New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

NF added class to save streamlines in vtk format #425

Closed
wants to merge 1 commit into
base: master
from

Conversation

Projects
None yet
3 participants
@Jan-Schreiber

Jan-Schreiber commented Sep 28, 2014

This is a class that provides to save streamlines (as generated e.g. with eudx) in the vtk file format.
Some features are:

  • setting an affine transform to save the streamlines in the
    data's coordinate system (rather than voxel coordinates)
  • writing in ascii or binary file format
  • saving colored streamlines for the local or global direction of the streamline
  • decorating the streamlines with one value for every streamline (e.g. the streamline's length)
  • decorating the streamline with a value for every vertex (e.g. the FA values)
  • colors and decorations can be viewed e.g. with paraview (http://www.paraview.org/)
  • errors are indicated by return code, no exceptions are thrown (or should I use exceptions?)

I am relatively new to python. So this is my initial project for dipy and a thorough review might be required.

@MarcCote

This comment has been minimized.

Contributor

MarcCote commented Sep 29, 2014

I think streamlines related stuff should in the library NiBabel. More precisely. it could be part of this PR NiBabel - Streamlines API which tries to provide an uniform interface to all streamlines formats (TRK, VTK, TCK, ...).

@Garyfallidis

This comment has been minimized.

Member

Garyfallidis commented Sep 29, 2014

@Jan-Schreiber thank you for this PR! Yes, we make strong effort that all file formats go to nibabel and all dMRI processing goes to dipy. Please coordinate with @MarcCote who has also made readers for VTK (but also TRK and TCK files) and see which problems you have probably solved that Marc hasn't done already. @matthew-brett is the lead developer of nibabel. I am sure he will be more than happy to help you on this. But first coordinate with Marc-Alex please. Thx Jan!!! :)

@Garyfallidis

This comment has been minimized.

Member

Garyfallidis commented Oct 1, 2014

Guys, is it okay if I close this PR here. As this need to go to nibabel?

@Jan-Schreiber

This comment has been minimized.

Jan-Schreiber commented Oct 3, 2014

Ok for me.
I'll check nibabel

On 10/01/2014 08:17 PM, Eleftherios Garyfallidis wrote:

Guys, is it okay if I close this PR here. As this need to go to nibabel?


Reply to this email directly or view it on GitHub
#425 (comment).

@Garyfallidis

This comment has been minimized.

Member

Garyfallidis commented Oct 3, 2014

Thank you @Jan-Schreiber . I will close this PR now. Let us know if you have dMRI processing code that you would like to share with the community in the future. Cheers!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment