The second image is transformed to fit on the first image.
| Bimage* p1 | first image. |
| Bimage* p2 | second image (transformed) |
| Vector3 | 3-valued vector for the size of sub-images. |
| float res_lo | low resolution limit for cross-correlation. |
| float res_hi | high resolution limit for cross-correlation. |
| int filter_flag | flag to filter micrograph extremes. |
| int refine_flag | flag to turn on refinement of shift. |