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eisfabian / PACEtomo

Parallel cryo electron tomography via beam image shift
GNU General Public License v3.0
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Trouble setting up polygon targeting in the 1.6 beta #18

Open bbarad opened 1 year ago

bbarad commented 1 year ago

Hi Fabian,

We decided to try the polygon targeting today, so we set up a polygon on a map and set targetPattern to true (but alignToP false). The guidance asked if we wanted to use a polygon, but once we said we wanted to run it, it defaulted to the target by shift routine. We tried saving a reference position (right outside the polygon) and it made the following tgts file, with only a single target (the tracking reference). What are we doing wrong?

Steps we took:

  1. Took a view mag image and made it a map.
  2. Drew a polygon on the map.
  3. Changed the 1.6 beta selectTargets script to include "targetPattern = True"
  4. Ran the selectTargets script.
  5. We were prompted to select a position by image shift for the tracking position. We took and saved a preview. The tgts file only has a single target included.

Is there something we are missing? We'd love to try out polygon selection! I've attached the tgts file and tgts_settings file if they help!

JTL005_4_L06_tgts_settings.txt JTL005_4_L06_tgts.txt

Only thing I see is that tgtPattern seems to be set to false in the settings even though we had it true in the selecttargets script? Thanks, Ben

eisfabian commented 1 year ago

Hi Ben!

Thanks for giving it a try! It looks like it found the proper vectors and it finished without an error? Did it open the GUI after?

That means that it thought that all your grid points were outside the polygon. How big was the polygon roughly? There might also be an issue with having the tracking target outside of the polygon since I haven't tried that.

The general idea is to set the tracking target manually and it then fills the grid in from there similar to the holey support setup excluding all points not in the polygon.

Best, Fabian

bbarad commented 1 year ago

It did make it through to the GUI so I think you are right that it just didn't place any pattern points.

The polygon should have been large enough for a ~2x3 grid of points, give or take, but probably not more than that. I'll give it a try with a larger lamella next time I am on, and will try with tracking inside/outside of polygon!