import lei

[jburel]

Using r7144

From test_images_good,
file: 050628-leica.lei

2010-06-01 15:24:21,789 841593     [2-thread-1] ERROR    ome.formats.importer.gui.ImportHandler  - Generic error while importing image.
java.lang.NullPointerException
	at loci.formats.FilePattern.getPrefixes(FilePattern.java:292)
	at loci.formats.AxisGuesser.<init>(AxisGuesser.java:125)
	at loci.formats.in.LeicaReader.parseFilenames(LeicaReader.java:786)
	at loci.formats.in.LeicaReader.initFile(LeicaReader.java:454)
	at loci.formats.FormatReader.setId(FormatReader.java:1066)
	at loci.formats.ImageReader.setId(ImageReader.java:644)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:485)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:177)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:485)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:238)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:485)
	at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:240)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:426)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:367)
	at ome.formats.importer.gui.ImportHandler.importImages(ImportHandler.java:215)
	at ome.formats.importer.gui.ImportHandler.access$100(ImportHandler.java:59)
	at ome.formats.importer.gui.ImportHandler$2.run(ImportHandler.java:134)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:417)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:269)
	at java.util.concurrent.FutureTask.run(FutureTask.java:123)
	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:65)
	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:172)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:651)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:676)

[mlinkert]

Works for me with ​bio-formats:r6436. If updating doesn't solve the problem, can you make sure that all of the associated TIFFs are in the same directory as the .lei? The stack trace indicates that at least one of the TIFFs cannot be found, which is a bit suspicious.

[jburel]

I have tried with the QA version
Still the same problem, the only image I can import from test_images_good/lei is the leica_stack.lei

[mlinkert]

So far, I've only been able to reproduce this problem by moving 050628-leica_* out of test_images_good/lei/, which again indicates that some of the TIFF files were missing when you imported. Can you confirm that 'ls /path/to/test_images_good/lei/ | grep -c 050628-leica' outputs 176?

I did make a few changes in ​bio-formats:r6465 which should prevent this exception and help us track down why the TIFFs are not being found in the first place. If you try importing with r6465 or later, you should see a bunch of debug messages that start with "Expected to find TIFF file"; if you could paste everything in your importer log starting with the first of those messages, that would be helpful.

[cxallan]

I deleted *ch02.tif and attempted an import. This results in a completed import and the following errors in the log:

2010-06-11 09:48:29,313 1708434    [2-thread-1] DEBUG               loci.formats.in.LeicaReader  - Expected to find TIFF file /Users/callan/testimages/hack/050628-leica_02-01_ch02.tif
2010-06-11 09:48:29,313 1708434    [2-thread-1] DEBUG               loci.formats.in.LeicaReader  -   file does not exist
...
2010-06-11 09:48:29,314 1708435    [2-thread-1] DEBUG               loci.formats.in.LeicaReader  - Expected to find TIFF file /Users/callan/testimages/hack/050628-leica_02-02_ch02.tif
2010-06-11 09:48:29,314 1708435    [2-thread-1] DEBUG               loci.formats.in.LeicaReader  -   file does not exist
...
2010-06-11 09:48:29,315 1708436    [2-thread-1] DEBUG               loci.formats.in.LeicaReader  - Expected to find TIFF file /Users/callan/testimages/hack/050628-leica_02-03_ch02.tif
2010-06-11 09:48:29,315 1708436    [2-thread-1] DEBUG               loci.formats.in.LeicaReader  -   file does not exist
...

If this is what you're expecting Melissa I'll close this. Thanks!

[mlinkert]

That looks correct to me, so feel free to close.

Replying to cxallan:

I deleted *ch02.tif and attempted an import. This results in a completed import and the following errors in the log:

2010-06-11 09:48:29,313 1708434    [2-thread-1] DEBUG               loci.formats.in.LeicaReader  - Expected to find TIFF file /Users/callan/testimages/hack/050628-leica_02-01_ch02.tif
2010-06-11 09:48:29,313 1708434    [2-thread-1] DEBUG               loci.formats.in.LeicaReader  -   file does not exist
...
2010-06-11 09:48:29,314 1708435    [2-thread-1] DEBUG               loci.formats.in.LeicaReader  - Expected to find TIFF file /Users/callan/testimages/hack/050628-leica_02-02_ch02.tif
2010-06-11 09:48:29,314 1708435    [2-thread-1] DEBUG               loci.formats.in.LeicaReader  -   file does not exist
...
2010-06-11 09:48:29,315 1708436    [2-thread-1] DEBUG               loci.formats.in.LeicaReader  - Expected to find TIFF file /Users/callan/testimages/hack/050628-leica_02-03_ch02.tif
2010-06-11 09:48:29,315 1708436    [2-thread-1] DEBUG               loci.formats.in.LeicaReader  -   file does not exist
...

If this is what you're expecting Melissa I'll close this. Thanks!

[jburel]

closing ticket