I’m trying to do a local refinement with simulated data. This is the first time I have tried using simulated data. The job fails very early. I haven’t had this issue with local refinement before. I just cloned and re-ran a job, and verified that this isn’t an issue with other particles.
The particles shapes match up. The volume, mask and particles are all the same pixel size.
[CPU: 99.4 MB] Importing job module for job type naive_local_refine...
[CPU: 216.7 MB] Job ready to run
[CPU: 216.7 MB] ***************************************************************
[CPU: 287.9 MB] Traceback (most recent call last):
File "cryosparc2_worker/cryosparc2_compute/run.py", line 85, in cryosparc2_compute.run.main
File "cryosparc2_worker/cryosparc2_compute/jobs/local_refine/run.py", line 92, in cryosparc2_compute.jobs.local_refine.run.run_naive_local_refine
File "cryosparc2_compute/particles.py", line 33, in init
self.N_input = int(self.data['blob/shape'][0,0])
KeyError: 'blob/shape'
Also, here’s a line from the .cs file of the simulated data
( 4148471469181798092, '/run/media/owner/Data1/P1/J1518/simulated_particles.mrcs', 19999, [200, 200], 1.02999997, 1., '', 0, 300., 2.70000005, 0.07, 9915.01660156, 10341.85546875, 0.56149507, 0., 1., 0., [ 0., 0.], [ 0., 0.], [ 0., 0.], [ 0., 0., 0., 0.], [ 0., 0., 0., 0.], 0., 0, [ 0., 0.], [-0.44879895, -3.14159274, -2.24399471], 0., 0., 0., 0., 0., 0., 0., 1., 0., 0., 0., 0., 0., 0, 0., [ 0., 0., 0.], [ 0., 0.], [ 0., 0., 0.])],
dtype=[('uid', '<u8'), ('blob/path', 'S57'), ('blob/idx', '<u4'), ('blob/shape', '<u4', (2,)), ('blob/psize_A', '<f4'), ('blob/sign', '<f4'), ('ctf/type', 'S1'), ('ctf/exp_group_id', '<u4'), ('ctf/accel_kv', '<f4'), ('ctf/cs_mm', '<f4'), ('ctf/amp_contrast', '<f4'), ('ctf/df1_A', '<f4'), ('ctf/df2_A', '<f4'), ('ctf/df_angle_rad', '<f4'), ('ctf/phase_shift_rad', '<f4'), ('ctf/scale', '<f4'), ('ctf/scale_const', '<f4'), ('ctf/shift_A', '<f4', (2,)), ('ctf/tilt_A', '<f4', (2,)), ('ctf/trefoil_A', '<f4', (2,)), ('ctf/tetra_A', '<f4', (4,)), ('ctf/anisomag', '<f4', (4,)), ('ctf/bfactor', '<f4'), ('alignments3D/split', '<u4'), ('alignments3D/shift', '<f4', (2,)), ('alignments3D/pose', '<f4', (3,)), ('alignments3D/psize_A', '<f4'), ('alignments3D/error', '<f4'), ('alignments3D/error_min', '<f4'), ('alignments3D/resid_pow', '<f4'), ('alignments3D/slice_pow', '<f4'), ('alignments3D/image_pow', '<f4'), ('alignments3D/cross_cor', '<f4'), ('alignments3D/alpha', '<f4'), ('alignments3D/alpha_min', '<f4'), ('alignments3D/weight', '<f4'), ('alignments3D/pose_ess', '<f4'), ('alignments3D/shift_ess', '<f4'), ('alignments3D/class_posterior', '<f4'), ('alignments3D/class', '<u4'), ('alignments3D/class_ess', '<f4'), ('alignments3D/localpose', '<f4', (3,)), ('alignments3D/localshift', '<f4', (2,)), ('alignments3D/localfulcrum', '<f4', (3,))])