[ome-devel] [ome-files] Getting Exceptions When Opening Files for setId(...)
Dennis Ai
dennis.ai at sri.com
Mon Jan 29 17:09:50 GMT 2018
Hi Roger,
1. I tried to set my environment variable OME_FILES_HOME to the root directory where I extracted the binary distribution. (“C:\Users\...\Documents\Visual Studio 2015\Projects\OMEFilesSharp\External\ome-files”). This gives me the same exception as before.
2. I was able to inspect the what() of the std::runtime_error and the message says, “Could not determine runtime path for “ome-xml-schema†directory”.
3. Seeing this, I tried to set the environment variable OME_XML_SCHEMADIR to “C:\Users\...\Documents\Visual Studio 2015\Projects\OMEFilesSharp\External\ome-files\share\xml\ome” and that resulted in the same exception as before.
4. I confirmed that I have the same files in the directories you described below.
% cd ome-files-bundle-0.5.0-VC14-x64-Release-b25
% ls share
doc man ome pkgconfig xml xsl
% ls share/xml/ome
2003-FC 2003-IR2 2003-RC1 2003-RC3 2003-RC5 2007-06 2008-04
2009-09 2010-06 2012-06 2015-01 catalog.xml
2003-IR1 2003-IR3 2003-RC2 2003-RC4 2003-RC6 2008-02 2008-09
2010-04 2011-06 2013-06 2016-06 external
% ls share/xml/ome/2016-06
catalog.xml ome.xsd
% ls share/xsl/ome
2003-FC-to-2007-06.xsl 2008-02-to-2008-09.xsl 2010-06-to-2003-FC.xsl
2011-06-to-2012-06.xsl 2013-06-to-2015-01.xsl units-conversion.xsl
2003-FC-to-2008-09.xsl 2008-09-to-2009-09.xsl 2010-06-to-2008-02.xsl
2012-06-to-2011-06.xsl 2015-01-to-2013-06.xsl
2007-06-to-2008-02.xsl 2009-09-to-2010-04.xsl 2010-06-to-2011-06.xsl
2012-06-to-2013-06.xsl 2015-01-to-2016-06.xsl
2007-06-to-2008-09.xsl 2010-04-to-2010-06.xsl 2011-06-to-2010-06.xsl
2013-06-to-2012-06.xsl 2016-06-to-2015-01.xsl
Any idea why I might still be running into issues? I’m happy to send you the source code if it might help figure out what’s going on.
Thanks,
Dennis
On 25/01/18 23:56, Dennis Ai wrote:
> Hi Roger,
>
> Sorry for not responding earlier, I guess I wasn’t subscribed to the
> list so I didn’t see your response in my email. Had to find it manually
> via the archive list. Following your advice, I tried:
>
> To give some context, my goal is to create a C# wrapper around ome-files
> (or at least certain functionality in ome-files), so that I can
> read/write OME-TIFF files. What I have done so far is:
>
> 1.Download OME Files 0.5.0
> <https://www.openmicroscopy.org/ome-files/downloads/> (Windows VC14
> 64-bit, self-contained super build) into a directory
> “C:\Users\...\Documents\Visual Studio 2015\Projects\OMEFilesSharp\External”.
>
> 2.Created a C++ DLL project in Visual Studio 2015 (hence the
> “OMEFiles.dll”) that effectively creates a wrapper around OMETIFFReader
> and OMETIFFWriter, and VariantPixelBuffer to get basic functionality
> working. I followed the instructions here
> <https://www.openmicroscopy.org/community/viewtopic.php?f=13 <https://www.openmicroscopy.org/community/viewtopic.php?f=13&t=8233&p=18005&hilit=ome+files+tutorial#p18005> &t=8233&p=18005&hilit=ome+files+tutorial#p18005>
> for getting the project to build properly.
>
> 3.The reason that the C++ DLL is necessary is that I needed to make the
> API compatible with C types, so that I could use CppSharp
> <https://github.com/mono/CppSharp> to generate automatic C# bindings.
Ah, that makes sense, thanks for the explanation.
> I tried to following your instructions, and did the following:
>
> 4.Adding ome::files::register_module_paths(); before I called setId(…).
> This resulted in the same stack trace and exceptions that I relayed before.
>
> 5.I set the OME_FILES_HOME environment variable to the root directory
> (“C:\Users\...\Documents\Visual Studio
> 2015\Projects\OMEFilesSharp\External\ome-files”), and to the binary
> sub-directory (““C:\Users\...\Documents\Visual Studio
> 2015\Projects\OMEFilesSharp\External\ome-files\bin”), along with adding
> the ome::files::register_module_paths() call, but that resulted in the
> same stack trace and exceptions that I relayed before too.
>
> 6.I did a search for “ome-model.xsl” and ““ome-model.xsd” and found
> neither in the downloaded super build.
It's in the ome-model component, and is in the provided binary builds:
In the ome-model sources:
% ls specification/src/main/resources/released-schema
2003-FC 2003-IR2 2003-RC1 2003-RC3 2003-RC5 2007-06 2008-04
2009-09 2010-06 2012-06 2015-01 2018-01-DEV external
2003-IR1 2003-IR3 2003-RC2 2003-RC4 2003-RC6 2008-02 2008-09
2010-04 2011-06 2013-06 2016-06 catalog.xml
% ls specification/src/main/resources/released-schema/2016-06
catalog.xml ome.xsd
% ls specification/src/main/resources/transforms
2003-FC-to-2007-06.xsl 2008-09-to-2009-09.xsl 2010-06-to-2011-06.xsl
2013-06-to-2012-06.xsl 2016-06-to-2018-01-DEV.xsl ome-transforms.xml
2003-FC-to-2008-09.xsl 2009-09-to-2010-04.xsl 2011-06-to-2010-06.xsl
2013-06-to-2015-01.xsl 2016-06-to-2018-01-DEV.xsl~ units-conversion.xsl
2007-06-to-2008-02.xsl 2010-04-to-2010-06.xsl 2011-06-to-2012-06.xsl
2015-01-to-2013-06.xsl 2018-01-DEV-to-2016-06.xsl util
2007-06-to-2008-09.xsl 2010-06-to-2003-FC.xsl 2012-06-to-2011-06.xsl
2015-01-to-2016-06.xsl 2018-01-DEV-to-2016-06.xsl~
2008-02-to-2008-09.xsl 2010-06-to-2008-02.xsl 2012-06-to-2013-06.xsl
2016-06-to-2015-01.xsl internal
In a binary build:
% cd ome-files-bundle-0.5.0-VC14-x64-Release-b25
% ls share
doc man ome pkgconfig xml xsl
% ls share/xml/ome
2003-FC 2003-IR2 2003-RC1 2003-RC3 2003-RC5 2007-06 2008-04
2009-09 2010-06 2012-06 2015-01 catalog.xml
2003-IR1 2003-IR3 2003-RC2 2003-RC4 2003-RC6 2008-02 2008-09
2010-04 2011-06 2013-06 2016-06 external
% ls share/xml/ome/2016-06
catalog.xml ome.xsd
% ls share/xsl/ome
2003-FC-to-2007-06.xsl 2008-02-to-2008-09.xsl 2010-06-to-2003-FC.xsl
2011-06-to-2012-06.xsl 2013-06-to-2015-01.xsl units-conversion.xsl
2003-FC-to-2008-09.xsl 2008-09-to-2009-09.xsl 2010-06-to-2008-02.xsl
2012-06-to-2011-06.xsl 2015-01-to-2013-06.xsl
2007-06-to-2008-02.xsl 2009-09-to-2010-04.xsl 2010-06-to-2011-06.xsl
2012-06-to-2013-06.xsl 2015-01-to-2016-06.xsl
2007-06-to-2008-09.xsl 2010-04-to-2010-06.xsl 2011-06-to-2010-06.xsl
2013-06-to-2012-06.xsl 2016-06-to-2015-01.xsl
> To be honest, C++ is not my strong suit. If there’s a better way to get
> set up in Windows, I’m all ears.
I think you are likely missing the datafiles, and it should be fairly
simple to resolve once it's clear what's missing and why.
When building from source with the superbuild, I think if you were to
run the superbuild "install" target, or look at the contents of the
"stage" directory, you'll get a full set of the binaries, libraries,
headers and datafiles needed for a functional installation.
Since you started with the binary build, the above files should all be
present, as shown above, unless they were omitted for some reason from
your "External" directory. Setting OME_FILES_HOME to the root where you
unpacked the binary distribution zip should be sufficient to make them
available.
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
Dennis Ai
Senior Strategic Advisor, SRI Biosciences
SRI International
333 Ravenswood Ave
Menlo Park, CA 94025
(847) 440-4765
SRI Biosciences™
A DIVISION OF SRI INTERNATIONAL
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