<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[,xc,yc,zc]>] | 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 |
[rfilt=<type>[,<val1>[,<val2>[,<val3>]]]] | Apply one of a variety of real-space filters |
[blfilt=<sigma1,sigma2,iter,localwidth>] | Apply bilateral filtering |
[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 |
[maskfile=<file>] | Multiplies the input by the specified file (must be same size) |
[norm] | Normalizes the output, mean->0 sigma->1 |
[bin=<thresh>] | use the threshold value to turn the 3D map into a binary map |
[mult=<constant>] | Scales the densities in the output |
[add=<constant>] | Adds a constant to the densities |
[noise=<level>] | Adds flatband noise at specified absolute level |
[signoise=<sig mult>] | Same, but level in terms of sigma |
[setsf=<SF file>] | Sets the structure factor based on a 1D x/y text file, must specify apix |
[vtk] | Output should be in VTK format, not MRC |
[amira] | Output should be in AMIRA format, not MRC |
[xplor] | Output should be in XPLOR format, not MRC |
[icos] | Output should be in ICOS format, not MRC |
[spider] | Output should be in Spider format, not MRC |
[imagic] | Output is an IMAGIC file |
[pif] | Output to a PIF (Purdue Image Format) file |
[gwin=<radius>] | Apply a Gaussian radial falloff, r is 1/e width |
[edgenorm] | Normalize the image based on the mean value at the edge of the box |
<input 1> | Input 1 to compare/process |
<input 2> | Input 2 to compare/process |
[apix=<A/pix>] | Specify the Angstr/pixel for S scaling |
[fsc=<out>] | Fourier shell correlation |
[phase=<out>] | mean phase difference (not residual!) |
[snr=<out>] | Relative signal to noise ratio between 2 images. |
[rfactor=<out>] | R factor between inputs |
[rms=<thresh>] | RMS variation above threshold |
[rdiv=<out>] | Radial plot of input 1/input 2 |
[rdivf=<out>] | Radial plot of input 1/input 2 |
[diffmap[=<~binary thr>]] | Generates a difference map in "diffmap.mrc" |
[sum=<output>] | Adds input files |
[pha1amp2=<out>] | Makes a new image with the phases from image 1 and the amplitudes from image2 |
[anim=<frames>] | Generates linearly interpolated intermediates between two maps |
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
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: