align2d

• This program will align a set of images to a reference

Usage

• align2d <fixed input> <input> <output> [fixn=<n>] [noflip] [precen] [seqali] [eulali] [pgm] [log] [edgenorm] [keepeulers]

Parameters

• <fixed input>	Reference image
  <input>	Images to be aligned
  <output>	Output filename
  [fixn=<n>]	Image number to use in fixed input stack
  [noflip]	Rotational/translational alignment without flips
  [precen]	No translational alignment
  [seqali]	Align 1st image to ref, 2nd to 1st, 3rd to 2nd, etc.
  [eulali]	Align each image to images with similar Eulers, referring to the 1st image in the file.
  [pgm]	Output in pgm format, note there should only be one input in this case
  [log]	Logs rotations/translations to align.log
  [edgenorm]	Perform an edgenormalization of both images before alignment
  [keepeulers]	Indicates that the input images have accurate Eulers which need to be preserved.

  Typical usage: align2d proj.hed cls000.hed tst.hed

Description

Pretty self explanatory. If the input is a stack, the first image is used.

EMAN Manual page, generated Mon Jan 8 17:35:59 2007