ -268,14 +252,6 @@
     "HTML(anim.to_jshtml())"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "6dc78225",
-   "metadata": {},
-   "source": [
-    "[Click here to see the Repulsion output](https://github.com/mrsonandrade/pyswarming/tree/main/Examples/pics/Repulsion.gif)"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "50eca133",
@@ -360,14 +336,6 @@
     "HTML(anim.to_jshtml())"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "c3c93292",
-   "metadata": {},
-   "source": [
-    "[Click here to see the Aggregation + Repulsion output](https://github.com/mrsonandrade/pyswarming/tree/main/Examples/pics/AggregationRepulsion.gif)"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "8b3ce0a4",
@@ -456,14 +424,6 @@
     "HTML(anim.to_jshtml())"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "3043d92c",
-   "metadata": {},
-   "source": [
-    "[Click here to see the Area Coverage output](https://github.com/mrsonandrade/pyswarming/tree/main/Examples/pics/AreaCoverage.gif)"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "7932e07f",
@@ -552,14 +512,6 @@
     "from IPython.display import HTML\n",
     "HTML(anim.to_jshtml())"
    ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "e0e03657",
-   "metadata": {},
-   "source": [
-    "[Click here to see the Collective Navigation output](https://github.com/mrsonandrade/pyswarming/tree/main/Examples/pics/CollectiveNavigation.gif)"
-   ]
   }
  ],
  "metadata": {

diff --git a/examples/example_joss_paper.py b/examples/example_joss_paper.py
@@ -66,7 +66,7 @@ def _animate(self, i):
         self.ax.set_ylabel('Y(m)')
         self.ax.grid()
         self.ax.set_aspect('equal')
-        self.ax.set_title('Aggregation + Heading Consensus behaviors')
+        self.ax.set_title('Aggregation + Heading Consensus + Repulsion behaviors', fontsize=9)
 
         # path history
         self.ax.plot(self.position_history[0][0], self.position_history[0][1], marker='.', lw=0, c='lightgray')
@@ -86,15 +86,15 @@ def _animate(self, i):
         self.ax.arrow(self.robot_positions[2][0], self.robot_positions[2][1], arrow_len*np.cos(self.robot_orientations[2][2]), arrow_len*np.sin(self.robot_orientations[2][2]), head_width=0.45, head_length=0.55, fc='k')
         self.ax.arrow(self.robot_positions[3][0], self.robot_positions[3][1], arrow_len*np.cos(self.robot_orientations[3][2]), arrow_len*np.sin(self.robot_orientations[3][2]), head_width=0.45, head_length=0.55, fc='k')
 
-        self.ax.text(0.7, -12.95, 'iter. %d' % (i), color='red')
+        self.ax.text(0.7, -12.95, 'iteration: %d' % (i), color='red')
 
         self.robot_positions_copy = self.robot_positions.copy()
         self.robot_orientations_copy = self.robot_orientations.copy()
 
         for r_ind in range(len(self.robot_positions)):
             r_i = self.robot_positions[r_ind]
             r_j = np.delete(self.robot_positions, np.array([r_ind]), axis=0)
-            self.robot_positions_copy[r_ind] += self.robot_linear_speed*(pb.aggregation(r_i, r_j))
+            self.robot_positions_copy[r_ind] += self.robot_linear_speed*((pb.aggregation(r_i, r_j)) + pb.repulsion(r_i, r_j, 3.0))
 
             theta_i = self.robot_orientations[r_ind]
             theta_j = np.delete(self.robot_orientations, np.array([r_ind]), axis=0)

diff --git a/paper/fig1.png b/paper/fig1.png
diff --git a/paper/fig2.png b/paper/fig2.png
diff --git a/paper/paper.bib b/paper/paper.bib
@@ -180,6 +180,16 @@ @article{chamanbaz:2017
   doi={10.3389/frobt.2017.00012}
 }
 
+@inproceedings{erez:2015,
+  title={Simulation tools for model-based robotics: Comparison of bullet, havok, mujoco, ode and physx},
+  author={Erez, Tom and Tassa, Yuval and Todorov, Emanuel},
+  booktitle={2015 IEEE international conference on robotics and automation (ICRA)},
+  pages={4397--4404},
+  year={2015},
+  organization={IEEE},
+  doi={10.1109/ICRA.2015.7139807}
+}
+
 @article{zoss:2018,
   title={Distributed system of autonomous buoys for scalable deployment and monitoring of large waterbodies},
   author={Zoss, BM and Mateo, D and Kuan, YK and Tokić, G and Chamanbaz, M and Goh, L and et al.},