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Summary: Review Request: vmtk - The Vascular Modeling Toolkit
https://bugzilla.redhat.com/show_bug.cgi?id=721112
Summary: Review Request: vmtk - The Vascular Modeling Toolkit Product: Fedora Version: rawhide Platform: All OS/Version: Linux Status: NEW Severity: medium Priority: medium Component: Package Review AssignedTo: nobody@fedoraproject.org ReportedBy: sanjay.ankur@gmail.com QAContact: extras-qa@fedoraproject.org CC: notting@redhat.com, package-review@lists.fedoraproject.org Classification: Fedora Story Points: ---
Spec URL: http://ankursinha.fedorapeople.org/vmtk/vmtk.spec SRPM URL: http://ankursinha.fedorapeople.org/vmtk/vmtk-0.9.0-1.fc15.src.rpm
Description: == Segmentation of vascular segments (or other anatomical structures) from medical images:
Gradient-based 3D level sets segmentation. A new gradient computation modality based on upwind finite differences allows the segmentation of small (down to 1.2 pixels/diameter) vessels. Interactive level sets initialization based on the Fast Marching Method. This includes a brand new method for selecting a vascular segment comprised between two points automatically ignoring side branches, no parameters involved. Segmenting a complex vascular tract comes down to selecting the endpoints of a branch, letting level sets by attracted to gradient peaks with the sole advection term turned on, repeating the operation for all the branches and merging everything in a single model.
== Geometric analysis and surface data processing of 3D models of blood vessels (and tubular objects in general)((The key algorithms have been published on medical imaging journals. You can find a complete reference to publications at David Steinman's and Luca Antiga's homepages)):
Compute centerlines and maximal inscribed sphere radius of branching tubular structures given their polygonal surface representation Split surface models into their constitutive branches based on centerline geometry Compute centerline-based geometric quantities (such as bifurcation angles, planarity, symmetry, branch curvature, tortuosity) and surface-based geometric quantities (such as distance to centerlines, surface curvature, deviation from tangency to maximal inscribed spheres) Robustly map branches to a rectangular parametric space Generate rectangular patches based on the parametric mapping for statistical analysis of geometric and CFD data over populations.
== Scripts, I/O tools and simple algorithms to easily work with images and meshes:
Read and write a number of image, surface and volume mesh formats. Includes a DICOM series reader with auto-flipping capabilities, Netgen mesh format reader, libMesh xda mesh format writer, Tetgen mesh generator wrapper, FIDAP FDNEUT mesh format reader and writer and a Newtetr input file generator Display images and meshes Incapsulate several VTK classes and make them available as pipeable scripts (e.g. Marching Cubes, surface smoothing, clipping, normal computation, connectivity, subdivision, distance between surfaces, ICP registration) Add cylindrical extensions to surface model boundaries as a preprocessing step for CFD simulations. Generate boundary layers of prismatic elements with varying thickness for CFD
=========================================================================
Some rpmlint issues. Fixing and uploading a new version in a day or two.
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https://bugzilla.redhat.com/show_bug.cgi?id=721112
Ankur Sinha sanjay.ankur@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Blocks| |673841(fedora-medical) Depends on| |720998(OpenNL) Alias| |vmtk
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--- Comment #1 from Ankur Sinha sanjay.ankur@gmail.com 2011-07-14 12:50:21 EDT --- Cleaned up rpmlint errors. Now there are only warnings
http://ankursinha.fedorapeople.org/vmtk/vmtk-0.9.0-2.fc15.src.rpm
http://ankursinha.fedorapeople.org/vmtk/vmtk.spec
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Richard Shaw hobbes1069@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- AssignedTo|nobody@fedoraproject.org |hobbes1069@gmail.com Flag| |fedora-review?
--- Comment #2 from Richard Shaw hobbes1069@gmail.com 2011-07-19 12:01:54 EDT --- I'll take this one for you.
Some quick observations.
1. The %description is WAY TO LONG.
2. I think the -devel package requires should include %{?_isa} since this isn't a noarch pacakge:
Requires: %{name}%{?_isa} = %{version}-%{release}
3. Could use more comments especially in %prep. I assume you're mainly removing bundled libraries there.
Don't worry about posting a new release just yet until I can do a more in-depth spec review.
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Ankur Sinha sanjay.ankur@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED
--- Comment #3 from Ankur Sinha sanjay.ankur@gmail.com 2011-07-19 13:39:58 EDT --- Thank you Richard! :)
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https://bugzilla.redhat.com/show_bug.cgi?id=721112
Richard Shaw hobbes1069@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Depends on| |567086(vxl), | |539387(InsightToolkit)
--- Comment #4 from Richard Shaw hobbes1069@gmail.com 2011-07-19 14:53:04 EDT --- I've made some progress trying to get it to build against the OpenNL package but I can't really test it because of:
rpmbuild -bc rpmbuild/vmtk/SPECS/vmtk.spec error: Failed build dependencies: InsightToolkit-devel is needed by vmtk-0.9.0-2.fc14.x86_64 vxl-devel is needed by vmtk-0.9.0-2.fc14.x86_64
Because of that I've added the review request of vxl and InsightToolkit as a blocker for this Review Request.
Back to this review :)
The only part of the project that appears to use OpenNL is the DifferentialGeometry sub-project.
I've added a cmake option, USE_EXTERN_OPENNL to the main CMakeLists.txt and I'm working on getting the headers and linking working in the CMakeLists.txt for DifferentialGeometry.
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https://bugzilla.redhat.com/show_bug.cgi?id=721112
--- Comment #5 from Ankur Sinha sanjay.ankur@gmail.com 2011-07-20 10:43:12 EDT --- Hi Richard,
(In reply to comment #4)
I've made some progress trying to get it to build against the OpenNL package but I can't really test it because of:
rpmbuild -bc rpmbuild/vmtk/SPECS/vmtk.spec error: Failed build dependencies: InsightToolkit-devel is needed by vmtk-0.9.0-2.fc14.x86_64 vxl-devel is needed by vmtk-0.9.0-2.fc14.x86_64
Because of that I've added the review request of vxl and InsightToolkit as a blocker for this Review Request.
I'm sorry, I forgot to mention that you need to build ITK and vxl for your fedora system before you can test it. I for example, have a local mock repo with these packages.
[root@ankur ~]# ls /tmp/mock-repo/InsightToolkit-* /tmp/mock-repo/vxl-* /tmp/mock-repo/InsightToolkit-3.20.0-5.fc16.i686.rpm /tmp/mock-repo/vxl-1.14.0-1.fc16.i686.rpm /tmp/mock-repo/InsightToolkit-3.20.0-5.fc16.src.rpm /tmp/mock-repo/vxl-1.14.0-1.fc16.src.rpm /tmp/mock-repo/InsightToolkit-debuginfo-3.20.0-5.fc16.i686.rpm /tmp/mock-repo/vxl-debuginfo-1.14.0-1.fc16.i686.rpm /tmp/mock-repo/InsightToolkit-devel-3.20.0-5.fc16.i686.rpm /tmp/mock-repo/vxl-devel-1.14.0-1.fc16.i686.rpm /tmp/mock-repo/InsightToolkit-doc-3.20.0-5.fc16.i686.rpm /tmp/mock-repo/vxl-doc-1.14.0-1.fc16.i686.rpm /tmp/mock-repo/InsightToolkit-examples-3.20.0-5.fc16.i686.rpm
Back to this review :)
The only part of the project that appears to use OpenNL is the DifferentialGeometry sub-project.
I've added a cmake option, USE_EXTERN_OPENNL to the main CMakeLists.txt and I'm working on getting the headers and linking working in the CMakeLists.txt for DifferentialGeometry.
The package works with the fedora OpenNL which I packaged recently. You don't need to make any tweaks. The changes I've made in the prep and build sections are enough.
At the moment, gdcm is broken in rawhide,(after the latest libpoppler soname bump) so I can't build it as well :/
Thanks, Ankur
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https://bugzilla.redhat.com/show_bug.cgi?id=721112
--- Comment #6 from Richard Shaw hobbes1069@gmail.com 2011-07-20 11:43:55 EDT --- (In reply to comment #5)
(In reply to comment #4)
I've made some progress trying to get it to build against the OpenNL package but I can't really test it because of:
rpmbuild -bc rpmbuild/vmtk/SPECS/vmtk.spec error: Failed build dependencies: InsightToolkit-devel is needed by vmtk-0.9.0-2.fc14.x86_64 vxl-devel is needed by vmtk-0.9.0-2.fc14.x86_64
Because of that I've added the review request of vxl and InsightToolkit as a blocker for this Review Request.
I'm sorry, I forgot to mention that you need to build ITK and vxl for your fedora system before you can test it. I for example, have a local mock repo with these packages.
Yup, I run a local repo as well. I'll try that.
The only part of the project that appears to use OpenNL is the DifferentialGeometry sub-project.
I've added a cmake option, USE_EXTERN_OPENNL to the main CMakeLists.txt and I'm working on getting the headers and linking working in the CMakeLists.txt for DifferentialGeometry.
The package works with the fedora OpenNL which I packaged recently. You don't need to make any tweaks. The changes I've made in the prep and build sections are enough.
Well, I was trying for a few reasons. One, I'm trying to improve my cmake-fu :) Also, hacking the link.txt is not ideal. If I can come up with a good cmake patch then maybe upstream will accept it (which is the best case).
Also, in retrospect, I'm wondering if we should have renamed the header file for OpenNL to be consistent with the library name, i.e.: nl.h -> opennl.h
What do you think?
Richard
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--- Comment #7 from Richard Shaw hobbes1069@gmail.com 2011-07-21 10:51:19 EDT --- Ok, after installing the other BuildRequires I got my cmake patch working!
Next issue: Are you on a 32bit or 64bit system? I noticed that "make install" doesn't put the libraries in /usr/lib64 on x86_64 systems. I added a %ifarch conditional to move /usr/lib to /usr/lib64 on x86_64 and ppc64 systems.
Second issue: I noticed it put all the python files in /usr/lib/vmtk/vmtk. I think all of these should go into %{python_sitelib}/vmtk, right?
Richard
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--- Comment #8 from Richard Shaw hobbes1069@gmail.com 2011-07-21 12:11:02 EDT --- Update:
I need your help to figure out what exactly is supposed to go into the -devel package.
I saw you had the python scripts going in there. Are they the "source" files for the python libraries or are they separate from them?
I find the whole /usr/lib/vmtk/vmtk structure that make install produces confusing...
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--- Comment #9 from Ankur Sinha sanjay.ankur@gmail.com 2011-07-21 14:11:47 EDT ---
Well, I was trying for a few reasons. One, I'm trying to improve my cmake-fu :) Also, hacking the link.txt is not ideal. If I can come up with a good cmake patch then maybe upstream will accept it (which is the best case).
Also, in retrospect, I'm wondering if we should have renamed the header file for OpenNL to be consistent with the library name, i.e.: nl.h -> opennl.h
What do you think?
Hrm, we certainly could do that. Although, we'd have to first look at it's effects. I'll look into it.
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--- Comment #10 from Ankur Sinha sanjay.ankur@gmail.com 2011-07-21 14:19:33 EDT --- (In reply to comment #7)
Ok, after installing the other BuildRequires I got my cmake patch working!
Next issue: Are you on a 32bit or 64bit system? I noticed that "make install" doesn't put the libraries in /usr/lib64 on x86_64 systems. I added a %ifarch conditional to move /usr/lib to /usr/lib64 on x86_64 and ppc64 systems.
I run mock builds for a 32 bit system. I haven't tried on an x86_64 yet.
I just looked at CMakeLists.txt. I think setting "VMTK_MODULE_INSTALL_LIB_DIR" would fix this. -DVMTK_MODULE_INSTALL_LIB_DIR:STRING=$RPM_BUILD_ROOT/%{_libdir}/ or something on these lines. Again, I'll try it out and confirm.
Second issue: I noticed it put all the python files in /usr/lib/vmtk/vmtk. I think all of these should go into %{python_sitelib}/vmtk, right?
Yes. Should. Again, setting VMTK_MODULE_INSTALL_LIB_DIR just might do the trick.
I'll try all of this out and post :)
Thanks, Ankur
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--- Comment #11 from Ankur Sinha sanjay.ankur@gmail.com 2011-07-21 14:21:05 EDT --- (In reply to comment #8)
Update:
I need your help to figure out what exactly is supposed to go into the -devel package.
I saw you had the python scripts going in there. Are they the "source" files for the python libraries or are they separate from them?
I find the whole /usr/lib/vmtk/vmtk structure that make install produces confusing...
I'll try getting in touch with upstream for suggestions.
I'm going to be unavailable until Monday. I'll only respond after that. I regret the inconvenience this will cause :/
Thanks, Ankur
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--- Comment #12 from Richard Shaw hobbes1069@gmail.com 2011-07-21 15:43:16 EDT --- (In reply to comment #10)
(In reply to comment #7)
Ok, after installing the other BuildRequires I got my cmake patch working!
Next issue: Are you on a 32bit or 64bit system? I noticed that "make install" doesn't put the libraries in /usr/lib64 on x86_64 systems. I added a %ifarch conditional to move /usr/lib to /usr/lib64 on x86_64 and ppc64 systems.
I run mock builds for a 32 bit system. I haven't tried on an x86_64 yet.
Ok, my updated spec/SRPM file[1] fixes that.
I just looked at CMakeLists.txt. I think setting "VMTK_MODULE_INSTALL_LIB_DIR" would fix this. -DVMTK_MODULE_INSTALL_LIB_DIR:STRING=$RPM_BUILD_ROOT/%{_libdir}/ or something on these lines. Again, I'll try it out and confirm.
Didn't work for me. It appears to just control the /usr or /usr/local part of the path, I set it to /lib64 (since it adds /usr seperately) and it ended up putting the files in /usr/lib64/lib/vmtk/vmtk...
Second issue: I noticed it put all the python files in /usr/lib/vmtk/vmtk. I think all of these should go into %{python_sitelib}/vmtk, right?
Yes. Should. Again, setting VMTK_MODULE_INSTALL_LIB_DIR just might do the trick.
Probably will not work but worth a try... The problem is all the .py files need to go in %{python_sitelib} which is /usr/lib/pythonX.X/site-packages/ while the .so python libraries need to go in %{python_sitearch} which can be the same as %{python_sitelib} for 32bit systems but is /usr/lib64... for 64 bit systems. This is easier just to manage manually.
The only side effect I've found so far is that one (and only one) of the python .so libraries actually has a SONAME and the .so symlink is getting pulled into the regular package instead of the -devel package. Should be easy to fix though, there are other bigger problems...
One of the "big" problems is actually with vtk, not vmtk. It provides a necessary library, libVPIC.so, but only in the -devel package, not in the main package. Because of that I had to add a Requires for vtk-devel which pulls in a bunch of dependencies we don't need just to get the one file we do need. I added a BZ reference in the comment so we can watch to see when it get's fixed.
The other problem seems to be that some of the libraries from vmtk can't find other libraries it provides. In other words, it's finding libraries in /usr/lib{,64} but not the ones in /usr/lib{,64}/vmtk... Not sure why that is happening.
That's enough for now I think!
[1] http://hobbes1069.fedorapeople.org/vmtk/vmtk-0.9.0-2.fc14.src.rpm
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Richard Shaw hobbes1069@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Depends on| |705885
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--- Comment #13 from Richard Shaw hobbes1069@gmail.com 2011-07-26 14:27:21 EDT --- Ankur,
I found out that I was wrong about the whole python_sitelib/sitearch thing. If there are ANY C python modules in the package then everything, including the pure python modules go in sitearch.
Richard
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Bug 721112 depends on bug 720998, which changed state.
Bug 720998 Summary: Review Request: OpenNL - A library for solving sparse linear systems https://bugzilla.redhat.com/show_bug.cgi?id=720998
What |Old Value |New Value ---------------------------------------------------------------------------- Resolution| |ERRATA Status|ON_QA |CLOSED
--- Comment #14 from Ankur Sinha sanjay.ankur@gmail.com 2011-08-13 03:30:55 EDT --- hi Richard,
I'm waiting on vxl to be packaged. Mario's working on it. I can't get vmtk to build in mock at the moment. Some issue with the vxl package.
Thanks, Ankur
Product: Fedora https://bugzilla.redhat.com/show_bug.cgi?id=721112
Bug 721112 depends on bug 567086, which changed state.
Bug 567086 Summary: Review Request: VXL - C++ Libraries for Computer Vision Research and Implementation https://bugzilla.redhat.com/show_bug.cgi?id=567086
What |Removed |Added ---------------------------------------------------------------------------- Status|ON_QA |CLOSED Resolution|--- |CURRENTRELEASE
Product: Fedora https://bugzilla.redhat.com/show_bug.cgi?id=721112
Miroslav Suchý msuchy@redhat.com changed:
What |Removed |Added ---------------------------------------------------------------------------- CC| |msuchy@redhat.com Flags| |needinfo?(sanjay.ankur@gmai | |l.com)
--- Comment #15 from Miroslav Suchý msuchy@redhat.com --- Ping? Any progress here? Or we can close this review?
Product: Fedora https://bugzilla.redhat.com/show_bug.cgi?id=721112
Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Flags|needinfo?(sanjay.ankur@gmai | |l.com) |
--- Comment #16 from Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com --- Hi,
VXL has *just* been included in the repositories. I'm away and will not be able to work on this review for another month. Please feel free to start a new review if you need to.
Thanks, Warm regards, Ankur
Product: Fedora https://bugzilla.redhat.com/show_bug.cgi?id=721112
Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- See Also| |https://bugzilla.redhat.com | |/show_bug.cgi?id=483663
--- Comment #17 from Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com --- Hrm, cannot still build it. Depends on ITK. Also found more bundled software *sigh* in the 1.0.1 release:
Doxygen OpenNL Stellar_1.0 tetgen1.4.3. I also see that tetgen is NOT free software, as noted in the review ticket:
https://bugzilla.redhat.com/show_bug.cgi?id=483663
I'm afraid this might mean we need to drop this package altogether. I'll see if I can speak to upstream about this.
I'll at least package stellar in the mean time: http://www.cs.berkeley.edu/~jrs/stellar/
Thanks, Warm regards, Ankur
Product: Fedora https://bugzilla.redhat.com/show_bug.cgi?id=721112
--- Comment #18 from Mario Ceresa mrceresa@gmail.com --- Thanks Ankur for your efforts in packaging vmtk. You might be able to use vmtk with netgen, which is free: http://www.vmtk.org/Tutorials/NetgenWay/
We hope to finish ITK anytime soon -if more bundled software doesn't show up, of course ;)
Best, Mario
Product: Fedora https://bugzilla.redhat.com/show_bug.cgi?id=721112
Bug 721112 depends on bug 539387, which changed state.
Bug 539387 Summary: Review Request: InsightToolkit - Medical imaging processing library https://bugzilla.redhat.com/show_bug.cgi?id=539387
What |Removed |Added ---------------------------------------------------------------------------- Status|ON_QA |CLOSED Resolution|--- |ERRATA
https://bugzilla.redhat.com/show_bug.cgi?id=721112
Dominik 'Rathann' Mierzejewski dominik@greysector.net changed:
What |Removed |Added ---------------------------------------------------------------------------- See Also|https://bugzilla.redhat.com | |/show_bug.cgi?id=483663 | Depends On| |483663
--- Comment #19 from Dominik 'Rathann' Mierzejewski dominik@greysector.net --- tetgen is free software now and I've just approved Sandro's package, so it can be unbundled from vmtk.
Referenced Bugs:
https://bugzilla.redhat.com/show_bug.cgi?id=483663 [Bug 483663] Review Request: tetgen - A tetrahedral mesh generator
https://bugzilla.redhat.com/show_bug.cgi?id=721112
Dominik 'Rathann' Mierzejewski dominik@greysector.net changed:
What |Removed |Added ---------------------------------------------------------------------------- Blocks| |505154 (FE-SCITECH)
Referenced Bugs:
https://bugzilla.redhat.com/show_bug.cgi?id=505154 [Bug 505154] Tracker: Review Requests for Science and Technology related packages
https://bugzilla.redhat.com/show_bug.cgi?id=721112 Bug 721112 depends on bug 483663, which changed state.
Bug 483663 Summary: Review Request: tetgen - A tetrahedral mesh generator https://bugzilla.redhat.com/show_bug.cgi?id=483663
What |Removed |Added ---------------------------------------------------------------------------- Status|ON_QA |CLOSED Resolution|--- |ERRATA
https://bugzilla.redhat.com/show_bug.cgi?id=721112
Richard Shaw hobbes1069@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- CC|hobbes1069@gmail.com | Assignee|hobbes1069@gmail.com |nobody@fedoraproject.org
https://bugzilla.redhat.com/show_bug.cgi?id=721112
Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|ASSIGNED |CLOSED Resolution|--- |WONTFIX Last Closed| |2018-01-07 16:46:08
--- Comment #20 from Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com --- I'm going to close this as WONTFIX. I'm not working on medical applications anymore so I'm not the best person to maintain this package now.
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