[ome-users] Bug report BioFormats - LiFlimReader.java

[Sebastien Besson (Staff)]

Hi Johan,

sorry for the late reply. We have received your sample file and will be adding it to our
testing data repository.

Thanks,
Sebastien

On 21 Apr 2016, at 07:40, Johan Herz <johan at lambertinstruments.com<mailto:johan at lambertinstruments.com>> wrote:

Dear Sebastien,

Thank you for your quick followup.
I have uploaded the following file: ExampleFile - LiFlimReader fix ExposureTime.fli

Looking forward to see it being fixed.


With best regards,

Johan Herz, Sales Engineer

Tel: +31-50-501-8461 | Skype: lambert-johan
Lambert Instruments BV|Leonard Springerlaan 19 (5th floor)|9727 KB Groningen|The Netherlands
Dutch Chamber of Commerce nr.: 52396940 | www.lambertinstruments.com<http://www.lambertinstruments.com/>

2016-04-20 23:19 GMT+02:00 Sebastien Besson (Staff) <s.besson at dundee.ac.uk<mailto:s.besson at dundee.ac.uk>>:
Dear Johan,

many thanks for your bug report. It looks like your assumption is correct and that
the metadata check for ExposureTime key is not stringent enough. I have
opened a Pull Request https://github.com/openmicroscopy/bioformats/pull/2364
with a proposed fix which I would expect to be available with Bio-Formats 5.2.0.

In order to facilitate our testing and to prevent future regressions, would it be
possible for you to upload a sample .fli file at http://qa.openmicroscopy.org.uk/qa/upload/
reproducing the problem?

Best regards,
Sebastien

On 20 Apr 2016, at 11:35, Johan Herz <johan at lambertinstruments.com<mailto:johan at lambertinstruments.com>> wrote:

Dear All,

To whom it may concern, I would like to report a Bug I encounter in Bioformats.
The following exception is thrown by Fiji:

java.lang.StringIndexOutOfBoundsException: String index out of range: -1
at java.lang.String.substring(String.java:1937)
at loci.formats.in.LiFlimReader.initOriginalMetadata(LiFlimReader.java:334)

I have a .fli file with the following header entry:
  'LockExposureTime = 0'
and while looking at the code in LiFlimReader.java I think that this conflicts with to following:

315  else if (metaKey.endsWith("ExposureTime")) {
316     int space = value.indexOf(" ");
317     double expTime = Double.parseDouble(value.substring(0, space));
318     String units = value.substring(space + 1).toLowerCase();
319     if (units.equals("ms")) {
320        expTime /= 1000;
321     }

I think for future releases of Bioformats this still can cause a conflict in case a different Header entry ends with "ExposureTime"

Please contact me for further questions and I will be looking forward to receiving a reply.

With best regards,

Johan Herz, Sales Engineer

Tel: +31-50-501-8461<tel:%2B31-50-501-8461> | Skype: lambert-johan
Lambert Instruments BV|Leonard Springerlaan 19 (5th floor)|9727 KB Groningen|The Netherlands
Dutch Chamber of Commerce nr.: 52396940 | www.lambertinstruments.com<http://www.lambertinstruments.com/>
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