Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Fix issue #40. Edited meshing module 2-8 pages. #41

Open
wants to merge 2 commits into
base: master
Choose a base branch
from
Open

Fix issue #40. Edited meshing module 2-8 pages. #41

wants to merge 2 commits into from

Conversation

francoisdh
Copy link
Contributor

@francoisdh
fixes issue #40. Edited meshing module 2-8 pages:
2028622 
      - docs/modules/ROOT/pages/meshing/module-2-surface-from-image.adoc
      - docs/modules/ROOT/pages/meshing/module-3-centerlines-gui-tool.adoc
      - docs/modules/ROOT/pages/meshing/module-4-centerlines-computing.adoc
      - docs/modules/ROOT/pages/meshing/module-5-centerlines-merging.adoc
      - docs/modules/ROOT/pages/meshing/module-6-image-generation.adoc
      - docs/modules/ROOT/pages/meshing/module-7-surface-remeshing.adoc
      - docs/modules/ROOT/pages/meshing/module-8-volume-meshing.adoc
@francoisdh francoisdh added type:bug An error, unexpected behavior, or misconfiguration domain:documentation Add or revise a unit of documentation labels Jul 2, 2018
prudhomm
prudhomm requested changes Jul 3, 2018
View reviewed changes
Copy link
Member

@prudhomm prudhomm left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

thanks for the work.

options should probably go in a table with

  • option name,
  • option default value
  • option description

docs/modules/ROOT/pages/meshing/module-2-surface-from-image.adoc Outdated
@@ -1,18 +1,22 @@
= Surface extraction

The goal here is to extract and create a 3D model of the surface of the blood vessels, using a level set method.
The level sets are initialiazed using either the isosurface of a given intensity value (*isosurface* method) or a given intensity range (*threshold* method).
The goal here is to extract and create a 3D model of the surface of the blood
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

The goal of this module is to extract...

docs/modules/ROOT/pages/meshing/module-2-surface-from-image.adoc Outdated
The level sets are initialiazed using either the isosurface of a given intensity value (*isosurface* method) or a given intensity range (*threshold* method).
The goal here is to extract and create a 3D model of the surface of the blood
vessels, using a level set method.
The level sets are initialiazed using either the isosurface of a given intensity
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

initialized

docs/modules/ROOT/pages/meshing/module-3-centerlines-gui-tool.adoc Outdated

Simply run this command or put it in your `.bashrc` (which is more convenient for repeated use).
Simply run this command or put it in your `.bashrc` (which is more convenient
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Run the following command or add it in $HOME/.bashrc

docs/modules/ROOT/pages/meshing/module-3-centerlines-gui-tool.adoc Outdated

Simply run this command or put it in your `.bashrc` (which is more convenient for repeated use).
Simply run this command or put it in your `.bashrc` (which is more convenient
for repeated use).

`source $INSTALL/bin/setupAngioTKEnvironment.sh`
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

use

source $INSTALL/bin/setupAngioTKEnvironment.sh

docs/modules/ROOT/pages/meshing/module-3-centerlines-gui-tool.adoc Outdated
@@ -32,7 +46,8 @@ Now, the exectutable `meshing_centerlinesmanagergui` can be launched directly.
The arguments to provide are:

- `--input.surface.path` (mandatory) specifies the surface file to work on.
- `--input.point-pair.path` (optional) specifies the point pairs file (typically: previously saved work)
- `--input.point-pair.path` (optional) specifies the point pairs file
(typically: previously saved work)

Thus, the typical command shoud be:
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

the typical command reads

docs/modules/ROOT/pages/meshing/module-4-centerlines-computing.adoc Outdated
@@ -1,12 +1,15 @@
= Center lines computing

We first need to compute each center line using both the extracted surface and the corresponding point pairs (which shoud have been defined in the first place, using link:Module_3_CenterlinesGUITool.adoc[the center lines editing tool])
We first need to compute each center line using both the extracted surface and
the corresponding point pairs (which shoud have been defined in the first place,
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

which have been defined using ...

docs/modules/ROOT/pages/meshing/module-4-centerlines-computing.adoc Outdated
We first need to compute each center line using both the extracted surface and the corresponding point pairs (which shoud have been defined in the first place, using link:Module_3_CenterlinesGUITool.adoc[the center lines editing tool])
We first need to compute each center line using both the extracted surface and
the corresponding point pairs (which shoud have been defined in the first place,
using link:Module_3_CenterlinesGUITool.adoc[the center lines editing tool]).
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

use xref !!! the link here won't work

docs/modules/ROOT/pages/meshing/module-7-surface-remeshing.adoc Outdated

.Distance comparison
image::distance_comparison.jpg[]

== Troubleshooting

Two bugs could arise:
- (Rarely) A partition remeshing failure: This can be fixed by adjusting *--open-surface.radius-uncertainty* and *gmsh.nb-points-in-circle=15*
- (Rarely) A partition remeshing failure: This can be fixed by adjusting
`open-surface.radius-uncertainty` and `gmsh.nb-points-in-circle`
- (Very rarely) A crash of unknown cause.

link:Meshing_Module_Description.adoc[Go back to The Meshing Module]
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

use xref!

docs/modules/ROOT/pages/meshing/module-8-volume-meshing.adoc Outdated
account for its thickness in future fluid-structure interation numerical
simulations.
We will also generate mesh input and output markers in a description file
(.desc).
The executable we use is named `meshing_volumefromstlandcenterlines`.
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

The executable is named ...

docs/modules/ROOT/pages/meshing/module-8-volume-meshing.adoc Outdated
NOTE: If the input surface has more than one connected component,
the algorithm will enter an infinite loop.
A solution is to split each connected component apart and to process them all
separately.

link:Meshing_Module_Description.adoc[Go back to The Meshing Module]
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

use xref.

have a What next? section

@francoisdh
Copy link
Contributor Author

francoisdh commented Jul 19, 2018 •
edited
Loading

Thank you @prudhomm, I have made changes according to your comments.

We should merge this as soon as possible to close issue #40 and have a better documentation online.

We can always improve the documentation later, for example with the options tables.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@prudhomm prudhomm prudhomm requested changes

@vincentchabannes vincentchabannes Awaiting requested review from vincentchabannes

Requested changes must be addressed to merge this pull request.

Assignees

@prudhomm prudhomm

Labels
domain:documentation Add or revise a unit of documentation type:bug An error, unexpected behavior, or misconfiguration
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

None yet
2 participants
@francoisdh @prudhomm