Saving tables in ImageJ2

fiji
imagej
imagej2

#1

Dear all,

I just ran into an issue: I tried to save a org.scijava table using ij.io.save() but it didn’t work. This is the code I tried:

And this is the error message which came up:

io.scif.FormatException: No compatible output format found for extension: C:/structure/temp/output.csv
	at io.scif.services.DefaultFormatService.getWriterByExtension(DefaultFormatService.java:270)
	at io.scif.services.DefaultDatasetIOService.canSave(DefaultDatasetIOService.java:94)
	at io.scif.io.DatasetIOPlugin.supportsSave(DatasetIOPlugin.java:69)
	at org.scijava.io.IOPlugin.supportsSave(IOPlugin.java:76)
	at org.scijava.io.IOService.getSaver(IOService.java:66)
	at org.scijava.io.DefaultIOService.save(DefaultIOService.java:80)
	at de.mpicbg.imagej.CellCountingWorkflow.run(CellCountingWorkflow.java:152)
	at org.scijava.command.CommandModule.run(CommandModule.java:199)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
	at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:238)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)

Am I doing something wrong? How are tables supposed to be saved?

Thanks a lot!

Cheers,
Robert


#2

You need the scijava-plugins-io-table component which is currently not included in Fiji, but will be once my PR in imagej is merged and the next round of updates happens. (Sorry for the brevity, I’m on mobile)


#3

Cool, thanks for working on this @imagejan

It’s this PR, right?

Looking forward to its merging :wink:

Cheers,
Robert


#4

Correct. See also these related topics:

… and these related GitHub issues: