If the template and target SkyFrames both have defined offset coordinate systems (i.e. the SkyRefIs attribute is set to either "Origin" or " Pole"), and they both have a non-zero value for AlignOffset, then alignment occurs within the offset coordinate systems (that is, a UnitMap will always be used to align the two SkyFrames). If either the template or target SkyFrame has zero (the default value) for AlignOffset, or if either SkyFrame has SkyRefIs set to "Ignored", then alignment occurring within the coordinate system specified by the AlignSystem attribute.
AST A Library for Handling World Coordinate Systems in Astronomy