[ome-users] bio-formats importer bug

Wed Jul 19 15:46:25 BST 2017

Hi David,

> If you had a smaller file (<2GB) which displayed the same behaviour
> would you be able to upload it for testing:
> https://www.openmicroscopy.org/qa2/qa/upload/

Did the 'AbI 1-200 1to4_Caption.tif' file I uploaded to QA come through? It
was smaller than 2GB.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/

On Wed, Jul 19, 2017 at 9:11 AM, David Gault (Staff) <d.gault at dundee.ac.uk>
wrote:

> Hi Vytas,
>
> That read time certainly doesn’t seem normal. We had also received a
> separate report yesterday of a file with a long read time.
> I had created a card on the Bio-Formats Trello inbox to investigate that
> issue and I will also link this thread topic to it incase the behaviour is
> related:
> https://trello.com/c/tjWeeyXb/161-tiff-long-delayed-load-time
>
> If you had a smaller file (<2GB) which displayed the same behaviour would
> you be able to upload it for testing:
> https://www.openmicroscopy.org/qa2/qa/upload/
>
> With Thanks,
> David Gault
>
> On 18 Jul 2017, at 17:06, vbindokas <vbindoka at BSD.UCHICAGO.EDU> wrote:
>
> 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> 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>
> Date: Mon, Jul 17, 2017 at 2:30 PM
> Subject: bio-formats importer bug
> To: Curtis Rueden <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 <%28773%29%20702-4875> [alt's: 773-834-9040 <%28773%29%20834-9040> or 773-834-2639 <%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
>
>
> email vbindoka at bsd.uchicago.edu
> web site for LMCF:http://digital.uchicago.edu
>
>
> _______________________________________________
> ome-users mailing list
> 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 <(773)%20702-4875> [alt's: 773-834-9040 <(773)%20834-9040> or 773-834-2639 <(773)%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
>
>
> email vbindoka at bsd.uchicago.edu
> web site for LMCF:http://digital.uchicago.edu
>
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
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