Hi Lia,
> Dear Luca,
>
> I decided not to convert into C++, for now. It's not worth it.
>
> Now i'm facing two problems: is there a way to automatize some parameters? I
> would like to know if i can change the python code, so i dont need to input
> the parameters manually at the console. In the vmtkimagevoiselector i can
> specify the coordinates of my cube, and if i could insert them in the code
> it became easier. Same thing with the vmtklevelsetsegmentation. The
> parameters are always the same, so can i insert them into the code? And how
> do i do that?
The best way to do what you want is to write a script that calls vmtk scripts
and passing the right parameters to them.
For instance, vmtkimagevoiselector accepts one argument -boxbounds
vmtkimagevoiselector -ifile foo.mha -boxbounds 100.0 12.0 56.0 58.0 34.0 37.0
-ofile foo_voi.mha
where box bounds is x_min x_max y_min y_max z_min z_max
Now, if you create a text file with the above line, say myscript.txt, and call
vmtk --file myscript.txt
the script will execute.
For a more advanced interaction with the PypeS internals directly from a Python
script you might write, you can take a look at this tutorial
http://www.vmtk.org/Tutorials/PypesProgrammatically/
You can also create your own scripts and include them in a pipe together with
standard vmtk scripts:
http://www.vmtk.org/Tutorials/PypesAdvanced/
> The other issue is: I want to measure the diameter of the ascending aorta in
> nine specifics points. I computed the centerline that gave me the central
> points and the radius in all points since the source till the target! But i
> just need nine points. Is there a way to do that?
The first thing to understand is how do you know what are the 8 points? Are
they going to be selected interactively?
> For this project i'm doing a lot of steps.. If i could avoid the most of
> them, it would be easier to automatize the process and to decrease the
> processing time. I mean, for compute the centerline its really necessary to
> run the vmtkimagevoiselector, vmtklevelsetsegmentation and
> vmtkmarchingcubes?
It is not necessary if, for instance, you have such a sharp image that you can
just extract the model by extracting an isosurface (using vmtkmarchingcubes
alone).
Or, if you can have a good initialization for vmtklevelsetsegmentation, you can
run vmtklevelsetsegmentation non-interactively, which would save most of your
time.
There are other ways to go in vmtk (vmtkpotentialfit, vmtknetworkeditor), but
probably you need to first clarify what deformable models are and when/why they
are needed
compared to just extracting an intensity isosurface. The more you know about
the theoretical background, the smoother will be your optimization process.
Best regards
Luca
>
> I'm sorry for the amount of questions, but i'm new at vmtk and programming..
>
> Best regards,
>
> Lia Silva
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