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Bug #16316

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"Add random amount to acquisition" also adjusts the focus target

Added by Eugene Chua 3 months ago. Updated 3 months ago.

Status:
New
Priority:
Normal
Assignee:
Category:
-
Target version:
Start date:
03/07/2024
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 3.6
Show in known bugs:
No
Workaround:

Description

In Exposure_Targeting node, "Add random amount to acquisition" seems to also add a random amount to the focus target. In my estimation it would be better to not do this to the focus target so that the holes are not accidentally exposed by the focus beam.

Actions #1

Updated by Eugene Chua 3 months ago

  • Assignee deleted (William Rice)
Actions #2

Updated by Anchi Cheng 3 months ago

  • Assignee set to William Rice

This is related to feature #13970. Bill, do you want to take it on ? If not, assign back to me.

Actions #3

Updated by William Rice 3 months ago

It's a bit complicated. The way it works is to add the random amount to all the acquisition targets before determining the focus target. It then calculates the ice thickness of the moved targets and eliminates based on that. Finally, it finds a focus target, either by convolution or by the "good", "any" or "center" decision if those are set. I could set it to move the targets after the focus hole is set, but then the thickness prediction will be wrong since it will be from the original position. For us, the moved focus position has not been a problem since we use it for screening, and for most positions, the focus is still far enough that it does not overlap a hole.

Actions #4

Updated by Eugene Chua 3 months ago

Hi Bill,

This makes sense. It’s not a big issue, and like you said doesn’t really cause problems especially when screening. Just something I noticed –

Best,
Eugene

From: <>
Date: Friday, March 8, 2024 at 7:32 PM
To: <>, Bridget Carragher <>, William Rice <>, Ed Eng <>, <>, Eugene Chua <>
Subject: [Leginon - Bug #16316] "Add random amount to acquisition" also adjusts the focus target
Issue #16316<https://emg.nysbc.org/issues/16316#change-63315> has been updated by William Rice.
________________________

It's a bit complicated. The way it works is to add the random amount to all the acquisition targets before determining the focus target. It then calculates the ice thickness of the moved targets and eliminates based on that. Finally, it finds a focus target, either by convolution or by the "good", "any" or "center" decision if those are set. I could set it to move the targets after the focus hole is set, but then the thickness prediction will be wrong since it will be from the original position. For us, the moved focus position has not been a problem since we use it for screening, and for most positions, the focus is still far enough that it does not overlap a hole.

________________________
Bug #16316: "Add random amount to acquisition" also adjusts the focus target<https://emg.nysbc.org/issues/16316#change-63315>

  • Author: Eugene Chua
  • Status: New
  • Priority: Normal
  • Assignee: William Rice
  • Category:
  • Target version: Appion/Leginon 3.7
  • Affected Version: Appion/Leginon 3.6
  • Show in known bugs: No
  • Workaround:

In Exposure_Targeting node, "Add random amount to acquisition" seems to also add a random amount to the focus target. In my estimation it would be better to not do this to the focus target so that the holes are not accidentally exposed by the focus beam.


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