[ome-users] Fwd: bio-formats importer bug

Mon Jul 17 21:05:26 BST 2017

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>
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.CellVoyagerReader.isThisType(CellVoyagerRead
er.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 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 <(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
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