This program will align a set of images to a reference
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