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Today's topic summary
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- [CCPPETMR/SIRF-SuperBuild] Travis, docker, osx improvements (#86) [2 Updates]
http://groups.google.com/group/ccp-petmr-codebot/t/c5d1e4bfc30939b7
- [CCPPETMR/SIRF] error in STIR when using an attenuation image in the AcquisitionSensitivityModel (#103) [3 Updates]
http://groups.google.com/group/ccp-petmr-codebot/t/2b059af9b9fcc97
- [CCPPETMR/SIRF-SuperBuild] make location of output of SuperBuild consistent (#16) [3 Updates]
http://groups.google.com/group/ccp-petmr-codebot/t/d158e6ba57395b85
- [CCPPETMR/SIRF] document usage of ports for Gadgetron (#105) [1 Update]
http://groups.google.com/group/ccp-petmr-codebot/t/82f3a9180fddc54f
- [CCPPETMR/SIRF] Release checklist (#93) [1 Update]
http://groups.google.com/group/ccp-petmr-codebot/t/caed9e00c8dd2080
- [CCPPETMR/CCPPETMR_VM] updating SIRF_VM_VERSION? (#50) [1 Update]
http://groups.google.com/group/ccp-petmr-codebot/t/9297208e6ae19c77
- [CCPPETMR/SIRF] chained normalisation unstable (#104) [2 Updates]
http://groups.google.com/group/ccp-petmr-codebot/t/23d5f8ac207498a6
- [CCPPETMR/SIRF] need to be consistent in spelling of normalisation (#98) [2 Updates]
http://groups.google.com/group/ccp-petmr-codebot/t/5bc3d8ba00f84493
- [CCPPETMR/SIRF] reconstruct_from_listmode is incomplete (#101) [2 Updates]
http://groups.google.com/group/ccp-petmr-codebot/t/2534871f09ff6fd1
- [CCPPETMR/SIRF] potential improvement in PETAttenuationModel::PETAttenuationModel (#102) [1 Update]
http://groups.google.com/group/ccp-petmr-codebot/t/9dee775ea1aea826
- [CCPPETMR/CCPPETMR_VM] Xorg failure on xenial64 machine (#49) [7 Updates]
http://groups.google.com/group/ccp-petmr-codebot/t/fb561c247d3cd683
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Topic: [CCPPETMR/SIRF-SuperBuild] Travis, docker, osx improvements (#86)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/c5d1e4bfc30939b7
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From: Richard Brown <[log in to unmask]>
Date: Feb 09 09:47AM
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/8de091d544bfc
@casperdcl ditto re removal of `brew tap homebrew/science` - if Travis is happy, I'm happy.
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From: Kris Thielemans <[log in to unmask]>
Date: Feb 10 12:10AM
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/90d2adf2f0912
KrisThielemans commented on this pull request.
> COPY user_sirf-ubuntu.sh .
RUN EXTRA_BUILD_FLAGS="-DCMAKE_BUILD_TYPE=Release -DUSE_SYSTEM_Boost=ON \
- -DUSE_SYSTEM_SWIG=ON
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Topic: [CCPPETMR/SIRF] error in STIR when using an attenuation image in the AcquisitionSensitivityModel (#103)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/2b059af9b9fcc97
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From: evgueni-ovtchinnikov <[log in to unmask]>
Date: Feb 09 04:05PM
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/8f2bb4b42b629
Closed #103.
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https://github.com/CCPPETMR/SIRF/issues/103#event-1466961401
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From: Kris Thielemans <[log in to unmask]>
Date: Feb 09 11:52PM
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/90c30b2424c2d
Reopened #103.
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From: Kris Thielemans <[log in to unmask]>
Date: Feb 10 12:07AM
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/90d00b5596141
I still have the same problem (with SIRF/devel and STIR/master)
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Topic: [CCPPETMR/SIRF-SuperBuild] make location of output of SuperBuild consistent (#16)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/d158e6ba57395b85
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From: Edoardo Pasca <[log in to unmask]>
Date: Feb 09 04:42PM
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/8f4bab36e72cf
with https://github.com/CCPPETMR/SIRF-SuperBuild/commit/f255b459fafab9d304df225c77db2a68c75b5855 I have set the build directories as
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From: Kris Thielemans <[log in to unmask]>
Date: Feb 09 03:46PM -0800
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/90bd4712e3045
You should check `petmr_data_path('pet')` in Python. That should be set to `/blabla/SIRF/data/examples/PET` (which is set via the env variable `SIRF_PATH`, which should be set to the location of the
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From: Kris Thielemans <[log in to unmask]>
Date: Feb 09 03:51PM -0800
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/90c1ba2a1cc0d
I've seen somewhere in the doc a reference to where the examples are etc, but I cannot find it anymore. In any case, this should be somehwere rather promiment. It's going to change with this PR, so
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Topic: [CCPPETMR/SIRF] document usage of ports for Gadgetron (#105)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/82f3a9180fddc54f
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From: Kris Thielemans <[log in to unmask]>
Date: Feb 09 11:22PM
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/90a837e1929ed
not sure where it is now. Should be in instructions for VM I guess. Also in instructions for Windows on Wiki
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Topic: [CCPPETMR/SIRF] Release checklist (#93)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/caed9e00c8dd2080
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From: Kris Thielemans <[log in to unmask]>
Date: Feb 09 11:19PM
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/90a6534b2bf5f
@KrisThielemans pushed 1 commit.
5c852bf Update ReleaseChecklist.md
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Topic: [CCPPETMR/CCPPETMR_VM] updating SIRF_VM_VERSION? (#50)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/9297208e6ae19c77
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From: Kris Thielemans <[log in to unmask]>
Date: Feb 09 11:08PM
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/909cb21940520
I don't think [UPDATE.sh](scripts/UPDATE.sh) currently will update the stored version in an existing VM. It's not clear if this is desired or not (arguably, the VM is the old, but after it's updated,
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Topic: [CCPPETMR/SIRF] chained normalisation unstable (#104)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/23d5f8ac207498a6
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From: evgueni-ovtchinnikov <[log in to unmask]>
Date: Feb 09 04:21PM
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/8f3975c9a1ec8
Chained normalisation misbehaves now (strange output from e.g. asm_sinograms.py, crashes).
Could it be because of OpenMP?
I switched off OpenMP option for STIR in CMake and deleted /openmp
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From: Kris Thielemans <[log in to unmask]>
Date: Feb 09 05:06PM
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/8f612c057eabe
yes, known bug in OPENMP version on STIR/master. The OPENMP branch should fix that...
Once you've configured CMake, it's kind of hard to change compiler flags. I'd recommend throwing your build
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Topic: [CCPPETMR/SIRF] need to be consistent in spelling of normalisation (#98)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/5bc3d8ba00f84493
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From: evgueni-ovtchinnikov <[log in to unmask]>
Date: Feb 09 04:09PM
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/8f2e57ec9671b
no longer an issue now that we are using AcquisitionSensitivityModel instead of normalisation
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From: evgueni-ovtchinnikov <[log in to unmask]>
Date: Feb 09 04:09PM
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/8f2e5cd1e3aea
Closed #98.
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https://github.com/CCPPETMR/SIRF/issues/98#event-1466968364
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Topic: [CCPPETMR/SIRF] reconstruct_from_listmode is incomplete (#101)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/2534871f09ff6fd1
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From: evgueni-ovtchinnikov <[log in to unmask]>
Date: Feb 09 08:07AM -0800
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/8f2caa9afd5d6
Closed #101.
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From: evgueni-ovtchinnikov <[log in to unmask]>
Date: Feb 09 04:07PM
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/8f2cb18eaa7ad
reconstruction from listmode demo with attenuation, ecat8 normalisation and randoms added
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Topic: [CCPPETMR/SIRF] potential improvement in PETAttenuationModel::PETAttenuationModel (#102)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/9dee775ea1aea826
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From: evgueni-ovtchinnikov <[log in to unmask]>
Date: Feb 09 04:06PM
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/8f2bb7b974f1c
Closed #102.
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Topic: [CCPPETMR/CCPPETMR_VM] Xorg failure on xenial64 machine (#49)
URL: http://groups.google.com/group/ccp-petmr-codebot/t/fb561c247d3cd683
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From: Edoardo Pasca <[log in to unmask]>
Date: Feb 09 01:34AM -0800
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/8dd55ef5abca2
I am reporting a strange error it has happened to me a couple of times.
1. I successfully create the VM, with everything working, including X.
2. I work on the VM for a while. After a few reboots
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From: Edoardo Pasca <[log in to unmask]>
Date: Feb 09 01:34AM -0800
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/8dd5b59c9ae3c
Currently I'm trying to install the VGA, but not really successfully.
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From: Kris Thielemans <[log in to unmask]>
Date: Feb 09 09:38AM
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/8dd900bace8c2
did you install https://github.com/dotless-de/vagrant-vbguest
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From: Edoardo Pasca <[log in to unmask]>
Date: Feb 09 02:01AM -0800
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/8dece579aa956
Yes I did, but that didn't fix the problem.
Anyhow, I've now installed the VGA from http://download.virtualbox.org/virtualbox/5.1.18/ mounting manually a iso file from a shared folder (not really
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From: Edoardo Pasca <[log in to unmask]>
Date: Feb 09 10:04AM
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/8def7aa4a957f
I'll give the vbguest a thorough read because it should help automating this fix.
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From: Casper da Costa-Luis <[log in to unmask]>
Date: Feb 09 02:42AM -0800
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/8e109fc3f731c
Don't know about vbox, but in docker (xenial64 on xenial64) I needed to mount the host's `/tmp/.X11-unix` and `/tmp/.docker.xauth` within the container. Certainly looks like a vbox, rather than xenial
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From: Edoardo Pasca <[log in to unmask]>
Date: Feb 09 11:24AM
URL: http://groups.google.com/group/ccp-petmr-codebot/msg/8e3576af9f23c
Closed #49.
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