Download output in series

Features and Functionality
1

Hello, are there any options for downloading volumes in ‘volume series’ format, specifically each iteration of NU-refine? I want to inspect each iteration, but downloading each one by one is not easy for me…

I mean, I want to download the volume series, but I also want to inspect the output of each iteration. like…3DVA.

2

Hi @Randomnick – for a few reasons, there is no straightforward way to do this in the UI, but I’ve put together the following CryoSPARC tools script that will collect MRCs (across iterations) from a refinement job and compress them into a zip file within the job folder. You’ll need to SCP the zip file yourself (i.e., no way to access it within the UI) EDIT: Script now also downloads the zipped file via the tools API. Hopefully this helps!

from cryosparc.tools import CryoSPARC
import zipfile

cs = CryoSPARC(
    host="[CS HOST URI]",
    base_port=[CS BASE PORT],
    email="[EMAIL]",
    password="[PASSWORD]"
)

assert cs.test_connection()

# Fill out as appropriate for homo / nu-refine job
project = cs.find_project("P321")
refine_job = project.find_job("J1428")

# Find all map files -- can also replace with "_map_half_A", "_map_half_B", "_map_sharp", as appropriate
map_paths_abs = [str(refine_job.dir / file) for file in refine_job.list_files() if file.endswith("_volume_map.mrc")]
print(map_paths_abs)

# Series will be a zip file in the job directory
series_path_abs =  str(refine_job.dir / (refine_job.uid + "_volume_map_series.zip"))
print(series_path_abs)

def zip_files(file_paths_abs, zip_path_abs):
    with zipfile.ZipFile(zip_path_abs, mode="w", compression=zipfile.ZIP_DEFLATED) as archive:
        for path in file_paths_abs:
            # this ensures that the directory structure is not in the zip file
            filename = path.split("/")[-1]
            archive.write(path, filename)
            
zip_files(map_paths_abs, series_path_abs)
print("Zipped maps into: {}".format(series_path_abs))

# Optional: download the zip file! Change target to the desired (local) filename
downloaded_file = refine_job.download_file(series_path_abs, target="/u/vperetroukhin/" + (refine_job.uid + "_volume_map_series.zip"))
print("Downloaded to: {}".format(downloaded_file))
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