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embl-cba / bd-cellview

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Processing images from selected gate only #15

Open schraivo opened 3 years ago

schraivo commented 3 years ago

@tischi

I think we misunderstood each other originally. We actually only need the images from the selected gate to be processed into jpeg. This will always be the case.

In case I need to process all, I can simply select a gate column which contains all events as TRUE (which I always generate in the script that also generated the tables which go into your tool).

tischi commented 3 years ago

In case I need to process all, I can simply select a gate column which contains all events as TRUE (which I always generate in the script that also generated the tables which go into your tool).

Good idea.

No problem I think I can easily implement that it only processes the selected gate.

tischi commented 3 years ago

The latest version on the server should do the job. Please test once we figured out the other issue with the ".." in the path.

schraivo commented 3 years ago

I tested it again. It now skips the images which are marked "FALSE" in a gate column, thanks!

Regarding the error: I think the error occurs if more that one table are processed. Example data: /Volumes/bdimsort/200807_Dewi_Nsp1/20200830_1634_HeLa RIEN pmaxGFP/output/reduced_gated.csv /Volumes/bdimsort/200807_Dewi_Nsp1/20200830_1648_HeLa RIEN NSP1 wt/output/reduced_gated.csv

Error message:

Screenshot 2020-09-23 at 19 04 43 Screenshot 2020-09-23 at 19 04 49
tischi commented 3 years ago

Can you give me write access in those folders?

tischi commented 3 years ago
  1. Don't worry about the write access, I copied the folder.
  2. It is a strange error that I cannot reproduce. I think it must be a difference of how MacOS and Linux handle relative paths with .. in Java. I updated the jars, hoping that it will work now. Could you please try?