imagej / imagej/imagej2

Reconcile case issues with module parameters

Open
#231 0 comments 1 reaction 0 assignees View on GitHub
Dominant language
Java
Stars
1.4k
Forks
350
PR merge metrics
No merged PRs in 30d

Description

From @tischi [on the Image.sc Forum](https://forum.image.sc/t/command-line-recording-of-imagej2-plugins/8789):
> I realized something with the IJ2 Macro Command recording, namely that it removes all capitalization in the parameters, resulting in recordings such as:
> ```
> run("Elastix", "elastixdirectory=/Applications/elastix_macosx64_v4.8 workingdirectory=/Users/tischer/Desktop/elastix-tmp fixedimagefile=/Users/tischer/Desktop/elastix-output/muscles.tif-transformed.tif movingimagefile=/Users/tischer/Desktop/elastix-output/muscles.tif-transformed.tif elastixparameters=Default usemask=false useinitialtransformation=false transformationtype=Translation numiterations=1 numspatialsamples=100 gaussiansmoothingsigmas=10,10,10 bsplinegridspacing=50,50,50 finalresampler=FinalLinearInterpolator outputmodality=[Save output as Tiff]");
> ```
> This is fine and works as a macro, however when trying to use this as a starting point for running the command from command line, it does not work. The reason is that on the command line the parameters do need the correct capitalization, e.g. `elastixdirectory` should actually be `elastixDirectory`, otherwise one gets an error.
>
> Would it maybe be possible to unify this?

Furthermore: SciJava module parameters are case-sensitive, whereas ImageJ1 macro parameters are case-insensitive.

Contributor guide

No contributing guide indexed for this repository

Research direction

Start by tracing IJ2 Macro Command recording and command-line SciJava module parameter parsing, focusing on how parameter names are normalized or matched. Compare the case rules for ImageJ1 macro parameters and SciJava module parameters, then define a consistent behavior that works for both recorded macros and command-line invocation.

Written by the indexing model from the issue text.

Assessment

Tech stack
java
Domain
api, cli
Issue type
Bug
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
30/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.