[ome-users] Bug report for version 2012-06 OME-XML in Fiji, seen in grid/collection stitching

Wed Nov 9 20:17:15 GMT 2016

Hi,

Michael: This problem would occur if WiscScan was ever deployed to use a
non-release version of Bio-Formats. Ask the WiscScan programmers to search
the Git commit history for changes to the Bio-Formats JAR files, to see
which versions were committed when.

OME team: it would be nice if Bio-Formats could make a "best effort" to
transform these sorts of files, by attempting to treat them as one or more
released schema versions before giving up on the XSLT forward transform.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/

On Wed, Nov 9, 2016 at 2:03 PM, Michael Pinkert <mpinkert at wisc.edu> wrote:

> Thanks for solving that Roger!
>
> That solution makes sense, though it is rather confusing that we would be
> encountering this problem now.  We've been using the software for years
> without problems, but I guess an update either messed up the references or
> made the improper reference a requirement when it wasn't before.
>
> I'll have to talk to the more knowledgeable coders on this issue, and look
> around to see if other people are still having this problem.
>
> Best regards,
> Michael Pinkert
>
> -----Original Message-----
> From: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On
> Behalf Of Roger Leigh
> Sent: Wednesday, November 9, 2016 4:20 AM
> To: ome-users at lists.openmicroscopy.org.uk
> Subject: Re: [ome-users] Bug report for version 2012-06 OME-XML in Fiji,
> seen in grid/collection stitching
>
> On 08/11/16 19:50, Michael Pinkert wrote:
> > Hi Mark,
> >
> > I just uploaded 9 files, from a much smaller sample image set.  I tried
> using the ImageJ/Fiji stitching algorithm again with this smaller sample
> size and it ran into the same problem, with the same warning.  It seems not
> to be reading the metadata correctly, because it was interpreting different
> Z-slices as different T-time points.
> >
> > This problem occurred after a recent Fiji/ImageJ update and applies to
> older sets of images that I've already stitched; I don't think there's
> anything wrong with the formatting of the images.
>
> Dear Michael,
>
> I've taken a look at your files, and the problem is that the XML schema is
> invalid.  Using bftools' xmlvalid program:
>
> % ./tools/xmlvalid ~/images/17416/FijiTester.ome.xml Parsing schema path
> https://raw.github.com/openmicroscopy/openmicroscopy/schema-
> 2012-06/components/specification/InProgress/ome.xsd
> Validating /home/rleigh/images/17416/FijiTester.ome.xml
> Error parsing schema at
> https://raw.github.com/openmicroscopy/openmicroscopy/schema-
> 2012-06/components/specification/InProgress/ome.xsd
> org.xml.sax.SAXParseException: schema_reference.4: Failed to read schema
> document 'https://raw.github.com/openmicroscopy/openmicroscopy/schema
> -2012-06/components/specification/InProgress/ome.xsd',
> because 1) could not find the document; 2) the document could not be read;
> 3) the root element of the document is not <xsd:schema>.
>
> % ./tools/xmlvalid ~/images/17416/FijiTester_C0_TP0_SP0_FW0.ome.tiff
> Parsing schema path
> https://raw.github.com/openmicroscopy/openmicroscopy/schema-
> 2012-06/components/specification/InProgress/ome.xsd
> Validating /home/rleigh/images/17416/FijiTester_C0_TP0_SP0_FW0.ome.tiff
> Error parsing schema at
> https://raw.github.com/openmicroscopy/openmicroscopy/schema-
> 2012-06/components/specification/InProgress/ome.xsd
> org.xml.sax.SAXParseException: schema_reference.4: Failed to read schema
> document 'https://raw.github.com/openmicroscopy/openmicroscopy/schema
> -2012-06/components/specification/InProgress/ome.xsd',
> because 1) could not find the document; 2) the document could not be read;
> 3) the root element of the document is not <xsd:schema>.
>
>
> The schema which is being used here is an invalid URL, and was never a
> released schema.  I'm not sure why any software would be using that.
>
> You can find sample files using the old 2012-06 schema here:
> http://downloads.openmicroscopy.org/images/OME-TIFF/2012-06/
> They are using a root element like this:
>
> <OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2012-06"
>       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
>       xmlns:ROI="http://www.openmicroscopy.org/Schemas/ROI/2012-06"
>       xmlns:SA="http://www.openmicroscopy.org/Schemas/SA/2012-06"
>       xmlns:SPW="http://www.openmicroscopy.org/Schemas/SPW/2012-06"
>       xmlns:Bin="http://www.openmicroscopy.org/Schemas/BinaryFile/2012-06"
>
> xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2012-06
>   http://www.openmicroscopy.org/Schemas/OME/2012-06/ome.xsd">
>
> while your samples do this:
>
> <OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2012-06"
>       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
>
> xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2012-06
> https://raw.github.com/openmicroscopy/openmicroscopy/schema-
> 2012-06/components/specification/InProgress/ome.xsd">
>
> It's the schemaLocation which is wrong, making the file invalid.  If you
> fix that up, and the rest of the file is valid for the 2012-06 schema, it
> should then work correctly.
>
>
> Kind regards,
> Roger
>
> --
> Dr Roger Leigh -- Open Microscopy Environment Wellcome Trust Centre for
> Gene Regulation and Expression, College of Life Sciences, University of
> Dundee, Dow Street,
> Dundee DD1 5EH Scotland UK   Tel: (01382) 386364
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
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