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Tyelab / bruker_control

Repository for code running the lab's multi-photon imaging experiments at the Bruker Ultima Investigator scope. Unites Arduino, Prairie View, and GenTL machine cameras in Python.
Mozilla Public License 2.0
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Transfer Script Copies "Single Image" Directories #130

Closed jmdelahanty closed 1 year ago

jmdelahanty commented 2 years ago

When the user does a live scan, Prairie View outputs a single image from that collection as a reference. I don't know if that behavior can be changed yet and it might not be something that actually needs changing, but for now it places that image into the team's microscopy directory because when you run an imaging session, the new save directory is set to E:\teamname_projectname\microscopy.

Until this behavior changes in Prairie View, the transfer script should check for those directories and both delete them (since we don't use them) as well as not transfer them through rsync.

Here's an example of what the .txt file looks like with this in place, which causes issues for bruker_pipeline when ripping is started:

/snlkt/specialk_lh/2p/raw/LHE060/20221018/20221018_LHE060_plane1_-346.875_raw-008
/snlkt/specialk_lh/2p/raw/LHE060/20221018/20221018_LHE060_plane1_-346.875_raw-009
/snlkt/specialk_lh/2p/raw/LHE064/20221018/20221018_LHE064_plane1_-306.7_raw-010
/snlkt/specialk_lh/2p/raw/LHE068/20221018/20221018_LHE068_plane1_-436.925_raw-011
/snlkt/specialk_lh/2p/raw/SingleImage-10142022-1054-2619/SingleImage-10142022-1054-2619/SingleImage-10142022-1054-2619
/snlkt/specialk_lh/2p/raw/SingleImage-10182022-1033-2619/SingleImage-10182022-1033-2619/SingleImage-10182022-1033-2619
/snlkt/specialk_lh/2p/raw/SingleImage-10182022-1225-2619/SingleImage-10182022-1225-2619/SingleImage-10182022-1225-2619

The last 3 directories are the problematic ones.

jmdelahanty commented 2 years ago

So there's less to do with the transfer script this is what I'd rather do. So it's what I'll try.