4.2

examples/advanced/cutWithMesh2.py

@@ -0,0 +1,21 @@
+"""Cut a cube with a surface
+to create a 'capping' mesh"""
+from vedo import *
+import numpy as np
+
+
+# Equation of the "gyroid" (https://en.wikipedia.org/wiki/Gyroid)
+x, y, z = np.mgrid[:30,:30,:30] * 0.4
+U = sin(x)*cos(y) + sin(y)*cos(z) + sin(z)*cos(x)
+
+# Create a Volume, take the isosurface at 0, smooth it and set mesh edges
+s = Volume(U).isosurface(0).smoothLaplacian().lineWidth(1)
+
+# Create a gridded cube
+c = CubicGrid(n=(29,29,29), spacing=(1,1,1)).alpha(1)
+
+s.cutWithMesh(c).color('silver')  # take what's inside of cube
+c.cutWithMesh(s).color('grey')    # take what's inside of isosurface
+
+# Show all the created objects
+show(s, c, __doc__, bg='darkseagreen', bg2='lightblue', axes=5)

examples/advanced/multi_viewer.py

@@ -40,7 +40,7 @@ def onLeftClick(mesh):
                    pos='bottom-left', c=ishape.color(), bg='k', font='Calco')
     instt = Text2D(instr, pos='bottom-right', c='dg', bg='g', font='Quikhand')
 
-    axes = addons.buildAxes(ishape, yzGrid=False)
+    axes = ishape.buildAxes(yzGrid=False)
     acts = [ishape, axes, sname, sprop, instt]
 
     plt1.backgroundColor('silver')

examples/advanced/splitmesh.py

@@ -1,11 +1,11 @@
 """Split a mesh by connectivity and
-order the pieces by increasing area.
+order the pieces by increasing area
 """
 from vedo import *
 
-em = load(datadir+"embryo.tif").isosurface(80)
+em = Volume(datadir+"embryo.tif").isosurface(80)
 
 # return the list of the largest 10 connected meshes:
 splitem = em.splitByConnectivity(maxdepth=40)[0:9]
 
-show( [(em, __doc__), splitem], N=2, axes=1 )
+show(splitem, __doc__, axes=1, viewup='z')

examples/basic/lights.py

@@ -1,16 +1,28 @@
-from vedo import Plotter, Plane, datadir
+"""Set custom lights to a 3D scene"""
+from vedo import Plotter, load, datadir, Point, Light, show
 
-vp = Plotter()
+man = load(datadir+'man.vtk').c('white').lighting('glossy')
 
-cow = vp.load(datadir+"cow.vtk").c("grey").scale(4).rotateX(-90)
-vp += Plane(pos=[0, -3.6, 0], normal=[0, 1, 0], sx=20).texture("grass")
-vp.show(viewup='y', interactive=0)
+p1 = Point([1,0,1], c='y')
+p2 = Point([0,0,2], c='r')
+p3 = Point([-1,-0.5,-1], c='b')
+p4 = Point([0,1,0], c='k')
 
-# vp.light() returns a vtkLight object with focal Point, fp, to mesh cow
-# fp can also be explicitly set as fp=[x,y,z]
-l = vp.addLight(pos=[-6, 6, 6], focalPoint=cow, deg=12, showsource=1)
+# Add light sources at the given positions
+l1 = Light(p1, c='y') # p1 can simply be [1,0,1]
+l2 = Light(p2, c='r')
+l3 = Light(p3, c='b')
+l4 = Light(p4, c='w', intensity=0.5)
 
-# can be switched on/off this way
-#l.SwitchOff()
+show(man, l1, l2, l3, l4, p1, p2, p3, p4,
+      __doc__, axes=1, viewup='z')
 
-vp.show(interactive=1)
+
+
+#####################################################
+##### Equivalent code using a Plotter instance: #####
+#####################################################
+# plt = Plotter(axes=1)
+# plt += [man, p1, p2, p3, p4, l1, l2, l3, l4]
+# plt.show(viewup='z')
+#####################################################

examples/basic/specular.py

@@ -3,7 +3,7 @@
 specular, specularPower, specularColor.
 """
 #https://lorensen.github.io/VTKExamples/site/Python/Rendering/SpecularSpheres
-from vedo import Plotter, Arrow, datadir
+from vedo import Plotter, Arrow, Light, datadir
 
 
 vp = Plotter(axes=1)
@@ -30,6 +30,5 @@
 print('Adding a light source..')
 p = (3, 1.5, 3)
 f = (3, 1.5, 0)
-vp.addLight(pos=p, focalPoint=f)
-vp += Arrow(p,f, s=0.01, c='gray', alpha=0.2)
+vp += [Arrow(p,f, s=0.01, c='gray', alpha=0.2), Light(pos=p, focalPoint=f)]
 vp.show()

examples/notebooks/notebooks_index.ipynb

@@ -21,7 +21,6 @@
        "-  <a href='advanced/gray_scott.ipynb' target='_blank'>advanced/gray_scott.ipynb</a>\n",
        "-  <a href='advanced/sierpinski.ipynb' target='_blank'>advanced/sierpinski.ipynb</a>\n",
        "-  <a href='advanced/thinplate_grid.ipynb' target='_blank'>advanced/thinplate_grid.ipynb</a>\n",
-       "-  <a href='advanced/value-iteration.ipynb' target='_blank'>advanced/value-iteration.ipynb</a>\n",
        "-  <a href='advanced/volterra.ipynb' target='_blank'>advanced/volterra.ipynb</a>\n",
        "-  <a href='basic/align1.ipynb' target='_blank'>basic/align1.ipynb</a>\n",
        "-  <a href='basic/align2.ipynb' target='_blank'>basic/align2.ipynb</a>\n",
@@ -31,9 +30,7 @@
        "-  <a href='basic/distance2mesh.ipynb' target='_blank'>basic/distance2mesh.ipynb</a>\n",
        "-  <a href='basic/manipulate_camera.ipynb' target='_blank'>basic/manipulate_camera.ipynb</a>\n",
        "-  <a href='basic/mirror.ipynb' target='_blank'>basic/mirror.ipynb</a>\n",
-       "-  <a href='basic/noname.ipynb' target='_blank'>basic/noname.ipynb</a>\n",
        "-  <a href='basic/pca.ipynb' target='_blank'>basic/pca.ipynb</a>\n",
-       "-  <a href='basic/shadow.ipynb' target='_blank'>basic/shadow.ipynb</a>\n",
        "-  <a href='basic/shrink.ipynb' target='_blank'>basic/shrink.ipynb</a>\n",
        "-  <a href='basic/sphere.ipynb' target='_blank'>basic/sphere.ipynb</a>\n",
        "-  <a href='dolfin/demo_cahn-hilliard.ipynb' target='_blank'>dolfin/demo_cahn-hilliard.ipynb</a>\n",
@@ -92,13 +89,6 @@
     "Markdown(l1)"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
   {
    "cell_type": "code",
    "execution_count": null,

examples/other/makeVideo.py

@@ -1,12 +1,12 @@
 """
 Make a video (needs ffmpeg or opencv)
  Set offscreen=True to only produce the video
- without any graphical window showing
+ without any graphic window showing
 """
 print(__doc__)
 from vedo import *
 
-# settings.screeshotScale = 2 # to get higher resolution
+# settings.screeshotScale = 2           # to get higher resolution
 
 # declare the class instance
 vp = Plotter(bg='beige', axes=10, offscreen=True)
@@ -26,6 +26,6 @@
 #Options are:  elevation_range=(0,80),
 #              azimuth_range=(0,359),
 #              zoom=None,
-#              cam1=None, cam2=None  # initial and final camera positions
+#              cam1=None, cam2=None   # initial and final camera positions
 
-video.close()                        # merge all the recorded frames
+video.close()                         # merge all the recorded frames

examples/other/nevergrad_opt.py

@@ -30,7 +30,7 @@ def callbk(optimizer, v, value):
 res = optimizer.minimize(func)  # best value
 printc('Minimum at:', res.value)
 
-ln = Line(pts, lw=3)
+ln = Line(pts, lw=3, c='r')
 fu = plot(f, xlim=[-3,4], ylim=[-3,4], alpha=0.5)
 
 show(fu, ln, __doc__)

examples/pyplot/plot_density4d.py

@@ -0,0 +1,35 @@
+# Plot a volume evolution in time
+# Credits: https://github.com/edmontz
+import numpy as np
+from scipy.fftpack import fftn, fftshift
+from vedo import Volume, ProgressBar, show, interactive
+
+def f(x, y, z, t):
+    r = np.sqrt(x*x + y*y + z*z + 2*t*t) + 0.1
+    return np.sin(9*np.pi * r)/r
+
+n = 64
+qn = 50
+vol = np.zeros((n, n, n))
+n1 = int(n/2)
+
+pb = ProgressBar(0, qn, c="r")
+for q in pb.range():
+    pb.print()
+
+    t = 2 * q / qn - 1
+    for k in range(n1):
+        z = 2 * k / n1 - 1
+        for j in range(n1):
+            y = 2 * j / n1 - 1
+            for i in range(n1):
+                x = 2 * i / n1 - 1
+                vol[i, j, k] = f(x, y, z, t)
+    volf = fftn(vol)
+    volf = fftshift(abs(volf))
+    volf = np.log(12*volf/volf.max()+ 1) / 2.5
+
+    vb = Volume(volf).mode(1).c("rainbow").alpha([0, 0.8, 1])
+    show(vb, bg="black", axes=1, viewup='z', interactive=False)
+
+interactive()

examples/pyplot/scatter3.py

@@ -3,30 +3,28 @@
 from vedo import *
 from numpy.random import randn
 
-
-### first scatter plot in blue
+### first cloud in blue, place it at z=0:
 x = randn(2000) * 3
 y = randn(2000) * 2
-
-# scatter cloud, place it at z=0:
 pts1 = Points([x,y], c="blue", alpha=0.5).z(0.0)
+bra1 = Brace([-7,-7], [7,-7], thickness=0.75,
+             comment='whole population', s=0.5, c='b')
 
-
-### second scatter plot in red
+### second cloud in red
 x = randn(1200) + 4
 y = randn(1200) + 2
 pts2 = Points([x,y], c="red", alpha=0.5).z(0.1)
+bra2 = Brace([8,2], [6,5], comment='red zone', c='r').z(0.3)
 
-
-### third scatter plot with marker in black
+### third cloud with a black marker
 x = randn(20) + 4
 y = randn(20) - 4
-mark = Marker('*', s=0.2, filled=True)
+mark = Marker('*', s=0.25)
 pts3 = Glyph([x,y], mark, c='k').z(0.2)
+bra3 = Brace([8,-6], [8,-2], comment='my stars').z(0.3)
 
+# some text message
+msg = Text("preliminary\nresults!", font='Quikhand', s=1.5)
+msg.c('black').rotateZ(20).pos(-10,3,.2)
 
-label = Text("preliminary\nresults!", font='Quikhand', s=1.5, pos=(-8,4,.2))
-label.c('black').rotateZ(20)
-
-show(pts1, pts2, pts3, label, __doc__,
-     title='A simple scatter plot', axes=1, viewup='2d')
+show(pts1, pts2, pts3, msg, bra1, bra2, bra3, __doc__, axes=1, zoom=1.2)

examples/pyplot/whiskers.py

@@ -1,31 +1,42 @@
 """Whisker plot with quantiles indication
 (horizontal line shows the mean value)"""
+from vedo import Axes, Brace, Line, Ribbon, show
 from vedo.pyplot import whisker
-from vedo import show, buildAxes
 import numpy as np
 
 # create 5 whisker bars with some random data
 ws = []
 for i in range(5):
-    xval = i*2
-    data = np.random.randn(25) + i/2
+    xval = i*2 # position along x axis
+    data = xval/4 + np.random.randn(25)
     w = whisker(data, bc=i, s=0.5).x(xval)
     ws.append(w)
+    # print(i, 'whisker:\n', w.info)
+
+# build some theoretical expectation to be shown as a grey band
+x = np.linspace(-1, 9, 100)
+y = x/5 + 0.2*np.sin(x)
+ye= y**2/5 + 0.1 # error on y
+line = Line(np.c_[x, y])
+band = Ribbon(np.c_[x, y-ye], np.c_[x, y+ye]).c('black').alpha(0.1)
+
+# build braces to inndicate stats significance and dosage
+bra1 = Brace([0, 3],[2, 3], comment='*~*', s=0.7, style='[')
+bra2 = Brace([4,-1],[8,-1], comment='dose > 3~\mug/kg', s=0.7)
 
 # build custom axes
-ax = buildAxes(xrange=[-1,9],
-               yrange=[-3,5],
-               htitle='\beta_c -expression: change in time',
-               xtitle=' ',
-               ytitle='Level of \beta_c  protein in \muM/l',
-               xValuesAndLabels=[(0,'experiment^A\nat t=1h'),
-                                 (4,'experiment^B\nat t=2h'),
-                                 (8,'experiment^C\nat t=4h'),
-                                ],
-               xLabelSize=0.02,
-               )
+axes = Axes(xrange=[-1,9],
+            yrange=[-3,5],
+            htitle='\beta_c -expression: change in time',
+            xtitle=' ',
+            ytitle='Level of \beta_c  protein in \muM/l',
+            xValuesAndLabels=[(0,'Experiment^A\nat t=1h'),
+                              (4,'Experiment^B\nat t=2h'),
+                              (8,'Experiment^C\nat t=4h'),
+                             ],
+            xLabelSize=0.02,
+           )
 
-show(ws, ax, __doc__)
-# print('whisker0:', ws[0].info)
+show(ws, bra1, bra2, line, band, __doc__, axes, zoom=1.1)