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