imagej / imagej/imagej-notebook

Provide a way to run the code inside a notebook from an ImageJ instance

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Dominant language
Java
Stars
4
Forks
2
PR merge metrics
No merged PRs in 30d

Description

When prototyping some analysis in a jupyter notebook (using SciJava Jupyter Kernel), it would be useful to also have the possibility to run the code contained in a notebook file from within ImageJ, e.g. to be able to run it in batch.

```groovy
#@ NotebookService nb

nbFile = new File("/path/to/myNotebook.ipynb")

nb.run(nbFile)
```

This would require some thought about how inputs are processed, as currently it's not possible to define script parameters (such as `#@ String s`) in a notebook (except auto-resolved inputs like services, e.g. `#@ OpService ops`).

Contributor guide

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Research direction

Start by tracing the NotebookService integration with the SciJava Jupyter Kernel and how ImageJ currently launches notebook code. Define how notebook inputs such as #@ String s should be handled, then verify that a notebook file can be run in batch from an ImageJ instance.

Written by the indexing model from the issue text.

Assessment

Tech stack
java, jupyter-notebook
Domain
tooling
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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