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Repo info
Activity
  • Apr 03 22:17

    prudhomm on master

    fix warning (compare)

  • Dec 20 2018 11:36

    vincentchabannes on feelpp-v0.106

    add option for smooth the radius (compare)

  • Dec 18 2018 16:11

    vincentchabannes on feelpp-v0.106

    up ITK version + use RPATH avoid to call wget at each times fix execution if does not have … (compare)

  • Dec 12 2018 15:38

    vincentchabannes on feelpp-v0.106

    download gmsh headers from gmsh… (compare)

  • Dec 06 2018 08:39

    vincentchabannes on feelpp-v0.106

    up centerlines fusion + fix war… (compare)

  • Nov 30 2018 12:45

    vincentchabannes on feelpp-v0.106

    up centerlines coloring add posibility to have a consta… up header (compare)

  • Nov 29 2018 22:02

    vincentchabannes on feelpp-v0.106

    change a little bit the partiti… (compare)

  • Nov 29 2018 16:10

    vincentchabannes on feelpp-v0.106

    fix call of python (seems due t… fix OpenSurface algo @francois… add vmtk cmake option and 1 more (compare)

  • Nov 23 2018 10:15

    vincentchabannes on feelpp-v0.106

    up vmtk version (use a recent c… use new cmake system with link … fix compilation with last feel++ (compare)

  • Jul 20 2018 09:19
    francoisdh closed #42
  • Jul 20 2018 09:19
    francoisdh commented #42
  • Jul 19 2018 11:48

    vincentchabannes on master

    fixed issue #42: requests RORPO… Merge pull request #43 from fee… (compare)

  • Jul 19 2018 11:48
    vincentchabannes closed #43
  • Jul 19 2018 10:24
    francoisdh review_requested #43
  • Jul 19 2018 10:24
    francoisdh review_requested #43
  • Jul 19 2018 10:24
    francoisdh assigned #43
  • Jul 19 2018 10:24
    francoisdh labeled #43
  • Jul 19 2018 10:24
    francoisdh labeled #43
  • Jul 19 2018 10:24
    francoisdh opened #43
  • Jul 19 2018 10:22

    francoisdh on issue-42-rorpo

    fixed issue #42: requests RORPO… (compare)

Christophe Prud'homme
@prudhomm
you can find it here
Christophe Prud'homme
@prudhomm
@francoisdh @jjomier we have to prepare the angiotk course for the summer school !
Christophe Prud'homme
@prudhomm
@francoisdh any news on the installation process ?
François Der Hovsepian
@francoisdh
Yes, I updated the building instructions and will push them in a few minutes.
Christophe Prud'homme
@prudhomm
@francoisdh @vincentchabannes the data from Baledent is on Atlas: /data/vivabrain/Baledent/*
François Der Hovsepian
@francoisdh
@prudhomm Thank you ! I will start working on it !
Christophe Prud'homme
@prudhomm
@jjomier what is the procedure to upload the data into midas ?
François Der Hovsepian
@francoisdh
@prudhomm @jjomier Is there a simple way to open all these dicom images as a 3D one in ParaView ? Or a way to concatenate and convert them all into a single MHA or NIfTI file ?
(ParaView 5.3.0 does not seem to handle the DICOMDIR, but opens slices fine individually, when told to read them as "DICOM (single)" files)
Christophe Prud'homme
@prudhomm
@vincentchabannes I setup buildkite for angiotk. however it will fail until we merge cmake-superbuild into master (or develop). When do you think you will merge ?
Vincent Chabannes
@vincentchabannes
@prudhomm thanks! I will try to merge today (I have still some minor up about the installation). I have tried in docker with feelpp-libs and it works. I have noticed an error in LD_LIBRARY_PATH and PYTHONPATH for paraview (paraview-5.0 -> paraview-5.3 in feelpp.env.sh). if you have time, can you update this?
Christophe Prud'homme
@prudhomm
where is the problem exactely ?
Vincent Chabannes
@vincentchabannes
Christophe Prud'homme
@prudhomm
@vincentchabannes feelpp/feelpp-env is currently being re-generated
Vincent Chabannes
@vincentchabannes
If I change this file, it’s automatically re-generated? I thought not
Christophe Prud'homme
@prudhomm
nope not yet. I need to set this up
Christophe Prud'homme
@prudhomm
@vincentchabannes c'est corrigé et mis à jour sur docker :) docker pull feelpp/feelpp-env
Vincent Chabannes
@vincentchabannes
merci!
Christophe Prud'homme
@prudhomm
ca a été vite car juste la couche feelpp.env.sh qui arrive a la fin était modifiée
Vincent Chabannes
@vincentchabannes
@prudhomm est-ce que l’on peut spécifier des options à cmake pour la génération de l’image?
François Der Hovsepian
@francoisdh
Bonjour à tous,
@vincentchabannes ai-je bien compris que la branche feature/cmake-superbuild qui vient d'être fusionnée avec master inclut toutes les dépendances ? Je suis en train de compiler pour pouvoir tester.
Vincent Chabannes
@vincentchabannes
oui, il faut juste compiler et installer feel++ (avec paraview par exemple) et ensuite tout le reste s'installe
François Der Hovsepian
@francoisdh
Ok super ! Donc pour la partie feel++, c'est comme avant, non ?
Vincent Chabannes
@vincentchabannes
oui comme avant(sur atlas tu as juste à charger le module feelpp-clang_gcc610.profile). Sinon l’image docker devrait bientot être dispo.
François Der Hovsepian
@francoisdh
C'est génial, merci.
Christophe Prud'homme
@prudhomm
@/all angiotk is now up up and running in docker !
Christophe Prud'homme
@prudhomm
@vincentchabannes could you test the images just to be sure everything is all right ?
Vincent Chabannes
@vincentchabannes
@prudhomm not really, we need to give some options in cmake (else all modules are disabled)
Vincent Chabannes
@vincentchabannes
and also docker pull feelpp/angiotk doesn’t work :
Using default tag: latest
Error response from daemon: repository feelpp/angiotk not found: does not exist or no pull access
Christophe Prud'homme
@prudhomm
@vincentchabannes sorry you have to pass the full tag: docker pull feelpp/angiotk:master-ubuntu-16.10
which options do we need to pass ? at feelpp level or angiotk level ?
Vincent Chabannes
@vincentchabannes
-DCMAKE_BUILD_TYPE=Release -DBUILD_MODULE_Meshing=ON -DBUILD_MODULE_Filtering=ON
and docker pull feelpp/angiotk:master-ubuntu-16.10 give me the same error
Christophe Prud'homme
@prudhomm
can you try now docker pull feelpp/angiotk?
I pushed the latest tag
Vincent Chabannes
@vincentchabannes
sorry, I forgot to run docker login. Now it’s good.
Christophe Prud'homme
@prudhomm
I will do the cmake stuff later this morning
Christophe Prud'homme
@prudhomm
@vincentchabannes the new docker images with the cmake flags has just been deployed. you can check ;)
François Der Hovsepian
@francoisdh
@prudhomm How can I test the docker image ? I just installed the latest version of docker for mac. docker pull feelpp/angiotk gives me the same error @vincentchabannes encountered. I read the documentation about docker login but I lack informations I should provide. I guess I should create an account somewhere and ask for access to the feelpp/angiotk docker registry ?
Christophe Prud'homme
@prudhomm
@francoisdh you need indeed to have an account on docker hub and that I give you the permission to access the image. It is still being developed/tested, your help is welcome
@vincentchabannes from feelpp/angiotk@8728833 is the module automatically set to be built in docker ? otherwise you need to change in .buildkite/pipeline.yml and add the proper cmake flag
ah ok you just committed it ;)
Vincent Chabannes
@vincentchabannes
@prudhomm je viens de faire de 2/3 tests, ça semble ok. J’ai pu aussi tester l’outil graphique avec virtualbox+docker.
Christophe Prud'homme
@prudhomm
Et ça marche ?
Vincent Chabannes
@vincentchabannes
oui, le rendu 3d rame un peu mais ça marche
Christophe Prud'homme
@prudhomm
Il faudrait avoir avoir des tests simples sur des data fabriquées à la main. Ce serait d'ailleurs utile pour le workshop
Vincent Chabannes
@vincentchabannes
@prudhomm j’ai remarqué que le tag latest de l’image docker n’était pas mis à jour
Christophe Prud'homme
@prudhomm
@vincentchabannes in fact the latest tag is associated with develop branch and not master. This could be changed of course. Master has the stable tag.
François Der Hovsepian
@francoisdh
@prudhomm I created a docker hub account: francoisdh
Christophe Prud'homme
@prudhomm
@francoisdh you have access as well @lsala . @jjomier do you have a docker account to access the docker images ?
Christophe Prud'homme
@prudhomm
@/all the docker image feelpp/angiotkis now public !