Comparison of SPIDER Alignment Operations

Operation	Multiple images	Multiple references	Shift	Rotation	Restricted Projections	Check Mirrored position	Source code	Notes
'AP SH'	+	+	+	+	+/-	+/-	apmaster.f, mrqli_ps.f, mrqli_ss.f	Exhaustive optimal search of rotations and shifts.
'AP REF'	+/-	+	+/-	+	+/-	+/-	apmaster.f, dsgr_pm.f, dsfs_p.f	Search of rotations followed by shifts for optimal rotation.
'AP I'	-	-	-	-	-	-	apmaster.f, aprings.f	Create rings file for'AP SH' & 'AP REF'
'AP MS'	+	+	+	-	-	-	multishift.f	Also checks 180 degree rotation
'AP SA'	+	-	+	-	-	-	saqb.f	Reference free
'AP SR'	+	-	+	+	-	-	gali.f	Reference free
'AP RA'	+	-	-	+	-	-	falb.f	Self-alignment
'AP C'	+	-	-	+	-	+/-	hali.f & hali_p.f	Also classifies images into groups. Replaces 'AP CA', 'AP CM'.
'OR A'	-	-	+	+	-	+/-	oracfmsk.f, oracfmskm.f, frng.f	Self-correlation
'OR Q'	+	+	+	+	-	+/-	oracfmskm.f, frng.f	Self-correlation
'OR SH'	-	-	+	+	-	+/-	apmaster.f, mrqli_ss.f	Same method as 'AP SH'. Replaces 'OR MQ', 'OR NQ'.
'OR R'	-	-	-	+	-	x	ormd.f, ormd_p.f	Same method as 'AP SH' without shifts. Replaces 'OR 2' & 'OR 2M'.

NOTE: 'AP SH' differs from 'AP REF' in that the former has an exhaustive search of all specified rotations and shifts, while the latter first finds the optimal rotation and then only searches for optimal shift for that rotation only.

Source file: align_overview.html     Updated: 18 June 2008     ArDean Leith