tests/issues/issue_1077.py

docs/changes.md

@@ -20,7 +20,7 @@
 - fix add tolerance to contains #1105 by @JeffreyWardman
 - fix minor bug in RoundedLine #1104 by @PinkMushroom
 - fix avoid overwriting screenshots with "S" key #1100 by @j042
-- add support for meshlib
+- add support for `meshlib`
 - add more kw options to `core.probe()`
 - increase precision in writing obj files as per #1119 by @ManuGraiph
 - add `plotter.freeze()` to freeze interaction of current renderer in #1122 by @sergei9838
@@ -48,14 +48,15 @@ examples/advanced/warp4b.py
 examples/other/magic-class1.py
 examples/other/iminuit2.py
 examples/other/meshlib1.py
+
+tests/issues/issue_1077.py
 ```
 
 ### Broken Examples
 Examples that are not fully functional and need some fixing:
 ```
 markpoint.py (misplaced leader indicator)
 cut_and_cap.py (incomplete capping)
-gyroscope1.py (broken physics)
 tests/issues/discussion_800.py (incomplete capping of tube)
 ```
 

examples/advanced/cut_with_points1.py

@@ -6,8 +6,8 @@
 settings.interpolate_scalars_before_mapping = True
 
 s = Sphere()
-s.color("white").alpha(0.25).backface_culling(True)
-s.pointdata['scalars1'] = np.sqrt(range(s.npoints))
+s.color("white").alpha(0.25).backface_culling()
+s.pointdata['myscalars'] = s.coordinates[:,1]
 print(s)
 
 # Pick a few points on the sphere
@@ -16,7 +16,7 @@
 
 # Cut the loop region identified by the points
 scut = s.clone().cut_with_point_loop(sv, invert=False).scale(1.01)
-scut.cmap("Paired", "scalars1").alpha(1).add_scalarbar()
+scut.cmap("Paired", "myscalars").alpha(1).add_scalarbar()
 print(scut)
 
 show(s, pts, scut, __doc__, axes=1, viewup="z")

examples/basic/align6.py

@@ -20,11 +20,12 @@
 # Set up a Plotter object with 2 subrenderers
 plt = Plotter(N=2)
 
-# Show the original mesh, axes, and cube in the left renderer with the script description
-plt.at(0).show(msh1, axes1, cube, __doc__)
+# Add the original mesh, axes, and cube in the left renderer with the script description
+plt.at(0).add(msh1, axes1, cube, __doc__)
 
-# Show the aligned mesh and axes in the right renderer, viewing from the top
-plt.at(1).show(msh2, axes2, viewup='z')
+# Add the aligned mesh and axes in the right renderer, viewing from the top
+plt.at(1).add(msh2, axes2, cube)
 
-# Enable interaction and close the plotter when done
+# Show all and close the plotter when done
+plt.show(viewup='z', zoom=0.6)
 plt.interactive().close()

examples/pyplot/pie_chart.py

@@ -0,0 +1,14 @@
+from vedo import settings, show
+from vedo.pyplot import pie_chart
+
+settings.default_font = "Komika"
+
+title     = "A pie chart plot"
+fractions = [0.1, 0.2, 0.3, 0.1, 0.3]
+colors    = [ 1,   2,   3,   4, 'white']
+labels    = ["stuff_1 ", "stuff_2 ", "comp^A ", "comp^B ", ""]
+
+pc = pie_chart(fractions, c=colors, labels=labels, title=title)
+pc2d = pc.clone2d("top-left", size=0.975, ontop=False)
+
+show(pc2d).close()

examples/simulations/gyroscope1.py

@@ -28,8 +28,7 @@
 
 shaft = Cylinder([[0, 0, 0], Ls * gaxis], r=0.03).c("dark green")
 rotor = Cylinder([(Ls - 0.55) * gaxis, (Ls - 0.45) * gaxis], r=R).c("tomato")
-bar   = Cylinder([Ls*gaxis/2-R*vector(0,1,0), Ls*gaxis/2+R*vector(0,1,0)], r=R/6).c("red5")
-gyro = shaft + rotor + bar  # group meshes into a single one of type Assembly
+gyro = shaft + rotor   # group meshes into a single one of type Assembly
 
 spring = Spring(top, gpos, r1=0.06, thickness=0.01).c("gray")
 plt += [gyro, spring]       # add it to Plotter.

examples/simulations/particle_simulator.py

@@ -97,14 +97,14 @@ def __init__(self, pos, charge, mass, radius, color, vel, fixed, negligible):
 #####################################################################################################
 if __name__ == "__main__":
 
-    plt = Plotter(title="Particle Simulator", bg="black", axes=0, interactive=False)
+    plt = Plotter(title="Particle Simulator", bg="black", interactive=False)
 
     plt += Cube().c('w').wireframe(True).lighting('off') # a wireframe cube
 
-    sim = ParticleSim(dt=1e-5, iterations=60)
+    sim = ParticleSim(dt=1e-5, iterations=50)
     sim.add_particle((-0.4, 0, 0), color="w", charge=3e-6, radius=0.01, fixed=True)  # the target
 
-    positions = np.random.randn(500, 3) / 60  # generate a beam of particles
+    positions = np.random.randn(100, 3) / 60  # generate a beam of particles
     for p in positions:
         p[0] = -0.5  # Fix x position. Their charge are small/negligible compared to target:
         sim.add_particle(p, charge=0.01e-6, mass=0.1e-6, vel=(1000, 0, 0), negligible=True)

examples/simulations/self_org_maps2d.py

@@ -9,7 +9,7 @@
 # -----------------------------------------------------------------------------
 import numpy as np
 import scipy.spatial
-from vedo import *
+from vedo import Sphere, Grid, Plotter, progressbar
 
 
 class SOM:
@@ -27,7 +27,7 @@ def learn(self, n_epoch=10000, sigma=(0.25,0.01), lrate=(0.5,0.01)):
         I = np.random.randint(0, len(self.samples), n_epoch)
         self.samples = self.samples[I]
 
-        for i in progressbar(range(n_epoch)):
+        for i in progressbar(n_epoch):
             # Get random sample
             data = self.samples[i]
 
@@ -49,9 +49,9 @@ def learn(self, n_epoch=10000, sigma=(0.25,0.01), lrate=(0.5,0.01)):
                     for j in range(n):
                         grdpts[i*n+j] = (x[i,j], y[i,j], z[i,j])
                 grd.vertices = grdpts
-                plt.azimuth(1.0).render()
+                if plt: plt.azimuth(1.0).render()
 
-        plt.interactive().close()
+        if plt: plt.interactive().close()
 
         return [self.codebook[:,i].reshape(n,n) for i in range(3)]
 
@@ -63,12 +63,13 @@ def learn(self, n_epoch=10000, sigma=(0.25,0.01), lrate=(0.5,0.01)):
     P = np.c_[X.ravel(), Y.ravel()]
     D = scipy.spatial.distance.cdist(P, P)
 
-    s = Sphere(res=90).cut_with_plane(origin=(0,-.3,0), normal='y').subsample(0.01)
+    sphere = Sphere(res=90).cut_with_plane(origin=(0,-.3,0), normal='y')
+    sphere.subsample(0.01).add_gaussian_noise(0.5).point_size(3)
 
     plt = Plotter(axes=6, interactive=False)
     grd = Grid(res=[n-1, n-1]).c('green2')
-    plt.show(__doc__, s.ps(1), grd)
+    plt.show(__doc__, sphere, grd)
 
     som = SOM((len(P), 3), D)
-    som.samples = s.vertices
+    som.samples = sphere.vertices.copy()
     som.learn(n_epoch=4000, sigma=(1, 0.01), lrate=(1, 0.01))

tests/issues/issue_1077.py

@@ -0,0 +1,16 @@
+from vedo import *
+
+aline = Line(Circle().coordinates)
+spline = Spline([(0,0,0), (1,1,1), (2,3,3), (1,1,4), (0,1,5)])
+spline.lw(5)
+pts = spline.coordinates
+
+surfs = []
+for i in range(1, len(pts)):
+    p0, p1 = pts[i-1:i+1]
+    surf = aline.sweep(p1 - p0)
+    surfs.append(surf)
+surface = merge(surfs, flag=True)
+surface.c("gold").lw(0.1).pickable(True)
+
+show(spline, surface, aline, axes=1).close()

tests/pipeline.txt

@@ -94,7 +94,8 @@ cd ~/Projects/server/trackviewer
     ./main_test.py
 ################
 cd /g/sharpe/software/clone_viewer2
-    ./clone_viewer3d.py
+cd ~/Projects/clonal_analysis/clone_viewer3
+    ./clone_viewer_gio3d.py
 ################
 cd ~/Projects/server/rio_organoid
     python main4.py
@@ -133,6 +134,7 @@ cd ~/Projects/server/brainrender/examples
 ################
 cd ~/Projects/clonal_analysis
     python -m analysis_plots2d
+    python tc_morph4_2d.py
 ################
 cd ~/Projects/server/gustaf
     git pull

vedo/applications.py

@@ -1476,12 +1476,12 @@ def __init__(
         self.idmousemove = self.add_callback("MouseMove", self._on_mouse_move)
         self.drawmode = False
         self.tol = tol  # tolerance of point distance
-        self.cpoints = np.array([])
+        self.cpoints = []
         self.points = None
         self.spline = None
         self.jline = None
         self.topline = None
-        self.top_pts = np.array([])
+        self.top_pts = []
 
     def init(self, init_points):
         """Set an initial number of points to define a region"""

vedo/cli.py

@@ -257,6 +257,7 @@ def exe_convert(args):
         "ply",
         "stl",
         "obj",
+        "off",
         "byu",
         "xml",
         "vti",

vedo/file_io.py

@@ -1254,6 +1254,16 @@ def write(objct: Any, fileoutput: str, binary=True) -> Any:
                     outF.write(f"l {ls}\n")
         return objct
 
+    elif fr.endswith(".off"):
+        with open(fileoutput, "w", encoding="UTF-8") as outF:
+            outF.write("OFF\n")
+            outF.write(str(objct.npoints) + " " + str(objct.ncells) + " 0\n\n")
+            for p in objct.vertices:
+                outF.write(" ".join([str(i) for i in p]) + "\n")
+            for c in objct.cells:
+                outF.write(str(len(c)) + " " + " ".join([str(i) for i in c]) + "\n")
+        return objct
+
     elif fr.endswith(".xml"):  # write tetrahedral dolfin xml
         vertices = objct.vertices.astype(str)
         faces = np.array(objct.cells).astype(str)

vedo/pyplot.py

@@ -34,7 +34,7 @@
     "plot",
     "histogram",
     "fit",
-    "donut",
+    "pie_chart",
     "violin",
     "whisker",
     "streamplot",
@@ -3282,7 +3282,7 @@ def _histogram_spheric(thetavalues, phivalues, rmax=1.2, res=8, cmap="rainbow",
     return newsg
 
 
-def donut(
+def pie_chart(
     fractions,
     title="",
     tsize=0.3,

vedo/utils.py

@@ -803,8 +803,7 @@ def vtk2numpy(varr):
             varr = varr.GetMatrix()
         except AttributeError:
             pass
-        n = 4
-        M = [[varr.GetElement(i, j) for j in range(n)] for i in range(n)]
+        M = [[varr.GetElement(i, j) for j in range(4)] for i in range(4)]
         return np.array(M)
     return vtk_to_numpy(varr)