From 1d0c2993beacf1f59d133e94b877c95419989dd8 Mon Sep 17 00:00:00 2001
From: SamTov <tovey.samuel@gmail.com>
Date: Wed, 15 May 2024 16:42:16 +0200
Subject: [PATCH] Update growing particle number example

---
 examples/growing_sphere_number.py | 59 +++++++++++++++++++++++++++++++
 znvis/particle/particle.py        |  6 ++--
 znvis/visualizer/visualizer.py    |  2 +-
 3 files changed, 63 insertions(+), 4 deletions(-)
 create mode 100644 examples/growing_sphere_number.py

diff --git a/examples/growing_sphere_number.py b/examples/growing_sphere_number.py
new file mode 100644
index 0000000..28d6a9f
--- /dev/null
+++ b/examples/growing_sphere_number.py
@@ -0,0 +1,59 @@
+"""
+ZnVis: A Zincwarecode package.
+License
+-------
+This program and the accompanying materials are made available under the terms
+of the Eclipse Public License v2.0 which accompanies this distribution, and is
+available at https://www.eclipse.org/legal/epl-v20.html
+SPDX-License-Identifier: EPL-2.0
+Copyright Contributors to the Zincwarecode Project.
+Contact Information
+-------------------
+email: zincwarecode@gmail.com
+github: https://github.com/zincware
+web: https://zincwarecode.com/
+Citation
+--------
+If you use this module please cite us with:
+
+Summary
+-------
+Tutorial script to visualize simple spheres over a random trajectory.
+"""
+
+import numpy as np
+
+import znvis as vis
+
+if __name__ == "__main__":
+    """
+    Run the simple spheres example.
+    """
+    material_1 = vis.Material(colour=np.array([30, 144, 255]) / 255, alpha=0.6)
+    # Define the first particle.
+    trajectory = np.random.uniform(-100, 100, (100, 1000, 3))
+    trajectory = []
+    p_number = 1
+    for t in range(1000):
+        trajectory.append(np.random.uniform(-100, 100, (p_number, 3)))
+
+        p_number = np.random.randint(p_number, 5 * p_number)
+
+        if p_number > 20000:
+            p_number = 20000
+
+    mesh = vis.Sphere(radius=2.0, resolution=3, material=material_1)
+    particle = vis.Particle(
+        name="Blue", mesh=mesh, position=trajectory, smoothing=False
+    )
+
+    # Create a bounding box
+    bounding_box = vis.BoundingBox(
+        center=np.array([0, 0, 0]), box_size=np.array([100, 100, 100])
+    )
+
+    # Construct the visualizer and run
+    visualizer = vis.Visualizer(
+        particles=[particle], frame_rate=20, bounding_box=bounding_box
+    )
+    visualizer.run_visualization()
diff --git a/znvis/particle/particle.py b/znvis/particle/particle.py
index 52fef30..3540880 100644
--- a/znvis/particle/particle.py
+++ b/znvis/particle/particle.py
@@ -105,13 +105,13 @@ def construct_mesh_list(self):
         """
         self.mesh_list = []
         try:
-            n_particles = int(self.position.shape[1])
-            n_time_steps = int(self.position.shape[0])
+            # n_particles = int(self.position.shape[1])
+            n_time_steps = int(len(self.position))
         except ValueError:
             raise ValueError("There is no data for these particles.")
 
         for i in track(range(n_time_steps), description=f"Building {self.name} Mesh"):
-            for j in range(n_particles):
+            for j in range(np.shape(self.position[i])[0]):
                 if j == 0:
                     if self.director is not None:
                         mesh = self._create_mesh(
diff --git a/znvis/visualizer/visualizer.py b/znvis/visualizer/visualizer.py
index bfa88f3..00f5502 100644
--- a/znvis/visualizer/visualizer.py
+++ b/znvis/visualizer/visualizer.py
@@ -93,7 +93,7 @@ def __init__(
         self.bounding_box = bounding_box() if bounding_box else None
 
         if number_of_steps is None:
-            number_of_steps = particles[0].position.shape[0]
+            number_of_steps = len(particles[0].position)
         self.number_of_steps = number_of_steps
 
         self.output_folder = pathlib.Path(output_folder).resolve()