Re: [vmtk-users] overlaying model and centerlines in vmtk?

Tue, 13 Dec 2011 12:50:56 -0800 

Hi Anna,
Sorry, I should have been more specific, that command won't work if you start your pipe with vmtkcenterlines--you will get the error you had below. You need to start with vmtksurfacereader and pipe that in to vmtkcenterlines. Try this instead: 


vmtksurfacereader -ifile YourFileName.vtp --pipe vmtkcenterlines --pipe 
vmtkrenderer --pipe vmtksurfaceviewer -opacity 0.25 --pipe 
vmtksurfaceviewer -i @vmtkcenterlines.o -array MaximumInscribedSphereRadius



That should work. Note that when it executes the first 
vmtksurfaceviewer, you will just see your semi-opaque surface with no 
centerlines, and then you have to press the 'E' key to go to the next 
command and add in the centerlines. Press 'E' a second time when you are 
done to exit.


I hope this works. If it doesn't, can you paste in your full pipe command?

Ian



On 12/13/2011 2:16 PM, Hoppe, Anna L wrote:

Hi Ian,


When I pipe the command you provided after  my vmtkcenterlines command 
I get the following VMTK output/error:

.
.
.
Computing centerlines.
Done executing vmtkcenterlines.
Writing VTK surface file.
Output vmtkcenterlines members:
    Id = 0
    Centerlines = vtkPolyData
    RadiusArrayName = MaximumInscribedSphereRadius
    EikonalSolutionArrayName = EikonalSolutionArray
    EdgeArrayName = EdgeArray
    EdgePCoordArrayName = EdgePCoordArray
    CostFunctionArrayName = CostFunctionArray
    DelaunayTessellation = vtkUnstructuredGrid
    VoronoiDiagram = vtkPolyData
    PoleIds = vtkIdList

Creating vmtkRenderer instance.
Automatic piping vmtkrenderer
Parsing options vmtkrenderer
Explicit piping vmtkrenderer
Input vmtkrenderer members:
    Id = 0
    Disabled = 0
    WindowSize = [800, 600]
    PointSmoothing = 1
    LineSmoothing = 1
    PolygonSmoothing = 0

    Background = [0.10000000000000001, 0.10000000000000001, 
0.20000000000000001]

Executing vmtkrenderer ...
Done executing vmtkrenderer.
Output vmtkrenderer members:
    Id = 0
    vmtkRenderer = vmtkRenderer

Creating vmtkSurfaceViewer instance.
Automatic piping vmtksurfaceviewer
    vmtkRenderer = vmtkrenderer-0.vmtkRenderer
Parsing options vmtksurfaceviewer
    Opacity = 0.25
Explicit piping vmtksurfaceviewer
Input vmtksurfaceviewer members:
    Id = 0
    Disabled = 0
    Surface = None
    SurfaceInputFileName =
    vmtkRenderer = vmtkRenderer
    Display = 1
    Opacity = 0.25
    ArrayName =
    ScalarRange = [0.0, 0.0]
    Legend = 0
    Grayscale = 0
    FlatInterpolation = 0
    DisplayCellData = 0
    Color = [-1.0, -1.0, -1.0]
    LineWidth = 1
    LegendTitle =
    SurfaceOutputFileName =
Executing vmtksurfaceviewer ...
Error: no Surface.


Am I supposed to be including an -ifile vesselnetwork.vtk after the 
first vmtksurfaceviewer command?


Thanks,
Anna

------------------------------------------------------------------------
*From:* Ian Campbell [iancampb...@gatech.edu]
*Sent:* Tuesday, December 13, 2011 11:39 AM
*To:* vmtk-users@lists.sourceforge.net
*Subject:* Re: [vmtk-users] overlaying model and centerlines in vmtk?

Hi Anna,


Funny you should ask--I was just doing this yesterday. If you would 
like to view a semi-transparent vessel surface with centerlines 
inside, add this command to your pipe after the vmtkcenterlines 
command and its arguments:


--pipe vmtkrenderer --pipe vmtksurfaceviewer -opacity 0.25 --pipe 
vmtksurfaceviewer -i @vmtkcenterlines.o -array MaximumInscribedSphereRadius


The vmtkrenderer command creates a persistent viewer instance, and the 
two following vmtksurfaceviewer plotting commands will be overlaid 
together in the window. You can play around with the opacity and array 
options to your liking. There is a very nice tutorial on centerlines 
on the VMTK website that does a much better job of explaining all this 
than I can: http://www.vmtk.org/Tutorials/Centerlines



Alternatively, if you would like to export your centerlines for 
external viewing in a program like Paraview, you can add -ofile 
filename.vtp to the vmtkcenterlines arguments to create a .vtp 
geometry file of just the centerlines. So your command would look 
something like


vmtksurfacereader -ifile input.vtp --pipe vmtkcenterlines -ofile centerlines.vtp


Then you can load your input.vtp file (or whatever file format your 
surface data might be...if not something Paraview can load, try 
exporting it to .vtp from VMTK using vmtksurfacewriter) and then load 
your centerlines.vtp files together in Paraview, set the surface 
opacity to some low value like 0.3, and you will be able to view your 
centerlines inside your surface.


I hope this helps,
Ian

On 12/13/2011 12:18 PM, Hoppe, Anna L wrote:

Hi VMTK users,


I am new to VMTK and I was wondering if there was a way in VMTK to 
view a vessel network overlayed on the corresponding centerlines?  
Right now I have successfully computed the centerlines for my vessel 
network using the vmtkcenterlines command, I have also viewed the 
computed centerlines using vmtkcenterlineviewer, I just wanted to 
overlay the vessel surface and the computed centerlines to check to 
see if they are correct...


Thanks for your help,
Anna


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