2.1

marcomusy · May 8, 2019 · b9341d6 · b9341d6
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diff --git a/README.md b/README.md
@@ -25,7 +25,7 @@ Intuitive and straightforward API which can be combined with VTK seamlessly
 in a program, whilst mantaining access to the full range of VTK native classes.
 
 It includes a [**large set of working examples**](https://github.com/marcomusy/vtkplotter/tree/master/examples)
-for the all following functionalities:
+for all the following functionalities:
 
   - Import meshes from VTK format, STL, Wavefront OBJ, 3DS, XML, Neutral, GMSH, OFF, PCD (PointCloud), volumetric TIFF stacks, DICOM, SLC, MHD, 2D images PNG, JPEG.
   - Export meshes as ASCII or binary to VTK, STL, OBJ, PLY formats.
@@ -39,7 +39,7 @@ for the all following functionalities:
   - Point-surface operations: find nearest points, determine if a point lies inside or outside a mesh.
   - Create primitive objects like: spheres, arrows, cubes, torus, ellipsoids... 
   - Generate *glyphs* (associating a mesh to each vertex of a source mesh).
-  - Create animations easily by just defining the position of the displayed objects in the 3D scene. Add trailing lines to moving objects automatically.
+  - Create animations easily by just defining the position of the displayed objects in the 3D scene. Add trailing lines and shadows to moving objects is also supported.
   - Straightforward support for multiple *sync-ed* or independent renderers in  the same window.
   - Registration (alignment) of meshes with different techniques.
   - Mesh smoothing with *Laplacian* and *WindowedSinc* algorithms.
@@ -97,7 +97,7 @@ git clone https://github.com/marcomusy/vtkplotter.git
 cd vtkplotter/examples
 python tutorial.py
 ```
-**More than 160 working examples can be found in directories** _(scroll down to see the screenshots):_ <br>
+**More than 170 working examples can be found in directories** _(scroll down to see the screenshots):_ <br>
 [**examples/basic**](https://github.com/marcomusy/vtkplotter/blob/master/examples/basic)<br>
 [**examples/advanced**](https://github.com/marcomusy/vtkplotter/blob/master/examples/advanced)<br>
 [**examples/volumetric**](https://github.com/marcomusy/vtkplotter/blob/master/examples/volumetric)<br>
@@ -109,6 +109,8 @@ python tutorial.py
 |:--------:|:-----|
 | ![rabbit](https://user-images.githubusercontent.com/32848391/50738808-5816ad00-11d8-11e9-9854-c952be6fb941.jpg)   | Apply a *Moving Least Squares* algorithm to obtain a smooth surface from a to a large cloud of scattered points in space ([script](https://github.com/marcomusy/vtkplotter/blob/master/examples/advanced/moving_least_squares2D.py)) <br />  `python advanced/moving_least_squares2D.py` |
 |                                                                                                                   |      |
+| ![airplanes](https://user-images.githubusercontent.com/32848391/57341963-b8910900-713c-11e9-898a-84b6d3712bce.gif)| Create 3D animations in just a few lines of code.<br>Trails and shadows can be added to moving objects easily. ([script](https://github.com/marcomusy/vtkplotter/blob/master/examples/simulations/airplanes.py)) <br /> `python simulations/airplanes.py`|
+|                                                                                                                   |      |
 | ![gyro](https://user-images.githubusercontent.com/32848391/39766016-85c1c1d6-52e3-11e8-8575-d167b7ce5217.gif)     | Simulation of a gyroscope hanging from a spring ([script](https://github.com/marcomusy/vtkplotter/blob/master/examples/simulations/gyroscope1.py)) <br /> `python simulations/gyroscope1.py`|
 |                                                                                                                   |      |
 | ![qsine2](https://user-images.githubusercontent.com/32848391/47751431-06aae880-dc92-11e8-9fcf-6659123edbfa.gif)   | Quantum-tunnelling effect integrating the Schroedinger equation with 4th order Runge-Kutta method. The animation shows the evolution of a particle in a box hitting a sinusoidal potential barrier. ([script](https://github.com/marcomusy/vtkplotter/blob/master/examples/simulations/tunnelling2.py)) <br /> `python simulations/tunnelling2.py`   |
@@ -119,6 +121,7 @@ python tutorial.py
 <br />
 
 
+
 ## References
 Scientific publications using `vtkplotter` so far:
 

diff --git a/examples/advanced/densifycloud.py b/examples/advanced/densifycloud.py
@@ -0,0 +1,20 @@
+"""Adds new points to an input point cloud. 
+The new points are created in such a way that
+all points in any local neighborhood are 
+within a target distance of one another. 
+"""
+from vtkplotter import *
+import numpy as np
+np.random.seed(3)
+
+npts = 200                       # nr. of points
+coords = np.random.rand(npts, 3) # range is [0, 1]
+scals = np.abs(coords[:, 2])     # let the scalar be the z of point itself
+
+apts = Points(coords, r=9).addPointScalars(scals, name='scals')
+
+densecloud = densifyCloud(apts, .05, closestN=10, maxIter=1)
+print(apts.N(), '->', densecloud.N())
+
+ppp = Points(densecloud.coordinates())
+show(apts, densecloud, Text(__doc__), axes=8)
diff --git a/examples/basic/README.md b/examples/basic/README.md
@@ -83,7 +83,9 @@ python example.py
 |    |    |
 | [![sliders3d](https://user-images.githubusercontent.com/32848391/52859555-4efcf200-312d-11e9-9290-6988c8295163.png)](https://github.com/marcomusy/vtkplotter/blob/master/examples/basic/sliders3d.py)<br/> `sliders3d.py`                | Use a 3D sliders to modify interactively the position of a mesh.|
 |    |    |
-| [![silhouette](https://user-images.githubusercontent.com/32848391/57179369-8e5df380-6e7d-11e9-99b4-3b1a120dd375.png)](https://github.com/marcomusy/vtkplotter/blob/master/examples/basic/silhouette.py)<br/> `silhouette.py`                |Show the silhouette of a mesh as seen along a specified direction. |
+| [![silhouette](https://user-images.githubusercontent.com/32848391/57179369-8e5df380-6e7d-11e9-99b4-3b1a120dd375.png)](https://github.com/marcomusy/vtkplotter/blob/master/examples/basic/silhouette.py)<br/> `silhouette.py`             |Show the silhouette of a mesh as seen along a specified direction. |
+|    |    |
+| [![shadow](https://user-images.githubusercontent.com/32848391/57312574-1d714280-70ee-11e9-8741-04fc5386d692.png)](https://github.com/marcomusy/vtkplotter/blob/master/examples/basic/shadow.py)<br/> `shadow.py`                         | Draw the shadow of a set of meshes on one of the Cartesian planes. |
 |    |    |
 | [![texturecubes](https://user-images.githubusercontent.com/32848391/50738847-be033480-11d8-11e9-8087-8ba949dbf228.jpg)](https://github.com/marcomusy/vtkplotter/blob/master/examples/basic/texturecubes.py)<br/> `texturecubes.py`       | Show a cube for each available texture name. Any jpg file can be used as texture. <br/>Built in textures: `['aqua', 'blue', 'bricks', 'gold1', 'gold2', 'grass', 'greenfloor', 'greentiles', 'ivy', 'leather1', 'leather2', 'marble', 'masonry', 'metal1', 'metal2', 'metalfloor1', 'metalfloor2', 'paper', 'water', 'white1', 'white2', 'white3', 'white4', 'wood1', 'wood2', 'wood3', 'wood4', 'wood5', 'wood6', 'wood7', 'wood8', 'wood9']` |
 |    |    |

diff --git a/examples/basic/shadow.py b/examples/basic/shadow.py
@@ -0,0 +1,9 @@
+"""Make a shadow of 2 meshes on the wall."""
+from vtkplotter import *
+
+a = load(datadir + "spider.ply").normalize().rotateZ(-90)
+s = Sphere(pos=[-0.4, 1.5, 0.3], r=0.3)
+
+shad = Shadow(a, s, direction="x").x(-4)
+
+show(a, s, shad, Text(__doc__), axes=1, viewup="z", bg="w")
diff --git a/examples/basic/silhouette.py b/examples/basic/silhouette.py
@@ -5,9 +5,9 @@
 
 s = Hyperboloid().rotateX(20)
 
-sx = s.clone().projectOnPlane('yz').addPos(-2,0,0).c('r')
-sy = s.clone().projectOnPlane('zx').addPos(0,-2,0).c('g')
-sz = s.clone().projectOnPlane('xy').addPos(0,0,-2).c('b')
+sx = s.clone().projectOnPlane('x').c('r').x(-3)
+sy = s.clone().projectOnPlane('y').c('g').y(-3)
+sz = s.clone().projectOnPlane('z').c('b').z(-3)
 
 show(s, sx, sy, sz,
      sx.silhouette(),

diff --git a/examples/other/dolfin/README.md b/examples/other/dolfin/README.md
@@ -19,6 +19,8 @@ python example.py  # on mac OSX try 'pythonw' instead
 |    |    |
 | [![submesh](https://user-images.githubusercontent.com/32848391/56675428-4e984e80-66bc-11e9-90b0-43dde7e4cc29.png)](https://github.com/marcomusy/vtkplotter/blob/master/examples/other/dolfin/demo_submesh.py)<br/> `demo_submesh.py`                   | How to extract matching sub meshes from a common mesh.  |
 |    |    |
+| [![scalemesh](https://user-images.githubusercontent.com/32848391/57393382-431c4b80-71c3-11e9-9a2c-8abb172f5468.png)](https://github.com/marcomusy/vtkplotter/blob/master/examples/other/dolfin/scalemesh.py)<br/> `scalemesh.py`                       | Scale a 2D mesh asymmetrically in one coordinate and elevate it along the z-axis with the solution. |
+|    |    |
 | [![pi_estimate](https://user-images.githubusercontent.com/32848391/56675429-4e984e80-66bc-11e9-9217-a0652a8e74fe.png)](https://github.com/marcomusy/vtkplotter/blob/master/examples/other/dolfin/pi_estimate.py)<br/> `pi_estimate.py`                 | Estimate _pi_ by integrating a circle surface. Latex formulas can be added to the renderer directly. |
 |    |    |
 | [![tet_mesh](https://user-images.githubusercontent.com/32848391/53026244-d2d31900-3462-11e9-835a-1fa9d66d3dae.png)](https://github.com/marcomusy/vtkplotter/blob/master/examples/other/dolfin/ex02_tetralize-mesh.py)<br/> `ex02_tetralize-mesh.py`    | Tetrahedral meshes generation with package _mshr_.  |

diff --git a/examples/other/dolfin/ex06_elasticity1.py b/examples/other/dolfin/ex06_elasticity1.py
@@ -42,7 +42,7 @@
 
 # ps = point size, only mesh vertices are shown 
 plot(u, mode='mesh', ps=10)
-clear()
 
 # plot displacements as white arrows, lw controls the mesh visibility
-plot(u, mode='arrows', color='w', alpha=0.5, cmap='gist_earth', lw=1)
+plot(u, mode='arrows', add=True,
+     color='w', alpha=0.5, cmap='gist_earth', lw=1)
diff --git a/examples/other/dolfin/run_all.sh b/examples/other/dolfin/run_all.sh
@@ -17,6 +17,9 @@ python calc_surface_area.py
 echo Running markmesh.py
 python markmesh.py
 
+echo Running scalemesh.py
+python scalemesh.py
+
 echo Running pi_estimate.py
 python pi_estimate.py
 

diff --git a/examples/other/dolfin/scalemesh.py b/examples/other/dolfin/scalemesh.py
@@ -0,0 +1,25 @@
+"""
+Scale a mesh asymmetrically in one coordinate
+"""
+from dolfin import *
+from mshr import *
+
+domain = Rectangle(Point(0.0, 0.0), Point(5.0, 0.01))
+mesh = generate_mesh(domain, 20)
+V = FunctionSpace(mesh, "CG", 2)
+
+e = Expression("sin(2*pi*(x[0]*x[0]+x[1]*x[1]))", degree=2)
+f = interpolate(e, V)
+
+####################################################
+from vtkplotter.dolfin import plot
+
+plt = plot(f,
+           warpZfactor=0.05, # add z elevation proportional to expression
+           style=1,
+           lw=0,
+           xtitle = 'y-coord is scaled by factor 100',
+           text=__doc__,
+           interactive=False)
+plt.actors[0].scale([1,100,1]) # retrieve actor object and scale y
+plt.show(interactive=True) # refresh scene
diff --git a/examples/other/dolfin/stokes.py b/examples/other/dolfin/stokes.py
@@ -9,7 +9,7 @@
 from vtkplotter.dolfin import plot, datadir, Latex
 
 t0 = time()
-print("calculating... please wait...")
+print("calculating... please wait... this takes time!")
 
 # Load mesh and subdomains
 mesh = Mesh(datadir+"dolfin_fine.xml")

diff --git a/examples/other/self_org_maps2d.py b/examples/other/self_org_maps2d.py
@@ -9,7 +9,7 @@
 # -----------------------------------------------------------------------------
 import numpy as np
 import scipy.spatial
-from vtkplotter import Points, Sphere, Grid, ProgressBar, Text, show
+from vtkplotter import *
 
 
 class SOM:
@@ -52,7 +52,8 @@ def learn(self, n_epoch=10000, sigma=(0.25,0.01), lrate=(0.5,0.01)):
                     for j in range(n):
                         grd.setPoint(i*n+j, (x[i,j], y[i,j], z[i,j]))
                 show(doc, pts, grd, axes=6, bg='w', azimuth=2, interactive=False)
-
+
+        interactive()
         return [self.codebook[:,i].reshape(n,n) for i in range(3)]
 
 # -------------------------------------------------------------------------------
@@ -69,4 +70,3 @@ def learn(self, n_epoch=10000, sigma=(0.25,0.01), lrate=(0.5,0.01)):
     som.samples = s.coordinates()
     som.learn(n_epoch=7000, sigma=(1, 0.01), lrate=(1, 0.01))
 
-    show(interactive=True)
diff --git a/examples/run_all.sh b/examples/run_all.sh
@@ -180,6 +180,9 @@ python basic/glyphs.py
 echo Running basic/glyphs_arrows.py
 python basic/glyphs_arrows.py   
 
+echo Running basic/shadow.py
+python basic/shadow.py   
+
 
 #################################### advanced
 echo Running advanced/fatlimb.py
@@ -248,50 +251,8 @@ python advanced/projectsphere.py
 echo Running advanced/convexHull.py
 python advanced/convexHull.py
 
-
-################################### simulations
-echo Running simulations/aspring.py
-python simulations/aspring.py
-
-echo Running simulations/cell_main.py
-python simulations/cell_main.py
-
-echo Running simulations/brownian2D.py
-python simulations/brownian2D.py
-
-echo Running simulations/gas.py
-python simulations/gas.py
-
-echo Running simulations/gyroscope1.py
-python simulations/gyroscope1.py
-
-echo Running simulations/gyroscope2.py
-python simulations/gyroscope2.py
-
-echo Running simulations/multiple_pendulum.py
-python simulations/multiple_pendulum.py
-
-echo Running simulations/hanoi3d.py
-python simulations/hanoi3d.py
-
-echo Running simulations/pendulum.py
-python simulations/pendulum.py
-
-echo Running simulations/wave_equation.py
-python simulations/wave_equation.py
-
-echo Running simulations/turing.py
-python simulations/turing.py
-
-echo Running simulations/particle_simulator.py
-python simulations/particle_simulator.py
-
-echo Running simulations/doubleslit.py
-python simulations/doubleslit.py
-
-echo Running simulations/tunnelling2.py
-python simulations/tunnelling2.py
-
+echo Running advanced/densifycloud.py
+python advanced/densifycloud.py
 
 ################################### volumetric
 echo Running volumetric/readVolumeAsIsoSurface.py
@@ -384,18 +345,6 @@ echo Running other/export_x3d.py
 python other/export_x3d.py
 
 
-##################################### not ran/ignored:
-#basic/annotations.py
-#basic/text_just.py
-#basic/lights.py
-#basic/ids.py
-#basic/surfIntersect.py
-#other/makeVideo.py
-#other/spherical_harmonics2.py 
-#other/remesh_ACVD.py 
-#other/tf_learn_embryo.py
-#other/self_org_maps2d.py
-
 #################################### 
 echo
 echo
@@ -427,4 +376,22 @@ echo '----------------------------'
 echo vtkplotter -s  "data/2??.vtk"
 vtkplotter      -s   data/2??.vtk
 
+echo '\n----------------------------'
+echo '----------------------------'
+echo 'cd simulations;  ./run_all.sh'
+echo 'cd other/dolfin; ./run_all.sh'
+echo '----------------------------'
+echo '----------------------------'
 
+
+##################################### not ran/ignored:
+#basic/annotations.py
+#basic/text_just.py
+#basic/lights.py
+#basic/ids.py
+#basic/surfIntersect.py
+#other/makeVideo.py
+#other/spherical_harmonics2.py 
+#other/remesh_ACVD.py 
+#other/tf_learn_embryo.py
+#other/self_org_maps2d.py
diff --git a/examples/simulations/README.md b/examples/simulations/README.md
@@ -29,6 +29,8 @@ python example.py  # on mac OSX try 'pythonw' instead
 |    |    |
 | [![hanoi](https://user-images.githubusercontent.com/32848391/56989284-58c1bd80-6b92-11e9-8f82-1ce95813f846.gif)](https://github.com/marcomusy/vtkplotter/blob/master/examples/simulations/hanoi3d.py)<br/> `hanoi3d.py`            | Solve the Tower of Hanoi puzzle (contributed by [G. Jacquenot](https://github.com/Gjacquenot)). |
 |    |    |
+| [![airplanes](https://user-images.githubusercontent.com/32848391/57341963-b8910900-713c-11e9-898a-84b6d3712bce.gif)](https://github.com/marcomusy/vtkplotter/blob/master/examples/simulations/airplanes.py)<br/> `airplanes.py` | Two acrobatic planes casting shadows and leaving a trail. |
+|    |    |
 | [![ruth](https://user-images.githubusercontent.com/32848391/50738891-db380300-11d8-11e9-84c2-0f55be7228f1.gif)](https://github.com/marcomusy/vtkplotter/blob/master/examples/simulations/particle_simulator.py)<br/> `particle_simulator.py` | Simulates interacting charged particles in 3D space. |
 |    |    |
 | [![tunneling1](https://vtkplotter.embl.es/gifs/tunnelling2.gif)](https://github.com/marcomusy/vtkplotter/blob/master/examples/simulations/tunnelling1.py)<br/> `tunnelling1.py`                                                    | Quantum Tunnelling effect using 4th order Runge-Kutta method with arbitrary potential shape. <br>The animation shows the evolution of a particle of relatively well defined momentum (hence undefined position) in a box hitting a potential barrier. The wave function is forced to be zero at the box walls. |
@@ -40,3 +42,6 @@ python example.py  # on mac OSX try 'pythonw' instead
 | [![wave](https://user-images.githubusercontent.com/32848391/50738956-7e891800-11d9-11e9-92d7-fa109b1b8551.gif)](https://github.com/marcomusy/vtkplotter/blob/master/examples/simulations/wave_equation.py)<br/> `wave_equation.py` | Simulate a collection of discrete coupled oscillators. We use this as a model of a vibrating string and compare two methods of integration: Euler and Runge-Kutta4.|
 |    |    |
 | [![](https://user-images.githubusercontent.com/32848391/44957809-b2c09500-aed6-11e8-9dc5-c2e52b632f94.gif)](https://github.com/marcomusy/pianoplayer)                                                                              | Finding and animating the optimal fingering to play a piano score with<br />[`pianoplayer 2.0`](https://github.com/marcomusy/pianoplayer)|
+
+
+
diff --git a/examples/simulations/airplanes.py b/examples/simulations/airplanes.py
@@ -0,0 +1,20 @@
+# Draw the shadow and trailing lines of 2 planes. This is not really
+# a simulation.. just a way to illustrate how to move objects around!
+from vtkplotter import *
+
+world = Box([0,0,0], 30, 15, 8).wire()
+
+p1 = load(datadir+"cessna.vtk").c("green").addTrail(lw=2, n=50)
+p2 = p1.clone().c("tomato").addTrail(lw=2, n=50) # make a copy
+
+# Setup the scene, creating the Plotter object is automatic
+show(world, p1, p2, axes=1, bg="white", viewup="z", resetcam=0, interactive=0)
+
+for x in arange(0, 3.5, 0.01):
+    p1.pos(9*x-15,  2-x, sin( 3-x)).rotateX(0+x) # make up some fancy movement
+    p2.pos(8*x-15, -2+x, sin(-3+x)).rotateX(2-x)
+
+    shad = Shadow(p1, p2, direction='z').z(-4) # fix z position of the shadow
+    show(world, p1, p2, shad)
+
+interactive()
diff --git a/examples/simulations/multiple_pendulum.py b/examples/simulations/multiple_pendulum.py
@@ -49,7 +49,7 @@
 Dt2 = Dt / 2  # Midpoint time step
 DiaSq = (2 * R) ** 2  # Diameter of bob squared
 
-printc("Press Esc to exit.", c="red")
+printc("Press F1 to exit.", c="red")
 
 while True:
     bob_x_m = list(map((lambda x, dx: x + Dt2 * dx), bob_x, x_dot))  # midpoint variables

diff --git a/examples/simulations/run_all.sh b/examples/simulations/run_all.sh
@@ -0,0 +1,58 @@
+#!/bin/bash
+# source run_all.sh
+#
+printf "\033c"
+
+echo #############################################
+echo    Press F1 at anytime to skip example
+echo #############################################
+echo
+echo
+echo
+
+
+################################### simulations
+echo Running aspring.py
+python aspring.py
+
+echo Running cell_main.py
+python cell_main.py
+
+echo Running brownian2D.py
+python brownian2D.py
+
+echo Running gas.py
+python gas.py
+
+echo Running gyroscope1.py
+python gyroscope1.py
+
+echo Running gyroscope2.py
+python gyroscope2.py
+
+echo Running multiple_pendulum.py
+python multiple_pendulum.py
+
+echo Running hanoi3d.py
+python hanoi3d.py
+
+echo Running airplanes.py
+python airplanes.py
+
+echo Running pendulum.py
+python pendulum.py
+
+echo Running wave_equation.py
+python wave_equation.py
+
+echo Running turing.py
+python turing.py
+
+echo Running particle_simulator.py
+python particle_simulator.py
+
+echo Running doubleslit.py
+python doubleslit.py
+
+echo Running tunnelling2.py
+python tunnelling2.py