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.


	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.