Context Navigation

Notice: In order to edit this ticket you need to be either: a Product Owner, The owner or the reporter of the ticket, or, in case of a Task not yet assigned, a team_member"

Task #6598 (closed)

Opened 8 years ago

Closed 8 years ago

Last modified 8 years ago

Bug: Bio-Formats ImageJ Plugin OME download

Reported by:	saloynton	Owned by:	mlinkert
Priority:	minor	Milestone:	OMERO-Beta4.3.2
Component:	General	Version:	n.a.
Keywords:	n.a.	Cc:	saloynton
Resources:	n.a.	Referenced By:	n.a.
References:	n.a.	Remaining Time:	0.0d
Sprint:	n.a.

Description

In making the selection

Open Plugins > OME > Download from OMERO
Enter the server details, port, username, password, and image id.

The following message was shown. I have also tested the same images opening them through Plugins > OMERO and the images open as expected.

java.lang.NullPointerException
	at loci.ome.io.OmeroReader.initFile(OmeroReader.java:249)
	at loci.formats.FormatReader.setId(FormatReader.java:1072)
	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:481)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)
	at loci.plugins.in.Importer.showDialogs(Importer.java:125)
	at loci.plugins.in.Importer.run(Importer.java:77)
	at loci.plugins.LociImporter.run(LociImporter.java:79)
	at ij.IJ.runUserPlugIn(IJ.java:183)
	at ij.IJ.runPlugIn(IJ.java:150)
	at ij.Executer.runCommand(Executer.java:124)
	at ij.Executer.run(Executer.java:61)
	at java.lang.Thread.run(Thread.java:680)

References

Attachments (1)

blurred image.png (170.2 KB) - added by saloynton 8 years ago.

Download all attachments as: .zip

Change History (16)

comment:1 Changed 8 years ago by mlinkert

This should have been fixed in [ebcdeb05f8f3a7cea3e18699290954c95d15a879/bioformats.git]. Scott, could you please try the latest trunk build and see if that solves the problem?

comment:2 Changed 8 years ago by Melissa Linkert <melissa@…>

(In [c090cf39e1efbe9249a16f830c323afe601b1377/bioformats.git]) Prevent exceptions when PositiveInteger/PositiveFloat? values are <= 0.

See #6598.

comment:3 Changed 8 years ago by Melissa Linkert <melissa@…>

(In [dfa48f8d53895dee2c1842d5c75bc313b2601e93/bioformats.git]) Pass the correct pixels ID to the RawPixelsStore?.

See #6598.

Changed 8 years ago by saloynton

Attachment blurred image.png added

comment:4 Changed 8 years ago by saloynton

Using build #3913 the image does now import but each channel appears blurred see screenshot.

comment:5 Changed 8 years ago by mlinkert

This is related to the stack trace that I pasted into Jabber. I could duplicate the problem with build 3913, but it works for me with build 3914.

comment:12 Changed 8 years ago by Melissa Linkert <melissa@…>

Remaining Time set to 0
Resolution set to fixed
Status changed from new to closed

(In [9e54577fdfec709a7896e83cbba1471a587af301/bioformats.git]) Fix one more NPE if the channel name is missing.

Closes #6598.

comment:13 Changed 8 years ago by Melissa Linkert <melissa@…>

(In [9e54577fdfec709a7896e83cbba1471a587af301/bioformats.git]) Fix one more NPE if the channel name is missing.

Closes #6598.

comment:14 Changed 8 years ago by Melissa Linkert <melissa@…>

(In [e1b0c49226585dcd691f907d9ad68f0083efe9e9/bioformats.git]) Fix one more NPE if the channel name is missing.

Closes #6598.
(cherry picked from commit 9e54577fdfec709a7896e83cbba1471a587af301)

comment:15 Changed 8 years ago by Melissa Linkert <melissa@…>