Tool to compute tracking metrics #11
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Could be improved. A default string could be used instead of the empty string because this will be used to generated the CSV results file.
A bit clumsy and the retrofit really shows.
When used in the Helper: - An abstract method does the computation and return the metrics. - A method in the mother class calls this method and takes care of saving the results to a CSV file. This diminishes slightly duplicated code, allows lowering visibility of some methods in MetricsRunner, but will also allow using the runners just to compute metrics oustide of the helper. Also for SPT runner: the units is specified at construction. Nevermind if we cannot get it right, it is just for display.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Right now the Helper computes the tracking metrics, but only within an optimization loop, sweeping over many tracking parameters. But I received two requests for a UI that simply computes the metrics, given a ground-truth and a test file.
This PR introduces a new plugin that does that:
The UI resembles the Helper's:
The user needs to specific a ground-truth (GT) path, and the path to a TrackMate file or a folder containing TrackMate files.
(Note: you can drag-and-drop files and folders onto the text field if you do not want to click the 'Browse' buttons.)
The GT path must be a folder for the CTC metrics.
For the SPT metrics, it can be a XML following the ISBI SPT challenge format, or directly a TrackMate file (which is handy).
The input can be a path to a TrackMate file, or to a folder in which all the TrackMate files will be tested against the GT.
The plugin shows results in the IJ log:
And saves them to a CSV file with possible one line per file in the folder.
