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]

<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

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