adjust volume transfer function

README.md

@@ -174,11 +174,22 @@ Check out the example galleries organized by subject here:
 ## ✏  Contributing
 
 Any contributions are **greatly appreciated**!
-If you have a suggestion that would make this better, please fork the repo and create a pull request.
+If you have a suggestion that would make this better,
+please fork the repo and create a pull request. This is how:
+```bash
+# 1. Fork the repository on GitHub then clone your fork locally:
+git clone https://github.com/your-username/vedo.git
+# 2. Create a new branch for your feature or bugfix:
+git checkout -b feature/my-feature
+# 3. Make your changes and commit them:
+git commit -m "Description of my feature"
+# 4. Push your changes to your fork:
+git push origin feature/my-feature
+# 5. Open a Pull Request on the main repository.
+```
 You can also simply open an issue with the tag "enhancement".
 
 
-
 ## 📜  References
 
 **Scientific publications leveraging `vedo`:**

docs/changes.md

@@ -27,6 +27,8 @@
 - changes in the scalarbar2d object.
 - fix purging of nan in pyplot.plot()
 - fix line trace to skip first point
+- adjust volume transfer function for transparency @Poisoned
+
 
 
 ## Soft-breaking Changes
@@ -84,3 +86,11 @@ mesh_map2cell.py
 texturecubes.py
 meshquality.py
 streamlines1.py
+
+#### volume alphas look bad
+erode_dilate.py
+euclidian_dist.py
+numpy2volume0.py
+numpy_imread.py
+slab_vol.py
+warp_scalars.py

tests/common/test_core1.py

@@ -76,20 +76,20 @@
 ###################################### shift
 cone.pos(5,6,7).shift(3,0,0)
 print('shift',[8,6,7], cone.pos())
-assert np.allclose([8,6,7], cone.pos())
+assert np.allclose([8,6,7], cone.pos(), atol=0.001)
 
 
 ###################################### x y z
 cone.pos(10,11,12)
 cone.x(1.1)
 print('x y z',[1.1,11,12], cone.pos())
-assert np.allclose([1.1,11,12], cone.pos())
+assert np.allclose([1.1,11,12], cone.pos(), atol=0.001)
 cone.y(1.2)
 print('x y z',[1.1,1.2,12], cone.pos())
-assert np.allclose([1.1,1.2,12], cone.pos())
+assert np.allclose([1.1,1.2,12], cone.pos(), atol=0.001)
 cone.z(1.3)
 print('x y z',[1.1,1.2,1.3], cone.pos())
-assert np.allclose([1.1,1.2,1.3], cone.pos())
+assert np.allclose([1.1,1.2,1.3], cone.pos(), atol=0.001)
 
 
 ###################################### rotate
@@ -160,7 +160,7 @@
 s2.vertices = pts2
 pts3 = s2.vertices
 print('vertices',sum(pts3-pts2))
-assert np.allclose(pts2, pts3)
+assert np.allclose(pts2, pts3, atol=0.001)
 
 
 ###################################### cells
@@ -220,7 +220,7 @@
 assert 3.3 < sphere.diagonal_size() < 3.5
 
 print('center_of_mass',sphere.center_of_mass())
-assert np.allclose(sphere.center_of_mass(), [0,0,0])
+assert np.allclose(sphere.center_of_mass(), [0,0,0], atol=0.001)
 
 print('volume',sphere.volume())
 assert 4.1 < sphere.volume() < 4.2
@@ -233,7 +233,7 @@
 pt = [12,34,52]
 print('closest_point',sphere.closest_point(pt), [0.19883616, 0.48003298, 0.85441941])
 assert np.allclose(sphere.closest_point(pt),
-                   [0.19883616, 0.48003298, 0.85441941])
+                   [0.19883616, 0.48003298, 0.85441941], atol=0.001)
 
 
 ###################################### find_cells_in_bounds
@@ -246,13 +246,13 @@
 T = cone.clone().pos(35,67,87).transform
 s3 = Sphere().apply_transform(T)
 print('transformMesh',s3.center_of_mass(), (35,67,87))
-assert np.allclose(s3.center_of_mass(), (35,67,87))
+assert np.allclose(s3.center_of_mass(), (35,67,87), atol=0.001)
 
 
 ######################################normalize
 s3 = sphere.clone().pos(10,20,30).scale([7,8,9]).normalize()
 print('normalize',s3.center_of_mass(), (10,20,30))
-assert np.allclose(s3.center_of_mass(), (10,20,30))
+assert np.allclose(s3.center_of_mass(), (10,20,30), atol=0.001)
 print('normalize',s3.average_size())
 assert 0.9 < s3.average_size() < 1.1
 
@@ -276,7 +276,7 @@
 
 ###################################### vertex_normals
 print('vertex_normals',sphere.vertex_normals[12], [9.97668684e-01, 1.01513637e-04, 6.82437494e-02])
-assert np.allclose(sphere.vertex_normals[12], [9.97668684e-01, 1.01513637e-04, 6.82437494e-02])
+assert np.allclose(sphere.vertex_normals[12], [9.97668684e-01, 1.01513637e-04, 6.82437494e-02], atol=0.001)
 
 
 ###################################### contains
@@ -286,9 +286,9 @@
 ###################################### intersectWithLine (fails vtk7..)
 # pts = sphere.intersectWithLine([-2,-2,-2], [2,3,4])
 # print('intersectWithLine',pts[0])
-# assert np.allclose(pts[0], [-0.8179885149002075, -0.522485613822937, -0.2269827425479889])
+# assert np.allclose(pts[0], [-0.8179885149002075, -0.522485613822937, -0.2269827425479889], atol=0.001)
 # print('intersectWithLine',pts[1])
-# assert np.allclose(pts[1], [-0.06572723388671875, 0.41784095764160156, 0.9014091491699219])
+# assert np.allclose(pts[1], [-0.06572723388671875, 0.41784095764160156, 0.9014091491699219], atol=0.001)
 
 
 ############################################################################
@@ -333,21 +333,21 @@
 q = transformations.cart2spher(*q)
 q = transformations.spher2cart(*q)
 print("cart2spher spher2cart", q)
-assert np.allclose(q, [5,2,3])
+assert np.allclose(q, [5,2,3], atol=0.001)
 q = transformations.cart2cyl(*q)
 q = transformations.cyl2cart(*q)
 print("cart2cyl cyl2cart", q)
-assert np.allclose(q, [5,2,3])
+assert np.allclose(q, [5,2,3], atol=0.001)
 q = transformations.cart2cyl(*q)
 q = transformations.cyl2spher(*q)
 q = transformations.spher2cart(*q)
 print("cart2cyl cyl2spher spher2cart", q)
-assert np.allclose(q, [5,2,3])
+assert np.allclose(q, [5,2,3], atol=0.001)
 q = transformations.cart2spher(*q)
 q = transformations.spher2cyl(*q)
 q = transformations.cyl2cart(*q)
 print("cart2spher spher2cyl cyl2cart", q)
-assert np.allclose(q, [5,2,3])
+assert np.allclose(q, [5,2,3], atol=0.001)
 
 ######################################
 print("OK with test_actors")

tests/snippets/test_elastic_pendulum.py

@@ -1,7 +1,9 @@
+"""Simulate an elastic pendulum.
+The trail is colored according to the velocity."""
 import numpy as np
 from scipy.integrate import solve_ivp
 import matplotlib.pyplot as plt
-from vedo import Plotter, Axes, Sphere, Spring, Image
+from vedo import Plotter, Axes, Sphere, Spring, Image, mag, sin, cos
 from vedo.addons import ProgressBarWidget
 
 
@@ -12,19 +14,17 @@
 
 # Define the system of ODEs
 def system(t, z):
-    x, x_dot, y, y_dot = z  # z = [x, x', y, y']
-    dx_dt = x_dot
-    dy_dt = y_dot
-    dx_dot_dt = (a + x) * y_dot ** 2 - k / m * x + g * np.cos(y)
-    dy_dot_dt = -2 / (a + x) * x_dot * y_dot - g / (a + x) * np.sin(y)
-    return [dx_dt, dx_dot_dt, dy_dt, dy_dot_dt]
+    x, dx_dt, y, dy_dt = z  # z = [x, x', y, y']
+    dxdot_dt = (a+x) * dy_dt**2 - k/m * x + g * cos(y)
+    dydot_dt = -2/(a+x) * dx_dt * dy_dt - g/(a+x) * sin(y)
+    return [dx_dt, dxdot_dt, dy_dt, dydot_dt]
 
 
 # Initial conditions: x(0), x'(0), y(0), y'(0)
-initial_conditions = [0.0, 0.0, 0.4, 0.0]
+initial_conditions = [0.0,   0.0,  0.4,   0.0]
 
 # Time span for the solution
-t_span = (0, 10)
+t_span = (0, 12)
 t_eval = np.linspace(t_span[0], t_span[1], 500) # range to evaluate solution
 
 # Solve the system numerically
@@ -33,28 +33,36 @@ def system(t, z):
 elong_values = solution.y[0]
 theta_values = solution.y[2]
 
-# Plot the results
+# Plot the results using matplotlib as a graph
 fig = plt.figure()
 plt.plot(t_values, elong_values, label="elongation(t)")
 plt.plot(t_values, theta_values, label="angle(t)")
 plt.xlabel("Time")
 plt.legend()
 
-# Use vedo to animate the system
+# Animate the system using the solution of the ODE
 plotter = Plotter(bg="blackboard", bg2="blue1", interactive=False)
-pbw = ProgressBarWidget(len(t_values))
+pbw  = ProgressBarWidget(len(t_values))
 axes = Axes(xrange=[-2, 2], yrange=[-a*2, 1], xygrid=0, xyframe_line=0, c="w")
-img = Image(fig).clone2d("top-right", size=0.5)
+img  = Image(fig).clone2d("top-right", size=0.5)
 sphere = Sphere(r=0.3, c="red5").add_trail(c="k5", lw=4)
-plotter.show(axes, sphere, img, pbw)
+plotter.show(axes, sphere, img, pbw, __doc__)
 
-for el, theta in zip(elong_values, theta_values):
-    x =  (a + el) * np.sin(theta)
-    y = -(a + el) * np.cos(theta)
+for elong, theta in zip(elong_values, theta_values):
+    x =  (a + elong) * sin(theta)
+    y = -(a + elong) * cos(theta)
     spring = Spring([0, 0], [x, y])
     sphere.pos([x, y]).update_trail()
-    plotter.remove("Spring").add(spring)
+
+    # color the trail according to the lenght of each segment
+    v = sphere.trail.vertices
+    lenghts1 = np.array(v[1:])
+    lenghts2 = np.array(v[:-1])
+    lenghts = mag(lenghts1 - lenghts2) # lenght of each segment
+    lenghts = np.append(lenghts, lenghts[-1])
+    sphere.trail.cmap("Blues_r", lenghts, vmin=0, vmax=0.1)
+
+    plotter.remove("Spring").add(spring).render()
     pbw.update()  # update progress bar
-    plotter.render()
 
 plotter.interactive()

vedo/shapes.py

@@ -3398,7 +3398,7 @@ def __init__(
 
         super().__init__(tuf.GetOutput(), c, alpha)
 
-        self.phong()
+        self.phong().lighting("metallic")
         self.base = np.array(start_pt, dtype=float)
         self.top  = np.array(end_pt, dtype=float)
         self.name = "Spring"

vedo/version.py

@@ -1 +1 @@
-_version = '2024.5.2+dev15'
+_version = '2024.5.2+dev17'