e2proc3d

Generic 3-D image processing program. The main tasks this program can be used for are:

Convert volumes from one format to another
Perform basic image processing operations such as filters, masks, normalization, etc.
Resize/rescale volumes
Compute FSC curves, structure factors, etc.

	medianshrink	bool	Downsamples the volume by a factor of n by computing the local median
	meanshrink	bool	Downsamples the volume by a factor of n by computing the local average
	meanshrinkbig	bool	Downsamples the volume by a factor of n without reading the entire volume into RAM. The output file (after shrinking) must fit into RAM. If specified, this must be the ONLY option on the command line. Any other options will be ignored. Output data type will match input data type. Works only on single image files, not stack files.
	meanshrinkbig	bool	Downsamples the volume by a factor of n without reading the entire volume into RAM. The output file (after shrinking) must fit into RAM. If specified, this must be the ONLY option on the command line. Any other options will be ignored. Output data type will match input data type. Works only on single image files, not stack files.
	scale	bool	Rescales the image by 'n', generally used with clip option.
	sym	bool	Symmetry to impose - choices are: c<n>, d<n>, h<n>, tet, oct, icos
	averager	bool	Averager used for --average and --sym options
	clip	bool	Make the output have this size by padding/clipping. 1, 3 or 6 arguments.
	fftclip	bool	Make the output have this size, rescaling by padding FFT.
	process	bool	apply a processor named 'processorname' with all its parameters/values.
	apix	bool	A/pixel for S scaling
	origin	bool	Set the coordinates for the pixel (0,0,0) for Chimera. THIS HAS NO IMPACT ON IMAGE PROCESSING !
	mult	bool	Scales the densities by a fixed number in the output
	multfile	bool	Multiplies the volume by another volume of identical size. This can be used to apply masks, etc.
	matchto	bool	Match filtration of input volume to this specified volume.
	outmode	bool	All EMAN2 programs write images with 4-byte floating point values when possible by default. This allows specifying an alternate format when supported (int8, int16, int32, uint8, uint16, uint32). Values are rescaled to fill MIN-MAX range.
	outnorescale	bool	If specified, floating point values will not be rescaled when writing data as integers. Values outside of range are truncated.
	mrc16bit	bool	(deprecated, use --outmode instead) output as 16 bit MRC file
	mrc8bit	bool	(deprecated, use --outmode instead) output as 8 bit MRC file
	add	bool	Adds a constant 'f' to the densities
	addfile	bool	Adds the volume to another volume of identical size
	calcfsc	bool	Calculate a FSC curve between two models. Output is a txt file. This option is the name of the second volume.
	filtertable	bool	Applies a 2 column (S,amp) file as a filter in Fourier space, assumed 0 outside the defined range.
	calcsf	bool	Calculate a radial structure factor. Must specify apix.
	calcradial	bool	Calculate the radial density by shell. Output file becomes a text file. 0 - mean amp, 2 - min, 3 - max, 4 - sigma
	setsf	bool	Set the radial structure factor. Must specify apix.
	tophalf	bool	The output only keeps the top half map
	inputto1	bool	All voxels in the input file are set to 1 after reading. This can be used with mask.* processors to produce a mask file of the correct size.
	icos5fhalfmap	bool	The input is the icos 5f top half map generated by the 'tophalf' option
	outtype	bool	Set output image format, mrc, imagic, hdf, etc
	first	bool	the first image in the input to process [0 - n-1])
	trans	bool	Translate map by dx,dy,dz
	resetxf	bool	Reset an existing transform matrix to the identity matrix
	align	bool	Align input map to reference specified with --alignref. As with processors, a sequence of aligners is permitted
	ralignzphi	string	Refine Z alignment within +-10 pixels and phi +-15 degrees (for C symmetries), specify name of alignment reference here not with --alignref
	alignref	bool	Alignment reference volume. May only be specified once.
	alignctod	string	Rotates a map already aligned for C symmetry so the best 2-fold is positioned for specified D symmetry. Does not impose specified symmetry.
	rot	string	Rotate map. Specify az,alt,phi or convention:par=val:par=val:... eg - mrc:psi=22:theta=15:omega=7
	icos5to2	bool	Rotate an icosahedral map from 5-fold on Z (EMAN standard) to 2-fold on Z (MRC standard) orientation
	icos2to5	bool	Rotate an icosahedral map from 2-fold on Z (MRC standard) to 5-fold on Z (EMAN standard) orientation
	last	bool	the last image in the input to process
	swap	bool	Swap the byte order
	average	bool	Computes the average of a stack of 3D volumes
	append	bool	Append output image, i.e., do not write inplace.
	ppid	int	Set the PID of the parent process, used for cross platform PPID
	unstacking	bool	Process a stack of 3D images, then output a a series of numbered single image files
	tomoprep	bool	Produces a special HDF file designed for rapid interactive tomography annotation. This option should be used alone.
-v	verbose	bool	verbose level [0-9], higner number means higher level of verboseness
	step	string	Specify <init>,<step>. Processes only a subset of the input data. For example, 0,2 would process only the even numbered particles

This program operates on single 3-D volume files, stacks of 3-D volume files, and EMAN2 BDB databases. It has many command-line options for specific tasks. The generic '--process' option is by far the most powerful, offering access to 180+ different image processing operations. For a list, type e2help.py processors.

For specific details on various options, use e2proc3d.py --help.

Examples

convert SPIDER format test.spi to HDF format:

e2proc3d.py test.spi test.hdf

extract a volume from a BDB database and convert to HDF format for visualization in Chimera

e2proc3d.py bdb:refine_01#threed_filt_04 volume.hdf

apply a 10 A low-pass filter to a volume in-place.

e2proc3d.py bdb:refine_01#threed_filt_04 bdb:refine_01#threed_filt_04 --process=filter.lowpass.gauss:cutoff_freq=0.1