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Task #9806 (closed)

Opened 12 years ago

Closed 12 years ago

Bug: bfconvert fails to write compressed big images

Reported by:	mlinkert	Owned by:	mlinkert
Priority:	critical	Milestone:	OMERO-4.4.7
Component:	Bio-Formats	Version:	n.a.
Keywords:	export	Cc:
Resources:	n.a.	Referenced By:	n.a.
References:	n.a.	Remaining Time:	n.a.
Sprint:	n.a.

Description

$ bfconvert -compression JPEG-2000 5794_001.svs test.ome.tiff

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 1834
	at loci.formats.codec.JPEG2000Codec.compress(JPEG2000Codec.java:123)
	at loci.formats.tiff.TiffCompression.compress(TiffCompression.java:328)
	at loci.formats.tiff.TiffSaver.writeImage(TiffSaver.java:371)
	at loci.formats.tiff.TiffSaver.writeImage(TiffSaver.java:265)
	at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:191)
	at loci.formats.out.OMETiffWriter.saveBytes(OMETiffWriter.java:198)
	at loci.formats.out.OMETiffWriter.saveBytes(OMETiffWriter.java:183)
	at loci.formats.FormatWriter.saveBytes(FormatWriter.java:136)
	at loci.formats.ImageWriter.saveBytes(ImageWriter.java:205)
	at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:523)
	at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:459)
	at loci.formats.tools.ImageConverter.main(ImageConverter.java:645)

and

$ bfconvert -compression JPEG 5794_001.svs test.ome.tiff

Exception in thread "main" java.awt.image.RasterFormatException: Data array too small (should be 1833 but is 611 )
	at sun.awt.image.IntegerComponentRaster.verify(IntegerComponentRaster.java:658)
	at sun.awt.image.IntegerComponentRaster.<init>(IntegerComponentRaster.java:211)
	at sun.awt.image.IntegerInterleavedRaster.<init>(IntegerInterleavedRaster.java:128)
	at sun.awt.image.IntegerInterleavedRaster.<init>(IntegerInterleavedRaster.java:95)
	at java.awt.image.Raster.createWritableRaster(Raster.java:997)
	at loci.formats.gui.AWTImageTools.constructImage(AWTImageTools.java:702)
	at loci.formats.gui.AWTImageTools.constructImage(AWTImageTools.java:653)
	at loci.formats.gui.AWTImageTools.makeRGBImage(AWTImageTools.java:591)
	at loci.formats.gui.AWTImageTools.makeImage(AWTImageTools.java:207)
	at loci.formats.gui.AWTImageTools.makeImage(AWTImageTools.java:494)
	at loci.formats.codec.JPEGCodec.compress(JPEGCodec.java:85)
	at loci.formats.tiff.TiffCompression.compress(TiffCompression.java:328)
	at loci.formats.tiff.TiffSaver.writeImage(TiffSaver.java:371)
	at loci.formats.tiff.TiffSaver.writeImage(TiffSaver.java:265)
	at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:191)
	at loci.formats.out.OMETiffWriter.saveBytes(OMETiffWriter.java:198)
	at loci.formats.out.OMETiffWriter.saveBytes(OMETiffWriter.java:183)
	at loci.formats.FormatWriter.saveBytes(FormatWriter.java:136)
	at loci.formats.ImageWriter.saveBytes(ImageWriter.java:205)
	at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:523)
	at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:459)
	at loci.formats.tools.ImageConverter.main(ImageConverter.java:645)

It looks like 'tileWidth' and 'tileHeight' aren't set correctly in TiffSaver?.

References

Change History (2)

comment:1 Changed 12 years ago by mlinkert

Keywords export added

comment:2 Changed 12 years ago by mlinkert

Resolution set to fixed
Status changed from new to closed

PR filed: https://github.com/openmicroscopy/bioformats/pull/198

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