Clean up cell detection and fail fast on invalid input#2026
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petebankhead merged 4 commits intoqupath:mainfrom Oct 29, 2025
Merged
Clean up cell detection and fail fast on invalid input#2026petebankhead merged 4 commits intoqupath:mainfrom
petebankhead merged 4 commits intoqupath:mainfrom
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Limited changes that should not make any difference in behavior (if I've done them properly).
Again, if I've done this properly then there should be no change in behavior.
qupath-core-processing/src/main/java/qupath/imagej/detect/cells/WatershedCellDetection.java
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alanocallaghan
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Oct 29, 2025
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I don't really understand a lot of the code still but this seems sensible and certainly resolves the worst examples of silently running on a different channel without even logging a warning.
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This firstly (conservatively) cleans up
WatershedCellDetectionwhile trying to avoid any change in behavior.Then it adds new logic to
parseArgument(ImageData<BufferedImage> imageData, String arg)that attempts to fail fast with an exception in the following cases:It is still possible to process a brightfield image while specifying a channel (stain) that doesn't exist, but I think that might be obscure enough to accept - and it will result in a warning being logged.
The main problem this aims to solve is that the user could use completely invalid parameters and still get sensible results because default channels were chosen.
See also #2025
Along the way, I also changed
so that it now throws an exception (rather than only logging a warning) if attempting to set a parameter that doesn't exist. This could potentially impact other commands, but I hope that if it does then its impact is positive.
This change could however be reverted, since in the end the cell detection adjustments don't rely upon it.