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content/post/3DSurfacesAndSketchFab.rst

+3D Surfaces and SketchFab
+=========================
+
+Surfaces
+--------
+
+For a while now, yt has had the ability to extract isosurfaces from volumetric
+data using a `marching cubes <http://en.wikipedia.org/wiki/Marching_cubes>`_
+algorithm.  The surfaces could be exported in `OBJ format
+<http://en.wikipedia.org/wiki/Wavefront_.obj_file>`_, values could be samples
+at the center of each face of the surface, and flux of a given field could be
+calculated over the surface.  This means you could, for instance, extract an
+isocontour in density and calculate the mass flux over that isocontour.  It
+also means you could export a surface from yt and view it in something like
+`Blender <http://www.blender.org/>`_, `MeshLab
+<http://meshlab.sourceforge.net/>`_, or even on your Android or iOS device in
+`MeshPad <http://www.meshpad.org/>`_ or `MeshLab Android
+<https://play.google.com/store/apps/details?id=it.isticnr.meshlab&hl=en>`_.
+One important caveat with marching cubes is that with adaptive mesh refinement
+data, you *will* see cracks across refinement boundaries unless a
+"crack-fixing" step is applied to match up these boundaries.  yt does not
+perform such an operation, and so there will be seams visible in 3D views of
+your isosurfaces.
+
+The methods to do so were methods on data objects -- ``extract_isocontours``,
+``calculate_isocontour_flux`` -- which returned just numbers or values.
+However, recently, I've created a new object called ``AMRSurface`` that makes
+this process much easier.  You can create one of these objects by specifying a
+source data object and a field over which to identify a surface at a given
+value.  For example:
+
+.. code-block:: python
+
+   from yt.mods import *
+   pf = load("/data/workshop2012/IsolatedGalaxy/galaxy0030/galaxy0030")
+   sphere = pf.h.sphere("max", (1.0, "mpc"))
+   surface = pf.h.surface(sphere, "Density", 1e-27)
+
+This object, ``surface``, can now be queried for values on the surface.  For
+instance:
+
+.. code-block:: python
+
+   print surface["Temperature"].min(), surface["Temperature"].max()
+
+will return the values 11850.7476943 and 13641.0663899.  These values are
+interpolated to the face centers of every triangle that constitutes a portion
+of the surface.  Note that reading a new field requires re-calculating the
+entire surface, so it's not the fastest operation.  You can get the vertices of
+the triangle by looking at the property ``.vertices``.
+
+Exporting to a File
+-------------------
+
+If you want to export this to a `PLY file
+<http://en.wikipedia.org/wiki/PLY_(file_format)>`_ you can call the routine
+``export_ply``, which will write to a file and optionally sample a field at
+every face or vertex, outputting a color value to the file as well.  This file
+can then be viewed in MeshLab, Blender or on the website `SketchFab
+<SketchFab.com>`_.  But if you want to view it on SketchFab, there's an even
+easier way!
+
+Exporting to SketchFab
+----------------------
+
+`SketchFab <http://sketchfab.com>`_ is a website that uses WebGL, a relatively
+new technology for displaying 3D graphics in any browser.  It's very fast and
+typically requires no plugins.  Plus, it means that you can share data with
+anyone and they can view it immersively without having to download the data or
+any software packages!  SketchFab provides a free tier for up to 10 models, and
+these models can be embedded in websites.
+
+There are lots of reasons to want to export to SketchFab.  For instance, if
+you're looking at a galaxy formation simulation and you publish a paper, you
+can include a link to the model in that paper (or in the arXiv listing) so that
+people can explore and see what the data looks like.  You can also embed a
+model in a website with other supplemental data, or you can use SketchFab to
+discuss morphological properties of a dataset with collaborators.  It's also
+just plain cool.
+
+The ``AMRSurface`` object includes a method to upload directly to SketchFab,
+but it requires that you get an API key first.  You can get this API key by
+creating an account and then going to your "dashboard," where it will be listed
+on the right hand side.  Once you've obtained it, put it into your
+``~/.yt/config`` file under the heading ``[yt]`` as the variable
+``sketchfab_api_key``.  If you don't want to do this, you can also supply it as
+an argument to the function ``export_sketchfab``.
+
+Now you can run a script like this:
+
+.. code-block:: python
+
+   from yt.mods import *
+   pf = load("redshift0058", file_style="%s.grid.cpu%%04i")
+   dd = pf.h.sphere("max", (200, "kpc"))
+   rho = 5e-27
+
+   bounds = [(dd.center[i] - 100.0/pf['kpc'],
+              dd.center[i] + 100.0/pf['kpc']) for i in range(3)]
+
+   surf = pf.h.surface(dd, "Density", rho)
+
+   upload_id = surf.export_sketchfab(
+       title = "RD0058 - 5e-27",
+       description = "Extraction of Density (colored by Temperature) at 5e-27 " \
+                   + "g/cc from a galaxy formation simulation by Ryan Joung."
+       color_field = "Temperature",
+       color_map = "hot",
+       color_log = True,
+       bounds = bounds
+   )
+
+and yt will extract a surface, convert to a format that SketchFab.com
+understands (PLY, in a zip file) and then upload it using your API key.  For
+this demo, I've used data kindly provided by Ryan Joung from a simulation of
+galaxy formation.  Here's what my newly-uploaded model looks like, using the
+embed code from SketchFab:
+
+.. raw:: html
+
+   <iframe frameborder="0" height="480" width="854" allowFullScreen
+   webkitallowfullscreen="true" mozallowfullscreen="true"
+   src="http://skfb.ly/l4jh2edcba?autostart=0&transparent=0&autospin=0&controls=1&watermark=1"></iframe>
+
+As a note, SketchFab has a maximum model size of 50MB for the free account.
+50MB is pretty hefty, though, so it shouldn't be a problem for most needs.
+We're working on a way to optionally upload links to the SketchFab models on
+the `yt Hub <https://hub.yt-project.org/>`_, but for now, if you want to share
+a cool model we'd love to see it!
+
+Thanks to SketchFab for such a cool service, and for helping us out along the
+way with their API.
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