Viz surfaces #1034

StongeEtienne · 2016-04-17T18:40:53Z

Surface visualization tools
Load/Save surface (polydata)
vtk polydata numpy support
surfaces tutorial

Update fork

…ested

save

…iz_surfaces

arokem · 2016-05-04T16:56:28Z

This is cool -- thanks for including this! Any chance to show an example of how this can be used to visualize some brain data? There are some VTK files in the mindboggle data-sets that might lend themselves to this, or we could create VTK files of brain surfaces for the Stanford HARDI data-set. I am curious to see how you would suggest using this together with streamlines.

StongeEtienne · 2016-05-04T17:14:59Z

Hello Ariel, I added an example file "doc/examples/viz_surfaces.py" to show how to
Generate, Read (load) and Write a vtkPolyData (".vtk"), it also support some other mesh/surface files format (".ply",".stl",".obj").
If you use FreeSurfer, you can use "mris_convert" to convert freesurfer mesh to ".vtk"
mris_convert lh.pial lh.pial.vtk

Once you have a vtkPolyData you can generate a vtkActor and use it in a scene/windows exactly like the streamlines actor.

Later on, I could add a tutorial with surface and streamlines visualization.
I also wanted to add Coloring tools interaction in-between streamlines and surface !
but I need to do some work on my own python library before (TriMeshPy)

arokem · 2016-05-04T19:31:02Z

On Wed, May 4, 2016 at 10:15 AM, StongeEtienne notifications@github.com
wrote:

Hello Ariel, I added an example file "doc/examples/viz_surfaces.py" to
show how to
Generate, Read (load) and Write a vtkPolyData (".vtk"), it also support
some other mesh/surface files format (".ply",".stl",".obj").
If you use FreeSurfer, you can use "mris_convert" to convert freesurfer
mesh to ".vtk"
mris_convert lh.pial lh.pial.vtk

Once you have a vtkPolyData you can generate a vtkActor and use it in a
scene/windows exactly like the streamlines actor.

Later on, I could add a tutorial with surface and streamlines
visualization.

I propose that we add this on this PR, if that's not too much to ask. The
cube example is compact, but it doesn't really show a user what they would
do with this functionality in the context of diffusion MRI analysis.

I also wanted to add Coloring tools interaction in-between streamlines and
surface !
but I need to do some work on my own python library before (TriMeshPy
https://github.com/StongeEtienne/trimeshpy)

Yep. Looks like you have your work cut out for you :-)

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#1034 (comment)

StongeEtienne · 2016-05-05T19:25:00Z

I think, for basic surface feature, I shouldn't add more details.
Because that would be an exact copy of the current tutorial, but with different file name.
In example to visualize a brain surface :

file_name = "my_brain.vtk"  # "my_cube.vtk"
polydata = io_vtk.load_polydata(file_name)
actor = ut_vtk.get_actor_from_polydata(polydata)

renderer = window.Renderer()
renderer.add(actor)

window.show(renderer, reset_camera=False)

Also I didn't want to add a brain_mesh files in your data, and I don't know how your data fetching system works.

StongeEtienne · 2016-07-02T20:38:35Z

@Garyfallidis Do you think you will have some time to look at this ?

Garyfallidis · 2016-07-02T20:56:32Z

Yes, will do asap. Hold on there!

Garyfallidis · 2016-09-08T02:36:38Z

dipy/viz/utils.py

@@ -228,3 +228,251 @@ def lines_to_vtk_polydata(lines, colors=None):
    poly_data.SetLines(vtk_lines)
    poly_data.GetPointData().SetScalars(vtk_colors)
    return poly_data, is_colormap
+
+
+##########################################


Non-standard comment style.

Garyfallidis · 2016-10-13T16:00:31Z

doc/examples/viz_surfaces.py

+Visualize surfaces; load/save, get/set and update vtkPolyData.
+========================================
+
+import usefull functions and dipy utils 


from dipy.viz.utils

Garyfallidis · 2016-10-13T16:01:09Z

doc/examples/viz_surfaces.py

@@ -0,0 +1,99 @@
+"""
+========================================
+Visualize surfaces; load/save, get/set and update vtkPolyData.


Just write
Visualize surfaces or Surface visualization

@StongeEtienne have you seen this?

Garyfallidis · 2016-10-13T16:01:39Z

doc/examples/viz_surfaces.py

+
+"""
+generate a empty vtkPolyData
+"""


Add an empty line between comments and code. Otherwise the tutorial will not render correctly.

Garyfallidis · 2016-10-13T16:02:03Z

doc/examples/viz_surfaces.py

+"""
+ut_vtk.set_polydata_vertices(my_polydata, my_vetices)
+ut_vtk.set_polydata_triangles(my_polydata, my_triangles)
+


One empty line between code.

coveralls · 2016-10-13T18:10:59Z

Changes Unknown when pulling 5a78436 on StongeEtienne:viz_surfaces into * on nipy:master*.

coveralls · 2016-10-13T18:10:59Z

Changes Unknown when pulling 5a78436 on StongeEtienne:viz_surfaces into * on nipy:master*.

codecov-io · 2016-10-13T18:11:12Z

Current coverage is 80.82% (diff: 15.94%)

No coverage report found for master at 7b6ce30.

Powered by Codecov. Last update 7b6ce30...5a78436

Garyfallidis · 2016-10-13T18:36:59Z

Okay thanks. Merging this and making a PR with some updates for the website.

arokem · 2016-10-13T18:40:30Z

For future reference: you might want to give a couple of days warning before you merge PRs. Something like "I will merge this in a couple of days, unless I hear from everyone" would be helpful. For example, my suggestion from May (#1034 (comment)) has been ignored in the revision.

StongeEtienne · 2016-10-13T18:51:19Z

Thanks Elef for the merge, @arokem I don't mind for the "warning before merge", but I already answer ( #1034 (comment) ) to your request in a comment right after, and this branch wasn't touch for a whole 5 months.

arokem · 2016-10-13T18:53:32Z

Sure - I was wrong about your answer. It has been a while...

Still - the principle still applies

StongeEtienne and others added 6 commits April 10, 2016 13:39

Merge pull request #1 from nipy/master

1a670a4

Update fork

add basic file and new branch

55af769

moved load and save in IO, polydata get and set in Utils, fixed and t…

e7040f4

…ested

Merge branch 'master' of https://github.com/nipy/dipy

b8e8221

save

Merge branch 'master' of https://github.com/StongeEtienne/dipy into v…

b7ad32f

…iz_surfaces

add some utility actor and polymapper, and tutorial

a440d95

StongeEtienne mentioned this pull request May 6, 2016

Feature request: read VTK format streamlines scilus/FiberCompression#13

Open

Garyfallidis reviewed Sep 8, 2016
View reviewed changes

Garyfallidis reviewed Oct 13, 2016

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Etienne St-Onge added 2 commits October 13, 2016 12:10

pep8 formatting

638af36

visualiSE -> ZE (US)

5a78436

Garyfallidis merged commit 8afb032 into dipy:master Oct 13, 2016

Garyfallidis mentioned this pull request Oct 14, 2016

Minor corrections for showing surfaces #1130

Merged

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Viz surfaces #1034

Viz surfaces #1034

StongeEtienne commented Apr 17, 2016

arokem commented May 4, 2016

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edited

arokem commented Oct 13, 2016

Viz surfaces #1034

Viz surfaces #1034

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StongeEtienne commented Apr 17, 2016

arokem commented May 4, 2016

StongeEtienne commented May 4, 2016

arokem commented May 4, 2016

StongeEtienne commented May 5, 2016 • edited

StongeEtienne commented Jul 2, 2016

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coveralls commented Oct 13, 2016

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codecov-io commented Oct 13, 2016

Current coverage is 80.82% (diff: 15.94%)

Garyfallidis commented Oct 13, 2016

arokem commented Oct 13, 2016

StongeEtienne commented Oct 13, 2016 • edited

arokem commented Oct 13, 2016

StongeEtienne commented May 5, 2016 •

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