Batch processing

[tischi]

How can we batch this across folders or tables?

[tischi]

We will only have the option to process from table.

[tischi]

• Try to get headless running
• Try out the idea of using Json to instantiate the class that does the job

[schraivo]

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 !

Best wishes,
Christian

[tischi]

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

[tischi]

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?

[tischi]

@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]

Batch processing on local computer should work now as well.

[schraivo]

@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]

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?

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]

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]

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]

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]

@tischi

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

• loading of tables WORKS
• preview images from different tables WORKS
• Process images from all tables on local computer: ERROR

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]

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]

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