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 the Meshing Module Description page.)

1. 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.)

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.

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.

2. 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.

Here again,INSTALL refers to the path where AngioTK was installed (see the building page)

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

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)

Thus, the typical command shoud be:

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

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 <home>/feel/meshing_centerlinesmanagergui/np_1/<model-name>_pointset.data

3. 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:

  • (optional) Prepare 2 different terminals, one for the CEGT, one for the center line generator.

3.1. 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)

  • 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.

    • 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.

3.2. 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.
    `--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.
    `--input.pointset.filename=pointset.data`
    `--output.directory=`
your desired output path

  • 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.

      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.

3.3. 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.