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Ticket #525 (closed defect: fixed)

Opened 2010-07-30T10:48:26-05:00

Last modified 2010-11-17T03:14:47-06:00

Files cannot be saved from ImageViewer unless '-omexml' option was passed to showinf

Reported by:	melissa	Owned by:	melissa
Priority:	major	Milestone:	~~bio-formats-4.3~~
Component:	bio-formats	Severity:	serious
Keywords:		Cc:	jmoore
Blocked By:		Blocking:

Description

To reproduce:

  showinf data/al3d/franz/Iron Plate.al3d

Select "File > Save". Enter any filename with a supported extension. This exception is produced: Exception in thread "ImageViewer-Saver"

java.lang.NegativeArraySizeException
        at loci.formats.FormatWriter.setId(FormatWriter.java:292)
        at loci.formats.out.APNGWriter.setId(APNGWriter.java:109)
        at loci.formats.ImageWriter.setId(ImageWriter.java:403)
        at loci.formats.WriterWrapper.setId(WriterWrapper.java:286)
        at loci.formats.gui.ImageViewer.save(ImageViewer.java:409)
        at loci.formats.gui.ImageViewer$2.run(ImageViewer.java:818)

Change History

comment:1 Changed 2010-08-04T15:18:51-05:00 by melissa

Status changed from new to closed
Resolution set to fixed

(In [6766]) Fixed file export from ImageViewer. Closes #525.

comment:2 Changed 2010-11-12T08:46:57-06:00 by melissa

Status changed from closed to reopened
Resolution fixed deleted
Milestone changed from bio-formats-4.2.1 to bio-formats-5.0

With this command:

  showinf -stitch data/pcx/generated/mri-stack0.pcx

This exception now appears when trying to save as OME-TIFF from the GUI:

Exception in thread "ImageViewer-Saver" java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
	at java.util.ArrayList.RangeCheck(ArrayList.java:547)
	at java.util.ArrayList.get(ArrayList.java:322)
	at ome.xml.model.Pixels.getChannel(Pixels.java:480)
	at loci.formats.ome.OMEXMLMetadataImpl.getChannelSamplesPerPixel(OMEXMLMetadataImpl.java:1010)
	at loci.formats.FormatWriter.getSamplesPerPixel(FormatWriter.java:401)
	at loci.formats.out.TiffWriter.getPlaneCount(TiffWriter.java:222)
	at loci.formats.FormatWriter.setId(FormatWriter.java:296)
	at loci.formats.out.OMETiffWriter.setId(OMETiffWriter.java:165)
	at loci.formats.ImageWriter.setId(ImageWriter.java:403)
	at loci.formats.WriterWrapper.setId(WriterWrapper.java:286)
	at loci.formats.gui.ImageViewer.save(ImageViewer.java:391)
	at loci.formats.gui.ImageViewer$2.run(ImageViewer.java:778)

comment:3 Changed 2010-11-16T13:19:22-06:00 by melissa

Milestone changed from bio-formats-5.0 to bio-formats-4.3

comment:4 Changed 2010-11-17T03:13:04-06:00 by melissa

Cc jmoore added; josh removed

comment:5 Changed 2010-11-17T03:14:47-06:00 by melissa

Status changed from reopened to closed
Resolution set to fixed

(In [7218]) Fixed ImageViewer's default metadata population; closes #525.