e2tomogram.py tiltseries/RatNeuron_07092025_ct3__SA60_Sh4.hdf --stage2prep --outsuffix=_SA --tltax=0.5 --zeroid=-1 --tltstep=2.033898 --npk=20 --tltkeep=1.0 --outsize=1k --niter=2,1,1,1 --bytile --pkkeep=0.9 --compressbits=6 --clipz=384 --bxsz=32 --filterres=40.0 --rmbeadthr=-1.0 --threads=2 --patchtrack=2 --extrapad
Reading tilt series tiltseries/RatNeuron_07092025_ct3__SA60_Sh4.hdf...
Temporary files will be written in tomorecon_01
Using fixed tilt step of 2.033898
Coarse translational alignment...
(59, 256, 256)
skip jumping tilts: [ 6 56]
iter 0: tx = 3.05, ty = 14.86
skip jumping tilts: [1]
iter 1: tx = 0.10, ty = 0.25
skip jumping tilts: [1]
iter 2: tx = 0.08, ty = 0.25
removing 0 bad tilts
tilt axis: -0.50
[]
Doing patch tracking
shrink by 2
Traceback (most recent call last):
File "/home3/pbaldwin/mambaforge/envs/eman3_Oct2024/bin/e2tomogram.py", line 2620, in
main()
File "/home3/pbaldwin/mambaforge/envs/eman3_Oct2024/bin/e2tomogram.py", line 531, in main
tpm01, l0= do_patch_tracking(imgs_pt, ttparams[ikeep], options)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home3/pbaldwin/mambaforge/envs/eman3_Oct2024/bin/e2tomogram.py", line 827, in do_patch_tracking
ptclimgs=ptclimgs.reshape((len(pks), -1, sz,sz))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: cannot reshape array of size 704692224 into shape (81,newaxis,256,256)
Warning: e2tomogram.py exited with code 256
e2tomogram.py tiltseries/RatNeuron_07092025_ct3__SA60_Sh4.hdf --stage2prep --outsuffix=_SA --tltax=0.5 --zeroid=-1 --tltstep=2.033898 --npk=20 --tltkeep=1.0 --outsize=1k --niter=2,1,1,1 --bytile --pkkeep=0.9 --compressbits=6 --clipz=384 --bxsz=32 --filterres=40.0 --rmbeadthr=-1.0 --threads=2 --patchtrack=2 --extrapad
Reading tilt series tiltseries/RatNeuron_07092025_ct3__SA60_Sh4.hdf...
Temporary files will be written in tomorecon_01
Using fixed tilt step of 2.033898
Coarse translational alignment...
(59, 256, 256)
skip jumping tilts: [ 6 56]
iter 0: tx = 3.05, ty = 14.86
skip jumping tilts: [1]
iter 1: tx = 0.10, ty = 0.25
skip jumping tilts: [1]
iter 2: tx = 0.08, ty = 0.25
removing 0 bad tilts
tilt axis: -0.50
[]
Doing patch tracking
shrink by 2
Traceback (most recent call last):
File "/home3/pbaldwin/mambaforge/envs/eman3_Oct2024/bin/e2tomogram.py", line 2620, in
main()
File "/home3/pbaldwin/mambaforge/envs/eman3_Oct2024/bin/e2tomogram.py", line 531, in main
tpm01, l0= do_patch_tracking(imgs_pt, ttparams[ikeep], options)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home3/pbaldwin/mambaforge/envs/eman3_Oct2024/bin/e2tomogram.py", line 827, in do_patch_tracking
ptclimgs=ptclimgs.reshape((len(pks), -1, sz,sz))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: cannot reshape array of size 704692224 into shape (81,newaxis,256,256)
Warning: e2tomogram.py exited with code 256