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View Code? Open in Web Editor NEWVirtual Angiography Toolkit
Home Page: http://docs.feelpp.org/angiotk/0.1
License: Apache License 2.0
Virtual Angiography Toolkit
Home Page: http://docs.feelpp.org/angiotk/0.1
License: Apache License 2.0
@omerveille (@hugues-talbot) your filter does not seem to remove the skull from the native images
Is it possible to do it ? do we have to tune your software ?
I propose to refactor the code in VolumeFromSTL in order to improve code readability and allow @francoisdh to have a look at the code.
In the src directory:
*_main.cpp
in an src/applications directory;What do you think about it ? @prudhomm @vincentchabannes @francoisdh
Using VMTK 1.3, the meshing_centerlines application segfaults.
feelpp/applications/models/fluid/main_fm.cpp
to simulate the fluid flowwe have to generate the json file for the fluid/fsi solvers from the marker file defined #6
/cc @vincentchabannes
The meshing modules documentation has some visual problems, especially the command line arguments sections, where two or more arguments are presented in the same line/paragraph instead of being spread with bullet points.
the application VolumeFromSTLAndCenterline
generates automatically a data file that provides marker named meshcreateinletoutlet.desc
, this file is then used to generates markers for boundary conditions
The current state of documentation is not very good. We should evaluate the current documentation and propose a proper design
We would like to remove the scaling of the spring example. The unit
defined at the first line of docs/modules/centerlines/examples/spring/spring.geo
should be 0.1
instead of 10
.
This would then allow to remove gmsh.scale=1e-2
option in Feel++ toolboxes spring examples: https://github.com/feelpp/toolbox/blob/master/examples/modules/cfd/examples/spring/spring.cfg
This 100x scaling was introduced as a workaround which should not be required anymore.
The geometry and mesh generation are done and documented from within Angiotk repository.
The generated mesh(es) should be uploaded to girder and then used in the subsequent steps
@vincentchabannes @francoisdh what do you think?
Documentation for AngioTK:
When trying to generate the documentation using antora and the site.yml file, we get an error.
$ antora site.yml
asciidoctor: ERROR: module-4-centerlines.adoc: line 22: only book doctypes can contain level 0 sections
asciidoctor: ERROR: module-4-centerlines.adoc: line 22: only book doctypes can contain level 0 sections
This should easily be fixed by splitting the file module-4-centerlines.adoc in two.
Integrate Odyssée's code into AngioTK
The center line radius can vary significantly in the image generated by imagefromcenterline, resulting in an incorrect surface in the next pipeline steps. For example, in the zebra fish, the dorsal aorta's radius is nearly halved.
Bonjour à tous,
J'ai une stagiaire pendant un mois à qui j'essaye de faire utiliser AngioTK...
Elle a un joli PC sous Linux-Ubuntu 16.4 (je crois).
Aujourd'hui nous avons réussi à installer Docker puis à copier l'image "master" d'angio-tk
(pas la "stable"...ça marchait pas, peut-être pour cela faut-il être dans le github privé...).
Ensuite, tout a presque bien fonctionné si ce n'est que RORPO n'a pas pu écrire le fichier de sortie pour de sombres histoires de droit ...J'ai essayé d'aller sur la page que François m'avait
envoyée pour utiliser "docker sans sudo" mais là non plus, cela ne marche pas...qu'est-ce que je rate ? Je pense ne pas savoir mon $USER quand on est dans docker ... est-ce un truc spécifique ?
j'avais un problème du même genre sur mon mac ...
Merci de votre aide, il faudrait vraiment que cela marche pour elle, elle
ne sera là que pendant un mois !
Amicalement
Stéphanie
Antora provides a framework to generate a static website for technical documentation.
We have already used this for Feel++. Check this out here http://docs.feelpp.org.
Initially, Angiotk will be integrated into Feel++ Docs then it will have its own website.
The move requires that we modify the structure of the repository.
/cc @feelpp/angiotk
Create asciidoc matrix presenting the results of each step of the pipeline for several datasets
Add some details about each pipeline step:
Using the feelpp/angiotk:stable Docker image, VMTK tools fail:
user@feelpp:~$ vmtkimagewriter
Unexpected error: <type 'exceptions.ImportError'>
Traceback (most recent call last):
File "/usr/local/bin/vmtkimagewriter", line 20, in <module>
from vmtk import pypeserver
ImportError: No module named vmtk
The problem can be fixed by appending the following path to the PYTHONPATH environment
variable:
export PYTHONPATH = $PYTHONPATH:/usr/local/lib/python3.5/site-packages
I guess this could be added to the docker image ?
AngioTK is now in Antora system, see #28, which uses asciidoc as a format for documentation.
However various adoc files are using markdown instead of asciidoc, please fix this
source code should use
[source,<lang>]
----
----
Sectioning should use =
instead of #
/cc @feelpp/angiotk
@jjomier Angiotk fails to build on Travis currently
AngioTK super build fails because of the recent updates in the RORPO repository. This will be solved by requesting the v1.0 git tag.
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