AlignementParametersNote

Note on alignment parameters

In Xmipp, we try to minimize interpolation of the pixel values by rotation or translation of the image matrix. Therefore, alignment parameters (in-plane rotation Psi, origin offsets Xoff and Yoff, and occasionaly a flag for the mirror operation) are stored in the header of 2D-images. Most Xmipp programs (exceptions is FindCenter!) then apply the corresponding transformation upon reading the image from disk. In this way, for the user it seems as if the transformation has been applied, but the images are never interpolated more than once. The following transformation is performed upon reading the images:

1. Shift the matrix by origin offsets Xoff and Yoff.
2. If the mirror-flag is set to 1: perform a mirror operation on the X-coordinates (flipX)
3. Rotate the matrix according to the following rules:

• if (Theta==0) rotate Phi+Psi degrees (untilted images)
• else rotate Psi degrees (tilted images)

The information stored in the image headers can be extracted and stored into (Spider-format) document files using the Header_extract and Header_assign programs. In this way, the docfiles provide a convenient way to backup your alignment results. Note that the option-mirror should be given explicitly in the header_assign program if you want to apply the mirror operations (for example after a maximum-likelihood refinement with mirror operations included).

Actual modification of the pixel matrix may be performed using theHeader_apply program (which applies the above mentioned transformation) or programs like shift, rotate and flip.

--Main.AlfredoSolano - 16 Jan 2007