= e2proc2d =

Generic 2-D image processing program. The main tasks this program can be used for are:

 * Convert images from one format to another
 * Perform basic image processing operations such as filters, masks, normalization, etc.
 * Resize/rescale images
 * Select subsets of image stacks

Options:
|| ||apix||float||A/pixel for S scaling||
|| ||average||bool||Averages all input images (without alignment) and writes a single output image||
|| ||averager||string||If --average is specified, this is the averager to use (e2help.py averager). Default=mean||
|| ||calcsf||string||calculate a radial structure factor for the image and write it to the output file, must specify apix. divide into <n> angular bins||
|| ||calccont||bool||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||string||Specify the output size in pixels xsize,ysize[,xcenter,ycenter], images can be made larger or smaller.||
|| ||exclude||string||Excludes image numbers in EXCLUDE file||
|| ||fftavg||string||Incoherent Fourier average of all images and write a single power spectrum image||
|| ||process||string||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||string||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||string||Works only on the image numbers in LIST file||
|| ||select||string||Works only on the images in named selection set from bdb:select||
|| ||inplace||bool||Output overwrites input, USE SAME FILENAME, DO NOT 'clip' images.||
|| ||interlv||string||Specifies a 2nd input file. Output will be 2 files interleaved.||
|| ||extractboxes||bool||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||bool||this is an experimental option||
|| ||outmode||string||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||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||
|| ||fixintscaling||string||When writing to an 8 or 16 bit integer format the data must be scaled. 'noscale' will assume the pixel values are already correct, 'sane' will pick a good range, a number will set the range to mean+=sigma*number||
|| ||multfile||string||Multiplies the volume by another volume of identical size. This can be used to apply masks, etc.||
|| ||norefs||bool||Skip any input images which are marked as references (usually used with classes.*)||
|| ||outtype||string||output image format, 'mrc', 'imagic', 'hdf', etc. if specify spidersingle will output single 2D image rather than 2D stack.||
|| ||radon||bool||Do Radon transform||
|| ||randomize||string||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||bool||Compute the 1-D rotational average of each image as a final step before writing the output||
|| ||rotate||float||Rotate clockwise (in degrees)||
|| ||rfp||bool||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||string||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||bool||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||string||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.||
|| ||writejunk||bool||Writes the image even if its sigma is 0.||
|| ||swap||bool||Swap the byte order||
|| ||threed2threed||bool||Process 3D image as a stack of 2D slices, then output as a 3D image||
|| ||threed2twod||bool||Process 3D image as a stack of 2D slices, then output as a 2D stack||
|| ||twod2threed||bool||Process a stack of 2D images, then output as a 3D image.||
|| ||unstacking||bool||Process a stack of 2D images, then output a a series of numbered single image files||
|| ||ppid||int||Set the PID of the parent process, used for cross platform PPID||
|| ||step||string||Specify <init>,<step>. Processes only a subset of the input data. For example, 0,2 would process only the even numbered particles||
||-v||verbose||int||verbose level [0-9], higner number means higher level of verboseness||
||-P||parallel||string||Run in parallel, specify type:n=<proc>:option:option||


This program operates on both single 2-D image files, image stacks, EMAN2 BDB databases, and can even treat 3-D volumes as a stack
of 2-D images for individual processing. 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 ''e2proc2d.py --help''.

=== Examples ===
convert IMAGIC format test.hed to HDF format:
{{{
e2proc2d.py test.hed test.hdf		
}}}

extract a subset of particles from a BDB database and convert to HDF format
{{{
e2proc2d.py bdb:particles#stack1 newfile.hdf --first=100 --last=150
}}}

apply a 10 A low-pass filter to a stack of particles and write output to a new file. 
{{{
e2proc2d.py ptcl.hdf ptcl.filt.hdf --process=filter.lowpass.gauss:cutoff_freq=0.1
}}}

invert the contrast in a BDB database. Overwrite the original images
{{{
e2proc2d.py bdb:particles#set1 bdb:particles#set1 --inplace --mult=-1
}}}