This will be useful to allow the user to perform some processings on the currently opened stack instead of choosing the stack from a list each time an image processing is launched : this will ease adjustment of image processing parameters.
This allows to now detect if the test succeeds or not. Also turned test_preprocessing into a proper unit test. This test is now much cleaner, as preprocessing.py does no longer require ij related code.
The 2 available plugins are:
- Define Raw Images Root: this plugin allows the user to tell lipase where the raw images are stored
- Estimate White: this plugin allows the user to trigger the computation of a white image estimate for the given sequence and the given channel (the sequence id an the channel ids are currently hardcoded but it is of course planned to make it user selectable)
These changes involved quite a lot of work:
- added the support of a lipase user settings file to store user dependent things such as the location of the lipase raw images (to allow the user to use lipase plugins without having to specify the raw images locations again an again)
- investigations on how to make different lipase plugins use a common lipase library: the library is packagesd into a jar file placed in Fiji/jars/lib, while the plugins (menu items) are placed into Fiji/plugins directory
- investigations on fiji script parameters (for plugins input output)
Guillaume Raffy
Guillaume Raffy