Hi all,
I am trying to convert a selected particles from a 2D classification using v2.15 of cryoSPARC to star file. The original coordinates of the particles (the particles.star) comes from Relion 3.0 in Scipion v2. I have imported that particles from Scipion to CS and then I run 2D classification in CS. Now, I would like to continue with the refinement in Relion. I have used the next command (using the last pyem version, v0.5):
csparc2star.py --copy-micrograph-coordinates particles.star particles_selected.cs P34_J165_passthrough_particles_selected.cs output_particles_CS.star --loglevel debug
Detected CryoSPARC 2+ .cs file
Reading primary file
Assigning parameters 2D classes or single 3D class
Assigning skew angle from 2D classification
Reading auxiliary file P34_J165_passthrough_particles_selected.cs
Classification parameters not found
Trying to merge: ctf/type, ctf/exp_group_id, 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/shift_A, ctf/tilt_A, ctf/trefoil_A, ctf/tetra_A, ctf/anisomag, ctf/bfactor
Merging: rlnOpticsGroup, rlnDefocusAngle, rlnDefocusU, rlnVoltage, rlnSphericalAberration, rlnPhaseShift, rlnCtfBfactor, rlnAmplitudeContrast, rlnDefocusV
Directly copied fields: ucsfImagePath, ucsfImageIndex, ucsfUid, rlnDetectorPixelSize, rlnRandomSubset, rlnOriginX, rlnOriginY, rlnAnglePsi, rlnClassNumber, rlnOpticsGroup, rlnDefocusAngle, rlnDefocusU, rlnVoltage, rlnSphericalAberration, rlnPhaseShift, rlnCtfBfactor, rlnAmplitudeContrast, rlnDefocusV, rlnMagnification
Converting DEFOCUSANGLE from degrees to radians
Converting PHASESHIFT from degrees to radians
Changing RANDOMSUBSET to 1-based index
Changing CLASS to 1-based index
Converting ANGLEPSI from degrees to radians
/services/tools/pyem/0.5/pyem-0.5/pyem/star.py:377: FutureWarning: Columnar iteration over characters will be deprecated in future releases.
df[Relion.IMAGE_NAME].str.split("@").str
/services/tools/pyem/0.5/pyem-0.5/pyem/star.py:386: FutureWarning: Columnar iteration over characters will be deprecated in future releases.
df[Relion.IMAGE_ORIGINAL_NAME].str.split("@").str
Coordinates merge key: None
Traceback (most recent call last):
File “/services/tools/pyem/0.5/pyem-0.5/csparc2star.py”, line 105, in
sys.exit(main(parser.parse_args()))
File “/services/tools/pyem/0.5/pyem-0.5/csparc2star.py”, line 68, in main
df = star.smart_merge(df, coord_star, fields=fields, key=key)
File “/services/tools/pyem/0.5/pyem-0.5/pyem/star.py”, line 108, in smart_merge
s2 = s2.set_index(key, drop=False)
File “/services/tools/pyem/0.5/lib/python3.6/site-packages/pandas/core/frame.py”, line 4550, in set_index
raise KeyError(f"None of {missing} are in the columns")
KeyError: ‘None of [None] are in the columns’
Any ideas what would it be wrong?
Thank you in advance,