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Bug 609 - Cannot save files as tiff
Cannot save files as tiff
Status: RESOLVED WORKSFORME
Product: Fiji
Classification: Unclassified
Component: Bio-Formats
unspecified
Macintosh Mac OS
: P5 major
Assigned To: Melissa Linkert
Depends on:
Blocks:
 
Reported: 2013-05-18 07:28 CDT by Kyoko3
Modified: 2013-07-07 10:34 CDT
1 user (show)

See Also:
Description Kyoko3 2013-05-18 07:28:33 CDT 
Hi there,

Recently, I have encountered the following exception message:

(Fiji Is Just) ImageJ 1.47q; Java 1.6.0_45 [64-bit]; Mac OS X 10.6.8; 22MB of 1273MB (1%)
 
java.lang.reflect.InvocationTargetException
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at ij.Command.runPlugIn(Command.java:148)
	at ij.Command.runCommand(Command.java:97)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:680)
Caused by: java.lang.IllegalStateException: FormatReader.getSeriesCount: Current file should not be null; call setId(String) first
	at loci.formats.FormatTools.assertId(FormatTools.java:713)
	at loci.formats.FormatReader.getSeriesCount(FormatReader.java:815)
	at loci.formats.FormatReader.setSeries(FormatReader.java:834)
	at loci.formats.ReaderWrapper.setSeries(ReaderWrapper.java:339)
	at loci.formats.ReaderWrapper.setSeries(ReaderWrapper.java:339)
	at loci.formats.ReaderWrapper.setSeries(ReaderWrapper.java:339)
	at loci.formats.ReaderWrapper.setSeries(ReaderWrapper.java:339)
	at loci.formats.ReaderWrapper.setSeries(ReaderWrapper.java:339)
	at loci.formats.ReaderWrapper.setSeries(ReaderWrapper.java:339)
	at loci.formats.ReaderWrapper.setSeries(ReaderWrapper.java:339)
	at loci.plugins.util.BFVirtualStack.getProcessor(BFVirtualStack.java:155)
	at ij.io.ImageWriter.write16BitVirtualStack(ImageWriter.java:102)
	at ij.io.ImageWriter.write(ImageWriter.java:276)
	at ij.io.TiffEncoder.write(TiffEncoder.java:119)
	at ij.io.TiffEncoder.write(TiffEncoder.java:139)
	at ij.io.FileSaver.saveAsTiffStack(FileSaver.java:184)
	at ij.io.FileSaver.saveAsTiff(FileSaver.java:89)
	at ij.plugin.filter.Writer.run(Writer.java:20)
	at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:262)
	at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:111)
	at ij.IJ.runPlugIn(IJ.java:168)
	... 8 more

This always happens when I want to save a 4D .ids file as a .tiff after editing. I am fairly certain that this didn't use to happen. I get the same message when I try to open the file with BioFormats, so I'm guessing that's where the problem lies.

Best,

Steff
Comment 1 Melissa Linkert 2013-05-21 12:27:53 CDT 
I have not been able to reproduce this problem so far.

Can you please make sure that your installation is completely up to date (you may need to run "Help > Update Fiji" several times)?  You may also need to follow the instructions here:

http://fiji.sc/bugzilla/﷒0﷓

If that does not solve the problem, then it would help to know exactly how you are opening the file (i.e. which options are selected in the "Bio-Formats Import Options" window), as well as exactly how you are saving the file to TIFF.