[SCIFIO] opening tiff files with ImageJ2

Thu Jan 16 14:37:00 CST 2014

Hi Martin,

thank you for that incredible fast reaction and fix!
>

You're welcome! Just wanted to post this on the list, so it goes on record.
;)

 I tried with the Scifio-dev update and it works perfectly fine.
>

Glad to hear it. It's always great to get feedback about SCIFIO/IJ2 - even
bug reports!

Take care,
Mark

On Thu, Jan 16, 2014 at 2:18 PM, Martin Höhne <martin.hoehne at uk-koeln.de>wrote:

>  Hi Mark,
>
>
>
> thank you for that incredible fast reaction and fix!
>
>
>
> As I said, currently we were still fine with Fiji/ImageJ1 opening the
> files. I just wanted to ensure that we still can open the files when
> ImageJ2 has replaced ImageJ1.
>
> I tried with the Scifio-dev update and it works perfectly fine.
>
>  Thanks again
>
> Martin
>
>
>
> *Von:* hinerm at gmail.com [mailto:hinerm at gmail.com] *Im Auftrag von *Mark
> Hiner
> *Gesendet:* Donnerstag, 16. Januar 2014 20:48
> *An:* Martin Höhne
> *Cc:* scifio at scif.io
> *Betreff:* Re: [SCIFIO] opening tiff files with ImageJ2
>
>
>
> 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
>
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