[ome-users] bio-formats importer bug

Tue Jul 18 11:51:10 BST 2017

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
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/

---------- 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<http://loci.formats.in/>.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<http://upload.imagej.net/> 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:(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/>

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