e2proc2d

usage: e2proc2d.py [options] <inputfile> ... <inputfile> <outputfile>

	MRC stack files MUST use the .mrcs extension to be treated as a set of 2-D images (or you must 
	use one of the --threed* options)

	If there is more than one input file, then outputfile is a pattern, where @
	in the pattern is replaced by the input file base name (minus any extension).

	Generic 2-D image processing and file format conversion program. Acts on stacks of 2-D images
	(multiple images in one file). All EMAN2 recognized file formats accepted (see Wiki for list).

	You can create a new 2-D or 3-D image from scratch instead of reading from a file by specifying 
	':<nx>:<ny>:<expression_in_x_y>' or ':<nx>:<ny>:<nz>:<expression_in_x_y_z>' as an input filename,
	where 0 <= x < nx, 0 <= y < ny, 0 <= z < nz, and the expression can be just a number.

	If performing certain operations which do not require an output file, specify "none" as the output file.

	Examples:

	convert IMAGIC format test.hed to HDF format:
	e2proc2d.py test.hed test.hdf

	convert all MRC format files in current directory to HDF format:
	e2proc2d.py *.mrc @.hdf

	convert a 'set' (.lst file) to an MRC stack file:
	e2proc2d.py sets/myset.lst myset.mrcs

	create a new image, initialized with 1.0, then mask it:
	e2proc2d.py :128:128:1 mymask.hdf --process mask.soft:outer_radius=50

	apply a 10 A low-pass filter to a stack of particles downsample the particles by a factor of 2
	and write output to a new file.
	e2proc2d.py ptcl.hdf ptcl.filt.hdf --process filter.lowpass.gauss:cutoff_freq=0.1 --meanshrink 2

	'e2help.py processors -v 2' for a detailed list of available procesors

Option	Type	Description
--version	None	show program's version number and exit
--apix	float	A/pixel for S scaling
--average	None	Averages all input images (without alignment) and writes a single output image
--avgseq	int	Averages sets of N sequential frames. eg - if N=4 and the input contains 100 images, the output would be 25 images
--averager	str	If --average is specified, this is the averager to use (e2help.py averager). Default=mean
--calcsf	str	calculate a radial structure factor for the image and write it to the output file, must specify apix. divide into <n> angular bins
--calccont	None	Compute the low resolution azimuthal contrast of each image and put it in the header as eval_contrast_lowres. Larger values imply more 'interesting' images.
--clip	str	Specify the output size in pixels xsize,ysize[,xcenter,ycenter], images can be made larger or smaller.
--exclude	str	Excludes image numbers, either a list of comma separated values, or a filename with one number per line, first image == 0
--fftavg	str	Incoherent Fourier average of all images and write a single power spectrum image
--process	str	apply a processor named 'processorname' with all its parameters/values.
--mult	float	Multiply image by a constant. mult=-1 to invert contrast.
--add	float	Adds a constant 'f' to the densities
--addfile	str	Adds the volume to another volume of identical size
--first	int	the first image in the input to process [0 - n-1])
--last	int	the last image in the input to process
--list	str	Works only on the image numbers in LIST file
--select	str	Works only on the images in named selection set from bdb:select
--randomn	int	Selects a random subset of N particles from the file to operate on.
--inplace	None	Output overwrites input, USE SAME FILENAME, DO NOT 'clip' images.
--interlv	str	Specifies a 2nd input file. Output will be 2 files interleaved.
--extractboxes	None	Extracts box locations from the image header to produce a set of .box files for only the particles in the .lst files
--meanshrink	float	Reduce an image size by an integral (1.5 also allowed) scaling factor using average. eg - 2 will reduce image size to 1/2. Clip is not required.
--medianshrink	int	Reduce an image size by an integral scaling factor, uses median filter. eg - 2 will reduce image size to 1/2. Clip is not required.
--fouriershrink	float	Reduce an image size by an arbitrary scaling factor by clipping in Fourier space. eg - 2 will reduce image size to 1/2.
--mraprep	None	this is an experimental option
--compressbits	int	HDF only. Bits to keep for compression. -1 for no compression
--outmode	str	All EMAN2 programs write images with 4-byte floating point values when possible by default. This allows specifying an alternate format when supported (float, int8, int16, int32, uint8, uint16, uint32). Values are rescaled to fill MIN-MAX range.
--outnorescale	None	If specified, floating point values will not be rescaled when writing data as integers. Values outside of range are truncated.
--mrc16bit	None	(deprecated, use --outmode instead) output as 16 bit MRC file
--mrc8bit	None	(deprecated, use --outmode instead) output as 8 bit MRC file
--fixintscaling	str	When writing to an 8 or 16 bit integer format the data must be scaled. 'noscale' will assume the pixel values are already correct, 'full' will insure the full range of values are included in the output, 'sane' will pick a good range, a number will set the range to mean+=sigma*number
--multfile	str	Multiplies the volume by another volume of identical size. This can be used to apply masks, etc.
--norefs	None	Skip any input images which are marked as references (usually used with classes.*)
--outtype	str	output image format, 'mrc', 'imagic', 'hdf', etc. if specify spidersingle will output single 2D image rather than 2D stack.
--radon	None	Do Radon transform
--randomize	str	Randomly rotate/translate the image. Specify: da,dxy,flip da is a uniform distribution over +-da degrees, dxy is a uniform distribution on x/y, if flip is 1, random handedness changes will occur
--rotavg	None	Compute the 1-D rotational average of each image as a final step before writing the output
--rotate	float	Rotate clockwise (in degrees)
--rfp	None	this is an experimental option
--fp	int	This generates rotational/translational 'footprints' for each input particle, the number indicates which algorithm to use (0-6)
--scale	float	Scale by specified scaling factor. Clip must also be specified to change the dimensions of the output map.
--anisotropic	str	Anisotropic scaling, stretches on one axis and compresses the orthogonal axis. Specify amount,angle. See e2evalrefine
--selfcl	int	Output file will be a 180x180 self-common lines map for each image.
--setsfpairs	None	Applies the radial structure factor of the 1st image to the 2nd, the 3rd to the 4th, etc
--split	int	Splits the input file into a set of n output files
--translate	str	Translate by x,y pixels
--headertransform	int	This will take the xform.align2d header value from each particle, and apply it. Pass 0 to perform the transform or 1 to perform the inverse.
--verbose, -v	int	verbose level [0-9], higher number means higher level of verboseness
--plane	str	Change the plane of image processing, useful for processing 3D mrcs as 2D images.
--writejunk	None	Writes the image even if its sigma is 0.
--swap	None	Swap the byte order
--threed2threed	None	Process 3D image as a stack of 2D slices, then output as a 3D image
--threed2twod	None	Process 3D image as a stack of 2D slices, then output as a 2D stack
--twod2threed	None	Process a stack of 2D images, then output as a 3D image.
--unstacking	None	Process a stack of 2D images, then output as a series of numbered single image files
--ppid	int	Set the PID of the parent process, used for cross platform PPID
--step	str	Specify <init>,<step>. Processes only a subset of the input data. For example, 0,2 would process only the even numbered particles
--eer2x	None	Render EER file on 8k grid.
--eer4x	None	Render EER file on 16k grid.
--parallel, -P	str	Run in parallel, specify type:n=<proc>:option:option

For more information go to emanwiki/EMAN2/Programs/e2proc2d.