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Export to CSV file in a headless mode #290

Merged
merged 2 commits into from
May 13, 2024
Merged

Export to CSV file in a headless mode #290

merged 2 commits into from
May 13, 2024

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tinevez
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@tinevez tinevez commented Apr 9, 2024

The CSV export methods in the table classes only exports what is directly shown in the tables, and use the GUI classes of Java. This causes errors when used in a script in a headless model. See the discussion:

https://forum.image.sc/t/error-headlessexception-when-trying-to-save-csv-file-of-tracking-data-from-trackmate-when-running-headlessly/94304/5

This commit adds a utility that exports the content of a model in a headless mode.

This:

CSVExporter.exportSpots( 'trackmate-output.csv', trackmate_model, False );

results in:
Screenshot 2024-04-09 at 18 18 55

Fix #288

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This pull request has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/error-headlessexception-when-trying-to-save-csv-file-of-tracking-data-from-trackmate-when-running-headlessly/94304/7

@tinevez tinevez merged commit a952d21 into master May 13, 2024
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@tinevez tinevez deleted the export-csv-headless branch May 13, 2024 15:05
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Make a headless routine that can export a model to CSV file in one go.
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