Class 2D - ValueError: total size of new array must be unchanged

[stephan]

Hi @prangley,

There was a bug in earlier versions of cryoSPARC where if you imported movies from separate folders that had non-unique names, cryoSPARC Patch Motion correction will incorrectly overwrite the files, which caused the particles to be also overwritten incorrectly, potentially causing the ValueError you see here in 2D Classification (the first time you would use the extracted particles).
The fix for this bug has been released in cryoSPARC v2.15.0. Unfortunately, you will need to re-run Patch Motion Correction and Extract From Micrographs (and all steps in between) in order to re-write the micrographs and particles that were incorrectly overwritten.

On the other hand, this bug also may arise from a corrupt data file, which was most likely the case why re-extracting the particle stack worked for @belousoff. If you know for certain the movie files you imported have unique file names (prior to v2.15.0), then it is worth checking the data integrity of the files you are trying to process.

To check the integrity of data files, see some helper scripts I’ve posted here:
For Raw .mrc Movies:

Value error with patch CTF estimation and manual picker

Hey @KSJ, Is it possible if you can run this code for me, and attach the file it creates? First, get together 2 paths dir_path: The path to the directory where you’ve saved the micrographs from EMPIAR 10059 output_path: The path to the file where the stats will be written to Then, in a shell, run cryosparcm icli, which will open up an interactive python shell. You can then copy and paste this code, with the two variables modified import os from cryosparc2_compute.blobio import mrc dir_pa…

For Particle .mrc stacks:

2D classification ValueError: total size of new array must be unchanged

Hey @Guillaume, Is it possible if you can run this code for me, and email me the file it creates (sarulthasan@structura.bio)? First, identify 3 variables, including the path to where the output of this script will be written to: project_uid : the uid of the project where the import particles job exists (e.g., P1) job_uid : the uid of the import particles job (e.g., J1) output_path : The path to the file where the stats will be written to (file will be created when the script is run) Then, …