[SCIFIO] opening tiff files with ImageJ2
Mark Hiner
hiner at wisc.edu
Thu Jan 16 13:47:41 CST 2014
Hi Martin,
There were two IFDs (id 1807 and 1808) which were unknown to us -
presumably related to the FusionCapt software you're using. As interpreted
by the TIFF spec they would cause reading past the EOF. There was a
safeguard in the SCIFIO parser to truncate such a read before the EOF, but
it wasn't implemented properly.
I fixed the bug,<https://github.com/scifio/scifio/commit/2b9f1be852c4b2bffee40a673924780022ac2c54>and
added a SCIFIO-dev
update site <http://fiji.sc/List_of_update_sites> for Fiji. Using this
update site will allow you to use the most recent SCIFIO. Generally, this
isn't guaranteed to be stable, but it should help if you want to view your
data in IJ2 between now and the next SCIFIO release.
Thanks again for reporting this issue. Let me know if anything else comes
up!
- Mark
On Wed, Jan 15, 2014 at 9:32 AM, Mark Hiner <hiner at wisc.edu> wrote:
> Hi Martin,
>
>
> PS - I hope this ist he right list to post. If not, maybe someone could
>> direct me to the best suited forum
>>
>
> This is definitely a problem in SCIFIO, so this was the right place to
> post! I've opened a new issue<https://github.com/scifio/scifio/issues/123>to track this problem and will look into it today.
>
> Because this looks to be a bug in Bio-Formats as well (which is not
> surprising - as the SCIFIO TIFF support is derived from Bio-Formats) I am
> also forwarding this to the OME-Users list.
>
> Thanks for the report!
>
> - Mark
>
>
> On Wed, Jan 15, 2014 at 6:36 AM, Martin Höhne <martin.hoehne at uk-koeln.de>wrote:
>
>> Dear list,
>>
>> We have 16 bit Tiff files from a camera (from a Chemoluminescence
>> detector. Fusion XL machine form Vilber Lourmat http://www.vilber.com/).
>> The images can be opened fine in Fiji (open or drag&drop). However,
>> importing via File>Import>BioFormats fails. I get this error:
>>
>> "Sorry, there was a problem during import". The log file is posted at the
>> end of this mail.
>>
>> We are fine with the normal opening, however the ImageJ2 seems to try to
>> open with the import function (2.0.0.0 beta7.6). I get this message:
>> "io.scif.img.ImgIOExceprion: java.io.EOFException: Attempting to read
>> beyond end of file"
>>
>> The image contains some metadata I can´t read when opening with ImageJ,
>> but only when opening the file with the Fusion software from Vilber.
>> For the attached file the metadata is at the end of this posting as well.
>>
>> The metadata is not so important, but it would be great if the images
>> could be opened with ImageJ2 as well.
>>
>> Thank you
>> Martin
>>
>> PS - I hope this ist he right list to post. If not, maybe someone could
>> direct me to the best suited forum
>>
>> System information:
>> Win7 64bit
>> Fiji, updatet 2014-01-15
>>
>> Log from import:
>> Fiji(legacy mode) File>Import>BioFormats:
>> loci.formats.FormatException: loci.common.ReflectException:
>> java.lang.reflect.InvocationTargetException
>> at
>> loci.formats.in.TiffJAIReader.openBufferedImage(TiffJAIReader.java:202)
>> at loci.formats.in.TiffJAIReader.initFile(TiffJAIReader.java:162)
>> at loci.formats.FormatReader.setId(FormatReader.java:1360)
>> at loci.formats.DelegateReader.setId(DelegateReader.java:275)
>> at
>> loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)
>> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)
>> at loci.plugins.in.Importer.showDialogs(Importer.java:141)
>> at loci.plugins.in.Importer.run(Importer.java:79)
>> at loci.plugins.LociImporter.run(LociImporter.java:81)
>> at ij.IJ.runUserPlugIn(IJ.java:196)
>> at ij.IJ.runPlugIn(IJ.java:160)
>> at ij.Executer.runCommand(Executer.java:131)
>> at ij.Executer.run(Executer.java:64)
>> at java.lang.Thread.run(Thread.java:662)
>> Caused by: loci.common.ReflectException:
>> java.lang.reflect.InvocationTargetException
>> at loci.common.ReflectedUniverse.exec(ReflectedUniverse.java:125)
>> at
>> loci.formats.in.TiffJAIReader.openBufferedImage(TiffJAIReader.java:197)
>> ... 13 more
>> Caused by: 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
>> ome.scifio.common.ReflectedUniverse.exec(ReflectedUniverse.java:317)
>> at loci.common.ReflectedUniverse.exec(ReflectedUniverse.java:122)
>> ... 14 more
>> Caused by: java.io.EOFException
>> at
>> com.sun.media.jai.codec.SeekableStream.readFully(SeekableStream.java:329)
>> at
>> com.sun.media.jai.codec.SeekableStream.readFully(SeekableStream.java:306)
>> at
>> com.sun.media.jai.codec.SeekableStream.readUnsignedIntLE(SeekableStream.java:708)
>> at
>> com.sun.media.jai.codec.TIFFDirectory.readUnsignedInt(TIFFDirectory.java:524)
>> at
>> com.sun.media.jai.codec.TIFFDirectory.initialize(TIFFDirectory.java:289)
>> at
>> com.sun.media.jai.codec.TIFFDirectory.<init>(TIFFDirectory.java:125)
>> at
>> com.sun.media.jai.codecimpl.TIFFImage.<init>(TIFFImage.java:318)
>> at
>> com.sun.media.jai.codecimpl.TIFFImageDecoder.decodeAsRenderedImage(TIFFImageDecoder.java:112)
>> ... 20 more
>>
>>
>> Metadata of attached image:
>> Good Laboratory Practice:GLP
>>
>> GENERAL INFORMATION
>> Title:
>> Comments:
>> Date: Freitag, 13. Dezember 2013
>> Time: 13:42:04
>> Image name:
>> C:\Users\nephrolab\Pictures\temp_western\mhoehne\eva24__1.TIF
>>
>> Software information: FusionCapt Advance Solo 4 16.07
>>
>> ACQUISITION PARAMETERS:
>>
>> Lens information:
>> Iris aperture:
>>
>> Camera information:
>> Integration time acquisition: : 0 min 50 sec 0 msec
>> Acquisition mode: Serial/r/n Image 1/10
>> Positive acquisition
>> Resolution used: Binning 2x2
>> Pixel depth 16 Bit per pixel
>> Software acquisition mode: Not defined
>> Vigneting filter : Aperture value 0.84
>> Sensor area used: : (0, 0, 2048,2048)
>> Configuration file used: C:\Users\nephrolab\Documents\Vilber
>> Lourmat\nephrolab_settings\2x2 binning.prt
>> Camera serial number: 275704
>> Tray position: Non applicable
>> Application name: 2x2 binning
>> Auto mode: User defined autoexposure coef 97%
>> USB status: No USB detected
>> Imaging system: FusionCapt Advance Solo 4 16.07
>> Camera serial number: 275704 - Firmware >2.0.0<
>> USB codage: No darkroom
>> Lens configuration: Non applicable
>> RGB status: Not installed
>> Skylight: Not installed
>>
>> Image manipulation
>>
>> Gray level inversion: No
>>
>>
>> _______________________________________________
>> SCIFIO mailing list
>> SCIFIO at scif.io
>> http://scif.io/mailman/listinfo/scifio
>>
>>
>
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