[ome-users] Fwd: Errors when loading Cellomics .DIB with non-standard filename

[Lee Kamentsky]

Thanks Melissa,


On Mon, Feb 24, 2014 at 8:09 PM, Melissa Linkert <
melissa at glencoesoftware.com> wrote:

> Hi Lee,
>
> > I do have one question as I'm implementing. This line:
> >
> https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats/src/loci/formats/in/CellomicsReader.java#L195
> >
> > prevents the reader from including all of a plate's files unless there
> is a
> > full plate map. It seems a little cruel... just want to make sure it
> > belongs there, I have one directory which is a full plate and another
> which
> > is just short of full.
>
> The main reason for that being in place was to prevent the reader from
> being confused when multiple files copied from different plates were
> present in the same directory.  It's not strictly necessary, and could
> definitely be replaced with something a little smarter (which I can
> certainly do in an upcoming pull request).
>
> It really is your call on that - we generally run with grouping off so it
doesn't affect us. I'd go with whatever best suits other users and results
in a predictable behavior.

--Lee

> Regards,
> -Melissa
>
> On Thu, Feb 13, 2014 at 10:33:03AM -0500, Lee Kamentsky wrote:
> > Hi all,
> > We packaged a Cellomics dataset as part of the Broad Bioimage Benchmark
> > Collection, BBBC018. It's available for download here:
> > http://www.broadinstitute.org/bbbc/BBBC018/BBBC018_v1_images.zip
> >
> > We renamed the files when we packaged it up - unfortunately. It's not the
> > first time that something like this has happened, not under our control.
> > When I unpack the zip and use showinf to read the image, I get the
> > following stack trace:
> >
> > c:\Temp\bioformats_5.0.0_rc2>showinf -no-upgrade
> > c:\Temp\BBBC018_v1_images\00733-actin.DIB
> > Checking file format [Cellomics C01]
> > Initializing reader
> > CellomicsReader initializing c:\Temp\BBBC018_v1_images\00733-actin.DIB
> > Exception in thread "main" java.lang.StringIndexOutOfBoundsException:
> > String index out of range: 1
> >         at java.lang.String.charAt(Unknown Source)
> >         at
> > loci.formats.in.CellomicsReader.getWellName(CellomicsReader.java:371)
> >         at
> > loci.formats.in.CellomicsReader.getChannel(CellomicsReader.java:395)
> >         at
> > loci.formats.in.CellomicsReader.initFile(CellomicsReader.java:149)
> >         at loci.formats.FormatReader.setId(FormatReader.java:1360)
> >         at loci.formats.ImageReader.setId(ImageReader.java:781)
> >         at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:576)
> >         at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:993)
> >         at loci.formats.tools.ImageInfo.main(ImageInfo.java:1075)
> > c:\Temp\bioformats_5.0.0_rc2>
> >
> > The problem here is that much of the code in the reader assumes that it
> > will get a reasonable file name and doesn't catch the cases where the
> > assumptions are violated. In this case, the code assumes that the well
> > metadata appears after the last underbar: "images\00733-actin.DIB" (it
> > should have a format like "A01f00o1.DIB").
> >
> > I'm going to submit a pull request for a patch to this - I have both the
> > directory of zip files and a representative directory of Cellomics files
> > with their correct file names and I want to make sure what I do works in
> > CellProfiler (https://github.com/CellProfiler/CellProfiler/issues/1043).
> >
> > I do have one question as I'm implementing. This line:
> >
> https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats/src/loci/formats/in/CellomicsReader.java#L195
> >
> > prevents the reader from including all of a plate's files unless there
> is a
> > full plate map. It seems a little cruel... just want to make sure it
> > belongs there, I have one directory which is a full plate and another
> which
> > is just short of full.
> >
> > --Lee
>
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
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