Daniel Russel wrote:
just to add the reason for storing voxels in a 1d array rather than 3d: in image processing, all computations are typically done in loops, i.e. neighboring voxels are accessed in succession. therefore, it should be faster in that case, and every program i know of (at least in the em community) handles it this way. if you refer to the grid as the coordinates a specific voxel corresponds to: it might well be that it is done sub-optimally done in EMbed. just test it with a reasonably large map (e.g. 100x100x100 voxels). if you result in a speed-up, changes are always welcome.It still has that. Just the index type is different. It also makes it easier to iterate over the whole thing.The differences from the grid used in EMBed are: - The voxel index is actually a triple if ints. This makes computing a point in a voxel fast without the large tables used in EMBed. I think this is the right choice speed wise, but we can always test (and it is trivial to change).The reason we had it as single array in EMBed is for consistency with external programs like fttw, EMAN. I think that we should keep it like that.
_______________________________________________ IMP-dev mailing list https://salilab.org/mailman/listinfo/imp-dev
-- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Friedrich Foerster % % Andrej Sali Lab % % University of California at San Francisco % % MC 2552 % % Byers Hall Room 501 % % 1700 4th Street % % San Francisco, CA 94158-2330, USA % % % % phone: +1 (415) 514-4258 % % fax: +1 (415) 514-4231 % % % % www.salilab.org/~frido % % % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%