Hello @DanielAsarnow,
I seem to be having a little trouble with pyem. I use the --passthrough command however there is still a request for it (please see below). Could you please let me know what I am doing wrong?
Thank you for your time!
Kellie
$ /data/CRYOSPARC/pyem/csparc2star.py --passthrough /data/CRYOSPARC/USERS/KELLIE/CRYOSPARC_projects/P1/J771/passthrough_particles.cs /data/CRYOSPARC/USERS/KELLIE/CRYOSPARC_projects/P1/J771/extracted_particles.cs from_cryosparc.star --loglevel debug
Detected CryoSPARC 2+ .cs file
Reading passthrough file
Particle passthrough detected
Concatenating passthrough fields: location/micrograph_uid, location/micrograph_path, location/micrograph_shape, location/center_x_frac, location/center_y_frac, ctf/type, ctf/accel_kv, ctf/cs_mm, ctf/amp_contrast, ctf/df1_A, ctf/df2_A, ctf/df_angle_rad, ctf/phase_shift_rad, ctf/scale, ctf/scale_const, ctf/cross_corr_ctffind4, ctf/ctf_fit_to_A, ctf/fig_of_merit_gctf, alignments3D/split, alignments3D/shift, alignments3D/pose, alignments3D/psize_A, alignments3D/error, alignments3D/error_min, alignments3D/resid_pow, alignments3D/slice_pow, alignments3D/image_pow, alignments3D/cross_cor, alignments3D/alpha, alignments3D/weight, alignments3D/pose_ess, alignments3D/shift_ess, alignments3D/class_posterior, alignments3D/class, alignments3D/class_ess, alignments2D/split, alignments2D/shift, alignments2D/pose, alignments2D/psize_A, alignments2D/error, alignments2D/error_min, alignments2D/resid_pow, alignments2D/slice_pow, alignments2D/image_pow, alignments2D/cross_cor, alignments2D/alpha, alignments2D/weight, alignments2D/pose_ess, alignments2D/shift_ess, alignments2D/class_posterior, alignments2D/class, alignments2D/class_ess, motion/type, motion/path, motion/idx, motion/frame_start, motion/frame_end, motion/zero_shift_frame, pick_stats/ncc_score, pick_stats/power, pick_stats/template_idx, pick_stats/angle_rad
Creating particle DataFrame from recarray
Directly copied fields: rlnDefocusAngle, rlnDetectorPixelSize, rlnCtfFigureOfMerit, rlnSphericalAberration, rlnAmplitudeContrast, rlnMicrographName, rlnCtfMaxResolution, rlnVoltage, rlnDefocusU, rlnPhaseShift, rlnDefocusV, rlnImageName, rlnMagnification
Converting normalized particle coordinates to absolute
Converted particle coordinates from normalized to absolute
Converting DEFOCUSANGLE from degrees to radians
Converting PHASESHIFT from degrees to radians
Collecting particle parameters from most likely classes
Columns must be same length as key
A passthrough file may be required (check inside the cryoSPARC 2+ job directory)
Columns must be same length as key
Traceback (most recent call last):
File “/data/CRYOSPARC/pyem/csparc2star.py”, line 42, in main
df = metadata.parse_cryosparc_2_cs(cs, passthrough=args.passthrough, minphic=args.minphic)
File “/data/CRYOSPARC/pyem/pyem/metadata.py”, line 349, in parse_cryosparc_2_cs
[cs[names[c]][i] for i, c in enumerate(cls)]))
File “/data/CRYOSPARC/miniconda2/lib/python2.7/site-packages/pandas/core/frame.py”, line 3116, in setitem
self._setitem_array(key, value)
File “/data/CRYOSPARC/miniconda2/lib/python2.7/site-packages/pandas/core/frame.py”, line 3138, in _setitem_array
raise ValueError(‘Columns must be same length as key’)
ValueError: Columns must be same length as key