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

[Michael Pinkert]

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

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