In this repository, we collect useful additions for the BigDataViewer in Fiji. These functionalities are accessible by enabling the PTBIOP Fiji update site, accessible via Help>Update>Manage Update Sites.
User documentation is located can be found at https://imagej.github.io/plugins/bdv/playground/bdv-playground
We tried to follow these general guidelines:
- Specific (atomic) functionality lives in a class implementing Runnable
- More mandatory parameters for the functionality are handed over as additional constructor parameters.
- Optional parameters are set with setter methods.
- The
run()method executes the concrete action. - Results are retrieved using getter methods. The getter methods may internally run the
run()method if necessary.
Pseudo-code example:
Class Action {
Action(BdvHandle)
setParameter(Parameter)
run()
getResult()
}
-
Furthermore, Demo code in the test sources directory should demonstrate the individual functionality, and how to be called programmatically.
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Higher level functions, which may execute several actions sequentially, are implemented as SciJava Commands. This enables additional user access.
- Read a source from disc
- Add a source to a BDV
- Log the current mouse position
- Log the current viewer transform
- Change the current viewer transform
- Take a screenshot
Here we document actions we would like to have. If you know similar functionality in other repositories, feel free to contribute it here or send us a link where we can adopt code! Thanks :-)
- Log intensity in current source at mouse position