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.
The resulting system is clearer and more generic (easier to change location of fiji or root images, as it is now located in one single place : the makefile). Some actions such as the installation of fiji are left as scripts outside the makefile.
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)
As a result, the implementation of estimate_white is getting closer to completion. However, the performance of fiji's gray morphology is very poor, which makes it practically unusable with the default settings provided in the original code (estimateWhiteFluoImageTelemos)
Bug 2623 - Faire un traitement automatique pour les images du projet lipase
- started to write estimate_white, with its unit test
- refactor: split lipase.py into modules
- cleanup : removed unused files and unused jenkins steps
- improved jenkinsfile
Bug 2623 - Faire un traitement automatique pour les images du projet lipase
As a result, lipase code is no longer using ijopencv.
ijopencv, based on javacpp provides poor compatibility with
opencv's cpython bindings, not to mention it's much less
convenient. Therefore, I'm not sure that I'll use ijopencv at all...
Guillaume Raffy
Guillaume Raffy