Bug #3758
open
uploaded signle direction tilt series causes error in preparation step for protomo2aligner
Added by Anchi Cheng about 9 years ago.
Updated about 9 years ago.
Affected Version:
Appion/Leginon 3.2
Description
missing accumulate_dose returned in orderImageList
- Status changed from Assigned to In Code Review
- Assignee changed from Anchi Cheng to Alex Noble
Please see if it makes sense.
You tried uploading a tilt-series to Appion/Leginon and my script failed because there is no recorded dose per image? What you changed has broken the 'Use Frame Aligned Images' option.
Could you show me how to upload a tilt-series properly to the database (with the correct angles and everything)? The proper way to solve this would be to allow the user to put the dose per image when uploading, even if it's not uniform across the tilt-series. I use the dose only to do dose compensation if the user wants, so I can warn the user that the dose might not be accurate so they should change the dose compensation parameters appropriately.
Actually this update has broken the file preparation step for all tilt-series collected with leginon. I'm reverting back and then fixing it a different way.
It was the use frame aligned images that broke the dose compensation. Revision 19357 broke the use frame aligned images. Thanks for finding the bug.
I'd like to replicate the issue because right now I'm unsure if it's something that needs to be fixed or needs to be tested. I've tested it with my normal processing workflow and it seems to work fine.
Alex,
Actually, my change should not impact other options. This particular bug is caused by you need five output but the original code only had four.
There is a problem with apProTomo.py, though.
apProTomo2.py function getImageFiles use string comparison to decide whether to llink or copy. In apProTomo2Prep, one of the call has boolean True for copy. Now if your ask if boolean True == "True", the answer is False. You may want to check how these are passed and what behavior you want. I started it but could not tell what exactly you want.
Never mind. I think I was confused. Let's get the Leginon flow and frame aligned images work. The ex-a hard code would be a bad way to find aligned image. I will need some details about how the aligned images are saved in your case. Started a new issue #3759 for it.
- Related to Feature #3762: upload tomography tilt series for protomo2 processing added
Yeah. I've never closed an issue...where's the close option?
It is one of the selection item in Status
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