Obj File Exporter for Surfaces
@ Jill Naiman | Saturday, Mar 30, 2013 | 4 minute read | Update at Thursday, Dec 3, 2020

How to export surfaces into an obj file (will it blend?!)

OBJ File Exporter for Surfaces

OBJ and MTL Files

If the ability to maneuver around an isosurface of your 3D simulation in Sketchfab cost you half a day of work (let’s be honest, 2 days), prepare to be even less productive. With a new
OBJ file exporter, you can now upload multiple surfaces of different transparencies in the same file. The following code snippet produces two files which contain the vertex info (surfaces.obj) and color/transparency info (surfaces.mtl) for a 3D galaxy simulation:

   from yt.mods import *

   pf = load("/data/workshop2012/IsolatedGalaxy/galaxy0030/galaxy0030")
   rho = [2e-27, 1e-27]
   trans = [1.0, 0.5]
   filename = './surfaces'

   sphere = pf.h.sphere("max", (1.0, "mpc"))
   for i,r in enumerate(rho):
       surf = pf.h.surface(sphere, 'Density', r)
       surf.export_obj(filename, transparency = trans[i], color_field='Temperature', plot_index = i)

The calling sequence is fairly similar to the export_ply function previously used to export 3D surfaces. However, one can now specify a transparency for each surface of interest, and each surface is enumerated in the OBJ files with plot_index. This means one could potentially add surfaces to a previously created file by setting plot_index to the number of previously written surfaces.

One tricky thing: the header of the OBJ file points to the MTL file (with the header command mtllib). This means if you move one or both of the files you may have to change the header to reflect their new directory location.

A Few More Options

There are a few extra inputs for formatting the surface files you may want to use.

(1) Setting dist_fac will divide all the vertex coordinates by this factor. Default will scale the vertices by the physical bounds of your sphere.

(2) Setting color_field_max and/or color_field_min will scale the colors of all surfaces between this min and max. Default is to scale the colors of each surface to their own min and max values.

Uploading to SketchFab

To upload to Sketchfab one only needs to zip the OBJ and MTL files together, and then upload via your dashboard prompts in the usual way. For example, the above script produces this beautiful rendering

Importing to MeshLab and Blender

The new OBJ formatting will produce multi-colored surfaces in both MeshLab and Blender, a feature not possible with the previous PLY exporter. To see colors in MeshLab go to the “Render” tab and select “Color -> Per Face”. Note in both MeshLab and Blender, unlike Sketchfab, you can’t see transparencies until you render.

…One More Option

If you’ve started poking around the actual code instead of skipping off to lose a few days running around your own simulations you may have noticed there are a few more options then those listed above, specifically, a few related to something called “Emissivity.” This allows you to output one more type of variable on your surfaces. For example:

   from yt.mods import *

   pf = load("/data/workshop2012/IsolatedGalaxy/galaxy0030/galaxy0030")
   rho = [2e-27, 1e-27]
   trans = [1.0, 0.5]
   filename = './surfaces'

   def _Emissivity(field, data):
       return (data['Density']*data['Density']*np.sqrt(data['Temperature']))
   add_field("Emissivity", function=_Emissivity, units=r"\rm{g K}/\rm{cm}^{6}")

   sphere = pf.h.sphere("max", (1.0, "mpc"))
   for i,r in enumerate(rho):
       surf = pf.h.surface(sphere, 'Density', r)
       surf.export_obj(filename, transparency = trans[i],
                       color_field='Temperature', emit_field = 'Emissivity',
		       plot_index = i)

will output the same OBJ and MTL as in our previous example, but it will scale an emissivity parameter by our new field. Technically, this makes our outputs not really OBJ files at all, but a new sort of hybrid file, however we needn’t worry too much about that for now.

This parameter is useful if you want to upload your files in Blender and have the embedded rendering engine do some approximate ray-tracing on your transparencies and emissivities. This does take some slight modifications to the OBJ importer scripts in Blender. For example, on a Mac, you would modify the file “/Applications/Blender/blender.app/Contents/MacOS/2.65/scripts/addons/io_scene_obj/import_obj.py”, in the function “create_materials” with:

                    elif line_lower.startswith(b'tr'):  # translucency
                        context_material.translucency = float_func(line_split[1])
                    elif line_lower.startswith(b'tf'):
                        # rgb, filter color, blender has no support for this.
                    elif line_lower.startswith(b'em'): # MODIFY: ADD THIS LINE
                        context_material.emit = float_func(line_split[1]) # MODIFY: THIS LINE TOO
                    elif line_lower.startswith(b'illum'):
                        illum = int(line_split[1])

To use this in Blender, you might create a Blender script like the following:

   import bpy
   from math import *

   bpy.ops.import_scene.obj(filepath='./surfaces.obj') # will use new importer

   # set up lighting = indirect
   bpy.data.worlds['World'].light_settings.use_indirect_light = True
   bpy.data.worlds['World'].horizon_color = [0.0, 0.0, 0.0] # background = black
   # have to use approximate, not ray tracing for emitting objects ...
   #   ... for now...
   bpy.data.worlds['World'].light_settings.gather_method = 'APPROXIMATE'
   bpy.data.worlds['World'].light_settings.indirect_factor=20. # turn up all emiss

   # set up camera to be on -x axis, facing toward your object
   scene = bpy.data.scenes["Scene"]
   scene.camera.location = [-0.12, 0.0, 0.0] # location
   scene.camera.rotation_euler = [radians(90.), 0.0, radians(-90.)] # face to (0,0,0)

   # render
   scene.render.filepath ='/Users/jillnaiman/surfaces_blender' # needs full path

This above bit of code would produce an image like so:

Our cool image

Note that the hottest stuff is brightly shining, while the cool stuff is less so (making the inner isodensity contour barely visible from the outside of the surfaces).

If the Blender image caught your fancy, you’ll be happy to know there is a greater integration of Blender and yt in the works, so stay tuned!

yt extension modules

yt has many extension packages to help you in your scientific workflow! Check these out, or create your own.


ytini is set of tools and tutorials for using yt as a tool inside the 3D visual effects software Houdini or a data pre-processor externally to Houdini.


Trident is a full-featured tool that projects arbitrary sightlines through astrophysical hydrodynamics simulations for generating mock spectral observations of the IGM and CGM.


pyXSIM is a Python package for simulating X-ray observations from astrophysical sources.


Analyze merger tree data from multiple sources. It’s yt for merger trees!


yt_idv is a package for interactive volume rendering with yt! It provides interactive visualization using OpenGL for datasets loaded in yt. It is written to provide both scripting and interactive access.


widgyts is a jupyter widgets extension for yt, backed by rust/webassembly to allow for browser-based, interactive exploration of data from yt.


yt_astro_analysis is the yt extension package for astrophysical analysis.

Make your own!!

Finally, check out our development docs on writing your own yt extensions!

Contributing to the Blog

Are you interested in contributing to the yt blog?

Check out our post on contributing to the blog for a guide!

We welcome contributions from all members of the yt community. Feel free to reach out if you need any help.

the yt data hub

The yt hub at https://girder.hub.yt/ has a ton of resources to check out, whether you have yt installed or not.

The collections host all sorts of data that can be loaded with yt. Some have been used in publications, and others are used as sample frontend data for yt. Maybe there’s data from your simulation software?

The rafts host the yt quickstart notebooks, where you can interact with yt in the browser, without needing to install it locally. Check out some of the other rafts too, like the widgyts release notebooks – a demo of the widgyts yt extension pacakge; or the notebooks from the CCA workshop – a user’s workshop on using yt.

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