This program performs various processing operations on images and sets of images

proc2d <input file> <output file> [first=<n>] [last=<n>] [list=<list file>] [exclude=<list file>] [nobad] [inplace] [edgenorm] [norm[=<mean>,<sigma>]] [invert] [flip] [rot=<angle>] [trans=<dx>,<dy>] [center] [acfcenter] [scale=<sca>] [clip=<newsize x&y>] [shrink=<n>] [meanshrink=<n>] [apix=<A/pix>] [lp=<filt r>] [hp=<filt r>] [tlp=<filt r>] [rfilt=<type>[,<val1>[,<val2>[,<val3>]]]] [blfilt=<sigma1,sigma2,iter,localwidth>] [filefilt=<file>] [mask=<radius>] [imask=<radius>] [noisemask] [gaussmask] [calcsf=[<n>,]<output>] [mrc] [mrc8bit] [pif] [hdf] [png] [em] [spider] [spider-single] [spiderswap] [spiderswap-single] [pgm[=<low>,<hi>]] [sharphp=<pixels>] [norefs] [rotav] [average] [fftavg=<file name>] [split=n] [ctfsplit] [interlv=<file 2 interleave>] [sym=<Cn>] [plt[=<plt file>]] [setsfpairs] [addnoise=<level>] [randomize=<dr>,<da>,<flip>] [snrfilt=<SF file>] [wiener=<SF file>[,<amp sca>[,<amp cont>]]] [wienernoc=<SF file>] [selfcl[=<steps>][,<mode>]] [comment=<str>] [radon] [rfp] [mraprep] [phot] [rsub]



Input file


Output file. Appends to output file unless inplace specified


Specify the first image in the input to process (0 - n-1)


Specify the last image in the input to process

[list=<list file>]

Works only on the image numbers contained in <list file>

[exclude=<list file>]

Excludes image numbers in <list file>


Exclude particles with simga=0


Output overwrites input, USE SAME FILENAME, DO NOT 'clip' images.


Output is always normalized, this will set 0 to the circular edge value rather than the overall mean


Normalize the result


Inverts the density


Vertical flip of image (inverts handedness)


Rotate by an angle (degrees)




Center image using center of mass


Center image using CCF with 180 deg rotation


Scale by specified scaling factor. Clip must also be specified to change the dimensions of the output map

[clip=<newsize x&y>]

Define the output image size (always square)


Reduce an image size by an integral scaling factor, uses median filter. Clip is not required.


Same as shrink, but takes the average instead of the median. Clip is not required.


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, r in angstroms if apix defined, pixels if undef

[tlp=<filt r>]

Arctan lowpass filter, r in angstroms if apix defined, pixels if undef


Apply one of a variety of real-space filters


Apply bilateral filtering


Filter with a Fourier filter specified in a 2 column text file


Circular mask


Circular inner mask


Fill the masked region with 1-sigma noise rather than zero


Make the mask a Gaussian falloff


This will calculate a radial structure factor for the image and write it to the specified output file, must specify apix. Optionally divide into <n> angular bins


Output a set of MRC files rather than a single IMAGIC stack


Output a set of 8-bit MRC files to conserve space


Output to a PIF (Purdue Image Format) file


Output to a HDF5 (Hierarchical Data Format) file.


Output to a PNG (Portable Network Graphics) file


Output to a EM image file


Output a Spider stack file rather than an IMAGIC stack


Output in individual Spider files rather than an IMAGIC file


Output a spider stack file in byte-swapped order (ie - PC vs SGI)


Output in individual Spider files in swapped order rather than an IMAGIC file


Output a set of PGM images rather than an IMAGIC stack


A highpass with a sharp cutoff (beware artifacts)


Skip any input images which are marked as references (usually used with classes.*)


Each image is rotationally averaged


Averages all input images (without alignment) and writes a single (normalized) output image

[fftavg=<file name>]

Incoherent Fourier average of all images and write a single power spectrum image


Splits the input file into a set of n output files


Splits the input file into output files with the same CTF parameters

[interlv=<file 2 interleave>]

Specifies a 2nd input file. Output will be 2 files interleaved.


Apply an n-fold rotational symmetry to each image

[plt[=<plt file>]]

output the orientations in IMAGIC .plt file format


Applies the radial structure factor of the 1st image to the 2nd, the 3rd to the 4th, etc


Add flatband gaussian noise with defined standard deviation


This will randomly rotate and translate each particle

[snrfilt=<SF file>]

Filter the images by the estimated SNR in each image.

[wiener=<SF file>[,<amp sca>[,<amp cont>]]]

Wiener filter the images using the estimated SNR with CTF amplitude correction.

[wienernoc=<SF file>]

Wiener filter the images without CTF amplitude correction.


Output file will be a 180x180 self-common lines map for each image.

[comment=<str>] Sets the comment string in the output file (if supported

[comment=<str>] Sets the comment string in the output file (if supported)


Do Radon transform










proc2d 3244.img start.hed invert apix=5 lp=18

proc2d start.hed start.hed invert inplace


This program is used to perform a variety of generic 2D image processing tasks. Like all of the EMAN programs, it will read any supported file format. By default it outputs to an Imagic file although there are options to change this. Note that, by default, images are appended to the end of the output file if it already exists. All images in one file MUST have the same size. ie - if you try to copy 50x50 images to the end of a file that already contains 100x100 images, an error will result. Note the 'first=' and 'last=' options allow a subset of the input file to be processed. The 'inplace' keyword may be used to cause output images to overwrite the input images rather than being appended to the end of the file.

Most of the processing is explained in sufficient detail above, but there are a few notes:

EMAN1/Programs/Proc2D (last edited 2008-11-26 04:42:30 by localhost)