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Writing a G-code generator for a 3-D printer? :^)
EMAN2 does have routines in its core library
(accessible from Python) which can do some aspects of this
process, but not everything. Certainly it can cut arbitrary
slices through a volume and threshold them to produce something
like a 2-D mask. I'd be happy to give you some example code for
this sort of thing in Python using EMAN if you like.
However, EMAN and most of the other CryoEM software
is pretty pixel-focused. It sounds like you are really after
something that does CSG (constructive solid geometry). The
disadvantage of the pixel/voxel approach is that you need huge
amounts of RAM for structures with a lot of detail. This depends
a lot on what your inputs and outputs will be. If you are
planning to take something like a 3-D volumetric reconstruction
of a molecule, and then generate slice-by-slice contours, then
EMAN could, indeed, help with everything but the 2-D contour
tracing. However, if you really do have a set of vertices and
surfaces defining a closed shape in 3-D, and wish to generate
contours for that, a CSG library is definitely a better choice.
You may check out CGAL:
which has python bindings
----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Professor, Dept. of Biochemistry and Mol. Biol.
Those who do
Co-Director National Center For
Macromolecular Imaging
ARE
Hello,
Consider a closed 3D surface constructed from a set of
vertices arranged into a set of polygons. I would like
to compute the image that forms on a plane slice through
this closed volume. My goal is to acquire the set of
contours that form on this surface.
Could anyone give me some ideas of how this could be
performed (efficiently)? Does an open source Python API
exist for this problem?
Thanks! ^_^
--
With kind regards,
Paul K Korir, PhD
Scientific Programmer
EMBL-EBI
Main Building, A2-35,
WTGC, Hinxton, Cambridge CB10 1SD
P: +44 1223 49 44 22
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