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IMOD WARPM

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gijsschot edited this page Nov 8, 2021 · 3 revisions

Interfacing PyTom and IMOD/WARPM

Creating Tomograms

In order to use PyTom and IMOD results interchangeably one has to be able to import/export the alignment parameters and the assiociated files that are used by either algorithm.

In order to import IMOD alignment results into pytom we need to combine two IMOD results files.

  1. taSolution.log
  2. align.xf

By using the following command PyTom can generate an alignmentResults.txt file, based on the results of IMOD. This file can be used during (sub)tomogram reconstruction. If the target directory is different from the directory where the tilt images are stored, one needs to provide this directory using the sortedFolder flag.

convert.py -f [taSolutions.log] -t [OUTPUT_FOLDER] -o txt --alignxf [IMOD_SHIFT_FILE.xf] --sortedFolder [FOLDER_WITH_SORTED_TILTIMAGES]
  • -f, --file Filename will convert this single file to the target format. Not to be used in combination with --directory
  • -t, --targetPath Path to new file, as a relative or absolute path to a directory, the filename will be the same as the original file.
  • -o, --outputFormat The format of the output file, will keep the same name but only change the extension.
  • --outname Optional filename output file. This name with replace the default alignmentResults.txt filename.

Specific flags for providing supporting data to for respective conversions.

  • --alignxf Final shift file from IMOD
  • --sortedFolder Sorted Images are located in this folder.

The GUI can also help you in this conversion.

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