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</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thanks. I’ll avoid DICOMs for now then. Brian – if you need a beta tester do shout!<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Derek<o:p></o:p></span></p><p class=MsoNormal><a name="_MailEndCompose"><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></a></p><p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> Matt McCormick [mailto:matt.mccormick@kitware.com] <br><b>Sent:</b> 18 March 2014 10:22<br><b>To:</b> Derek Magee<br><b>Cc:</b> community@itk.org; Brian Helba<br><b>Subject:</b> Re: [ITK Community] Compiling with system libopenjpeg<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal style='margin-bottom:12.0pt'><o:p> </o:p></p><div><p class=MsoNormal>On Mon, Mar 17, 2014 at 5:07 PM, Derek Magee <<a href="mailto:D.R.Magee@leeds.ac.uk" target="_blank">D.R.Magee@leeds.ac.uk</a>> wrote:<o:p></o:p></p><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>So, the answer is “no you can’t” I think, which leads me on to two more questions:</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p></div></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>"Yes, you can!". :-). It may take a little effort, though...<o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p></div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm'><div><div><p style='margin-left:18.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>1)</span><span style='font-size:7.0pt;color:#1F497D'> </span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>My current workaround is to manually remove itkopenjpeg from the linker by modifying my CMake thus:</span><o:p></o:p></p><p style='margin-left:18.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><p><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>message("ITK Libs: ${ITK_LIBRARIES}")</span><o:p></o:p></p><p><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><p><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>#target_link_libraries(IServer ${ITK_LIBRARIES})</span><o:p></o:p></p><p><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><p><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>target_link_libraries(IServer "what is printed out, but removing itkopenjpeg") </span><o:p></o:p></p><p><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><p><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>As I know if I don’t do this it causes openslide (which uses the system openjpeg) to crash, I’m assuming the reverse is true for ITK. Does anyone know what functionality uses openjpeg/jpeg2000? (i.e. what file formats to avoid for now!)</span><o:p></o:p></p></div></div></blockquote><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>GDCM Image IO uses openjpeg/jpeg2000. You can manually specify the ITK modules needed and exclude GDCM [1]. <o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p></div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm'><div><div><p><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><p style='margin-left:18.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>2)</span><span style='font-size:7.0pt;color:#1F497D'> </span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Is this an issue with openslide or ITK? (“</span>The current version of OpenJPEG needs to updated to be closer to upstream” is a bit ambiguous and could mean a) ITK only works with (an) old version(s) of openjpeg, b) ITK works with a hacked version of openjpeg, c) Something needs updating in openjpeg as it is “broken” ). And, should I raise an issue with the appropriate developers? (If so how?)<o:p></o:p></p></div></div></blockquote><div><p class=MsoNormal>ITK works with an old, hacked version of OpenJPEG. Brian Helba (in CC) is working on updating the version and going towards vanilla upstream. Collaboration with him would be the best long term solution.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Thanks,<o:p></o:p></p></div><div><p class=MsoNormal>Matt<o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>[1] <a href="http://www.kitware.com/blog/home/post/557">http://www.kitware.com/blog/home/post/557</a><o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div></div></div></div></div></body></html>