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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link="#0563C1" vlink="#954F72"><div class=WordSection1><pre><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Hi Roger,<o:p></o:p></span></pre><pre><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><o:p> </o:p></span></pre><pre style='margin-left:.5in;text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>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.<o:p></o:p></span></pre><pre style='margin-left:.5in;text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>I was able to inspect the what() of the std::runtime_error and the message says, “Could not determine runtime path for “ome-xml-schemaâ€</span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'></span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'> directory”.<o:p></o:p></span></pre><pre style='margin-left:.5in;text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>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.<o:p></o:p></span></pre><pre style='margin-left:.5in;text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>I confirmed that I have the same files in the directories you described below.<o:p></o:p></span></pre><pre><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><o:p> </o:p></span></pre><pre>% cd ome-files-bundle-0.5.0-VC14-x64-Release-b25<o:p></o:p></pre><pre>% ls share<o:p></o:p></pre><pre>doc man ome pkgconfig xml xsl<o:p></o:p></pre><pre>% ls share/xml/ome<o:p></o:p></pre><pre>2003-FC 2003-IR2 2003-RC1 2003-RC3 2003-RC5 2007-06 2008-04<o:p></o:p></pre><pre>2009-09 2010-06 2012-06 2015-01 catalog.xml<o:p></o:p></pre><pre>2003-IR1 2003-IR3 2003-RC2 2003-RC4 2003-RC6 2008-02 2008-09<o:p></o:p></pre><pre>2010-04 2011-06 2013-06 2016-06 external<o:p></o:p></pre><pre>% ls share/xml/ome/2016-06<o:p></o:p></pre><pre>catalog.xml ome.xsd<o:p></o:p></pre><pre>% ls share/xsl/ome<o:p></o:p></pre><pre>2003-FC-to-2007-06.xsl 2008-02-to-2008-09.xsl 2010-06-to-2003-FC.xsl<o:p></o:p></pre><pre>2011-06-to-2012-06.xsl 2013-06-to-2015-01.xsl units-conversion.xsl<o:p></o:p></pre><pre>2003-FC-to-2008-09.xsl 2008-09-to-2009-09.xsl 2010-06-to-2008-02.xsl<o:p></o:p></pre><pre>2012-06-to-2011-06.xsl 2015-01-to-2013-06.xsl<o:p></o:p></pre><pre>2007-06-to-2008-02.xsl 2009-09-to-2010-04.xsl 2010-06-to-2011-06.xsl<o:p></o:p></pre><pre>2012-06-to-2013-06.xsl 2015-01-to-2016-06.xsl<o:p></o:p></pre><pre>2007-06-to-2008-09.xsl 2010-04-to-2010-06.xsl 2011-06-to-2010-06.xsl<o:p></o:p></pre><pre>2013-06-to-2012-06.xsl 2016-06-to-2015-01.xsl<o:p></o:p></pre><pre><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><o:p> </o:p></span></pre><pre><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>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.<o:p></o:p></span></pre><pre><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><o:p> </o:p></span></pre><pre><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Thanks,<o:p></o:p></span></pre><pre><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Dennis<o:p></o:p></span></pre><pre><o:p> </o:p></pre><pre>On 25/01/18 23:56, Dennis Ai wrote:<o:p></o:p></pre><pre>><i> Hi Roger,<o:p></o:p></i></pre><pre>><i><o:p> </o:p></i></pre><pre>><i> Sorry for not responding earlier, I guess I wasn’t subscribed to the<o:p></o:p></i></pre><pre>><i> list so I didn’t see your response in my email. Had to find it manually<o:p></o:p></i></pre><pre>><i> via the archive list. Following your advice, I tried:<o:p></o:p></i></pre><pre>><i><o:p> </o:p></i></pre><pre>><i> To give some context, my goal is to create a C# wrapper around ome-files<o:p></o:p></i></pre><pre>><i> (or at least certain functionality in ome-files), so that I can<o:p></o:p></i></pre><pre>><i> read/write OME-TIFF files. What I have done so far is:<o:p></o:p></i></pre><pre>><i><o:p> </o:p></i></pre><pre>><i> 1.Download OME Files 0.5.0<o:p></o:p></i></pre><pre>><i> <<a href="https://www.openmicroscopy.org/ome-files/downloads/">https://www.openmicroscopy.org/ome-files/downloads/</a>> (Windows VC14<o:p></o:p></i></pre><pre>><i> 64-bit, self-contained super build) into a directory<o:p></o:p></i></pre><pre>><i> “C:\Users\...\Documents\Visual Studio 2015\Projects\OMEFilesSharp\External”.<o:p></o:p></i></pre><pre>><i><o:p> </o:p></i></pre><pre>><i> 2.Created a C++ DLL project in Visual Studio 2015 (hence the<o:p></o:p></i></pre><pre>><i> “OMEFiles.dll”) that effectively creates a wrapper around OMETIFFReader<o:p></o:p></i></pre><pre>><i> and OMETIFFWriter, and VariantPixelBuffer to get basic functionality<o:p></o:p></i></pre><pre>><i> working. I followed the instructions here<o:p></o:p></i></pre><pre>><i> <<a href="https://www.openmicroscopy.org/community/viewtopic.php?f=13&t=8233&p=18005&hilit=ome+files+tutorial#p18005">https://www.openmicroscopy.org/community/viewtopic.php?f=13&t=8233&p=18005&hilit=ome+files+tutorial#p18005</a>><o:p></o:p></i></pre><pre>><i> for getting the project to build properly.<o:p></o:p></i></pre><pre>><i><o:p> </o:p></i></pre><pre>><i> 3.The reason that the C++ DLL is necessary is that I needed to make the<o:p></o:p></i></pre><pre>><i> API compatible with C types, so that I could use CppSharp<o:p></o:p></i></pre><pre>><i> <<a href="https://github.com/mono/CppSharp">https://github.com/mono/CppSharp</a>> to generate automatic C# bindings.<o:p></o:p></i></pre><pre><o:p> </o:p></pre><pre>Ah, that makes sense, thanks for the explanation.<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>><i> I tried to following your instructions, and did the following:<o:p></o:p></i></pre><pre>><i><o:p> </o:p></i></pre><pre>><i> 4.Adding ome::files::register_module_paths(); before I called setId(…).<o:p></o:p></i></pre><pre>><i> This resulted in the same stack trace and exceptions that I relayed before.<o:p></o:p></i></pre><pre>><i><o:p> </o:p></i></pre><pre>><i> 5.I set the OME_FILES_HOME environment variable to the root directory<o:p></o:p></i></pre><pre>><i> (“C:\Users\...\Documents\Visual Studio<o:p></o:p></i></pre><pre>><i> 2015\Projects\OMEFilesSharp\External\ome-files”), and to the binary<o:p></o:p></i></pre><pre>><i> sub-directory (““C:\Users\...\Documents\Visual Studio<o:p></o:p></i></pre><pre>><i> 2015\Projects\OMEFilesSharp\External\ome-files\bin”), along with adding<o:p></o:p></i></pre><pre>><i> the ome::files::register_module_paths() call, but that resulted in the<o:p></o:p></i></pre><pre>><i> same stack trace and exceptions that I relayed before too.<o:p></o:p></i></pre><pre>><i><o:p> </o:p></i></pre><pre>><i> 6.I did a search for “ome-model.xsl” and ““ome-model.xsd” and found<o:p></o:p></i></pre><pre>><i> neither in the downloaded super build.<o:p></o:p></i></pre><pre><o:p> </o:p></pre><pre>It's in the ome-model component, and is in the provided binary builds:<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>In the ome-model sources:<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>% ls specification/src/main/resources/released-schema<o:p></o:p></pre><pre>2003-FC 2003-IR2 2003-RC1 2003-RC3 2003-RC5 2007-06 2008-04<o:p></o:p></pre><pre>2009-09 2010-06 2012-06 2015-01 2018-01-DEV external<o:p></o:p></pre><pre>2003-IR1 2003-IR3 2003-RC2 2003-RC4 2003-RC6 2008-02 2008-09<o:p></o:p></pre><pre>2010-04 2011-06 2013-06 2016-06 catalog.xml<o:p></o:p></pre><pre>% ls specification/src/main/resources/released-schema/2016-06<o:p></o:p></pre><pre>catalog.xml ome.xsd<o:p></o:p></pre><pre>% ls specification/src/main/resources/transforms<o:p></o:p></pre><pre>2003-FC-to-2007-06.xsl 2008-09-to-2009-09.xsl 2010-06-to-2011-06.xsl<o:p></o:p></pre><pre>2013-06-to-2012-06.xsl 2016-06-to-2018-01-DEV.xsl ome-transforms.xml<o:p></o:p></pre><pre>2003-FC-to-2008-09.xsl 2009-09-to-2010-04.xsl 2011-06-to-2010-06.xsl<o:p></o:p></pre><pre>2013-06-to-2015-01.xsl 2016-06-to-2018-01-DEV.xsl~ units-conversion.xsl<o:p></o:p></pre><pre>2007-06-to-2008-02.xsl 2010-04-to-2010-06.xsl 2011-06-to-2012-06.xsl<o:p></o:p></pre><pre>2015-01-to-2013-06.xsl 2018-01-DEV-to-2016-06.xsl util<o:p></o:p></pre><pre>2007-06-to-2008-09.xsl 2010-06-to-2003-FC.xsl 2012-06-to-2011-06.xsl<o:p></o:p></pre><pre>2015-01-to-2016-06.xsl 2018-01-DEV-to-2016-06.xsl~<o:p></o:p></pre><pre>2008-02-to-2008-09.xsl 2010-06-to-2008-02.xsl 2012-06-to-2013-06.xsl<o:p></o:p></pre><pre>2016-06-to-2015-01.xsl internal<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>In a binary build:<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>% cd ome-files-bundle-0.5.0-VC14-x64-Release-b25<o:p></o:p></pre><pre>% ls share<o:p></o:p></pre><pre>doc man ome pkgconfig xml xsl<o:p></o:p></pre><pre>% ls share/xml/ome<o:p></o:p></pre><pre>2003-FC 2003-IR2 2003-RC1 2003-RC3 2003-RC5 2007-06 2008-04<o:p></o:p></pre><pre>2009-09 2010-06 2012-06 2015-01 catalog.xml<o:p></o:p></pre><pre>2003-IR1 2003-IR3 2003-RC2 2003-RC4 2003-RC6 2008-02 2008-09<o:p></o:p></pre><pre>2010-04 2011-06 2013-06 2016-06 external<o:p></o:p></pre><pre>% ls share/xml/ome/2016-06<o:p></o:p></pre><pre>catalog.xml ome.xsd<o:p></o:p></pre><pre>% ls share/xsl/ome<o:p></o:p></pre><pre>2003-FC-to-2007-06.xsl 2008-02-to-2008-09.xsl 2010-06-to-2003-FC.xsl<o:p></o:p></pre><pre>2011-06-to-2012-06.xsl 2013-06-to-2015-01.xsl units-conversion.xsl<o:p></o:p></pre><pre>2003-FC-to-2008-09.xsl 2008-09-to-2009-09.xsl 2010-06-to-2008-02.xsl<o:p></o:p></pre><pre>2012-06-to-2011-06.xsl 2015-01-to-2013-06.xsl<o:p></o:p></pre><pre>2007-06-to-2008-02.xsl 2009-09-to-2010-04.xsl 2010-06-to-2011-06.xsl<o:p></o:p></pre><pre>2012-06-to-2013-06.xsl 2015-01-to-2016-06.xsl<o:p></o:p></pre><pre>2007-06-to-2008-09.xsl 2010-04-to-2010-06.xsl 2011-06-to-2010-06.xsl<o:p></o:p></pre><pre>2013-06-to-2012-06.xsl 2016-06-to-2015-01.xsl<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>><i> To be honest, C++ is not my strong suit. If there’s a better way to get<o:p></o:p></i></pre><pre>><i> set up in Windows, I’m all ears.<o:p></o:p></i></pre><pre><o:p> </o:p></pre><pre>I think you are likely missing the datafiles, and it should be fairly<o:p></o:p></pre><pre>simple to resolve once it's clear what's missing and why.<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>When building from source with the superbuild, I think if you were to<o:p></o:p></pre><pre>run the superbuild "install" target, or look at the contents of the<o:p></o:p></pre><pre>"stage" directory, you'll get a full set of the binaries, libraries,<o:p></o:p></pre><pre>headers and datafiles needed for a functional installation.<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>Since you started with the binary build, the above files should all be<o:p></o:p></pre><pre>present, as shown above, unless they were omitted for some reason from<o:p></o:p></pre><pre>your "External" directory. Setting OME_FILES_HOME to the root where you<o:p></o:p></pre><pre>unpacked the binary distribution zip should be sufficient to make them<o:p></o:p></pre><pre>available.<o:p></o:p></pre><pre><o:p> </o:p></pre><pre><o:p> </o:p></pre><pre>Regards,<o:p></o:p></pre><pre>Roger<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>--<o:p></o:p></pre><pre>Dr Roger Leigh -- Open Microscopy Environment<o:p></o:p></pre><pre>Wellcome Trust Centre for Gene Regulation and Expression,<o:p></o:p></pre><pre>College of Life Sciences, University of Dundee, Dow Street,<o:p></o:p></pre><pre>Dundee DD1 5EH Scotland UK Tel: (01382) 386364<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>The University of Dundee is a registered Scottish Charity, No: SC015096<o:p></o:p></pre><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><b>Dennis Ai</b><o:p></o:p></p><p class=MsoNormal><span style='font-size:9.0pt'>Senior Strategic Advisor, SRI Biosciences</span><o:p></o:p></p><p class=MsoNormal><span style='font-size:9.0pt'>SRI International</span><o:p></o:p></p><p class=MsoNormal><span style='font-size:9.0pt'>333 Ravenswood Ave</span><o:p></o:p></p><p class=MsoNormal><span style='font-size:9.0pt'>Menlo Park, CA 94025</span><o:p></o:p></p><p class=MsoNormal><span style='font-size:9.0pt'>(847) 440-4765</span><o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><p class=MsoNormal><b><span style='font-size:14.0pt;font-family:"Helvetica",sans-serif'>SRI </span></b><span style='font-size:14.0pt;font-family:"Helvetica",sans-serif'>Biosciences</span><sup><span style='font-size:10.0pt;font-family:"Helvetica",sans-serif'>™</span></sup><o:p></o:p></p><p class=MsoNormal><span style='font-size:6.0pt;font-family:"Helvetica",sans-serif'>A DIVISION OF SRI INTERNATIONAL</span><o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>