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DOC/RF - update/standardize tracking examples #1432

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gabknight opened this issue Feb 14, 2018 · 3 comments

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@gabknight
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commented Feb 14, 2018

Some idea to ease the introduction to the various tractography algorihtms/examples

  • Standardize tracking example names starting with tracking_.
  • Add figures to all examples (e.g. probabilistic_fiber_tracking.py has none)
  • Uniformize the way streamlines are generated, saved and visualised e.g.:
pft_streamline_generator = ParticleFilteringTracking(dg,
                                                     cmc_classifier,
                                                     seeds,
                                                     affine,
                                                     max_cross=1,
                                                     step_size=step_size,
                                                     maxlen=1000,
                                                     pft_back_tracking_dist=2,
                                                     pft_front_tracking_dist=1,
                                                     particle_count=15,
                                                     return_all=False)
streamlines = Streamlines(pft_streamline_generator)
save_trk("pft_streamline.trk", streamlines, affine, shape)


renderer.clear()
renderer.add(actor.line(streamlines, line_colors(streamlines)))
window.record(renderer, out_path='pft_streamlines.png', size=(600, 600))

if interactive:
    window.show(renderer)

Current tracking examples:

  • :ref:example_introduction_to_basic_tracking
  • :ref:example_probabilistic_fiber_tracking
  • :ref:example_deterministic_fiber_tracking
  • :ref:example_tracking_tissue_classifier
  • :ref:example_particle_filtering_fiber_tracking
  • :ref:example_sfm_tracking
@skoudoro

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commented Feb 14, 2018

great ideas :-)

Uniformize the way streamlines are generated, saved and visualised e.g.:

I think this point is done on #1379. Could you have a look? I can correct this.

@jhlegarreta

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commented Feb 19, 2018

If Cython is not needed (still having issues compiling files) and once #1379 merged, I can propose a patch set to address the rest of the issues.

@gabknight

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commented Feb 20, 2018

Ok! No cython is needed for this. Let's wait for #1379 and #1431 to be merged.

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