Hi all,
Thanks @DanielAsarnow and @olibclarke for clarifications. CryoSPARC Patch Motion does in fact write out motion trajectories (as plain numpy array files in the job output dir) but Relion or other programs will not know how to read these.
Also the reason for the --swapxy (I believe - looking through pyem code) is that in cryoSPARC, we use the convention that 2D/3D arrays are always stored in C-order, with the fastest axis being the “x” axis, and we use a right hand coordinate system. That means that 2D arrays are stored with their slow (first) axis being Y, and second (fast) axis being X. Therefore the “shape” of a 2D array will be [ny,nx] and a 3D array shape will be [nz,ny,nx].
Vectors that describe a position (in 2D or 3D) also follow the right-hand convention, meaning that they are stored in standard geometry order, (x,y,z). So particle locations are stored as (x,y) pairs, while the shape of the micrograph is stored as [ny,nx] to maintain the conventions.