@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:

• Move all the applications *_main.cpp in an src/applications directory;
• Split the volumefromstl.hpp in the include directory into as many files as there are classes.
• Split the volumefromstl.cpp file which contains all the classes implementation into as many files as there are classes in it.
• Create a src/libraries directory where we put all the source files that are part of the angiotk_meshing_volumefromstl library.
• Ensure that everything builds correctly with CMake

What do you think about it ? @prudhomm @vincentchabannes @francoisdh

Documentation for AngioTK:

• Build instructions
• General description of AngioTK
• Description of the different modules
  • Input and output of the modules
  • Document the different options available
• Document the graphical tool for editing centerlines
• Document how output files are stored for the Pipeline and how files are stored for the result matrix
• Creation of Angiotk Book

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.

• update docker instructions to run the latest image
• update building instructions (including building Feel++ on atlas)

@jjomier Angiotk fails to build on Travis currently

https://magnum.travis-ci.com/feelpp/angiotk

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.

• add all the scripts and configuration files used during the workshop.
• add a user guide to help users to run the pipeline and to reproduce the various steps presented during the summer school workshop.

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 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?

The current state of documentation is not very good. We should evaluate the current documentation and propose a proper design

Integrate Odyssée's code into AngioTK

• use feelpp/applications/models/fluid/main_fm.cpp to simulate the fluid flow
• + test fluid structure interaction

we have to generate the json file for the fluid/fsi solvers from the marker file defined #6
/cc @vincentchabannes

Create asciidoc matrix presenting the results of each step of the pipeline for several datasets

• Include configuration and environment details (user, date, versions,...) used for the whole run.
  Information
  • version of angiotk if it exists or commit ids
  • author of the batch run
  • date/time
  • time for global execution
  • machine
  • dataset name (we have to define the notion of dataset) eg Vivabrain
    • number of dataset inside the dataset
  • statistics about the data set
    • number of successful reconstruction
    • number of incomplete reconstruction
    • number of total failures

Add some details about each pipeline step:

• Use boolean 'success' variable to assign a background color to the relevant cell.
• Include the complete command used in each cell (this could later be changed to a 'rebuild' button in the web page)
• Round all execution times.

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 super build fails because of the recent updates in the RORPO repository. This will be solved by requesting the v1.0 git tag.

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

Using VMTK 1.3, the meshing_centerlines application segfaults.

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

• Make sure every dataset runs up to the centerlines step
• create minimal centerlines file for every dataset

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.

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.

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