[ome-users] problem opening tiff

[Sebastien Besson (Staff)]

Hi Adam,

thanks for the bug report which we were able to reproduce with the
uploaded file. A proposed fix [1] was opened to correct the bug and
will be under review shortly.

Best regards,
Sebastien

[1] https://github.com/openmicroscopy/bioformats/pull/1902

On 29 Jul 2015, at 20:12, Adam Webb <Adam.Webb at lightsource.ca<mailto:Adam.Webb at lightsource.ca>> wrote:

Hi,

I have gotten an error opening a 16 bit tiff. This is similar to the one I posted previously (http://lists.openmicroscopy.org.uk/pipermail/ome-users/2015-May/005386.html). The message is similar.

(Fiji Is Just) ImageJ 2.0.0-rc-34/1.50a; Java 1.6.0_24 [64-bit]; Windows NT (unknown) 6.2; 62MB of 24000MB (<1%)
java.lang.NumberFormatException: null
                at java.lang.Integer.parseInt(Integer.java:417)
                at java.lang.Integer.parseInt(Integer.java:499)
                at loci.formats.in.SimplePCITiffReader.initStandardMetadata(SimplePCITiffReader.java:179)
                at loci.formats.in.BaseTiffReader.initMetadata(BaseTiffReader.java:98)
                at loci.formats.in.BaseTiffReader.initFile(BaseTiffReader.java:577)
                at loci.formats.FormatReader.setId(FormatReader.java:1426)
                at loci.formats.ImageReader.setId(ImageReader.java:835)
                at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:424)
                at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:406)
                at io.scif.AbstractParser.parse(AbstractParser.java:253)
                at io.scif.AbstractParser.parse(AbstractParser.java:336)
                at io.scif.AbstractParser.parse(AbstractParser.java:52)
                at io.scif.AbstractReader.setSource(AbstractReader.java:270)
                at io.scif.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:90)
                at io.scif.img.ImgOpener.createReader(ImgOpener.java:547)
                at io.scif.img.ImgOpener.openImgs(ImgOpener.java:146)
                at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:123)
                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.interceptFileOpen(DefaultLegacyHooks.java:329)
                at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:152)
                at ij.IJ.runPlugIn(IJ.java)
                at ij.Executer.runCommand(Executer.java:132)
                at ij.Executer.run(Executer.java:65)
                at java.lang.Thread.run(Thread.java:662)


The image is from the same camera as before but might be a newer version of HCImage. I noticed that the metadata is somewhat different in this file compared to the previous ba_image. (This was QA 11088)  I have uploaded the file bone_tmp1981_00011.tif to the QA system.

Cheers,
Adam


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