ts_export_particles without raw data

[Mart Last]

Hi,

I'm trying something that I think should be possible (?) but can't figure out how to do. After doing the whole raw data to tomograms workflow in WarpTools I've offloaded my raw frames to a hard disk to free up memory. But I do still have the frame averages in warp_frameseries/average which as raw a version of the data as I suppose I need.

When I run WarpTools ts_export_particles I get errors due to missing raw data files:

System.IO.DirectoryNotFoundException: Could not find a part of the path '/cephfs/mlast/compu_projects/easymode/datasets/034_DICTYO/raw/TS_008_052_-60.0.tif'

Which I'm guessing is because the tomostar files point at files like:

  ../warp_frameseries/TS_004_056_-64.0.tif

Which don't exist, but corresponding ../warp_frameseries/*.xml's do and they in turn point at the missing ../raw/ directory.

So my question is: is there a simple way to tell Warp to sample from the previously generated frame averages instead of from the raw data? (A way that is simpler than just copying the data back onto the cluster 🙃) Any input much appreciated!

Best,

Mart

[Hamidreza Rahmani]

Hi Mart,

Have you tried making dummy soft links or text files with the correct name in the rawdata directory?

I am not sure if this will work but maybe WarpTools only checks if that path exists and moves on to aligned micrographs.

Best,

Hamid

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[Mart Last]

Hi Hamid,

That's a good suggestion, I'll try... at some point, I actually just deleted the frame averages when I got a bit overzealous with cleaning up  storage... will update this thread once I run into the same problem again and get to try your suggestion.

Op dinsdag 25 november 2025 om 16:23:41 UTC schreef hami...@gmail.com: