proc3d

Misc. 3d image processing

proc3d <input file>

proc3d <input file> <output file> [shrink=<div>] [scale=<factor>] [clip=<x,y,z>] [rot=<alt,az,phi>] [trans=<dx,dy,dz>] [center] [acfcen] [apix=<A/pix>] [lp=<filt r>] [hp=<filt r>] [tlp=<filt r>] [unhp=<filt r>] [filefilt=<file>] [flip] [sym=<c?,icos,etc>] [mask=<radius>] [imask=<radius>] [automask=<thr1>,<thr2>] [automask2=<rad>,<thr>,<N>] [norm] [mult=<constant>] [noise=<level>] [signoise=<sig mult>] [vtk] [spider] [gwin=<radius>]

proc3d <input 1> <input 2> [apix=<A/pix>] [fsc=<out>] [phase=<out>] [rfactor=<out>] [rms=<thresh>] [rdiv=<out>] [diffmap[=<~binary thr>]] [sum=<output>]

Parameters:


<input file>Get info/stats on this file

<input file>Source file
<output file>Destination file
[shrink=<div>]Shrinks the image by an integral scaling factor, median filter
[scale=<factor>]Rescales the image, generally used with clip=
[clip=<x,y,z>]Make the output have this size, no scaling
[rot=<alt,az,phi>]Rotate the volume, angles in degrees
[trans=<dx,dy,dz>]Translate the volume
[center]Centers volume using center of mass
[acfcen]Centers volume using cross correlation with mirrored model
[apix=<A/pix>]Specify the Angstr/pixel for S scaling
[lp=<filt r>]Gaussian lowpass filter, r in angstroms if apix defined, pixels if undef
[hp=<filt r>]Arctan highpass filter
[tlp=<filt r>]Gaussian/artan mix lowpass
[unhp=<filt r>]Undoes the hp= filter
[filefilt=<file>]Applies a filter defined by an x/y text file
[flip]Mirrors the object across the x-y plane
[sym=<c?,icos,etc>]Applies the specified symmetry to the map
[mask=<radius>]Applies a circular mask at the given radius
[imask=<radius>]Applies an inside mask at the given radius
[automask=<thr1>,<thr2>]Tries to mask out only interesting density
[automask2=<rad>,<thr>,<N>]Same goal as automask
[norm]Normalizes the output, mean->0 sigma->1
[mult=<constant>]Scales the densities in the output
[noise=<level>]Adds flatband noise at specified absolute level
[signoise=<sig mult>]Same, but level in terms of sigma
[vtk]Output should be in VTK format, not MRC
[spider]Output should be in Spider format, not MRC
[gwin=<radius>]Apply a Gaussian radial falloff, r is 1/e width

<input 1>Input to be compared
<input 2><input 2>
[apix=<A/pix>]Specify the Angstr/pixel for S scaling
[fsc=<out>]Fourier shell correlation
[phase=<out>]mean phase difference (not residual!)
[rfactor=<out>]R factor between inputs
[rms=<thresh>]RMS variation above threshold
[rdiv=<out>]Radial plot of input 1/input 2
[diffmap[=<~binary thr>]]Generates a difference map in "diffmap.mrc"
[sum=<output>]Adds input files

Usage:

proc3d threed.5a.mrc

proc3d threed.1.mrc threed.1a.mrc unhp=1 lp=15

proc3d threed.1a.mrc threed.2a.mrc apix=4.67 fsc=corr12.dat

Description

This program performs a variety of 3d image processing operations. Like all EMAN programs, it will automatically read any supported file format. It can be invoked in one of 3 ways. The first form simply provides statistical information on a single volume data set.

The second form will copy an input file to and output file after processing it in various ways. Most of the processing is explained in sufficient detail above, but there are a few notes:


EMAN Manual page, generated Mon Jan 10 15:41:44 2000