Dear Luca,
Thanks for Your reply.
On 18/09/12 11:47, Luca Antiga wrote:
Hi Roman,
I'm not sure, it could be the fact that Paraview shows cell-based data by
coloring the whole cell with a uniform color, but it may also be that there's
a bug with setting topology values somewhere.
Can you share the network file so that I can take a direct look?
Sure, it's attached.
Many thaks for looking into this.
Roman
On Sep 14, 2012, at 3:26 PM, Dr. Roman Grothausmann wrote:
On 03/09/12 11:39, Luca Antiga wrote:
Dear Roman,
thanks for your appreciation of vmtk, it's good to have you onboard.
It is indeed possible to use manually specified endpoints for vmtkcenterlines,
but there's some glue code that needs to be written in-between.
vmtknetworkextraction outputs a polydata dataset composed of interconnected
lines, whose endpoints are the coordinates you're interested in. In order to
extract endpoints from the Network you should look for cells that have either
one of the Topology array values equal to -1 and extract the corresponding
coordinates.
I tried to check this with paraview and its python-calculator using:
(Topology[:,0] +1) * (Topology[:,1] +1) and colouring the result with a colour
range from 0 to 1 (blue to red, see screen shot). It seems not all cells
containing endpoints have one of the topology values == -1, or have I done
something wrong?
Thanks for any help or hints
Roman
Once you have the coordinates, you can specify them even at the command
line using vmtkcenterlines using -seedselector pointlist -seeds x y z -targets
x0 y0 z0 x1 y1 z1 ...
Let me know if you need support/advice for the extraction of the endpoints. In
fact this could be a nice addition to vmtk.
Best,
Luca
On Sep 3, 2012, at 11:26 AM, Dr. Roman Grothausmann wrote:
Dear mailing list members,
vmtk is really cool. I'm just about getting to know its features
especially those for centre line extraction.
I found this email from Luca:
http://sourceforge.net/mailarchive/message.php?msg_id=29119553 to use
vmtknetworkextraction for this purpose.
Now I wonder, if it is possible to use the endpoints of the result of
vmtknetworkextraction as the endpoints for vmtkcenterlines?
Or is there a way to save the manually selected start and end points of
vmtkcenterlines to use these when experimenting with other options of
vmtkcenterlines?
Many thanks for vmtk and for any help or hints.
Roman
--
Dr. Roman Grothausmann
Tomographie und Digitale Bildverarbeitung
Tomography and Digital Image Analysis
Institut für Funktionelle und Angewandte Anatomie, OE 4120
Medizinische Hochschule Hannover
Carl-Neuberg-Str. 1
30625 Hannover
Tel. +49 511 532-9574
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Tomographie und Digitale Bildverarbeitung
Tomography and Digital Image Analysis
Institut für Funktionelle und Angewandte Anatomie, OE 4120
Medizinische Hochschule Hannover
Carl-Neuberg-Str. 1
30625 Hannover
Tel. +49 511 532-9574
<endpoints.jpg>------------------------------------------------------------------------------
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Tomographie und Digitale Bildverarbeitung
Tomography and Digital Image Analysis
Institut für Funktionelle und Angewandte Anatomie, OE 4120
Medizinische Hochschule Hannover
Carl-Neuberg-Str. 1
30625 Hannover
Tel. +49 511 532-9574
<?xml version="1.0"?>
<VTKFile type="PolyData" version="0.1" byte_order="LittleEndian" compressor="vtkZLibDataCompressor">
<PolyData>
<Piece NumberOfPoints="317" NumberOfVerts="0" NumberOfLines="68" NumberOfStrips="0" NumberOfPolys="0" >
<PointData>
<DataArray type="Float64" Name="Radius" format="appended" RangeMin="0" RangeMax="9.6867031594" offset="0" />
</PointData>
<CellData>
<DataArray type="Int64" Name="Topology" NumberOfComponents="2" format="appended" RangeMin="1" RangeMax="64.350602173" offset="2336" />
</CellData>
<Points>
<DataArray type="Float32" Name="Points" NumberOfComponents="3" format="appended" RangeMin="92.762125182" RangeMax="192.17313621" offset="2632" />
</Points>
<Verts>
<DataArray type="Int64" Name="connectivity" format="appended" RangeMin="" RangeMax="" offset="6420" />
<DataArray type="Int64" Name="offsets" format="appended" RangeMin="" RangeMax="" offset="6436" />
</Verts>
<Lines>
<DataArray type="Int64" Name="connectivity" format="appended" RangeMin="" RangeMax="" offset="6452" />
<DataArray type="Int64" Name="offsets" format="appended" RangeMin="" RangeMax="" offset="7200" />
</Lines>
<Strips>
<DataArray type="Int64" Name="connectivity" format="appended" RangeMin="" RangeMax="" offset="7440" />
<DataArray type="Int64" Name="offsets" format="appended" RangeMin="" RangeMax="" offset="7456" />
</Strips>
<Polys>
<DataArray type="Int64" Name="connectivity" format="appended" RangeMin="" RangeMax="" offset="7472" />
<DataArray type="Int64" Name="offsets" format="appended" RangeMin="" RangeMax="" offset="7488" />
</Polys>
</Piece>
</PolyData>
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</AppendedData>
</VTKFile>
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