[ome-users] bio-formats importer bug

Tue Jul 18 17:06:08 BST 2017

Thanks for looking at the issue.

I can confirm that the crash no longer occurs if I nest the files 2 
folders up from root. However, FIJI has been trying to read a 3.5GB test 
file for now over 40 MINUTES and is now only at "reading plane 3/3".  
Ifranview64 AND windows picture viewer app both can open the same file 
in about 15 SECONDS. Something is still wrong....

best regards,

Vytas

On 7/18/2017 5:51 AM, David Gault (Staff) wrote:
> Hi Curtis and Vytas,
>
> This error is seen when attempting to open a file from the root 
> directory. While Bio-Formats attempts to identify the format type some 
> of the readers will search for associated files in parent folders. 
> This error is then seen if those locations do not exist. Moving the 
> files up from the root directory (at least 2 levels) should provide a 
> work around to enable you to open the files normally.
>
> This is a scenario which should be handled better without an exception 
> being thrown. I have created a card on the Bio-Formats Trello inbox to 
> further investigate a long term fix.
>
> With Thanks,
> David Gault
>
>> On 17 Jul 2017, at 21:05, Curtis Rueden <ctrueden at WISC.EDU 
>> <mailto:ctrueden at WISC.EDU>> wrote:
>>
>> Hi,
>>
>> Below is a Bio-Formats bug report from Vytas Bindokas (CCed).
>>
>> I also uploaded the sample image ('AbI 1-200 1to4_Caption.tif') to 
>> the OME QA system on his behalf.
>>
>> Regards,
>> Curtis
>>
>> --
>> Curtis Rueden
>> LOCI software architect - https://loci.wisc.edu/software 
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__loci.wisc.edu_software&d=DwMFAg&c=Nd1gv_ZWYNIRyZYZmXb18oVfc3lTqv2smA_esABG70U&r=pD-sSh_e9cMzytxHgN9Gfakl4sCheZunFOz7i3o-Ewk&m=7ukIxNxspqJuFY_Dl5sx9ganU_k-_lqSbbNrEu8Y3es&s=Oq_3SA9xhnjYUkrQMeN09J0NZ-iZDvAgGe0MgkNYK7Y&e=>
>> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden 
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__imagej.net_User-3ARueden&d=DwMFAg&c=Nd1gv_ZWYNIRyZYZmXb18oVfc3lTqv2smA_esABG70U&r=pD-sSh_e9cMzytxHgN9Gfakl4sCheZunFOz7i3o-Ewk&m=7ukIxNxspqJuFY_Dl5sx9ganU_k-_lqSbbNrEu8Y3es&s=tVkA4OcKqF_EmMYkanSV7srrKtDxjYlGGhwG14neeIA&e=>
>> Did you know ImageJ has a forum? http://forum.imagej.net/ 
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__forum.imagej.net_&d=DwMFAg&c=Nd1gv_ZWYNIRyZYZmXb18oVfc3lTqv2smA_esABG70U&r=pD-sSh_e9cMzytxHgN9Gfakl4sCheZunFOz7i3o-Ewk&m=7ukIxNxspqJuFY_Dl5sx9ganU_k-_lqSbbNrEu8Y3es&s=DVXZdDIESTW8arorbMOrlCLaoCGs4DGSnJl-jmfoeGI&e=>
>>
>>
>> ---------- Forwarded message ----------
>> From: *vbindokas* <vbindoka at bsd.uchicago.edu 
>> <mailto:vbindoka at bsd.uchicago.edu>>
>> Date: Mon, Jul 17, 2017 at 2:30 PM
>> Subject: bio-formats importer bug
>> To: Curtis Rueden <ctrueden at wisc.edu <mailto:ctrueden at wisc.edu>>
>>
>>
>> Hello Curtis,
>>
>> I'm sure you're busy, so can you please forward to LOCI dev team? 
>> [GUI reporter tool still not working]
>>
>> Back in March we were able to open automated scanner TIF exports 
>> using bio-formats, however recent attempts result in red ink:
>>
>> (Fiji Is Just) ImageJ 2.0.0-rc-61/1.51n; Java 1.8.0_66 [64-bit]; 
>> Windows 7 6.1; 1130MB of 15000MB (7%)
>> java.lang.NullPointerException
>>     at loci.common.Location.<init>(Location.java:104)
>>     at loci.common.Location.getParentFile(Location.java:623)
>>     at loci.formats.in 
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__loci.formats.in_&d=DwMFAg&c=Nd1gv_ZWYNIRyZYZmXb18oVfc3lTqv2smA_esABG70U&r=pD-sSh_e9cMzytxHgN9Gfakl4sCheZunFOz7i3o-Ewk&m=7ukIxNxspqJuFY_Dl5sx9ganU_k-_lqSbbNrEu8Y3es&s=fzRZjgHCLt5i4SWaooY1yOLpTb_pebsVBTzRhfCbRlo&e=>.CellVoyagerReader.isThisType(CellVoyagerReader.java:256)
>>     at loci.formats.ImageReader.getReader(ImageReader.java:185)
>>     at 
>> loci.plugins.in.ImportProcess.createBaseReader(ImportProcess.java:618)
>>     at 
>> loci.plugins.in.ImportProcess.initializeReader(ImportProcess.java:484)
>>     at loci.plugins.in.ImportProcess.execute(ImportProcess.java:137)
>>     at loci.plugins.in.Importer.showDialogs(Importer.java:140)
>>     at loci.plugins.in.Importer.run(Importer.java:76)
>>     at loci.plugins.LociImporter.run(LociImporter.java:78)
>>     at ij.IJ.runUserPlugIn(IJ.java:217)
>>     at ij.IJ.runPlugIn(IJ.java:181)
>>     at ij.Executer.runCommand(Executer.java:137)
>>     at ij.Executer.run(Executer.java:66)
>>     at java.lang.Thread.run(Thread.java:745)
>>
>> I've uploaded a sample via the Help UI;
>>
>> <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
>> <html><head>
>> <title>201 Created</title>
>> </head><body>
>> <h1>Created</h1>
>> <p>Resource /*AbI%201-200%201to4_Caption.tif *has been created.</p>
>> <hr />
>> <address>Apache/2.4.18 (Ubuntu) Server at upload.imagej.net 
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__upload.imagej.net_&d=DwMFAg&c=Nd1gv_ZWYNIRyZYZmXb18oVfc3lTqv2smA_esABG70U&r=pD-sSh_e9cMzytxHgN9Gfakl4sCheZunFOz7i3o-Ewk&m=7ukIxNxspqJuFY_Dl5sx9ganU_k-_lqSbbNrEu8Y3es&s=Z-p6JYY2UNRli6My0Ud_u2n5kWhdfoynPG-80b96TVc&e=> 
>> Port 80</address>
>> </body></html>
>>
>> I can open this file in IrafanView and resave it there-- that resave 
>> opens normally in fiji.  It's a work-around, but time and space 
>> consuming.
>>
>> BEST REGARDS!~
>>
>> Vytas
>>
>> -- 
>> __
>>
>> Vytas Bindokas, Ph.D.
>> Research Assoc. Prof.,
>> Director, BSD Light Microscopy Core Facility
>> phone:773-702-4875 <tel:%28773%29%20702-4875>  [alt's:773-834-9040 <tel:%28773%29%20834-9040>  or773-834-2639 <tel:%28773%29%20834-2639>]
>>
>>       [address for letters ONLY (see shipping addr below):]
>> Dept Pharmacol Physiol Sci MC0926
>> 947 E 58th Street
>> The University of Chicago
>> Chicago IL 60637
>> Room Abbott 129
>>
>>
>> shipping address (main KCBD site):
>> V. Bindokas
>> 900 E 57th Street
>> KCBD room 1250, Microscopy Core
>> The University of Chicago
>> Chicago IL 60637
>>
>>
>> emailvbindoka at bsd.uchicago.edu <mailto:vbindoka at bsd.uchicago.edu>
>> web site for LMCF:
>> http://digital.uchicago.edu <http://digital.uchicago.edu/>
>>
>> _______________________________________________
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>> ome-users at lists.openmicroscopy.org.uk 
>> <mailto:ome-users at lists.openmicroscopy.org.uk>
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096 

-- 
__

Vytas Bindokas, Ph.D.
Research Assoc. Prof.,
Director, BSD Light Microscopy Core Facility
phone: 773-702-4875 [alt's: 773-834-9040 or 773-834-2639]

      [address for letters ONLY (see shipping addr below):]
Dept Pharmacol Physiol Sci MC0926
947 E 58th Street
The University of Chicago
Chicago IL 60637
Room Abbott 129

shipping address (main KCBD site):
V. Bindokas
900 E 57th Street
KCBD room 1250, Microscopy Core
The University of Chicago
Chicago IL 60637

email vbindoka at bsd.uchicago.edu
web site for LMCF:
http://digital.uchicago.edu

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