Hi Darren,<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">I'm
a little puzzled by the farsight build wiki. It appears to be nothing
more than an ITK build, so what's special about "farsight" that it
should be identified as something more than Insight (ITK)?<br>
</blockquote><div><br>FARSIGHT is an effort to provide an image analysis toolkit for microscopy, based on ITK. There is an (incomplete) list of modules included in FARSIGHT listed at:<br><br> <a href="http://www.farsight-toolkit.org/wiki/Table_of_Contents">http://www.farsight-toolkit.org/wiki/Table_of_Contents</a><br>
<br>It is still very early days for FARSIGHT, with the SVN repository just opening up in recent weeks, so everything is still pretty rough around the edges.<br><br>Badri Roysam, the head of the project, can comment further on goals and directions if you are interested.<br>
<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">As for OSX, there are no build instructions (most of the linux
instructions might apply, but actually it's a lot more complicated
because OSX can an rpath nightmare when it comes to shared libs). I
think the entire farsight build wiki could be replaced, for OSX, with a
one line MacPorts command:<br>
<br><span style="font-family: courier new,monospace;">sudo port install InsightToolkit</span><br><br>This will probably do everything at all stages identified on this wiki thread:<div class="im"></div></blockquote><div><br>
As far as compililng ITK, yes, if the MacPorts version of ITK includes the CableSWIG stuff with WrapITK. (My understanding is that FARSIGHT needs that for its Python interface.)<br><br>There are still more instructions to be written on compiling FARSIGHT itself, once all the dependencies are set up.<br>
<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im"><a href="http://farsight-toolkit.org/wiki/FARSIGHT_Tutorials/Building_Software" target="_blank">http://farsight-toolkit.org/wiki/FARSIGHT_Tutorials/Building_Software</a><br>
<br></div>The MacPorts system will take care of all the dependencies
(cmake, python, cableswig). Please see this ITK wiki page for more
details:<br><a href="http://www.vtk.org/Wiki/ITK_MacPorts_Package_Maintainers" target="_blank">http://www.vtk.org/Wiki/ITK_MacPorts_Package_Maintainers</a><br>
<br>Moreover, _please_ link to that page from the farsight tutorial on
the build process, it might save everyone a lot of time and headaches
(because I know just how painful it was to put it all together in
MacPorts).<br>
</blockquote><div><br>Noted on the Building_Software page.<br><br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">If you need to develop ITK using macports, that might be done too,
but it requires a little bit of tweaking on the macports installation
process. The macports installation uses several phases and a developer
could stop after the build phase. At that point, you have a complete
source tree and a separate build tree. So you could try this:<br>
<br><span style="font-family: courier new,monospace;">sudo port build InsightToolkit</span><br><br>Then go look in the build tree, under <span style="font-family: courier new,monospace;">/opt/local/var/macports/build/</span><br>
</blockquote><div><br>Cool; I saw this note on the ITK_MacPorts_Package_Maintainers page too, so hopefully people who care will notice that.<br> </div></div>-Curtis<br><br><div class="gmail_quote">On Wed, Jun 24, 2009 at 3:08 PM, Darren Weber <span dir="ltr"><<a href="mailto:darren.weber.lists@gmail.com">darren.weber.lists@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>I'm a little puzzled by the farsight build wiki. It appears to be nothing more than an ITK build, so what's special about "farsight" that it should be identified as something more than Insight (ITK)?<br>
<br>As for OSX, there are no build instructions (most of the linux instructions might apply, but actually it's a lot more complicated because OSX can an rpath nightmare when it comes to shared libs). I think the entire farsight build wiki could be replaced, for OSX, with a one line MacPorts command:<br>
<br><span style="font-family: courier new,monospace;">sudo port install InsightToolkit</span><br><br>This will probably do everything at all stages identified on this wiki thread:<div class="im"><br><a href="http://farsight-toolkit.org/wiki/FARSIGHT_Tutorials/Building_Software" target="_blank">http://farsight-toolkit.org/wiki/FARSIGHT_Tutorials/Building_Software</a><br>
<br></div>The MacPorts system will take care of all the dependencies (cmake, python, cableswig). Please see this ITK wiki page for more details:<br><a href="http://www.vtk.org/Wiki/ITK_MacPorts_Package_Maintainers" target="_blank">http://www.vtk.org/Wiki/ITK_MacPorts_Package_Maintainers</a><br>
<br>Moreover, _please_ link to that page from the farsight tutorial on the build process, it might save everyone a lot of time and headaches (because I know just how painful it was to put it all together in MacPorts).<br>
<br>If you need to develop ITK using macports, that might be done too, but it requires a little bit of tweaking on the macports installation process. The macports installation uses several phases and a developer could stop after the build phase. At that point, you have a complete source tree and a separate build tree. So you could try this:<br>
<br><span style="font-family: courier new,monospace;">sudo port build InsightToolkit</span><br><br>Then go look in the build tree, under <span style="font-family: courier new,monospace;">/opt/local/var/macports/build/</span><br>
<br>Take care,<br><font color="#888888">Darren</font><div><div></div><div class="h5"><br><br><br><br><br><div class="gmail_quote">On Wed, Jun 24, 2009 at 11:55 AM, Curtis Rueden <span dir="ltr"><<a href="mailto:ctrueden@wisc.edu" target="_blank">ctrueden@wisc.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Darren,<div><br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">What's the latest on this project? Is there a wiki how-to on this?<br>
</blockquote></div><br></div>The project is currently under active development. Currently, the plugin works with ITK 3.12 on Mac OS X and Linux. Soon it will compile with Visual Studio on Windows as well (pending a commit from me -- and thanks to Alex Gouaillard for his help tracking down some Windows issues).<br>
<br>There are a number of improvements I am in the process of making, including support for RGB and vector images, and dimensions beyond 3D. I would also like to make the build easier to do, as much as possible at least.<br>
<br>You can access the code by checking out the LOCI Software codebase from SVN:<br><br> <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk" target="_blank">https://skyking.microscopy.wisc.edu/svn/java/trunk</a><br>
<br>The relevant components are in components/native/bf-cpp and components/native/itk-plugin. See the readme.txt files for details. Please note that as of this writing, the skyking server is down due to a large-scale power outage on the UW-Madison campus (some construction mishap, I think).<br>
<br>There is also a preliminary set of wiki pages on how to compile the plugin on the FARSIGHT wiki at:<br><br> <a href="http://farsight-toolkit.org/wiki/FARSIGHT_Tutorials/Building_Software/Bio-Formats" target="_blank">http://farsight-toolkit.org/wiki/FARSIGHT_Tutorials/Building_Software/Bio-Formats</a><br>
<br>Note that you do not actually need to build FARSIGHT to use the ITK plugin as is (the wiki pages are written with the idea that the plugin will be used within FARSIGHT, but there is no requirement to do so). The plugin is merely an ITK ImageIO plugin, and should work with any code that uses itkImageFileReader.<br>
<br>Lastly, a bug introduced in ITK CVS five weeks ago (which should be fixed soon) will prevent the plugin from working properly with image data beyond 2D in certain cases.<br><br>I will keep the list posted on my progress.<br>
<br>-Curtis<br><br><div class="gmail_quote"><div>On Wed, Jun 24, 2009 at 1:48 PM, Darren Weber <span dir="ltr"><<a href="mailto:darren.weber.lists@gmail.com" target="_blank">darren.weber.lists@gmail.com</a>></span> wrote:<br>
</div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div>
<div><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>
Curtis is working on making bioformats usable from ITK</blockquote></div><br><br></div></div><div>What's the latest on this project? Is there a wiki how-to on this?<br><br></div>Thanks,<br><font color="#888888">Darren<br>
<br>
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