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

[Johan Herz]

Okay, Thank you :)

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

2016-04-25 12:09 GMT+02:00 Sebastien Besson (Staff) <s.besson at dundee.ac.uk>:

> 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> 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
>
> 2016-04-20 23:19 GMT+02:00 Sebastien Besson (Staff) <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>
>> 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 | 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
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>>
>>
>>
>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>
>
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
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