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padding fix
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13 files changed

+211
-139
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‎examples/basic/voronoi1.py‎

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Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@
55
points = np.random.random((500, 2))
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77
pts = Points(points).subsample(0.02) # impose a min distance of 2%
8-
vor = voronoi(pts, pad=0.01)
8+
vor = voronoi(pts, padding=0.01)
99
vor.cmap('Set3', "VoronoiID", on='cells').wireframe(False)
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1111
lab = vor.labels("VoronoiID", cells=True, scale=0.01)

‎examples/notebooks/align1.ipynb‎

Lines changed: 9 additions & 18 deletions
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@@ -2,7 +2,7 @@
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"cells": [
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{
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"cell_type": "code",
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"execution_count": 1,
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"execution_count": 4,
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"metadata": {
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"scrolled": true
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},
@@ -11,31 +11,22 @@
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"name": "stdout",
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"output_type": "stream",
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"text": [
14-
"\u001b[1m\u001b[32;1mave. squared distance = 43.20515185350062\u001b[0m\n"
14+
"ave. squared distance = 43.20515185350062\n"
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]
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},
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{
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"data": {
19-
"application/vnd.jupyter.widget-view+json": {
20-
"model_id": "d0e95ecc66c24e2faaa347a292b971d8",
21-
"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
25-
"Plot(antialias=True, axes=['x', 'y', 'z'], axes_helper=1.0, background_color=16777215, camera=[2, -3, 0.2, 0.0…"
20+
"<vedo.plotter.Plotter at 0x7f3a5a98dfa0>"
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]
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},
23+
"execution_count": 4,
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"metadata": {},
29-
"output_type": "display_data"
25+
"output_type": "execute_result"
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}
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],
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"source": [
33-
"\"\"\"\n",
34-
"Align 2 shapes and for each vertex of the first draw\n",
35-
"and arrow to the closest point of the second.\n",
36-
"The source transformation is accessible with getTransform()\n",
37-
"rigid=True doesn't allow scaling\n",
38-
"\"\"\"\n",
29+
"\"\"\"Align 2 shapes: a simple line to a polygonal mesh\"\"\"\n",
3930
"from vedo import *\n",
4031
"\n",
4132
"limb = Mesh(dataurl + \"270.vtk\").alpha(0.5)\n",
@@ -44,7 +35,7 @@
4435
"# make a clone copy of the rim line and align it to the surface\n",
4536
"arim = rim.clone().alignTo(limb, rigid=True).c(\"g\").ps(20)\n",
4637
"\n",
47-
"plt = Plotter(backend='k3d') # or panel, k3d, itk, ipyvtk, or None\n",
38+
"plt = Plotter(backend=None) # or k3d, itk, ipyvtk, or None\n",
4839
"plt += [limb, rim, arim]\n",
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"\n",
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"# compute how well it fits\n",
@@ -59,7 +50,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 5,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -83,7 +74,7 @@
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.9.10"
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"version": "3.9.7"
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}
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},
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"nbformat": 4,

‎examples/notebooks/distance2mesh.ipynb‎

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"cells": [
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 2,
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"metadata": {},
7-
"outputs": [],
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"outputs": [
8+
{
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"name": "stdout",
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"output_type": "stream",
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"text": [
12+
"\u001b[32;1m_________________________________________________________________\u001b[0m\n",
13+
"\u001b[2m\u001b[7m\u001b[1m\u001b[32;1mMesh/Points\u001b[0m \n",
14+
"\u001b[1m\u001b[32;1m name: \u001b[0m\u001b[32;1mSphere\u001b[0m\n",
15+
"\u001b[1m\u001b[32;1m points: \u001b[0m\u001b[32;1m1058\u001b[0m\n",
16+
"\u001b[1m\u001b[32;1m cells: \u001b[0m\u001b[32;1m2112\u001b[0m\n",
17+
"\u001b[1m\u001b[32;1m polygons: \u001b[0m\u001b[32;1m2112\u001b[0m\n",
18+
"\u001b[1m\u001b[32;1m position: \u001b[0m\u001b[32;1m(0.0, 0.0, 0.0)\u001b[0m\n",
19+
"\u001b[1m\u001b[32;1m scale: \u001b[0m\u001b[32;1m(1.00, 1.00, 1.00)\u001b[0m\n",
20+
"\u001b[1m\u001b[32;1m center of mass: \u001b[0m\u001b[32;1m(0, 0, 0)\u001b[0m\n",
21+
"\u001b[1m\u001b[32;1m average size: \u001b[0m\u001b[32;1m1.00000\u001b[0m\n",
22+
"\u001b[1m\u001b[32;1m diagonal size: \u001b[0m\u001b[32;1m3.45872\u001b[0m\n",
23+
"\u001b[1m\u001b[32;1m bounds: \u001b[0m\u001b[32;1mx=(-0.998, 0.998)\u001b[0m\u001b[32;1m y=(-0.998, 0.998)\u001b[0m\u001b[32;1m z=(-1.00, 1.00)\u001b[0m\n",
24+
"\u001b[1m\u001b[32;1m scalar mode:\u001b[0m \u001b[32;1mDefault coloring = Default\u001b[0m\n",
25+
"\u001b[1m\u001b[32;1m active array: \u001b[0m\u001b[32;1mDistance (point data) \u001b[0m\n",
26+
"\u001b[1m\u001b[32;1m point data: \u001b[0m\u001b[32;1mname=Normals (3 FLOAT, np.float32),\u001b[0m\u001b[32;1m range=(-0.998,0.998)\u001b[0m\n",
27+
"\u001b[1m\u001b[32;1m point data: \u001b[0m\u001b[32;1mname=Distance (1 DOUBLE, np.float64),\u001b[0m\u001b[32;1m range=(1.50,3.50)\u001b[0m\n",
28+
"[2.54950976 2.54950976 2.41422468 ... 2.14595456 2.27999987 2.41536531]\n"
29+
]
30+
},
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{
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"data": {
33+
"application/vnd.jupyter.widget-view+json": {
34+
"model_id": "b796eb2c20d146398cdebb41c8ac8dae",
35+
"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
39+
"ViewInteractiveWidget(height=960, layout=Layout(height='auto', width='100%'), width=960)"
40+
]
41+
},
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"metadata": {},
43+
"output_type": "display_data"
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}
45+
],
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"source": [
947
"\"\"\"Compute the (signed) distance from one mesh to another.\"\"\"\n",
1048
"\n",
1149
"from vedo import *\n",
1250
"\n",
1351
"s1 = Sphere().flat() # flat shading\n",
14-
"s2 = Cube(pos=(1,0,0), c='white', alpha=0.2)\n",
52+
"s2 = Cube(pos=(3,0,0), c='white', alpha=0.2)\n",
1553
"\n",
1654
"# add scalars to the sphere that correspond to their distance from the cube\n",
17-
"s1.distanceTo(s2, signed=True, invert=False)\n",
55+
"s1.distanceTo(s2, signed=True, invert=False).addScalarBar()\n",
1856
"\n",
19-
"#s1.printInfo()\n",
20-
"#print(s1.getPointArray(\"Distance\"))\n",
57+
"s1.print()\n",
58+
"print(s1.pointdata[\"Distance\"])\n",
2159
"\n",
2260
"plt = show(s1, s2, viewup='z', axes=1, backend='ipyvtk')\n",
2361
"plt"
2462
]
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},
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{
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"cell_type": "code",
28-
"execution_count": null,
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"execution_count": 3,
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"metadata": {},
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"outputs": [],
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"source": [
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"plt.close()"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
@@ -49,7 +94,7 @@
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.8.8"
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"version": "3.9.7"
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}
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},
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"nbformat": 4,

‎examples/notebooks/legosurface.ipynb‎

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‎examples/notebooks/numpy2volume.ipynb‎

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@@ -14,31 +14,35 @@
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},
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "485788b1c34a4c9a9fb0f4a6b0633217",
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"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
18-
"<vedo.plotter.Plotter at 0x7f459c235850>"
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"ViewInteractiveWidget(height=960, layout=Layout(height='auto', width='100%'), width=960)"
1924
]
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},
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"execution_count": 1,
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"metadata": {},
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"output_type": "execute_result"
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"output_type": "display_data"
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}
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],
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"source": [
2731
"# Make a Volume from a numpy object\n",
2832
"#\n",
2933
"import numpy as np\n",
3034
"from vedo import *\n",
31-
"#embedWindow('itkwidgets') # backends are: itkwidgets, k3d or False\n",
3235
"\n",
3336
"X, Y, Z = np.mgrid[:30, :30, :30]\n",
37+
"\n",
3438
"# scaled distance from the center at (15, 15, 15)\n",
3539
"scalar_field = ((X-15)**2 + (Y-15)**2 + (Z-15)**2)/225/3\n",
3640
"print('scalar min, max =', np.min(scalar_field), np.max(scalar_field))\n",
3741
"\n",
3842
"vol = Volume(scalar_field)\n",
3943
"lego = vol.legosurface(vmin=.3, vmax=.6)\n",
4044
"\n",
41-
"plt = show(lego, axes=1, backend=None)\n",
45+
"plt = show(lego, axes=1, backend='ipyvtk')\n",
4246
"plt"
4347
]
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},
@@ -61,7 +65,7 @@
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.8.8"
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"version": "3.9.7"
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}
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},
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"nbformat": 4,

‎examples/notebooks/pca.ipynb‎

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Original file line numberDiff line numberDiff line change
@@ -2,21 +2,44 @@
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"cells": [
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 1,
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"\u001b[1m\u001b[32;1minside points # 2502\u001b[0m\n",
13+
"\u001b[1m\u001b[31;1moutside points # 2498\u001b[0m\n",
14+
"\u001b[1masphericity: 0.5282829679821651\u001b[0m\n"
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]
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},
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "518be2799b674814b33da00638af9079",
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"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
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"ViewInteractiveWidget(layout=Layout(height='auto', width='100%'), width=1000)"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"source": [
933
"\"\"\"\n",
1034
"Draw the PCA (Principal Component Analysis) ellipsoid that contains\n",
11-
"50% of a cloud of Points, then check if points are inside the surface.\n",
12-
"Extra info is stored in object.info['sphericity'], 'va', 'vb', 'vc'.\n",
35+
"50% of a cloud of a pointcloud, then check how many points are inside the surface.\n",
1336
"\"\"\"\n",
1437
"from vedo import *\n",
1538
"import numpy as np\n",
1639
"\n",
17-
"plt = Plotter(backend='ipyvtk')\n",
40+
"plt = Plotter(backend='ipyvtk', size=(1000,500))\n",
1841
"\n",
19-
"pts = np.random.randn(500, 3) # random gaussian point cloud\n",
42+
"pts = np.random.randn(5000, 3) * [3,2,1]# random gaussian point cloud\n",
2043
"\n",
2144
"elli = pcaEllipsoid(pts, pvalue=0.5) # group of [ellipse, 3 axes]\n",
2245
"plt += elli\n",
@@ -28,13 +51,13 @@
2851
"\n",
2952
"printc(\"inside points #\", ipts.N(), c='g')\n",
3053
"printc(\"outside points #\", opts.N(), c='r')\n",
31-
"printc(\"a-sphericity:\", elli.asphericity())\n",
54+
"printc(\"asphericity:\", elli.asphericity())\n",
3255
"plt.show(axes=1)"
3356
]
3457
},
3558
{
3659
"cell_type": "code",
37-
"execution_count": null,
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"execution_count": 2,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -51,7 +74,7 @@
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
@@ -65,7 +88,7 @@
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.8.8"
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"version": "3.9.7"
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}
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},
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"nbformat": 4,

‎examples/other/export_x3d.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,7 @@
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txt = Text3D(__doc__, font='Bongas', s=350, c='red2', depth=0.05)
1212
txt.pos(2500, 300, 500)
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14-
plt.show(embryo, txt, txt.box(pad=250), axes=1, viewup='z', zoom=1.2)
14+
plt.show(embryo, txt, txt.box(padding=250), axes=1, viewup='z', zoom=1.2)
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1616
# This exports the scene and generates 2 files:
1717
# embryo.x3d and an example embryo.html to inspect in the browser

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