Saving large files in ome.tif or ids/ics

Posted by Jason Miller on Apr 30, 2015; 9:27pm
URL: http://imagej.273.s1.nabble.com/Saving-large-files-in-ome-tif-or-ids-ics-tp5012659.html

Hi all-

This may be a Bioformats issue as well, so I will separately e-mail the OME
folks, but similar to recent past posts on this list, I'm having trouble
saving files that are > 4GB into ome.tif or IDS/ICS formats. I have a 5GB
file, open as a virtual file, and when I go to export via Bioformats
Exporter to IDS/ICS format, I get the following error:

(Fiji Is Just) ImageJ 2.0.0-rc-15/1.49p; Java 1.6.0_24 [64-bit]; Windows 7
6.1; 98MB of 12209MB (<1%)

java.lang.IllegalArgumentException: Negative position
at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:600)
at
loci.common.NIOByteBufferProvider.allocateDirect(NIOByteBufferProvider.java:131)
at
loci.common.NIOByteBufferProvider.allocate(NIOByteBufferProvider.java:116)
at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:551)
at loci.common.NIOFileHandle.seek(NIOFileHandle.java:273)
at
loci.common.RandomAccessOutputStream.seek(RandomAccessOutputStream.java:79)
at loci.formats.out.ICSWriter.saveBytes(ICSWriter.java:139)
at loci.formats.FormatWriter.saveBytes(FormatWriter.java:126)
at loci.plugins.out.Exporter.run(Exporter.java:629)
at loci.plugins.LociExporter.run(LociExporter.java:77)
at
ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:263)
at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:112)
at ij.IJ.runUserPlugIn(IJ.java:201)
at ij.IJ.runPlugIn(IJ.java:163)
at ij.Executer.runCommand(Executer.java:131)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:662)


When I go to export to ome.tif format, I get the same error previously
reported on this list:
loci.formats.FormatException: File is too large; call setBigTiff(true)

Is it possible to retain the ome.tif format for >4GB? In my case, this is
for importing into Huygens for deconvolution.

Thanks so very much
-Jason
--

Jason Miller, MD, PhD

University of Michigan Kellogg Eye Center

--

Home address:

117 Worden Ave

Ann Arbor, MI 48103

Cell: [phone]

E-mail: *[hidden email] <[hidden email]>*


"When I was 5 years old, my mother always told me that happiness was the
key to life. When I went to school, they asked me what I wanted to be when
I grew up. I wrote down, 'Happy.' They told me I didn't understand the
assignment. I told them they didn't understand life." - John Lennon

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html