Python Visualization from 3D array - python

Quick background: I'm a pretty proficient programmer when it comes to MATLAB, but am experimenting with learning python for fun and out of curiousity. I'm working on windows (will be dual booting again soon after this experience...) and am using anaconda (3.6), as I needed Scipy and, being new, figuring out the setup on windows was difficult at best.
I am working on 3D path planning for UAVs. I have a 3D array (say 1000x500x50) where unobstructed space has a value of zero and "no fly zones" have a value of 1. I can create variable terrains representative of a forest with trees, varrying floors, etc. and I'd like a simple way to view this environment. I could sort of get away with doing this as a point cloud by subsampling, increasing density, and then displaying it, but that is a less than ideal solution.
I've been perusing mayavi as a possible method for doing this, but I haven't been able to find examples of this kind of scale. I did write a script to draw a patch for each face of each obstructed cube, and this does work but is horribly inefficinet. Just looking for a better solution if one exists. Also, mayavi doesn't seem to be supported in anaconda yet (at least in 3.6), so I'd like a little more of a lead before I start switching builds again. Thanks everyone!

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How to create a 3d model out of a series of 2d images? using python

So lets say I have a objects like a face. I take multiple pictures of the face all at different angles and from far and close. I have a sort of idea of how to make a 3d model out of these pictures but don't know how to accomplish them. My idea goes likes this.
First make code that gets the image object and gets rid of all background "noise".
Second find what part of the 3d model the picture is about and place a tag on the image for where it should fit.
Third collect and overlap all the images together to create a 3d object.
Anyone have any idea how to accomplish any of these steps or any ideas how to create a 3d model out of a series of images? I use python 3.10.4.
It seems that you are asking if there are some Python modules that would help to implement a complete photogrammetry process.
Please note that, even in the existing (and commercial) photogrammetry solutions, the process is not always fully-automated, sometimes it require some manual tweaking & point cloud selection.
Anyway, to the best of my knowledge, what you asked requires to implement the following steps:
detecting common features between the different photographs
infer the position in space of the camera that took each photograph
generate a point cloud of the photographs based on their relative position in space and the common features
convert the point cloud in a 3D mesh.
Possibly, all of these steps can be implemented in Python but I'm not aware that such a "off-the-shelf" module does exist.
There's this commercial solution called: Metashape from Agisoft, it has a python module you can use, but beware that it has its pitfalls (it threw segmentation fault for me at the end of processing which makes things... icky) and the support kind of ignores bigger problems and you can expect that they would ignore your ticket. Still, does the job quite well.

Representing volumes using isosurfaces

I would like to represent a bunch of particles (~100k grains), for which I have the position (including rotation) and a discretized level set function (i.e. the signed distance of every voxel from surface). Due to the large sample, I'm searching for eficient solutions to visualize it.
I first went for vtk, using its python interface, but I'm not really sure if it's the best (and simplest) way to do it since, as far as I know, there is no direct implementation for getting an isosurface from a 3D data set. In the beginning I was thinking usind marching cubes, but then I still would have to use a threshold or to interpolate in order to get the voxels that are on the surface and label them in order to be used by the marching cubes.
Now I found mayavi which has a python function
mlab.pipeline.iso_surface()
I however did not find much documentation on it and was wondering how it behaves in terms of performance.
Does someone have experience with this kind of tools? Which would be the best solution (in terms of efficiency and, secondly, in terms of simplicity - I do not know the vtk library, but if there is a huge difference in performance I can dig into it, also without python interface).

how to get opengl 3d model sectional drawing?

I have load an obj file to render my opengl model using pyopengl and pygame. The 3D model show successfully.
Below is the 3D model i render with obj file, Now i cut my model into ten pieces through y axis , my question is how to get the sectional drawing in each piece?
I'm really very new to openGL, Is there any way can do that?
There are two ways to do this and both use clipping to "slice" the object.
In older versions of OpenGL you can use user clip planes to "isolate" the slices you desire. You probably want to rotate the object before you clip it, but it's unclear from your question. You will need to call glClipPlane() and you will need to enable it using glEnable with the argument GL_CLIP_PLANE0, GL_CLIP_PLANE1, ...
If you don't understand what a plane equation is you will have to read up on that.
In theory you should check to see how many user clip planes exist on your GPU by calling glGetIntegerv with argument GL_MAX_CLIP_PLANES but all GPUs support at least 6.
Since user clip planes are deprecated in modern Core OpenGL you will need to use a shader to get the same effect. See gl_ClipDistance[]
Searching around on Google should get you plenty of examples for either of these.
Sorry not to provide source code but I don't like to post code unless I am 100% sure it works and I don't have the time right now to check it. However I am 100% sure you can easily find some great examples on the internet.
Finally, if you can't make it work with clip planes and some hacks to make the cross sections visible then this may indeed be complicated because creating closed cross sections from an existing model is a hard problem.
You would need to split the object, and then rotate the pieces so that they are seen from the side. (Or move the camera. The two ideas are equivalent. But if you're coding this from scratch, you don't really have the abstraction of a 'camera'.) At that point, you can just render all the slices.
This is complicated to do in raw OpenGL and python, essentially because objects in OpenGL are not solid. I would highly recommend that you slice the object into pieces ahead of time in a modeling program. If you need to drive those operations with scripting, perhaps look into Blender's python scripting system.
Now, to explain why:
When you slice a real-life orange, you expect to get cross sections. You expect to be able to see the flesh of the fruit inside, with all those triangular pieces.
There is nothing inside a standard polygonal 3D model.
Additionally, as the rind of a real orange has thickness, it is possible to view the rind from the side. In contrast, one face of a 3D model is infinitely thin, so when you view it from the side, you will see nothing at all. So if you were to render the slices of this simple model, from the side, each render would be completely blank.
(Well, the bits at the end will have 'caps', like the ends of a loaf a bread, but the middle sections will be totally invisible.)
Without a programming library that has a conception of what a cut is, this will get very complicated, very fast. Simply making the cuts is not enough. You must seal up the holes created by slicing into the original shape, if you want to see the cross-sections. However, filling up the cross sections has to be done intelligently, otherwise you'll wind up with all sorts of weird shading artifacts (fyi: this is caused by n-gons, if you want to go discover more about those issues).
To return to the original statement:
Modeling programs are designed to address problems such as these, so I would suggest you leverage their power if possible. Or at least, you can examine how Blender implements this functionality, as it is open source.
In Blender, you could make these cuts with the knife tool*, and then fill up the holes with the 'make face' command (just hit F). Very simple, even for those who are not great at art. I encourage you to learn a little bit about 3D modeling before doing too much 3D programming. It personally helped me a lot.
*(The loop cut tool may do the job as well, but it's hard to tell without understanding the topology of your model. You probably don't want to get into understanding topology right now, so just use the knife)

CFD work with Python

I am a meteorologist, and lately I am trying to investigate the possibility of building my one sondes.
In order to do that, I have the following work plan :
I would like to generate 3D models pyformex. An alternative is openSCAD. But I start with pyformex - to generate simple cylindrical sonde shapes with associated extra features, e.g. intake tube or such.
Next, I will like to split it in Meshes, using PyDistMesh; as well as prepare a raytraced point cloud model with Xrt.
In the third step, I would like to perform the CFD works.
Now, my questions :
Are there some other simple Python Libraries to generate 3D models? I would like a very simple system, where i can issue commands like p = Parallelogram (length, height, width), or p.position(x,y,z) etc. It would be nice to have built in mouse interaction - that is, a built in drawing component, which I can use to display the model, and rotate/ zoom/pan with mouse.
Any other mesh generation tools?
For this step, I would need a multiphysics system. I tried to use OpenFOAM, it is too huge (to hack through). I have taken a look at SU2, but it seems to focus more on aerospace engineering, than Fluid Dynamics (I would like to simulate the flight of the sonde - which is closer to aerospace engineering, as well as the state of the atmosphere). Fluidity seems to suit my needs better, but I dont find a python fork thereof. So are there some general purpose, not too bloated up, multiphysics python library for geophysical and general hydrodynamic simulations? I have taken a look a MOOSE, also dont find a python binding for it.
Scientific visualization : Are there some 3 or 4 (or may be higher dimensional) visualization libraries? I would prefer to issue simple commands as Plot instead of first generating a window / form, and then putting the graphs on it, if possible.
FINALLY, and most importantly, if the same can be done by C++ or Fortan, or some other language besides java, I would also consider using those.
Have a look at http://freecadweb.org/. This seems to be under active development. It is a fairly complete open source CAD package written in python. I believe it also has tools for meshing.
For cfd, you might want to consider openfoam - http://www.openfoam.com/. This is an open source cfd package with the obligatory steep learning curve. There seem to be some python libraries to be available that link to it, however I'm not sure how active these are:
http://openfoamwiki.net/index.php/Contrib/PyFoam
http://pythonflu.wikidot.com/

Is there a python library to generate STL file for 3D printing?

I am currently in a project where a lot of 3D printing designs need to be done. They are all parameterized, so I'd like to write a python code to generate those design files (in .STL format) for me. I was wondering that, is there a python package that can do this? Because currently I am all doing those by hand using SolidWorks.
Thanks!
Yes there is... It's called FreeCAD.
The assembly module is already in the devel version (as of 06/15/2014) and will be of production quality really soon for real assemblies!
http://freecadweb.org/
Yes, more than one.
In my humble experience, I tried many Open Source tools for parametric CAD modeling using Python (FreeCAD, Rhino-Grasshopper, Blender, Salome).
All of them are valid options and the best one is represented by your ability to either model or code.
I recently favour SALOME (www.salome-platform.org) because of the straight forward "dump study" option, the continue development and the good API documentation.
Particularly I did some 3d prints using the exportSTL command once I had a solid worthy of printing and it was ok.
Nevertheless, if you intend to work on surfaces rather than solids, I don't think you will find anything worthy Open Source (Rhino has a little price to pay).
There is also a new one ! called pymadcad
It's a library meant to do complete CAD stuff only with python scripts.
At contrary to FreeCAD, Pymadcad is natively dealing with triangular meshes so it makes it very easy to import/export .stl files.
There is a growing amount of surface generation functions (extrusion, revolution, tube, screw, smooth surface, ...). And there is also all the stuff to generate and deal with 3D primtives such as Lines, Arc, ...
Here is a brief look at the features

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