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embl-cba / bd-cellview

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Batch processing #6

Open tischi opened 4 years ago

tischi commented 4 years ago

How can we batch this across folders or tables?

tischi commented 4 years ago

We will only have the option to process from table.

tischi commented 4 years ago
schraivo commented 3 years ago

From Tischi:

There are now two versions of imagej-utils.

  1. You need now 0.5.5 (the newer one)
  2. You need to delete 0.5.4 in case it is in your Fiji/jars folder => there must be only one image-utils.jar !
PastedGraphic-1

Best wishes, Christian

tischi commented 3 years ago

@schraivo How many tables would you typically like to process in one batch?

tischi commented 3 years ago

See also question above but also have a look at the new user interface below. I want to enable processing of multiple tables. Does this make sense?

image

tischi commented 3 years ago

@schraivo I updated imflow-0.1.0-SNAPSHOT.jar to contain the new UI. Please test the preview functionalities. Batch processing is not working yet.

tischi commented 3 years ago

Batch processing on local computer should work now as well.

schraivo commented 3 years ago

@schraivo How many tables would you typically like to process in one batch?

Hi Tischi, it will be around 5-10 Tables at most.

schraivo commented 3 years ago

See also question above but also have a look at the new user interface below. I want to enable processing of multiple tables. Does this make sense?

image

In principle exactly what we're looking for. But how is it working? Let's say I have two table selected: Can I set thresholds for each table separately? The idea of selecting a table is cool though, very flexible!!

schraivo commented 3 years ago

Batch processing on local computer should work now as well.

Cool, will test one thing after the other today. Hard to catch up with your speed :)

tischi commented 3 years ago

In principle exactly what we're looking for. But how is it working? Let's say I have two table selected: Can I set thresholds for each table separately?

No you cannot select different thresholds. This is just meant for batch processing of table where you use the same thresholds. If you need different thresholds you would need to start the plugin a second time and select the other tables, which I think that makes sense.

schraivo commented 3 years ago

Yes makes sense, just to be sure I got it correctly. I am trying it at the moment, so far everything works. The idea with the dataset table list is awesome.

schraivo commented 3 years ago

@tischi

I tested the batch processing on local computer (VM Linux):

The ERROR shows that the path is not generated correctly: There are additional ".." between the experiment path and the relativ path extracted from the table, e.g. /g/bdimsort/bla/bla/output/../images/bla.tiff (correct: /g/bdimsort/bla/bla/output/images/bla.tiff).

tischi commented 3 years ago

The ERROR shows that the path is not generated correctly: There are additional ".." between the experiment path and the relativ path extracted from the table, e.g. /g/bdimsort/bla/bla/output/../images/bla.tiff (correct: /g/bdimsort/bla/bla/output/images/bla.tiff).

Could you post the whole error message from the console window?

tischi commented 3 years ago

...and tell me which table you are processing? Then I can also try myself...