Anyone an idea if there were changes in the latest cryosparc update (v2.3.2) regarding the file format?
Reading of the passthrough file after refinement fails.
$ /home/user/pyem/csparc2star.py P6/J62/cryosparc_P6_J62_011_particles.cs --passthrough P6/J62/passthrough_particles.cs csparc_J62_pass.star --loglevel debug
Detected CryoSPARC 2+ .cs file
Reading passthrough file
Particle passthrough detected
Concatenating passthrough fields: 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, location/micrograph_uid, location/micrograph_path, location/micrograph_shape, location/center_x_frac, location/center_y_frac, pick_stats/ncc_score, pick_stats/power, pick_stats/template_idx, pick_stats/angle_rad
/home/user/pyem/pyem/util/util.py:74: FutureWarning: Numpy has detected that you may be viewing or writing to an array returned by selecting multiple fields in a structured array.
This code may break in numpy 1.16 because this will return a view instead of a copy – see release notes for details.
joint[:, offset:offset + size] = a.view(np.uint8).reshape(n, size)
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 with subpixel origin
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 “/home/user/pyem/csparc2star.py”, line 42, in main
df = metadata.parse_cryosparc_2_cs(cs, passthrough=args.passthrough, minphic=args.minphic)
File “/home/user/pyem/pyem/metadata.py”, line 326, in parse_cryosparc_2_cs
[cs[names[c]][i] for i, c in enumerate(cls)]))
File “/home/user/miniconda2/lib/python2.7/site-packages/pandas/core/frame.py”, line 3116, in setitem
self._setitem_array(key, value)
File “/home/user/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