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Fix issue #40. Edited meshing module 2-8 pages. #41
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francoisdh
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Jul 2, 2018
- Solves a few problems described in issue Meshing modules documentation problems #40,
- improves some code snippets,
- corrects a few typos.
- 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
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thanks for the work.
options should probably go in a table with
- option name,
- option default value
- option description
@@ -1,18 +1,22 @@ | |||
= Surface extraction | |||
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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 |
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The goal of this module is to extract...
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 |
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initialized
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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 |
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Run the following command or add it in $HOME/.bashrc
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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). | ||
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`source $INSTALL/bin/setupAngioTKEnvironment.sh` |
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use
source $INSTALL/bin/setupAngioTKEnvironment.sh
@@ -32,7 +46,8 @@ Now, the exectutable `meshing_centerlinesmanagergui` can be launched directly. | |||
The arguments to provide are: | |||
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- `--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) | |||
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Thus, the typical command shoud be: |
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the typical command reads
@@ -1,12 +1,15 @@ | |||
= Center lines computing | |||
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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, |
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which have been defined using ...
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]). |
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use xref !!! the link here won't work
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.Distance comparison | ||
image::distance_comparison.jpg[] | ||
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== Troubleshooting | ||
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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. | ||
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link:Meshing_Module_Description.adoc[Go back to The Meshing Module] |
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use xref!
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`. |
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The executable is named ...
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. | ||
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link:Meshing_Module_Description.adoc[Go back to The Meshing Module] |
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use xref.
have a What next? section