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

[Lee Kamentsky]

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
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