[ome-users] Saving large files in ome.tif or ids/ics

[Jason Miller]

Hi all-

I have cross-posted this issue to both this list and the ImageJ list, as
I'm not sure which is the best place to ask the question.

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: (415) 225-2134

E-mail: *jason.miller at stanfordalumni.org <jason.miller at stanfordalumni.org>*


"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



-- 

Jason Miller, MD, PhD

University of Michigan Kellogg Eye Center

--

Home address:

117 Worden Ave

Ann Arbor, MI 48103

Cell: (415) 225-2134

E-mail: *jason.miller at stanfordalumni.org <jason.miller at stanfordalumni.org>*


"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
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