[ome-users] bio-formats importer bug

Thu Jul 20 10:17:41 BST 2017

Hi Curtis,

We did indeed receive the 'AbI 1-200 1to4_Caption.tif’ that was submitted. From testing it does not appear to display the exceptionally long load time that was being reported with the larger file.

With Thanks,
David Gault

On 19 Jul 2017, at 15:46, Curtis Rueden <ctrueden at WISC.EDU<mailto:ctrueden at WISC.EDU>> wrote:

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<mailto: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<mailto: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<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> or 773-834-2639<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

email vbindoka 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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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<tel:(773)%20702-4875> [alt's: 773-834-9040<tel:(773)%20834-9040> or 773-834-2639<tel:(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<mailto:vbindoka at bsd.uchicago.edu>
web site for LMCF:
http://digital.uchicago.edu<http://digital.uchicago.edu/>

The University of Dundee is a registered Scottish Charity, No: SC015096

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The University of Dundee is a registered Scottish Charity, No: SC015096
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