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Ticket #1870 (closed defect: fixed)

Opened 2013-05-14T14:56:54-05:00

Last modified 2013-06-04T11:44:13-05:00

SCIFIO barfs on this PNG file

Reported by:	bdezonia	Owned by:	hinerm
Priority:	major	Milestone:	~~imagej2-b7-ndim-data~~
Component:	SCIFIO	Version:
Severity:	serious	Keywords:
Cc:		Blocked By:
Blocking:	#1563

Description

I'm on the scifiocells branches. The attached PNG, which opens fine in IJ1, causes an exception to be thrown in IJ2

java.lang.ArrayIndexOutOfBoundsException: 258

at ome.scifio.formats.APNGFormat$Parser.typedParse(APNGFormat.java:481)
at ome.scifio.formats.APNGFormat$Parser.typedParse(APNGFormat.java:1)
at ome.scifio.AbstractParser.parse(AbstractParser.java:371)
at ome.scifio.AbstractParser.parse(AbstractParser.java:115)
at ome.scifio.AbstractParser.parse(AbstractParser.java:1)
at ome.scifio.AbstractReader.setSource(AbstractReader.java:251)
at ome.scifio.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:98)
at ome.scifio.io.img.ImgOpener.createReader(ImgOpener.java:450)
at ome.scifio.io.img.ImgOpener.initializeReader(ImgOpener.java:515)
at ome.scifio.io.img.ImgOpener.openImg(ImgOpener.java:288)
at ome.scifio.io.img.ImgOpener.openImg(ImgOpener.java:240)
at imagej.io.DefaultIOService.loadDataset(DefaultIOService.java:166)
at imagej.io.DefaultIOService.load(DefaultIOService.java:124)
at imagej.core.commands.io.OpenFile.run(OpenFile.java:87)
at imagej.command.CommandModule.run(CommandModule.java:163)
at imagej.module.ModuleRunner.run(ModuleRunner.java:169)
at imagej.module.ModuleRunner.call(ModuleRunner.java:126)
at imagej.module.ModuleRunner.call(ModuleRunner.java:1)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
at java.lang.Thread.run(Thread.java:680)

Attachments

EL_ImageToProcess2.png (312.6 KB) - added by bdezonia 2013-05-14T14:57:24-05:00.

Change History

Changed 2013-05-14T14:57:24-05:00 by bdezonia

attachment EL_ImageToProcess2.png added

comment:1 Changed 2013-05-15T10:07:20-05:00 by hinerm

The PLTE parsing wasn't dividing array indices.. so if the PLTE length was 768, it would try to populate 3x size 256 arrays at indices 0, 3, 6.. up to 768.

Fixed now to populate indices 0, 1, 2... up to the actual lut length and not the combined lut length.

Works locally on latest scifiocells branch.

comment:2 Changed 2013-05-17T14:48:02-05:00 by bdezonia

Blocking 1563 added; 1457 removed
Milestone changed from imagej2-b8-analysis to imagej2-b7-ndim-data

comment:3 Changed 2013-05-17T15:16:12-05:00 by bdezonia

Verified the fix works on the upstream branch of scfio-cells. When merged to master this ticket can close.

comment:4 Changed 2013-06-04T11:44:13-05:00 by bdezonia

Status changed from new to closed
Resolution set to fixed

Merged. Closing.