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

docs/modules/ROOT/pages/meshing/module-2-surface-from-image.adoc

@@ -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 of this module is to extract and create a 3D model of the surface of the blood
+vessels, using a level set method.
+The level sets are initialized using either the isosurface of a given intensity
+value (*isosurface* method) or a given intensity range (*threshold* method).
 A marching cube algorithm then extracts the surface.
 
 == Surface subdivision
 
 The resulting surface can be subdivided using 3 methods:
 
-*linear*:: (original points are preserved and linear subdivisions are created in between),
+*linear*:: (original points are preserved and linear subdivisions are created in
+  between),
 *butterfly*:: (original points are preserved and new points are added)
 *loop*:: (original points are displaced and new points are added).
 
-NOTE: The difference between the last two is the smoothness they tend to bend the surface to: C^1 for *butterfly*, C^2 for *loop*.
+NOTE: The difference between the last two is the smoothness they tend to bend
+the surface to: C^1 for *butterfly*, C^2 for *loop*.
 
 The executable we use is named `meshing_surfacefromimage`.
 
@@ -26,12 +30,33 @@ The executable we use is named `meshing_surfacefromimage`.
 - `--input.image.filename`: (string) Input image
 - `--output.path`: (string) Output file
 - `--config-file`: (string) Configuration file
-- `--force-rebuild=1` :(int) 0 to avoid computing if target file already exists, 1 to overwrite it
-- `--pre-process.resize-from-reference-image.path`: (string) Reference image to resize.
-- `--method=threshold` (string) method to use for level set initialization among: threshold or isosurface- `--image-fusion.operator=max` (string) method operator among : max, min, multiply, substract- `--threshold.lower` (double) lower bound for the threshold limit- `--threshold.higher` (double) higher bound for the threshold limit- `--apply-connectivity.largest-region=1` (bool) 1 to keep the *n* largest connected regions, 0 to keep everything- `--apply-connectivity.number=1` (int) Number *n* used above.
-- `--post-process.subdivide-surface` (bool) 1 to enable surface subdivision, 0 to disable it
-- `--post-process.smooth-surface` (bool) 1 to enable surface smoothing, 0 to disable it
-- `--subdivide-surface.method=butterfly` (string) Name of the surface subdivision method to use, among: linear, butterfly, loop- `--subdivide-surface.subdivisions=1` (int) Number of subdivisions- `--smooth-surface.method=taubin` (string) Name of the surface smoothing method to use, among : taubin, laplace- `--smooth-surface.iterations=30` (int) Number of iterations- `--smooth-surface.taubin.passband=0.1` (double) Low-pass filter threshold for the Taubin method- `--smooth-surface.laplace.relaxation=0.01` (double) Relaxation factor for the Laplace method
+- `--force-rebuild=1` :(int) 0 to avoid computing if target file already exists,
+ 1 to overwrite it
+- `--pre-process.resize-from-reference-image.path`: (string) Reference image to
+ resize.
+- `--method=threshold` (string) method to use for level set initialization
+among: threshold or isosurface.
+- `--image-fusion.operator=max` (string) method operator among : max, min,
+multiply, substract.
+- `--threshold.lower` (double) lower bound for the threshold limit.
+- `--threshold.higher` (double) higher bound for the threshold limit.
+- `--apply-connectivity.largest-region=1` (bool) 1 to keep the *n* largest
+connected regions, 0 to keep everything.
+- `--apply-connectivity.number=1` (int) Number *n* used above.
+- `--post-process.subdivide-surface` (bool) 1 to enable surface subdivision,
+0 to disable it
+- `--post-process.smooth-surface` (bool) 1 to enable surface smoothing, 0 to
+disable it
+- `--subdivide-surface.method=butterfly` (string) Name of the surface
+subdivision method to use, among: linear, butterfly, loop.
+- `--subdivide-surface.subdivisions=1` (int) Number of subdivisions.
+- `--smooth-surface.method=taubin` (string) Name of the surface smoothing
+method to use, among : taubin, laplace.
+- `--smooth-surface.iterations=30` (int) Number of iterations.
+- `--smooth-surface.taubin.passband=0.1` (double) Low-pass filter threshold for
+the Taubin method.
+- `--smooth-surface.laplace.relaxation=0.01` (double) Relaxation factor for the
+Laplace method
 
 
 == Troubleshooting
@@ -42,4 +67,4 @@ Please report any problem you may encounter.
 
 
 
-link:Meshing_Module_Description.adoc[Go back to The Meshing Module]
+xref:Meshing_Module_Description.adoc[Go back to The Meshing Module]

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

@@ -1,97 +1,147 @@
 = The Center line Editing Graphical Tool
 
-The Centerline Editing Graphical Tool's (CEGT) purpose is to assist the user in centerlines creation and edition.
-At this time (november 2016), it essentially remains a manual task, and a critical step in the pipeline (see the Center lines definition section in link:Meshing_Module_Description.adoc[the Meshing Module Description page].)
+The Centerline Editing Graphical Tool's (CEGT) purpose is to assist the user in
+centerlines creation and edition.
+At this time (November 2016), it essentially remains a manual task, and a
+critical step in the pipeline (see the Center lines definition section in
+  xref:Meshing_Module_Description.adoc[the Meshing Module Description page].)
 
 == Overview
 
-Although the CEGT is started using command line (and outputs useful messages there too), all operations are performed in its GUI (graphical user interface.)
+Although the CEGT is started using command line (and outputs useful messages
+there too), all operations are performed in its GUI (graphical user interface.)
 
-The user is presented with the initial blood vessels mesh generated in the previous step.
+The user is presented with the initial blood vessels mesh generated in the
+previous step.
 
 The goal is to define center lines for each vein/artery.
-To define a center line, the user has to define key points along the desired center line, and pair them along the way, in order to create a polygonal chain through the blood vessel.
+To define a center line, the user has to define key points along the desired
+center line, and pair them along the way, in order to create a polygonal chain
+through the blood vessel.
 
-During this process, the user also adjusts the radius of the inscribed sphere for each key point.
+During this process, the user also adjusts the radius of the inscribed sphere
+for each key point.
 
-When all the center lines keypoints are well defined, the next pipeline module generates the center lines and carries on automatically.
+When all the center lines keypoints are well defined, the next pipeline module
+generates the center lines and carries on automatically.
 
 == Starting command line
 
-The CEGT is located in `$INSTALL/Modules/Meshing/bin/meshing_centerlinesmanagergui`.
-An optional but helping first step is to export all environment variables using the appropriate supplied bash script located at `$INSTALL/bin/setupAngioTKEnvironment.sh.`
+The CEGT is located in
+`$INSTALL/Modules/Meshing/bin/meshing_centerlinesmanagergui`.
+An optional but helping first step is to export all environment variables
+using the appropriate supplied bash script located at
+`$INSTALL/bin/setupAngioTKEnvironment.sh.`
 
-Here again,`INSTALL` refers to the path where AngioTK was installed (see link:Building.adoc[the building page])
+Here again,`INSTALL` refers to the path where AngioTK was installed
+(see xref:Building.adoc[the building page])
 
-Simply run this command or put it in your `.bashrc` (which is more convenient for repeated use).
+Run the following command or add it to `$HOME/.bashrc`
 
-`source $INSTALL/bin/setupAngioTKEnvironment.sh`
+[source, sh]
+----
+source $INSTALL/bin/setupAngioTKEnvironment.sh
+----
 
 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:
+Thus, the typical command reads:
 
-`meshing_centerlinesmanagergui --input.surface.path model.stl --input.point-pair.path pointpair.data`
+[source, sh]
+----
+meshing_centerlinesmanagergui \
+  --input.surface.path model.stl \
+  --input.point-pair.path pointpair.data
+----
 
 for example, using the provided Phantom example:
 
-`meshing_centerlinesmanagergui --input.surface.path Phantom/angiotk/surfacefromimage/model.stl --input.point-pair.path pointpair.data`
+[source, sh]
+----
+meshing_centerlinesmanagergui \
+  --input.surface.path Phantom/angiotk/surfacefromimage/model.stl \
+  --input.point-pair.path pointpair.data
+----
 
-IMPORTANT: when no point-pair file is specified, saving your progress will result is creation of two files: `<home>/feel/meshing_centerlinesmanagergui/np_1/<model-name>_pointpair.data`
+IMPORTANT: Saving your progress will result in the creation of two files:
+`<home>/feel/meshing_centerlinesmanagergui/np_1/<model-name>_pointpair.data`
 `<home>/feel/meshing_centerlinesmanagergui/np_1/<model-name>_pointset.data`
+*This means that your original file will NOT be modified, unless you manually
+replace it!*
+
 
 == Recommended workflow
 
-At this time (May 2016), center line generation is completely dependent and very sensitive to the provided pointsets.
-Therefore, a cautious stepwise workflow is strongly advised, and you should frequently check you progress with the center line generator and ParaView:
+At this time (May 2016), center line generation is completely dependent and very
+ sensitive to the provided pointsets.
+Therefore, a cautious stepwise workflow is strongly advised, and you should
+frequently check you progress with the center line generator and ParaView:
 
-- (optional) Prepare 2 different terminals, one for the CEGT, one for the center line generator.
+- (optional) Prepare 2 different terminals, one for the CEGT, one for the
+center line generator.
 
 === In the center line editing graphical tool
 - Start the GUI in one terminal
-- (optional) Press the 'h' key to display help (this should toggle an on-screen list of commands)
+- (optional) Press the 'h' key to display help (this should toggle an on-screen
+  list of commands)
 - Use click&drag to rotate the mesh around, identify a blood vessel to work on.
 - Press the '2' key to switch to _point insertion mode_
-    * Click on the mesh near the end of the chosen blood vessel. This should create a sphere which center is the key point.
-    * Adjust the position and size of the sphere using the following keys: left/right, up/down, o/l and p/m (all of which are also visible in the on-screen help)
-    * Press 'y' to validate the sphere parameters. To further modify these, simply click back on the sphere and proceed as if it was a newly created one.
+    * Click on the mesh near the end of the chosen blood vessel.
+    This should create a sphere which center is the key point.
+    * Adjust the position and size of the sphere using the following keys:
+    left/right, up/down, o/l and p/m (all of which are also visible in the
+      on-screen help)
+    * Press 'y' to validate the sphere parameters.
+    To further modify these, simply click back on the sphere and proceed as if
+    it was a newly created one.
     * To connect or disconnect two points, click on both of them and press 'd'.
-- After adding/connecting a few points, you should save your work by pressing 's'. This will write two files: a point-pair file a point-set file. Now you can check center line generation.
+- After adding/connecting a few points, you should save your work by pressing
+'s'.
+This will write two files: a point-pair file a point-set file.
+Now you can check center line generation.
 
 === In the center line generator
 
-- Launch the center line generator with the relevant options to test your center line definition points:
-
-    `meshing_centerlines`
-
-    `--input.surface.filename=model.stl`
-    this is the model used in the CEGT.
-
+==== Command line
+Launch the center line generator with the relevant options to test your center
+ line definition points:
 
-    `--input.pointpair.filename=pointpair.data`
-    use this option to use a point-pair file (recommended), or the next one to use a point-set file.
+[source,sh]
+----
+meshing_centerlines \
+  --input.surface.filename=model.stl \ <1>
+  --input.pointpair.filename=pointpair.data \ <2>
+  --input.pointset.filename=pointset.data \ <3>
+  --output.directory=<outputpath> \ <4>
+----
+<1> This is the 3D model used in the CEGT.
+<2> Use a point-pair file (recommended),
+<3> or a point-set file.
+<4> Your desired output path
 
-    `--input.pointset.filename=pointset.data`
+==== Troubleshooting
 
-    `--output.directory=`
-    your desired output path
+Pay attention to the following error, during the `Computing centerlines` step:
 
-- Pay attention to the following errors:
-    * During the `Computing centerlines `step:
-        `Warning: In /data/software/src/vmtk/vtkVmtk/ComputationalGeometry/`
-        `vtkvmtkSteepestDescentLineTracer.cxx, line 240`
-        `vtkvmtkSteepestDescentLineTracer (0x24ef850): `
-        `Degenerate descent detected. Target not reached.`
+[source,sh]
+----
+Warning: In /data/software/src/vmtk/vtkVmtk/ComputationalGeometry/
+vtkvmtkSteepestDescentLineTracer.cxx, line 240
+vtkvmtkSteepestDescentLineTracer (0x24ef850):
+Degenerate descent detected. Target not reached.
+----
 
-        This means the center line is invalid and won't be used.
-        Try changing the positions of the input points or adding more points in between.
+This means the center line is invalid and won't be used.
+Try changing the positions of the input points or adding more points in between.
 
 
 === In ParaView
 
-- Check your results by opening the produced `model_centerlines.vtk` in ParaView. Go back to the CEGT to edit your points if necessary, or to create new ones.
+- Check your results by opening the produced `model_centerlines.vtk` in ParaView.
+Go back to the CEGT to edit your points if necessary, or to create new ones.

docs/modules/ROOT/pages/meshing/module-4-centerlines-computing.adoc

@@ -1,12 +1,14 @@
 = 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 have been defined using xref:Module_3_CenterlinesGUITool.adoc[the center lines editing tool]).
 
-The executable we use is named `meshing_centerlines`.
+The executable we use is named `angiotk_meshing_centerlines`.
 
 == Supported file formats
 
-- input: a 3 model in STereoLithography (.stl) and a text file containing point pairs (pointpair.data) or a gmsh-readable file (.geo or 1D mesh (.msh))
+- input: a 3D model in STereoLithography (.stl) and a text file containing point
+pairs (pointpair.data) or a gmsh-readable file (.geo or 1D mesh (.msh))
 - output: a VTK file (.vtk)
 
 == Parameters
@@ -15,7 +17,9 @@ The executable we use is named `meshing_centerlines`.
 - `--input.pointpair.filename`: (string) Input point pairs text file
 - `--output.directory`: (string) Output directory for the VTK file
 - `--config-file`: (string) Configuration file
-- `--force-rebuild=1`: (int) 0 to avoid computing if target file already exists, 1 to overwrite it
-- `--delaunay-tessellation.output.directory`: (string) Output directory for the Delaunay tessellation
-- `--delaunay-tessellation.force-rebuild=1`: (int) 0 to avoid computing if target file already exists, 1 to overwrite it
-
+- `--force-rebuild=1`: (int) 0 to avoid computing if target file already exists,
+ 1 to overwrite it
+- `--delaunay-tessellation.output.directory`: (string) Output directory for the
+Delaunay tessellation
+- `--delaunay-tessellation.force-rebuild=1`: (int) 0 to avoid computing if
+target file already exists, 1 to overwrite it

docs/modules/ROOT/pages/meshing/module-5-centerlines-merging.adoc

@@ -11,23 +11,34 @@ This is done by `meshing_centerlinesmanager`
 == Parameters
 
 - `--input.surface.filename`: (string) Input surface
-- `--input.centerlines.filename`: (string) Input center line (add this once for each center line file to merge)
+- `--input.centerlines.filename`: (string) Input center line (add this once for
+  each center line file to merge)
 - `--output.directory`: (string) Output directory for the VTK file
 - `--config-file`: (string) Configuration file
-- `--force-rebuild=1`: (int) 0 to avoid computing if target file already exists, 1 to overwrite it
-- `--delaunay-tessellation.output.directory`: (string) Output directory for the Delaunay tessellation
-- `--delaunay-tessellation.force-rebuild=1`: (int) 0 to avoid computing if target file already exists, 1 to overwrite it
+- `--force-rebuild=1`: (int) 0 to avoid computing if target file already exists,
+ 1 to overwrite it
+- `--delaunay-tessellation.output.directory`: (string) Output directory for the
+Delaunay tessellation
+- `--delaunay-tessellation.force-rebuild=1`: (int) 0 to avoid computing if
+target file already exists, 1 to overwrite it
 - `remove-branch-ids` (vector of int) Optional, branch IDs to remove
-- `--threshold-radius.min=-1`: (double) minimum radius- `--threshold-radius.max=-1`: (double) maximum radius- `--avoid-tubular-colision.apply=0`: (bool) 1 to enable tubular collisions avoidance mechanism, 0 to disable it
-- `--avoid-tubular-colision.distance-min=0.4`: (double) minimum distance between tubular branches (to avoid collisions)
-- `--avoid-tubular-colision.radius-min=0.4`: (double) minimum radius (to avoid collisions)
-- `--smooth-resample.apply=1`: (bool) 1 to enable smoothing resampling, 0 to disable it
+- `--threshold-radius.min=-1`: (double) minimum radius
+- `--threshold-radius.max=-1`: (double) maximum radius
+- `--avoid-tubular-colision.apply=0`: (bool) 1 to enable tubular collisions
+avoidance mechanism, 0 to disable it
+- `--avoid-tubular-colision.distance-min=0.4`: (double) minimum distance between
+ tubular branches (to avoid collisions)
+- `--avoid-tubular-colision.radius-min=0.4`: (double) minimum radius (to avoid
+   collisions)
+- `--smooth-resample.apply=1`: (bool) 1 to enable smoothing resampling, 0 to
+disable it
 - `--smooth-resample.geo-points-spacing=4.0`: (double) spacing between points
 - `--smooth-resample.mesh-size=1.0`: (double)
 
 == Troubleshooting
 
 Collisions may happen depending on blood vessels radius and proximity.
-Adjusting *avoid-tubular-colision.radius-min* and *avoid-tubular-colision.distance-min* should solve the problem.
+Adjusting `avoid-tubular-colision.radius-min` and
+`avoid-tubular-colision.distance-min` should solve the problem.
 
-link:Meshing_Module_Description.adoc[Go back to The Meshing Module]
+xref:Meshing_Module_Description.adoc[Go back to The Meshing Module]