Rework the helper tool. #14
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Right now, it lives in the branch 'omnipose' of the TrackMate-Cellpose repo.
PretrainedModel is now an interface, with PretrainedModelCellpose a concrete implementation as an enum.
…s versions. This kind of error is very likely to happen in the near future, we might as well give a hint to the user.
Simply delete the parameter file and relaunch the GUI.
Happens in Trackastra for the save folder settings. It might be better not including them in the settings map at all.
The list of modules is somewhat long now.
There are now many detectors and trackers, we need to fit everything in a convenient manner.
so that the parent config panel can be scrolled.
Trackastra integration
It's possible to make a tracking configuration that will generate a branching event in a track. With this we will have two spots in the same timepoint and in the same track. This is ok for the CTC metrics but not for the SPT metrics, that trigger an exception. With this commit we gracefully catch it and write that the tracking parameters generate an invalid tracking results for SPT. And continue the sweep.
Spot filters and track filters are stored in the results tables if present. They are used to compare settings against others, and are properly reported in the results table. This has become especially important in the light of the new SPT metrics integration, that has a metric for penalizing false positive.
Using a JSON file to specify where and what, like this:
{
"metrics": "SPT",
"ground_truth_path": "/Users/tinevez/Desktop/HPyloriGT/SHicham_Video1_crop_GT_05.xml",
"source_image_path": "/Users/tinevez/Desktop/HPyloriGT/SHicham_Video1_crop.tif",
"save_folder": "/Users/tinevez/Desktop/HPyloriGT/",
"helper_task_definition_path": "/Users/tinevez/Desktop/HPyloriGT/helperrunnersettings.json",
"log_file": "/Users/tinevez/Desktop/HPyloriGT/log.txt",
"spt_max_linking_distance": 2.0,
"target_channel": 1
}
So that we can use a param sweep model with classes that are not a TrackMateModule.
However the runner seems to get it wrong. Investigate.
Now the TrackMate helper targets the new v8 of TrackMate.
This helped fix an error that resulted in skipping computation when no filters were set.
when comparing detector settings. The hash code of the logger does not affect the tracking accuracy, and should not be relevant when deciding whether a parameter set has already been tested.
When iterating over spot and track filter configurations, we were passing the feature *name* instead of the feature *key* to TrackMate. This caused TrackMate to actually skip all filtering, but silently, and printing a meaningful message to the user stating that it was done. This commit fixes the issue.
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Integrate future modules:
Can perform parameter sweep over spot and track filters.
Large refactoring.