segment3d

Split a 3d map into several pieces.

segment3d <input file> <output file> <n seg> [ampw] [thr=<val>] [split] [maxit=<n>] [itxp=<n>] [vector=<outfile>] [gaussmod=<mrc out>] [randomize]

Parameters:


<input file>Source file
<output file>Destination file
<n seg>Number of segments to split map into
[ampw]Apply a straight line integral amplitude weight to the distance parameter
[thr=<val>]Only segment voxels above the given threshold
[split]Separate out the individual segments
[maxit=<n>]Specify maximum iterations before giving up on convergence
[itxp=<n>]After the segmentation, iteratively extend the segments into regions below threshold, n is the number of voxels of expansion
[vector=<outfile>]Write segment centers to a text file x,y,z,dx,dy,dz
[gaussmod=<mrc out>]Construct a 3d model from Gaussians centered at the group centers.
[randomize]This will randomize the gaussians by rotating them randomly with a fixed radius

Usage:

segment3d threed.1a.mrc seg.mrc 12 thr=1

Description

This program will take a 3D map and attempt to intelligently split that map into 'segments'. That is, every voxel in the map will be assigned to one of segments. The assignment is performed in such a way that high density regions will be grouped together. This is accomplished using a k-means clustering algorithm.


EMAN Manual page, generated Tue Oct 8 21:38:48 2002