8. Delete Rejected Exposures

How to remove original movies and motion-corrected micrographs that were culled in an Exposure Curation job.

Danger

Improper use of this code may result in data loss. Please ensure the relevant data is backed up.

First, initialize the CryoSPARC client.

from cryosparc.tools import CryoSPARC

cs = CryoSPARC(host="cryoem0.sbi", base_port=40000)
assert cs.test_connection()

Connection succeeded to CryoSPARC command_core at http://cryoem0.sbi:40002
Connection succeeded to CryoSPARC command_vis at http://cryoem0.sbi:40003
Connection succeeded to CryoSPARC command_rtp at http://cryoem0.sbi:40005

Select a project and find its directory.

from pathlib import Path

project = cs.find_project("P251")
project_dir = Path(project.dir())

Select a “Manually Curate Exposures” job within the selected project and load its exposures_rejected output.

job = project.find_job("J93")
exposures_rejected = job.load_output("exposures_rejected")

Note

To instead clean up rejected exposures from a CryoSPARC Live session, first export exposures from the Session view at Details > Actions > Export Exposures. This results in a “Live Exposure Export” job in the session workspace. Select that job and load the rejected_exposures output instead.

The following loop prints the absolute path of associated files that may be deleted for each exposure.

for exposure in exposures_rejected.rows():
    for group in (
        "movie_blob",
        "micrograph_blob",
        "micrograph_blob_non_dw",
        "background_blob",
        "micrograph_thumbnail_blob_1x",
        "micrograph_thumbnail_blob_2x",
    ):
        field = group + "/path"
        if field in exposure:
            rel_path = exposure[field]
            abs_path = project_dir / rel_path
            print(rel_path)
            # abs_path.resolve().unlink()  # DANGER: UNCOMMENT TO PERFORM CLEANUP

J1/imported/009270517818331954156_14sep05c_00024sq_00003hl_00002es.frames.tif
J2/motioncorrected/009270517818331954156_14sep05c_00024sq_00003hl_00002es.frames_patch_aligned_doseweighted.mrc
J2/motioncorrected/009270517818331954156_14sep05c_00024sq_00003hl_00002es.frames_patch_aligned.mrc
J2/motioncorrected/009270517818331954156_14sep05c_00024sq_00003hl_00002es.frames_background.mrc
J2/thumbnails/009270517818331954156_14sep05c_00024sq_00003hl_00002es.frames_thumb_@1x.png
J2/thumbnails/009270517818331954156_14sep05c_00024sq_00003hl_00002es.frames_thumb_@2x.png
J1/imported/018045652812341181121_14sep05c_00024sq_00003hl_00005es.frames.tif
J2/motioncorrected/018045652812341181121_14sep05c_00024sq_00003hl_00005es.frames_patch_aligned_doseweighted.mrc
J2/motioncorrected/018045652812341181121_14sep05c_00024sq_00003hl_00005es.frames_patch_aligned.mrc
J2/motioncorrected/018045652812341181121_14sep05c_00024sq_00003hl_00005es.frames_background.mrc
J2/thumbnails/018045652812341181121_14sep05c_00024sq_00003hl_00005es.frames_thumb_@1x.png
J2/thumbnails/018045652812341181121_14sep05c_00024sq_00003hl_00005es.frames_thumb_@2x.png
J1/imported/013858401686983345121_14sep05c_c_00003gr_00014sq_00004hl_00004es.frames.tif
J2/motioncorrected/013858401686983345121_14sep05c_c_00003gr_00014sq_00004hl_00004es.frames_patch_aligned_doseweighted.mrc
J2/motioncorrected/013858401686983345121_14sep05c_c_00003gr_00014sq_00004hl_00004es.frames_patch_aligned.mrc
J2/motioncorrected/013858401686983345121_14sep05c_c_00003gr_00014sq_00004hl_00004es.frames_background.mrc
J2/thumbnails/013858401686983345121_14sep05c_c_00003gr_00014sq_00004hl_00004es.frames_thumb_@1x.png
J2/thumbnails/013858401686983345121_14sep05c_c_00003gr_00014sq_00004hl_00004es.frames_thumb_@2x.png
J1/imported/014372787500169110452_14sep05c_c_00003gr_00014sq_00005hl_00005es.frames.tif
J2/motioncorrected/014372787500169110452_14sep05c_c_00003gr_00014sq_00005hl_00005es.frames_patch_aligned_doseweighted.mrc
J2/motioncorrected/014372787500169110452_14sep05c_c_00003gr_00014sq_00005hl_00005es.frames_patch_aligned.mrc
J2/motioncorrected/014372787500169110452_14sep05c_c_00003gr_00014sq_00005hl_00005es.frames_background.mrc
J2/thumbnails/014372787500169110452_14sep05c_c_00003gr_00014sq_00005hl_00005es.frames_thumb_@1x.png
J2/thumbnails/014372787500169110452_14sep05c_c_00003gr_00014sq_00005hl_00005es.frames_thumb_@2x.png
J1/imported/013353543220334248239_14sep05c_c_00003gr_00014sq_00007hl_00005es.frames.tif
J2/motioncorrected/013353543220334248239_14sep05c_c_00003gr_00014sq_00007hl_00005es.frames_patch_aligned_doseweighted.mrc
J2/motioncorrected/013353543220334248239_14sep05c_c_00003gr_00014sq_00007hl_00005es.frames_patch_aligned.mrc
J2/motioncorrected/013353543220334248239_14sep05c_c_00003gr_00014sq_00007hl_00005es.frames_background.mrc
J2/thumbnails/013353543220334248239_14sep05c_c_00003gr_00014sq_00007hl_00005es.frames_thumb_@1x.png
J2/thumbnails/013353543220334248239_14sep05c_c_00003gr_00014sq_00007hl_00005es.frames_thumb_@2x.png

To delete the rejected files, either un-comment the very last line and re-run the loop, or manually rm each path from the command line. For the latter strategy, resolve symlinks to ensure the original data gets deleted:

cd /path/to/project
rm -f $(readlink -f ${RELATIVE_PATH_TO_DELETE})  # for each file to delete...