Vtk plot #312

xavArtley · 2019-03-16T08:01:20Z

Panel model for vtk representations

A minimal example is the following

Should not work for the moment (need next bokeh version)

TODO:
Add tests
clean api to work with vtk renderers

Examples:

xavArtley · 2019-03-16T08:57:34Z

Exmaple inspired from :
https://vtk.org/Wiki/VTK/Examples/Python/Cylinder

panel/pane/vtk.py

philippjfr · 2019-03-16T15:02:34Z

Looks like a great start! Note that I'd expect the Vtk pane to accept Vtk object directly and convert them to a VtkPlot model internally. Generally users should not be creating bokeh models directly since they are not meant to be reused, while a pane can be reused as often as desired.

jbednar

I'm very happy to have VTK support in Panel; that should be very handy. I don't have much opinion about the actual code that interfaces to VTK, other than that there seems to be a lot of it! :-) . And I haven't tested to see how well it works in practice.

panel/models/__init__.py

panel/models/audio.ts

panel/models/vtk.py

panel/pane/vtk.py

jbednar · 2019-03-16T16:54:34Z

panel/pane/vtk.py

@@ -0,0 +1,519 @@
+# coding: utf-8


This file has quite a bit of code; was it really all developed from scratch for Panel? Or was it adapted from some other starting point? If the latter, probably need to include the license of the original code.

the code is an adaptation from this Macro
https://raw.githubusercontent.com/Kitware/vtk-js/master/Utilities/ParaView/export-scene-macro.py
It allows to convert a paraview scene to a zip file

Most of developpement are inspired from
https://kitware.github.io/vtk-js/examples/SceneExplorer.html

I'm not very aware about licensing

Ok, I think you'd need to paste in the license from: https://github.com/Kitware/vtk-js/blob/master/LICENSE

(And should include the link to the original example, for reference.)

xavArtley · 2019-03-16T17:47:45Z

There are two parts to the vtk panel work:

first part consists of taking a VTK rendering window and converting it in a zip file stream encoded in a string.
for this I adapted this macro https://raw.githubusercontent.com/Kitware/vtk-js/master/Utilities/ParaView/export-scene-macro.py
then the string is sent with bokeh communication pipeline and a vtkjs scene is reconstructed using the SceneLoader of vtkjs and embedded in a bokeh HTMLBox (https://kitware.github.io/vtk-js/examples/SceneExplorer.html)

xavArtley · 2019-03-16T19:09:28Z

Now panel are construct using:

import vtk
import panel as pn
pn.extension('vtk')
from vtk.util.colors import tomato

cylinder = vtk.vtkCylinderSource()
cylinder.SetResolution(8)
cylinderMapper = vtk.vtkPolyDataMapper()
cylinderMapper.SetInputConnection(cylinder.GetOutputPort())
cylinderActor = vtk.vtkActor()
cylinderActor.SetMapper(cylinderMapper)
cylinderActor.GetProperty().SetColor(tomato)
cylinderActor.RotateX(30.0)
cylinderActor.RotateY(-45.0)
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
ren.AddActor(cylinderActor)
ren.SetBackground(0.1, 0.2, 0.4)
ren.ResetCamera()
ren.GetActiveCamera().Zoom(1.5)

VTK(renWin)

or

import panel as pn
pn.extension('vtk')
import urllib

data_url = urllib.request.urlopen(r'https://raw.githubusercontent.com/Kitware/vtk-js/master/Data/StanfordDragon.vtkjs')
pn.pane.VTK(data_url)

philippjfr · 2019-03-16T21:10:11Z

data_url = urllib.request.urlopen(r'https://raw.githubusercontent.com/Kitware/vtk-js/master/Data/StanfordDragon.vtkjs')

With a file extension as specific as vtkjs I'd be happy for the pane to accept filepaths and URLs which end in .vtkjs and then fetch it internally using requests.

philippjfr · 2019-03-16T21:14:01Z

Another question, you say that the data is converted to a zip file stream. Are there any other formats which are potentially more efficient, e.g. could you imagine extracting any binary buffers such as arrays and sending those independently via a ColumnDataSource and then reconstituting it client-side?

xavArtley · 2019-03-16T21:26:33Z

Another question, you say that the data is converted to a zip file stream. Are there any other formats which are potentially more efficient, e.g. could you imagine extracting any binary buffers such as arrays and sending those independently via a ColumnDataSource and then reconstituting it client-side?

Yes I think we could create a scene and add and update actors through this process. But it exceeds my current skills.

Actually it could be something similar of the second part of this gif

The second object is divided in three parts.
The files are results of a FE simulation and the raw binary vtk where about 100MB each
Each vtkjs file was ~10MB

philippjfr · 2019-03-16T21:27:42Z

Yes I think we could create a scene and add and update actors through this process. But it exceeds my current skills.

Okay, once you're finished with this PR, let's just file an issue providing a rough outline of such an approach. Certainly doesn't have to happen in this PR.

codecov-io · 2019-03-16T21:39:48Z

Codecov Report

Merging #312 into master will decrease coverage by 2.62%.
The diff coverage is 41.09%.

@@            Coverage Diff             @@
##           master     #312      +/-   ##
==========================================
- Coverage   89.41%   86.79%   -2.63%     
==========================================
  Files          83       77       -6     
  Lines        6776     7105     +329     
==========================================
+ Hits         6059     6167     +108     
- Misses        717      938     +221

Impacted Files	Coverage Δ
panel/config.py	`48% <ø> (ø)`	⬆️
setup.py	`0% <0%> (ø)`	⬆️
panel/models/vtk.py	`100% <100%> (ø)`
panel/pane/__init__.py	`100% <100%> (ø)`	⬆️
panel/pane/vtk.py	`28.61% <28.61%> (ø)`
panel/tests/test_vtk.py	`96.22% <96.22%> (ø)`
panel/tests/test_links.py	`97.4% <0%> (-2.6%)`	⬇️
panel/links.py	`83.92% <0%> (-0.82%)`	⬇️
panel/tests/test_param.py	`99.66% <0%> (-0.34%)`	⬇️
panel/tests/test_layout.py	`100% <0%> (ø)`	⬆️
... and 30 more

Continue to review full report at Codecov.

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xavArtley · 2019-03-16T22:12:37Z

philippjfr · 2019-03-17T04:26:55Z

Resolved the merge conflict I introduced as part of the KaTeX/MathJax PR.

xavArtley · 2019-03-17T07:15:18Z

Locally tests passed for me

But I don't know what's the error on CI servers

xavArtley · 2019-03-17T11:40:07Z

example reference:
https://lorensen.github.io/VTKExamples/site/Python/
To test and see limits of the panel

philippjfr · 2019-03-17T15:16:36Z

It looks like the CI is crashing when the VTK render window is loaded, does that expect a windowing system to exist by any chance?

xavArtley · 2019-03-17T16:10:58Z

I hope it's not the windowing system system,
I set the off screen mode before rendering
https://github.com/pyviz/panel/blob/717d084f643c3bea933a6cf31e18a9252d854168/panel/pane/vtk.py#L373

philippjfr · 2019-03-17T16:48:50Z

I think it is down to missing windowing, I've seen a couple of issues filed by people seeing similar errors despite the fact that they used SetOffScreenRendering.

philippjfr · 2019-03-21T20:19:34Z

Okay rebased, just run:

git fetch
git reset origin/vtk_plot --hard

xavArtley · 2019-03-21T22:04:44Z

Linking carmera between views should not be hard if we expose camera settings in vtk model
adding pan on the left click of the mouse seems doable, need to look more in detail of this example
https://kitware.github.io/vtk-js/examples/InteractorStyleManipulator.html
The size of thw widget must be set in VTK panel object

dharhas · 2019-03-21T22:12:31Z

With some experimentation I realized 'shift + left button' pans in the code I pasted.

I was able to set the size on the pane object, i.e. pn.pane.VTK(renWin, height=800, width=800)

Linked camera would be really useful. I have a set of unstructured objects at different mesh resolutions that I want to create a panel dashboard to compare.

jourdain · 2019-03-21T22:46:26Z

Guys is awesome and great work!
Sorry I was out in the wild the last couple of days without network or computer so I couldn't provide pointers sooner.

@xavArtley the python serializer that you found is indeed a better approach and will be improved while things progress on our end. It should be paired with the SynchronizedRenderWindow. Right now it is used with wslink (our WebSocket connection to VTK or ParaView backend) but can be adapted to exchange data with whatever communication protocol you would like.

Please find below some links of the usage of it.

Feel free to reach out on the vtk.js bug tracker as well...

dharhas · 2019-03-22T15:26:27Z

So how close is this to being merged? i.e. what is still needed?

philippjfr · 2019-03-22T16:16:10Z

It sounds like a lot of the existing serialization code could be swapped out for the code that @jourdain helpfully pointed to. The next release is scheduled for about a week from today, @xavArtley do you think you'll be able to do that swapping before then? If not I'd be okay with merging it using the current serialization approach and filing an issue to swap that out at a later date.

xavArtley · 2019-03-22T17:29:57Z

Seems unlikely I can pass some times on this PR next week.
I have several work deadline next week

philippjfr · 2019-03-22T18:10:47Z

Okay, how would you feel about merging this in its current state (after I've made a quick pass to clean it up), and then improve the serialization in a subsequent PR?

xavArtley · 2019-03-22T19:14:59Z

Can we wait the end of the week? Le ven. 22 mars 2019 à 19:10, Philipp Rudiger <notifications@github.com> a écrit :

…

Okay, how would you feel about merging this in its current state (after I've made a quick pass to clean it up), and then improve the serialization in a subsequent PR? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#312 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ARrDS2Hyq2tjKJkeHLk7BeUr9uXoSWfFks5vZRyngaJpZM4b3rP7> .

xavArtley · 2019-03-24T09:02:10Z

@philippjfr do you know if it is possible in bokehjs to trigger a python function to transfer data from python to javascript?

philippjfr · 2019-03-24T14:34:40Z

@philippjfr do you know if it is possible in bokehjs to trigger a python function to transfer data from python to javascript?

Not sure there is a straightforward mechanism particularly on the model itself. You could add a sync boolean property to the model and then subscribe to it on the Pane, because at the model level you don't know whether to sync via a JS callback (which triggers an event python side) or via a bokeh server callback.

xavArtley · 2019-03-24T15:19:15Z

After passing some times this week end on refactoring serializers, I need more time to reconstruct vtk rendering on the javascript side.
So I think you can merge when you want and we will open another PR to improve it

philippjfr · 2019-03-24T18:02:27Z

So I think you can merge when you want and we will open another PR to improve it

Okay, I'll maybe make a pass over it tonight and will merge tomorrow.

philippjfr · 2019-03-26T15:41:38Z

Okay, I'll merge this now and let you improve it in a subsequent PR.

github-actions · 2025-09-12T19:16:50Z

This pull request has been automatically locked since there has not been any recent activity after it was closed. Please open a new issue for related bugs.

xavArtley added type: enhancement Minor feature or improvement to an existing feature status: paused Paused labels Mar 16, 2019

philippjfr reviewed Mar 16, 2019

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xavArtley force-pushed the vtk_plot branch 2 times, most recently from 738f980 to 4b3a728 Compare March 16, 2019 19:07

xavArtley force-pushed the vtk_plot branch from 00d780e to e11e9ce Compare March 16, 2019 21:02

xavArtley force-pushed the vtk_plot branch from 27cf57a to df91f01 Compare March 16, 2019 21:29

xavArtley force-pushed the vtk_plot branch from 9b3cb97 to 312b184 Compare March 16, 2019 23:01

philippjfr force-pushed the vtk_plot branch from 27bc191 to be60f22 Compare March 17, 2019 04:26

xavArtley force-pushed the vtk_plot branch 2 times, most recently from fbc0236 to d9c393c Compare March 17, 2019 06:58

xavArtley and others added 8 commits March 21, 2019 20:19

test _dump data array

c2db28c

urlopen compatibility py2.7

77afe81

test correction in python 2 dict keys are not ordered

e9a8aff

Implementation of vtk default scalar mode behavior

5767b92

Wait after layout to create and render the vtk view

a1970d9

Updates to Vtk model

4fe742e

try to correct vtk layout (without success)

0a77f87

Don't recreate a vtk element each time the layout is recomputed

e8626ff

philippjfr force-pushed the vtk_plot branch from 6812854 to e8626ff Compare March 21, 2019 20:19

philippjfr merged commit a6cb109 into master Mar 26, 2019

This was referenced Mar 31, 2019

A question about 3d interaction jupyterhub/binderhub#760

Closed

Interactive notebook rendering pyvista/pyvista#144

Merged

xavArtley mentioned this pull request Apr 25, 2019

Help to use SynchronizableRenderWindow Kitware/vtk-js#1063

Closed

philippjfr deleted the vtk_plot branch September 9, 2019 16:37

github-actions bot locked as resolved and limited conversation to collaborators Sep 12, 2025

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