Fiji: exception when reading .ome.tiff by drag&drop

scifio
bug
fiji
Tags: #<Tag:0x00007fb87be8f310> #<Tag:0x00007fb87be8f1d0> #<Tag:0x00007fb87be8f090>

#1

Dear all,

a fresh installation of the latest Fiji with SCIFIO enabled fails to read this .ome.tiff image. The Bioformats Importer reads successfully. Is this the right place to report this?

Best,
Lorenz

Warning:  org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser: Property 'http://www.oracle.com/xml/jaxp/properties/entityExpansionLimit' is not recognized.
Warning:  org.apache.xerces.parsers.SAXParser: Feature 'http://javax.xml.XMLConstants/feature/secure-processing' is not recognized.
Warning:  org.apache.xerces.parsers.SAXParser: Property 'http://javax.xml.XMLConstants/property/accessExternalDTD' is not recognized.
Warning:  org.apache.xerces.parsers.SAXParser: Property 'http://www.oracle.com/xml/jaxp/properties/entityExpansionLimit' is not recognized.
Warning:  org.apache.xerces.parsers.SAXParser: Property 'http://javax.xml.XMLConstants/property/accessExternalDTD' is not recognized.
Warning:  org.apache.xerces.parsers.SAXParser: Property 'http://www.oracle.com/xml/jaxp/properties/entityExpansionLimit' is not recognized.
[WARNING] Image ID 'D:\Lorenz\2016 06 06 stainings\3 - bleach_new_switch track every z-stack__AQ__W0001__P0001__T0004.czi': missing plane #0.  Using TiffReader to determine the number of planes.
[INFO] Reading IFDs
[INFO] Populating metadata
[INFO] Checking comment style
[INFO] Reading IFDs
[INFO] Populating metadata
[INFO] Checking comment style
Exception in thread "DrawAndDrop" java.lang.ArrayIndexOutOfBoundsException: 1
	at io.scif.ome.formats.OMETIFFFormat$Reader.openPlane(OMETIFFFormat.java:1116)
	at io.scif.ome.formats.OMETIFFFormat$Reader.openPlane(OMETIFFFormat.java:1082)
	at io.scif.AbstractReader.openPlane(AbstractReader.java:167)
	at io.scif.filters.ChannelFiller.openPlane(ChannelFiller.java:171)
	at io.scif.filters.ChannelFiller.openPlane(ChannelFiller.java:151)
	at io.scif.filters.PlaneSeparator.openPlane(PlaneSeparator.java:305)
	at io.scif.filters.AbstractReaderFilter.openPlane(AbstractReaderFilter.java:244)
	at io.scif.img.ImgOpener.read(ImgOpener.java:836)
	at io.scif.img.ImgOpener.read(ImgOpener.java:818)
	at io.scif.img.ImgOpener.read(ImgOpener.java:818)
	at io.scif.img.ImgOpener.read(ImgOpener.java:818)
	at io.scif.img.ImgOpener.read(ImgOpener.java:798)
	at io.scif.img.ImgOpener.readPlanes(ImgOpener.java:785)
	at io.scif.img.ImgOpener.openImgs(ImgOpener.java:383)
	at io.scif.img.ImgOpener.openImgs(ImgOpener.java:269)
	at io.scif.img.ImgOpener.openImgs(ImgOpener.java:146)
	at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:124)
	at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:109)
	at io.scif.io.DatasetIOPlugin.open(DatasetIOPlugin.java:75)
	at io.scif.io.DatasetIOPlugin.open(DatasetIOPlugin.java:50)
	at net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:135)
	at net.imagej.legacy.DefaultLegacyHooks.interceptDragAndDropFile(DefaultLegacyHooks.java:363)
	at ij.plugin.DragAndDrop.openFile(DragAndDrop.java)
	at ij.plugin.DragAndDrop.run(DragAndDrop.java:159)
	at java.lang.Thread.run(Thread.java:745)

#2

Thank you for the report. I have filed scifio/scifio-ome-xml#25 to track this. Unfortunately, it will probably be a while before anyone at LOCI can look into it.