Renamed MDOCs

[asarnow]

I collected some data with redundant tilt series names in SerialEM (e.g. ts1.mrc.mdoc), so I made symbolic links renamed with a unique leading string. Most of them are processed successfully but a number of them fail with an error message like:

15 | Traceback (most recent call last):
-- | --
16 | File "/opt/pyp/bin/run/pyp", line 3448, in <module>
17 | tomo_swarm(args.path, args.file, args.debug, args.keep, args.skip)
18 | File "/opt/pyp/src/pyp/utils/timer.py", line 78, in wrapper_timer
19 | return func(*args, **kwargs)
20 | File "/opt/pyp/bin/run/pyp", line 1446, in tomo_swarm
21 | ] = preprocess.read_tilt_series(
22 | File "/opt/pyp/src/pyp/preprocess/core.py", line 173, in read_tilt_series
23 | raise Exception(f"{tilt_image_filename} indicated inside {name}.mdoc is not found in {project_raw_path}")
24 | Exception: 23dec02b_ts1.mrc indicated inside 23dec02b_ts1.mdoc is not found in /data/veesler/nextpyp/shared/users/asarnow/projects/Spike_all_counting-hIIvI0aF2RZwKfMgOCs6v75z/tomo-preprocessing-f2JIJRcXboknzKLR/raw

Are some of my MDOCs being interpreted as MDOC-per-tilt instead of MDOC-per-tilt-series? Might there be an edit I can make to fix that?

[tofushan]

Hi,

If you are using mdoc file to parse metadata (i.e., tilt angle, tilt axis angle, acquisition), the tilted images indicated inside the mdoc file need to match your image files. Taking one mdoc file from EMPIAR-10987 as an example, FE33_3_1837_-51.0_Dec09_23.37.35.mrc needs to be present so that nextPYP can find the corresponding tilted images.

In the mdoc file:
SubFramePath = X:\Dosefractions\Fabian\2021_12_09_FE33_3\Frames\FE33_3_1837_-51.0_Dec09_23.37.35.mrc

If you have mdoc file per tilt-series, be sure there are no other mdoc files having the same leading strings. For example, 23dec02b_ts1_xxxx.mdoc will be treated as a mdoc file for a tilted image if you are using 23dec02b_ts1.mdoc for tilt-series 23dec02b_ts1. Same rationale applied to mdoc file per tilted image, they need to have the same leading strings.

[tofushan]

Do you have any other mdoc files that have names like 23dec02b_ts1*.mdoc and were also picked up by the glob function?

[asarnow]

Aha...there are indeed, the 10th through 19th tilt-series, e.g. 23dec02b_ts10.mrc.mdoc, 23dec02b_ts11.mrc.mdoc, etc.

The tsX increments are created automatically by SerialEM when you set up tiltseries targets, it will either append a number starting from 1 to the tiltseries root name that is given, or if that name already ends in a number it will continue from there.

[tofushan]

Great! We can fix it in the next release. Thanks for reporting!

[asarnow]

Awesome, thanks for being patient with me!

[abartesaghi]

This was addressed in version 0.6.4.