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Protocol rework#271

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JoQCcoz merged 18 commits intoNIEHS:devfrom
JoQCcoz:protocol-rework
May 20, 2024
Merged

Protocol rework#271
JoQCcoz merged 18 commits intoNIEHS:devfrom
JoQCcoz:protocol-rework

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@JoQCcoz JoQCcoz commented May 20, 2024

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JoQCcoz and others added 18 commits April 30, 2024 21:14
Fixed an issue with the new selection algorithms when the grid is all black and no target is found.
Fixed an issue with resuming a run stopped after atlas processing but before completion.
Graylevel selector was running on nomalized images where the brightest pixel was normalized to 255.
This had for effect to make each square independent of the others and impossible to select a good range of graylevel throughout the grid.
Fixed issue where the target registration was off when the hole recentering isn't close enough to center.
It should now calculate the offset and correct it when calculating the registration.
Selectors will now be run when manual targets are added.
Removed regular-pattern holes from lattice calculation. Users would normally have had to delete all the holes before running the lattice extension.
Remove autofocus and drift from run_grid and added it to the protocol_commands.
Also added these commands to all default protocols.
@JoQCcoz JoQCcoz merged commit 3089624 into NIEHS:dev May 20, 2024
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