Medical-sig May 2013

medical-sig@lists.stg.fedorahosted.org

4 participants
2 discussions

Fwd: [Seg3D] Re: Re: Re: Re: Packaging seg3d for Fedora - Problem with boost::mutex
by Mario Ceresa 24 May '13

24 May '13

Dear all, I had an interesting talk with Seg3D mantainers on the possibility to accept patches to build against system version of the many bundled libs. However, as you can see from the forwarded mails, they seem not willing to help with that nor to accept any related patches. I'm not sure what to do here: shall I package it regardless? I fear I'll end up mantaining a fork of the program... What would you suggest here? Thanks and regards, Mario ---------- Forwarded message ---------- From: Ayla Khan <ayla(a)sci.utah.edu> Date: 22 May 2013 07:09 Subject: [Seg3D] Re: Re: Re: Re: Packaging seg3d for Fedora - Problem with boost::mutex To: seg3d(a)sci.utah.edu Hi Mario, Many of the libraries we include with Seg3D have been modified, even if the modifications are as basic as replacing their default builds with CMake and doing some symbol mangling to make libraries play well with ITK. Our Boost distribution includes a project from the Boost sandbox that will not be available in a generic distribution. ITK has been customized as well. Including specific versions of third-party libraries allows us to maintain stable Seg3D builds across multiple platforms (Windows, Mac OSX and different Linux distributions) with the least amount of effort for SCI developers. We are also tightly coupled to Boost, ITK and Teem, so it is preferable from our point of view to build against versions that we control. Having a binary distribution for Fedora would be helpful - it's certainly been a good thing for our Windows and OS X users, however keeping our dependencies uniform across supported platforms has eliminated many of the deployment headaches we used to have in the past. Ayla On May 7, 2013, at 3:27 AM, Mario Ceresa wrote: > Thanks Dan and Ayla for your prompt response! When do you plan to release 2.1.5? > > As for the 3rd party libs, unfortunately, Fedora has a strict policy > of not bundled and not static libs: > https://fedoraproject.org/wiki/Packaging:No_Bundled_Libraries > https://fedoraproject.org/wiki/Packaging:Guidelines#Packaging_Static_Librar… > > The only exceptions granted are usually for libraries that are heavily > modified. Does any of the 3rd party libs in "external" meet this? > > Including seg3d in a distribution like Fedora it is usually a positive > force: it means a large user base, continuous feedback, builds ready > available for x86, arm and ppc archs, access to last releases of all > libs, prompt bug reports and many submitted patches. It also relieves > you part of the burden to assist users with bugs: package maintainers > will usually catch them up early and report to you, sometimes along > with a proposed fix. Thus you can concentrate more on working on your > software instead of all the maintenance tasks. > > You can think about it as an investment :). > > However, it needs a bit of involvement by your side because I cannot > maintain a complete fork of seg3d. > > In the end I don't think the process is so complicated: we just need > to ensure we can choose at build time whether to link seg3d with the > included static libs or against system wide ones. I can send a patch > for this, if you are willing to review it. Then, if any > bugs/regression arises, we will work towards a fix. > > I do hope that this would be the beginning of a long joint collaboration! > > With best regards, > > Mario > > > > > > > > On 7 May 2013 07:07, Ayla Khan <ayla(a)sci.utah.edu> wrote: >> Hi Mario, >> >> You should check out the 2.1.5 release branch ( https://code.sci.utah.edu/svn/seg3d2/branches/2.1.5) or wait until I merge the updates from the 2.1.5 release candidate back to the trunk once the release is done. We're currently targeting a modified Boost 1.53.0 library (see the Modifications.txt file in the src/Externals/boost directory). Keep in mind that Seg3D is designed to work with statically linked libraries built from the third-party dependencies that we include with it's sources and does not support the use of other versions. I would strongly recommend using our libraries and then attempting to work with Fedora's Qt system libraries. >> >> Ayla >> >> >> On May 6, 2013, at 12:42 PM, Dan White wrote: >> >>> Here is the fix for that error from our svn branch. Ayla can provide more info, since it looks like there were multiple boost-upgrade-related Seg3d2 source compiler fixes in addition to this one. >>> >>> https://gforge.sci.utah.edu/gf/project/seg3d2/scmsvn/?action=browse&path=%2… >>> >>> >>> On 5/6/2013 5:44 AM, Mario Ceresa wrote: >>>> Hi all, >>>> first of all, thank you for your work on seg3d: it's really a nice >>>> software and helps a lot for image segmentation! >>>> >>>> I would like to package it for fedora, however, I have several build >>>> problems. Once is especially difficult for me to figure out and I'd >>>> appreciate some help. >>>> >>>> I have a: >>>> * no matching function for call to >>>> ‘boost::shared_lock<boost::shared_mutex>::swap(Core::MaskDataBlock::shared_lock_type) >>>> >>>> in Application/Filters/Actions/ActionAndFilter.cc:149. I past the full >>>> compiler error: >>>> * http://ur1.ca/dpo7o >>>> >>>> You can find in github a fork of the code with some of the changes so far: >>>> * https://github.com/mrceresa/seg3d2 >>>> >>>> They are almost only in the cmake build system to enable use of Fedora >>>> system-wide libs such as: >>>> >>>> * boost 1.50 >>>> * gdcm 2.0.18 >>>> * ITK 4.3.1 >>>> >>>> Which is required for packaging. >>>> >>>> This was the cmake build line: >>>> ccmake ../seg3d2 -DCMAKE_CXX_FLAGS="-fpermissive" >>>> -DCMAKE_VERBOSE_MAKEFILE=ON -DBUILD_WITH_PYTHON=OFF >>>> >>>> Thanks for your attention and best regards, >>>> >>>> Mario Ceresa >>> >>

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Last updates
by Mario Ceresa 23 May '13

23 May '13

Dear all, several important changes happened recently in fedora medical. The following packages were added: * InsightToolkit (ITK)- Kitware flagship medical image analysis library * Orthanc - Lightweight PACS * octave-dicom - Dicom package for octave * gdcm bumped up to last release Especially ITK was a big jump after almost 4 years of review! It now unblocks a wide range of medical imaging software such as: * elastix - image registration * GinkoCAD - DICOM viewer * ITKSnap - Segmentation * Seg3D 2 - Segmentation * vmtk - Vascular modeling kit * msvtk - Multi-scale visualization toolkit On another side, Orthanc enables Fedora to act as a PACS to interchange dicom images between several peers. I think it would be nice to concentrate now in having a working and integrated dicom viewer (GinkoCAD) and segmentation program (Seg3D2 or ITKSnap). Maybe, with some effort, we might even propose three features for one of the next fedora releases: * "medical image platform clinic" which would include: a) improved dicom compatilibity (already done with dcmtk, gdcm, octave-dicom) b) pacs support (orthanc, already done) + GinkoCAD c) InsightToolkit (already done) d) segmentation tools (ITKSnap + Seg3d 2) * "medical image platform research" which would include: a) 3D slicer b) registration tools (elastix + ants) c) statistical shape models (statismo + shapeworks) d) vascular analysis (vmtk) e) guided surgery (openigtlink, already done + IGSTK) * "biomechanical platform" which would include: a) Meshing (Biomesh3d, cleaver, stellar) b) FEM code (Elmer, Kratos, OpenPalm, OpenFOAM) c) Salome modeler An updated page with current status of all these packages is: https://fedoraproject.org/wiki/Medical_Imaging Probably some of those packages are already included in Debian/Ubuntu and we can contact our fellow packagers for help with patches. Is there anyone interested in all of this? Best, Mario

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Medical-sig May 2013