AW: [Insight-users] I need help please!! DeformableMesh3DFilter
Waltraud Henrich
henrich@ira.uka.de
Tue, 21 Jan 2003 15:33:50 +0100
Hallo Ting,
first of all I want to thank you for your reply.
Actually I would like to work with the DeformableMesh3DFilter class but
still have some trouble with it. Maybe you can give me a hand on that. =
There
are a few questions I would like to ask you:
I have a 3D image which I want to segment and I don't think that I have =
to
create the image.=20
In some place I've read that I have to create a binary image. But I =
don't
see how to do so? What is that for? Do I really need this for the
segmentation at all?=20
The other day (20th January), I've read that the binary image resulted =
from
a initial segmentation using the confidence connected image filter. Is =
that
a good solution? Can you think of a better way to get the binary image =
?
Could you explain how the segmentation works in itk ?=20
( What is my result?... (m_bmmeshsource)???)
Thanks a lot in advance.
Waltraut
-----Urspr=FCngliche Nachricht-----
Von: Ting Chen [mailto:chenting@graphics.cis.upenn.edu]
Gesendet: Sonntag, 12. Januar 2003 20:24
An: Waltraud Henrich
Cc: insight-users@public.kitware.com
Betreff: Re: [Insight-users] I need help please!! =
DeformableMesh3DFilter
HI! Waltraut,
There are some major change in itkDeformableTest in the past few weeks.
1. the itkdeformable3Dmeshfilter no longer support balloon force (I may =
add
the balloon force in again some time later), so there is no need for =
the
m_Center parameters anymore. Now the model is driven by the gradient =
force
derived from the original image. We are using marhcing cubes method to
create the initial deformable mesh. However, it is possible that the =
mesh
and gradient is of different size. ng
For example, when we segment a 100 by 100 image. before we calculate =
the
gradient map, we shrink it with the scale (2, 2) to reduce the =
processing
time, the reuslt gradient map is of the size 50 by 50 now. and the
deformable mesh is still created based on the binary mask in a 100 by =
100
image. so now we need a (0.5, 0.5) m_scale to make the mesh and =
gradient map
work together.
2. a itk2DDeformabletest is added in itk, which shows how to use
itkspheresource and itkballoonforcefilters in 2D, however, by making =
some
modifications it can be converted into 3D. if you like, I can also do =
the
work for you.
please contact me if there are further questions
ting
----- Original Message -----
From: "Waltraud Henrich" <henrich@ira.uka.de>
To: "'Ting Chen '" <chenting@graphics.cis.upenn.edu>
Cc: <insight-users@public.kitware.com>
Sent: Sunday, January 12, 2003 6:02 AM
Subject: AW: [Insight-users] I need help please!! =
DeformableMesh3DFilter
>
>
> Hallo
>
>
> I have recognized that if i add SetScale() then I get a sphere. But =
the
> speher is allways the same wherever I click on the image. When I =
click on
> the image I get my x,y,z coordinates for my SetCenter(x,y,z).
> I unterstood it like this: that when I click on the image the sphere
begins
> to grow biginning from that point up to the gradient image. Is that =
right?
> I have noticed that m_Center appeared in the old version of
> itkDeformableMesh3DFilter.txx that is:
> m_ObjectLabel =3D m_Potential->GetPixel(m_Center)
> but it doesen't appear at all in the new Version. Why?
> But in the new Version m_Scale appears not so in the old version.
> My last version is from 28.11.2002.
>
> Thanks a lot.
>
> Waltraut Henrich
>
> -----Originalnachricht-----
> Von: Ting Chen
> An: Waltraud Henrich
> Gesendet: 09.01.03 22:02
> Betreff: Re: [Insight-users] I need help please!! =
DeformableMesh3DFilter
>
> Hi! I write the code for deformable 3D mesh. I checked the code after
> reviewing your last email.
>
> I checked in a new version of itkDeformableTest and
> itkedeformable3Dmeshfilter on 12/19 to fix some possible bugs. I am
> sorry it
> did not solve your problem.
> the fact that I did not develope an itk2vtk application make it
> difficult
> for me to understand what could be the possible problems.
> I will try explain the code as clear as possible to help you to =
search
> for
> the problems.
>
>
> ----- Original Message -----
> From: "Waltraud Henrich" <henrich@ira.uka.de>
> To: <insight-users@public.kitware.com>
> Sent: Thursday, January 09, 2003 5:31 AM
> Subject: [Insight-users] I need help please!! DeformableMesh3DFilter
>
>
> >
> > Hallo,
> >
> > at 16 December I had written my problem in the mailing list.
> Unfortunately
> > I received still no answer and I did not repair the problem .
> > I have a newer version of ITK and I downloaded =
InsightToolkit-1.0.0
> to
> > 28.11.2002.
> > Where can I look for the errors?
> > What are the meaning of the parameters: Stiffness, Scale,Time Step =
and
> Step
> > Threshold in the ItkDeformableMesh3DFilter?
> stiffness help to set the stiffness on the deformable surface.
> the scale factors are used to make the deformable mesh with with
> gradient
> maps of different size.
>
> the time step control the magnitude of deformation in each iteration.
> the
> step threshold define however steps is need to stop the filter. I am =
not
> sure if this parameter is still in the newest version of itk.
> one anothere thing is that I notice you are using a setcenter =
function,
> which are not included in 12/19's update. i am not sure what could be
> the
> problem, did you use cvs to update the code from time to time?
>
> hope to talk with more about the existing problems. thanks for your
> efforts.
>
>
> ting
>
>
>
> > In the example itkDeformableTest.cxx it does not use these =
parameters.
> Why?
> they ARE used in itkdeformabletest, I checked in a new verion of
> itkdeformabletest on 12/19 and I used all theses parameter there.
>
>
> > Is sufficient in such a way?
> > I have tried it also without these parameters and it does not go.
> > I tried with this parameter:
> >
> >
> > double m_stiff[2];
> > m_stiff[0]=3D0.001;
> > m_stiff[1]=3D0.04;
> >
> > myIndexType m_center=3D{{SEEDX, SEEDY, SEEDZ}};
> >
> > Deformable3DFilterType::Pointer m_bfilter =3D
> > Deformable3DFilterType::New();
> >
> > m_bfilter->SetCenter(m_center);
> > m_bfilter->SetStiffness(m_stiff);
> > m_bfilter->SetTimeStep(0.001);
> > m_bfilter->SetStepThreshold(20);
> > m_bfilter->SetGradient(gradient->GetOutput());
> > m_bfilter->SetInput(m_spheresource->GetOutput());
> > m_bfilter->SetInput(initmesh);
> > m_bfilter->Update();
> >
> > The mail from 16.12 was:
> > "
> > 1) I work with itkDeformableMesh3DFilter and now I get the
> OutputWindow.
> >
> > Debug: In
> >
> =
d:\programme\development\insighttoolkit-1.0.0\code\common\itkpointset.tx=
> x,
> > line 74
> > Mesh (088D9178): returning Points container of VectorContainer
> (013B4AA8)
> > Reference Count: 2
> > Modified Time: 9838
> > Debug: Off
> > Observers:
> > none
> >
> >
> >
> > Debug: In
> >
> =
D:\Programme\Development\InsightToolkit-1.0.0\Code\Common\itkDataObject.=
> cxx,
> > line 239
> > Mesh (088D9178): disconnecting source 088D7D98, source output =
index 0
> >
> > Debug: In
> >
> =
D:\Programme\Development\InsightToolkit-1.0.0\Code\Common\itkObject.cxx,=
> > line 288
> > Mesh (088D9178): UnRegistered, ReferenceCount =3D 0
> >
> > Debug: In
> > =
d:\programme\development\insighttoolkit-1.0.0\code\common\itkmesh.txx,
> line
> > 1061
> > Mesh (088D9178): Mesh Destructor
> >
> > Debug: In
> > =
d:\programme\development\insighttoolkit-1.0.0\code\common\itkmesh.txx,
> line
> > 1078
> > Mesh (088D9178): Mesh ReleaseCellsMemory method
> >
> > Debug: In
> > =
d:\programme\development\insighttoolkit-1.0.0\code\common\itkmesh.txx,
> line
> > 1104
> > Mesh (088D9178): m_CellsContainer->GetReferenceCount()=3D 1
> >
> > Debug: In
> > =
d:\programme\development\insighttoolkit-1.0.0\code\common\itkmesh.txx,
> line
> > 1149
> > Mesh (088D9178): CellsAllocatedDynamicallyCellByCell
> >
> > Debug: In
> > =
d:\programme\development\insighttoolkit-1.0.0\code\common\itkmesh.txx,
> line
> > 1168
> > Mesh (088D9178): Mesh ReleaseBoundariesMemory method
> >
> > Debug: In
> > =
d:\programme\development\insighttoolkit-1.0.0\code\common\itkmesh.txx,
> line
> > 1195
> > Mesh (088D9178): Mesh ReleaseBoundariesMemory(unsigned int) method
> >
> > Debug: In
> > =
d:\programme\development\insighttoolkit-1.0.0\code\common\itkmesh.txx,
> line
> > 1286
> > Mesh (088D9178): Boundaries already deleted.
> >
> > Debug: In
> > =
d:\programme\development\insighttoolkit-1.0.0\code\common\itkmesh.txx,
> line
> > 1195
> > Mesh (088D9178): Mesh ReleaseBoundariesMemory(unsigned int) method
> >
> > Debug: In
> > =
d:\programme\development\insighttoolkit-1.0.0\code\common\itkmesh.txx,
> line
> > 1286
> > Mesh (088D9178): Boundaries already deleted.
> >
> > Debug: In
> > =
d:\programme\development\insighttoolkit-1.0.0\code\common\itkmesh.txx,
> line
> > 1195
> > Mesh (088D9178): Mesh ReleaseBoundariesMemory(unsigned int) method
> >
> > Debug: In
> > =
d:\programme\development\insighttoolkit-1.0.0\code\common\itkmesh.txx,
> line
> > 1286
> > Mesh (088D9178): Boundaries already deleted.
> >
> > Debug: In
> >
> =
D:\Programme\Development\InsightToolkit-1.0.0\Code\Common\itkObject.cxx,=
> > line 447
> > Object (088D9178): Destructing!
> >
> >
> > 2) When I save vtkUnstructuredGrid in a file and when I look this =
file
> I
> get
> > following:
> >
> > # vtk DataFile Version 3.0
> > vtk output
> > ASCII
> > DATASET UNSTRUCTURED_GRID
> > POINTS 402 float
> > -1.#INF -1.#INF 1.#INF -1.#INF -1.#INF 1.#INF -1.#INF -1.#INF =
1.#INF
> > -1.#INF -1.#INF 1.#INF -1.#INF -1.#INF 1.#INF -1.#INF -1.#INF =
1.#INF
> > -1.#INF -1.#INF 1.#INF -1.#INF -1.#INF 1.#INF -1.#INF -1.#INF =
1.#INF
> > -1.#INF -1.#INF 1.#INF -1.#INF -1.#INF 1.#INF -1.#INF -1.#INF =
1.#INF
> > -1.#INF -1.#INF 1.#INF -1.#INF -1.#INF 1.#IN.......etc
> >
> > My problem is that in vtk2itkDouble.cxx this coordinates are #INF..
> >
> > pcoordinates[0] =3D pp[0];
> > pcoordinates[1] =3D pp[1];
> > pcoordinates[2] =3D pp[2];
> >
> > Can you tell me where the problem is?
> >
> > 3) I can disply my SphereSource with vtk2itkDouble. The coordinates
> are OK
> > here."
> >
> > Thanks a lot.
> >
> > Waltraut Henrich
> >
> >
> >
> >
> >
> > _______________________________________________
> > Insight-users mailing list
> > Insight-users@public.kitware.com
> > http://public.kitware.com/mailman/listinfo/insight-users
> >
>
> _______________________________________________
> Insight-users mailing list
> Insight-users@public.kitware.com
> http://public.kitware.com/mailman/listinfo/insight-users