Marching_cubes with pymcubes, skimage and sverchok

[kalwalt]

Pymcubes is a python module with a marching cubes algorithm. In the simple example that i provide it simply plot a sphere. You can set the bounds, the number of samples in each dimension, and the iso surface level. The sphere is defined by the function f; of course you can use what function you desire.
You must install the module in the python 3 location and then import it with the sys importing statement.

import sys
mcubes_path = r"/usr/local/lib/python3.5/dist-packages" #it depend on your OS but just paste the path where is mcubes
if not mcubes_path in sys.path:
    sys.path.append(mcubes_path)    
import mcubes

change your path accordingly.
to install pymcubes i used pip:

pip3 install pymcubes

it requires also pycollada and cython.

"""
in bounds s d=10 n=2
in iso_val s d=8.0 n=2
in samples s d=100 n=2
out vertices v
out triangles s
"""


import numpy as np
import sys
mcubes_path = r"/usr/local/lib/python3.5/dist-packages" #it depend on your OS but just paste the path where is mcubes
if not mcubes_path in sys.path:
    sys.path.append(mcubes_path)    
import mcubes

# Create the volume
def f(x, y, z):
    return x**2 + y**2 + z**2

# Create a data volume (30 x 30 x 30)
#X, Y, Z = np.mgrid[:100, :100, :100]
# u = (X-50)**2 + (Y-50)**2 + (Z-50)**2 - 25**2

# Extract the 0-isosurface
#verts, tri = mcubes.marching_cubes(u, 0)

# Extract the 16-isosurface
verts, tri = mcubes.marching_cubes_func(
        (-bounds, -bounds, -bounds), (bounds, bounds, bounds),  # Bounds
        samples, samples, samples,              # Number of samples in each dimension
        f,                          # Implicit function
        iso_val)                         # Isosurface value

vertices, triangles = verts.tolist(), tri.tolist()

you can take the script also here

[kalwalt]

multi schwarz ( i think it is called so...) with just a function call.
this is the formula used:

math.cos(x) + math.cos(y) + math.cos(z)

notice the isovalue used ( do not use high values).

script here

[kalwalt]

hyperboloid with function:

x**2 + y**2 - z**2 - 0.3

[zeffii]

it can do metaballs? :)

[kalwalt]

it can do metaballs? :)

maybe, i will try to add a set of multi spheres,...

[kalwalt]

Bingo!

with this script:

"""
in bounds s d=10 n=2
in iso_val s d=8.0 n=2
in samples s d=100 n=2
in factor s d=0.9 n=2
out vertices v
out triangles s
"""


import numpy as np
import sys
mcubes_path = r"/usr/local/lib/python3.5/dist-packages" #it depend on your OS but just paste the path where is scipy
if not mcubes_path in sys.path:
    sys.path.append(mcubes_path)    
import mcubes
import math

# Create the volume
def f(x, y, z):
    
    return ((x-factor)*(x-factor)+y*y+z*z-1)*((x+factor)*(x+factor)+y*y+z*z-1)-0.3

# Extract the 16-isosurface
verts, tri = mcubes.marching_cubes_func(
        (-bounds, -bounds, -bounds), (bounds, bounds, bounds),  # Bounds
        samples, samples, samples,              # Number of samples in each dimension
        f,                          # Implicit function
        iso_val)                         # Isosurface value

vertices, triangles = verts.tolist(), tri.tolist()

This only create two spheres but it can be developed a multi spheres version.
https://github.com/kalwalt/sverchok_nodes_collection/blob/master/scripts/pymcubes/metaballs_test.py

[kalwalt]

Scikit image module has also marching cubes functions http://scikit-image.org/docs/dev/auto_examples/edges/plot_marching_cubes.html
but i didn't tryed yet. I found this modules as possible replacement for polyvox lib that i used before #1168 as this has some issues....

[zeffii]

i'd like to see an example of multi verts for metaballs. very cool stuff.

[kalwalt]

i'd like to see an example of multi verts for metaballs. very cool stuff.

i will do later if i can.

[nortikin]

hm, will try at home just essentially needed stuff

[kalwalt]

ok thank you. I'm looking for the multi metaballs example.
one difficult is that the function f must be in the form f(x, y, z) as described in the struct of the pywrapper.ccp:

struct PythonToCFunc
{
    PyObject* func;
    PythonToCFunc(PyObject* func) {this->func = func;}
    double operator()(double x, double y, double z)
    {
        PyObject* res = PyObject_CallFunction(func, "(d,d,d)", x, y, z); // py::extract<double>(func(x,y,z));
        if(res == NULL)
            return 0.0;
        
        double result = PyFloat_AsDouble(res);
        Py_DECREF(res);
        return result;
    }
};

https://github.com/pmneila/PyMCubes/blob/master/mcubes/src/pywrapper.cpp#L8

[scorpion451]

anyone know a reason the script would fail to load mcubes on Windows?
I swapped out the file path to "C:\Program Files\Python36\Lib\site-packages" but it keeps giving me an error about not being able to find mcube._mcube

[enzyme69]

can it remesh Particles into something meshy?

[kalwalt]

@scorpion451 i don't know. But where is mcubes folder? in

C:\Program Files\Python36\Lib\site-packages

?

in my mcubes folder i have three files:

exporter.py
__init__.py
_mcubes.cpython-35m-x86_64-linux-gnu.so  # _this in Windows should be a .dll file_

can it remesh Particles into something meshy?

really i don't know @enzyme69: i'm testing the lib for now.

[zeffii]

@scorpion451 i suspect the problem could also be a mismatch between python 3.5 and your 3.6

[kalwalt]

TorusIso

"""
in bounds s d=10 n=2
in iso_val s d=8.0 n=2
in samples s d=100 n=2
in r_i s d=5.0 n=2
in r_o s d=1.0 n=2
out vertices v
out triangles s
"""


import numpy as np
import sys
mcubes_path = r"/usr/local/lib/python3.5/dist-packages" #it depend on your OS but just paste the path where is mcubes
if not mcubes_path in sys.path:
    sys.path.append(mcubes_path)    
import mcubes
import math

# Create the volume
def f(x, y, z):
    
    # (sqrt(x*x+y*y)-3)^2+z*z-1 formula from MathMod
    res=(math.sqrt(x*x+y*y)-r_i)**2+z*z-r_o

    return res

# Extract the 16-isosurface

verts, tri = mcubes.marching_cubes_func(
    (-bounds, -bounds, -bounds), (bounds, bounds, bounds),  # Bounds
    samples, samples, samples,              # Number of samples in each dimension
    f,                          # Implicit function
    iso_val)                         # Isosurface value

vertices, triangles = [verts.tolist()], [tri.tolist()]

https://github.com/kalwalt/sverchok_nodes_collection/blob/master/scripts/pymcubes/torus_iso.py

[kalwalt]

Testing the scikit marching_cubes function:

Example taken from here:
http://scikit-image.org/docs/dev/auto_examples/edges/plot_marching_cubes.html
Skimage marching cubes documentation:
http://scikit-image.org/docs/dev/api/skimage.measure.html#marching-cubes
The script i used:

"""
in sp s d=0.0 n=2
in iso_val s d=0.0 n=2
in step s d=1 n=2
in a s d=6 n=2
in b s d=10 n=2
in c s d=16 n=2
out vertices v
out faces s
"""


import numpy as np
import sys
scikit_path = r"/usr/local/lib/python3.5/dist-packages" # it depend on your OS but just paste the path where is scikit
if not scikit_path in sys.path:
    sys.path.append(scikit_path)
from skimage import measure
from skimage.draw import ellipsoid


# Generate a level set about zero of two identical ellipsoids in 3D
ellip_base = ellipsoid(a, b, c, levelset=True)
ellip_double = np.concatenate((ellip_base[:-1, ...],
                               ellip_base[2:, ...]), axis=0)

# Use marching cubes to obtain the surface mesh of these ellipsoids
verts, faces, normals, values = measure.marching_cubes(
    ellip_double, level=iso_val,spacing=(sp, sp, sp), step_size=step)

vertices, faces = [verts.tolist()], [faces.tolist()]

https://github.com/kalwalt/sverchok_nodes_collection/blob/master/scripts/skimage/ellipsoid_skimage.py

[scorpion451]

@kalwalt double checked, and I do have mcubes in my C:\Program Files\Python36\Lib\site-packages folder, with

exporter.py
__init__.py
_mcubes.cp36-win_amd64.pyd # .pyd is theoretically a "better dll" format for windows python

I just updated Python, so I'm going to try rolling back to 3.5.2, see if that makes any difference.
EDIT: Turns out blender had been launching using my old python install because the update didn't change the path properly. Problem maybe solved.

[scorpion451]

Okay, so now that I've got it working and played with it for a while:
How can we make f = (interpolation/lerp/closest vertex/etc of an existing mesh)?
Add that and a quadder to this, and I am seeing the holy grail of retopo tools here.

[kalwalt]

Okay, so now that I've got it working and played with it for a while:

@scorpion451 Happy, that you got it working!

How can we make f = (interpolation/lerp/closest vertex/etc of an existing mesh)?

This is sure possible. Probably given the Bounding Box of the mesh you can calculate the distance of every vertex from the center of the BB, so finding the values for the marching cubes algorithm. This is a feature that would fine have with Sverchok. but for now we can only develop some script or macro, because pymcubes can't be installed in blender python. I suggest also to try the scikit-image module as mentioned in a previous post in this issue. For now I'm testing the two modules to see what is more convenient to use.

[nortikin]

Unexpected error: <class 'ImportError'>
on line:  2
Traceback (most recent call last):
  File "/home/ololo/.config/blender/2.78/scripts/addons/sverchok/nodes/generator/script1_lite.py", line 348, in process_script
    exec(self.script_str, locals(), locals())
  File "<string>", line 16, in <module>
ImportError: No module named 'mcubes._mcubes'

mcubes_path = r"/usr/lib/python3.6/site-packages/" #it depend on your OS but just paste the path where is scipy
if not mcubes_path in sys.path:
    sys.path.append(mcubes_path)    
import mcubes

the same 3.6

[kalwalt]

@nortikin i think should match the python versions. Blender use python 3.5 (at least 2.78a) your system python installed is as i can see 3.6.

[nortikin]

the same 3.6 problem, i see

[kalwalt]

if you can you should install python 3.5 on your system and after the pymcubes module

[nortikin]

Traceback (most recent call last):
  File "/home/ololo/.config/blender/2.78/scripts/addons/sverchok/nodes/generator/script1_lite.py", line 348, in process_script
    exec(self.script_str, locals(), locals())
  File "<string>", line 16, in <module>
ImportError: No module named 'mcubes._mcubes'

have now 3.5

[nortikin]

how to point blender on locan python?

[kalwalt]

@nortikin now how is your mcubes_path?

[nortikin]

@kalwalt r"/usr/lib/python3.5/site-packages/mcubes/"

[nortikin]

  File "/usr/lib/python3.5/site-packages/mcubes/__init__.py", line 2, in <module>
    from ._mcubes import marching_cubes, marching_cubes_func
ImportError: No module named 'mcubes._mcubes'

from ._mcubes import marching_cubes, marching_cubes_func
from .exporter import export_mesh, export_obj
cannot see this file, only _mcubes.cpython-35m-x86_64-linux-gnu.so

[kalwalt]

try:

-r"/usr/lib/python3.5/site-packages/"
+r"/usr/lib/python3.5/site-packages"

[zeffii]

stick a plate of glass ontop of that and you got a coffee table.

[kalwalt]

try also;

# instead of multiplying
v = Z * u
# try yo add
v = Z + u

[kalwalt]

I did this only changing:

-v = Z * u
+v = Z + u

and adjusting the isovalue, note the difference with the previous image.

[paulofalcao]

Cool stuff, if I also send normals / colors or others attributes per vertex, how can I use them in sverchok / blender ?

[kalwalt]

Cool stuff, if I also send normals / colors or others attributes per vertex

Hi @paulofalcao, no pymcubes can't send normals or other vertex informations. Polyvox lib has this feature but the python bindings unfortunately not. I would update the bindings to the latest but Polyvox, the original lib in C++, is heavily templated and i don't feel very comfortable with.

how can I use them in sverchok / blender ?

i think you can do what you want with it. You can apply other nodes, baking in the scene and use all the modifiers and other blender tools.

[paulofalcao]

i think you can do what you want with it. You can apply other nodes, baking in the scene and use all the modifiers and other blender tools.

Thanks, that's what I was trying to do with a simple example like this:

"""
in bounds s d=10 n=2
in iso_val s d=0.0 n=2
in samples s d=100 n=2
in sphere_size s d=5.0 n=2
out vertices v
out triangles s
out normals v
out colors v
"""


import numpy as np
import sys
mcubes_path = r"/usr/local/lib/python3.6/site-packages/PyMCubes-0.0.6-py3.6-macosx-10.11-x86_64.egg"  # it depend on your OS but just paste the path where is mcubes
if not mcubes_path in sys.path:
    sys.path.append(mcubes_path)
import mcubes
import math


# Signed Distance Function
def sdf(x, y, z):
    x = x + math.sin(y*2.0)*1.0
    res = math.sqrt(x*x + y*y + z*z) - sphere_size
    return res

def norm(p):
    e = 0.001
    v = sdf(p[0],p[1],p[2])
    return np.linalg.norm([v-sdf(p[0]+e,p[1],p[2]),
                           v-sdf(p[0],p[1]+e,p[2]),
                           v-sdf(p[0],p[1],p[2]+e)])

def cor(p):
    return [math.sin(p[0]*0.5)+0.5,
            math.sin(p[1]*0.7)+0.5,
            math.sin(p[2]*0.9)+0.5]

# Extract the 16-isosurface
verts, tri = mcubes.marching_cubes_func(
    (-bounds, -bounds, -bounds), (bounds, bounds, bounds),  # Bounds
    samples, samples, samples,            # Number of samples in each dimension
    sdf,                                  # Signed Distance Function
    iso_val)                              # Isosurface value

vertices = [verts.tolist()]
triangles =  [tri.tolist()]
normals = map(norm,vertices)
colors = map(cor,vertices)

[kalwalt]

@paulofalcao great! but colors and normals i think won't works as it is now. Anyway you could plug into a viewer bmesh and a vertex color new to display the color information onto the mesh. But i will show you tomorrow, maybe opening another issue thread, as i have no time now

[paulofalcao]

@kalwalt, OK thanks. I was just playing around with these stuff :)

[nortikin]

consulted with pymcubes developer, i had blender 32 bit, system 64 bit, so it was not working )))

[kalwalt]

consulted with pymcubes developer, i had blender 32 bit, system 64 bit, so it was not working )))

Did you tried with blender 64 bit?

[nortikin]

yes, it importing ok

[enzyme69]

I would not mind a coffee shop with such futuristic furniture! I think this 3D voxel mesher is what I need to meditate soon. I always want it since Cycles can do volumetric.

[enzyme69]

With difficulty:

• can install mcubes finally
• numpy version was different, copy paste from outside into blender

Somewhat works:

def heart(x,y,z):
    # some kind of heart 3D function
    
    res = 320 * ((-x**2 * z**3 -9*y**2 * z**3/80) + (x**2 + 9*y**2/4 + z**2-1)**3)
    return res

[zeffii]

also.. i can't get mcubes installed

if you want answers, paste / copy (not screenshot) the output of a working SNLite piped into a Debug node, and SNLite that doesn't work

and by "doesn't work" i mean, it doesn't display anything for VDMK. also show the whole Error messages, but maybe not the parts of the message that repeat, or have already been printed earlier.

[zeffii]

also.. disconnect the VDMK2 when you connect the debug print node

[enzyme69]

@zeffii Yes, I think the issue was: data list was empty: [[]] --> this gives "int not iterable" error. By adjusting parameter, etc, I finally got something.

False alarm.

something to do with this:
verts, tri = mcubes.marching_cubes(v, iso_val)

verts, tri = mcubes.marching_cubes(v, 0) --> empty list
verts, tri = mcubes.marching_cubes(v, 0.5) --> something appears!
verts, tri = mcubes.marching_cubes(v, 0.8) --> something appears!

I wish you can play with this "marching cube" stuff, interesting~

[enzyme69]

[kalwalt]

hi @enzyme69 glad that you work with it ! pay attention to the iso values. As i remember it is very sensible. Sorry for my long delay here. I have no time to work or experimenting with sverchok and programming in general...

[nortikin]

[nortikin]

(y**2 / math.sin(z*y) + 2**x)**2

[nortikin]

https://vk.com/wall-35076122_9416

[enzyme69]

What would be cool is a way to read or export Cycles Volumetric back into Sverchok. Maybe OSL can help with this? --

…

------------------------------------------------------------ - Jimmy Gunawan http://blendersushi.blogspot.com.au http://mayaspiral.blogspot.com.au http://houdoodles.blogspot.com.au http://puppetar.blogspot.com.au

[akalyan3]

import mcubes command generating the following error:

Traceback (most recent call last):
File "<blender_console>", line 1, in
File "/Users/adityak/anaconda2/envs/conda-python-blender/lib/python3.5/site-packages/mcubes/init.py", line 2, in
from ._mcubes import marching_cubes, marching_cubes_func
ImportError: cannot import name 'marching_cubes'

Any help would be appreciated!

[enzyme69]

@akalyan3 You need to ensure that the module is callable from inside Blender or Script node.

Have you downloaded the PyMCubes module and install it into your computer and testing it using Python outside Blender? Ensuring also the Python version is good.

Then once it's good, you can call it using the lines mentioned above by @kalwalt

import sys
mcubes_path = r"/usr/local/lib/python3.5/dist-packages" #it depend on your OS but just paste the path where is mcubes
if not mcubes_path in sys.path:
    sys.path.append(mcubes_path)    
import mcubes

[akalyan3]

@enzyme69 Thanks for that. That resolved the issue. But I ran into another one :P
Traceback (most recent call last):
File "<blender_console>", line 1, in
File "/Users/adityak/anaconda2/envs/conda-python-blender/lib/python3.5/site-packages/mcubes/exporter.py", line 29, in export_mesh
vert_src = collada.source.FloatSource("verts-array", vertices, ('X','Y','Z'))
AttributeError: module 'collada' has no attribute 'source'

I'm trying to export a Schwarz.

[nortikin]

export? try other exporter from blender.