BUG: Open with in Insight

[pwalczysko]

Noticed by Alex Herbert during the Paris meeting.

Insight 'Open with' function ends with error in ImageJ

Workflow:

• go to any image in Insight (NOT in insight-ij plugin !)
• right-click in central pane and select Open with > Other
• browse to you ImageJ installation (with 5.0.2 release biofirmats) and select the application
• the ImageJ opens as expected
• immediately, an error in ImageJ appears saying "Image: cannot open tiled tiffs"

According to mlinkert, this is because ImageJ cannot open tiled tiffs. OMERO exports tiled tiffs in any case when Open with function is executed in Insight. IJ tries to open such image even when not capable of doing so, instead to defer this to his plugins.

Note that the opening of the same image using insight-ij plugin is successful.

Apparently, it does not matter which format or even size of image you choose, I tried .png and .dv (the dv was 512 x 512 but 2 z planes).

[pwalczysko]

This bug persists. If opening from Insight (5.1 to trout) a dv, the spinner spins indefinitely. If from IJ plugin, it reports "IJ cannot open tiled tiff".
Note that this does not concern the main insight-ij opening functionality, just the "Open with" feature.

[jburel]

Changing component since we use the B-F plugin to open the image.

[mlinkert]

The easiest way to do this at the moment is to change the command that is executed internally from:

/path/to/ImageJ /tmp/file.ome.tiff

to:

/path/to/ImageJ -eval "run('Bio-Formats Importer', 'open=[/tmp/file.ome.tiff]');"

This bypasses ImageJ's own TIFF reader in favor of Bio-Formats; the issue at the moment is that ImageJ's own TIFF reader can't handle the file, but it reports the error in such a way that it won't fall back to other TIFF-capable plugins. So far I haven't worked out any other way of telling ImageJ to ignore the error and move on to the next plugin in its list.

I'm not completely familiar with the "open with" code in Insight though, so feedback on which of the following makes more sense (or some other alternative) would be much appreciated:

1. check the executable path in org.openmicroscopy.shoola.env.ui.UserNotifierImpl?.openApplication; if it case-insensitively matches "imagej", then alter the arguments to match the above.

2. add a specific "ImageJ" menu item in the "Open with" menu; if the user clicks that, they still need to specify their ImageJ installation (though maybe it can be cached?), but it allows the command line arguments to be changed only if that menu item is clicked without affecting everything that uses UserNotifierImpl?.

I guess the only other option is to stop writing tiled TIFFs, but that's a pretty far-reaching change.

[jburel]

Melissa: Thanks for the investigation.

I take the ticket back and see who we can adjust that.

[mlinkert]

Changing the component back to Insight so that this is allowed for the OMERO freeze (and not the earlier Bio-Formats freeze).

[jburel]

see ​https://github.com/openmicroscopy/openmicroscopy/pull/3748