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cp data.hdf data_copy.hdf

sxali2d_c.py data_copy.hdf ali2d_c --ir=1 --ou=30 --rs=1 --xr=3 --yr=3 --ts=1 --center=1 --maxit=10 || exit

sxali2d_e.py data_copy.hdf ali2d_e --ou=30 --br=1 --center=1 --eps=0.0001 --maxit=10 || exit

sxali2d_ra.py data_copy.hdf --ir=1 --ou=30 --rs=1 --maxit=10 --check_mirror --rand_seed=10 || exit

sxtransform2d.py data_copy.hdf data_aligned.hdf || exit

sxk_means.py data_aligned.hdf Kmeans 25 --trials=10 --init_method=Random --opt_method=MOV --maxit=100 --rand_seed=10 || exit

sxali2d_m.py data_aligned.hdf Kmeans/average.hdf ali2d_m  --ir=1 --ou=30 --rs=1 --xr=3 --yr=3 --ts=1 --center=1 --maxit=10 --rand_seed=10 || exit

sxfind_struct.py multi_ref.hdf voronri --delta=20 --rand_seed=10 || exit

sxrecons3d_n.py voronri/result.hdf pre_vol.spi || exit

sxali_2D_to_3D.py data_aligned.hdf || exit

sxali3d_d.py data_aligned.hdf pre_vol.spi ali3d_d --ir=1 --ou=30 --rs=1 --xr='2 2' --yr='-1' --ts='1 0.5' --delta='10 6' --an="-1" --center=1 --maxit=5 --ref_a=S --sym=c1 || exit

sxali3d_e.py data_aligned.hdf ali3d_d/vol0010.spi ali3d_e --ou=30 --dtheta=2 --maxit=5 --sym=c1 --chunk=1.0 || exit

sxssnr3d.py data_aligned.hdf vol_var ssnr_text --ou=30 --rw=1 --npad=1 --sign=1 --sym=c1 || exit