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

[Johan Herz]

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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