VTK volume viewer export color mapper informations to python side #1073

xavArtley · 2020-02-05T14:46:47Z

With this PR we begin to have a real 3d slicer

import panel as pn
pn.extension('vtk')
import holoviews as hv
hv.extension('bokeh')
import pyvista as pv
from pyvista import examples
# Download a volumetric dataset
head = examples.download_head()
arr = head.active_scalar.reshape(head.dimensions, order='F')
interpolation_level = pn.widgets.IntSlider(value=5, start=1, end=20, name='Interpolation Level')
vol = pn.panel(head, sizing_mode='stretch_both', height=400, display_slices=True, rescale=True, display_volume=False,
              orientation_widget=True)
import scipy.ndimage as sn

@pn.depends(vol.param.slice_i,vol.param.slice_j,vol.param.slice_k,vol.param.mapper, interpolation_level.param.value)
def print_mapper(si, sj, sk, mapper, interp_level):
    im_interp = lambda x: sn.zoom(x, zoom=interp_level, order=1)
    low = mapper['low'] if mapper else arr.min()
    high = mapper['high'] if mapper else arr.max()
    cmap = mapper['palette'] if mapper else 'fire'
    
    im_i = hv.Image(im_interp(arr[si,::-1,:]), bounds=(head.extent[4],head.extent[2],head.extent[5],head.extent[3]), kdims=['z','y'], vdims='Intensity')
    im_j = hv.Image(im_interp(arr[::-1,sj,:]), bounds=(head.extent[4],head.extent[0],head.extent[5],head.extent[1]), kdims=['z','x'], vdims='Intensity')
    im_k = hv.Image(im_interp(arr[::-1,:,sk]), bounds=(head.extent[2],head.extent[0],head.extent[3],head.extent[1]), kdims=['y','x'], vdims='Intensity')
    return (im_i + im_j + im_k).opts(hv.opts.Image(clim=(low, high), cmap=cmap, invert_axes=True, data_aspect=1))
    
    
pn.Column(
    pn.Row(
        pn.Column(vol.controls(jslink=False,
                               parameters=['render_background', 'rescale', 'slice_i', 'slice_j', 
                                           'slice_k', 'display_volume', 'display_slices']),
                  interpolation_level),
        vol
    ),
    print_mapper
)

philippjfr · 2020-02-05T18:59:26Z

Ready to merge?

xavArtley · 2020-02-05T20:12:48Z

No I'd like to modify documentation before

xavArtley · 2020-02-06T05:27:54Z

What do you think to had something like that to the gallery?

import param
import panel as pn
import holoviews as hv
import pyvista as pv
from pyvista import examples
from scipy.ndimage import zoom

pn.extension('vtk')
hv.extension('bokeh')


class ImageSmoother(param.Parameterized):
    
    smooth_fun = param.Parameter(default=None)
    order = param.Selector(default=1, objects=[1,2,3])
    zoom = param.Integer(default=2, bounds=(1,10))
    
    def __init__(self, **params):
        super().__init__(**params)
        self._update_fun()
    
    @param.depends('order', 'zoom', watch=True)
    def _update_fun(self):
        self.smooth_fun = lambda x: zoom(x, zoom=self.zoom, order=self.order)
    
    @property
    def stream(self):
        return hv.streams.Params(self, parameters=['smooth_fun'])



# Download a volumetric dataset
vol = examples.download_head()
volume = pn.panel(vol, sizing_mode='stretch_both', height=400, display_slices=True, orientation_widget=True)
volume_controls = volume.controls(jslink=False, parameters=['render_background', 'display_volume', 'display_slices',
                                                            'slice_i', 'slice_j', 'slice_k', 'rescale'])
toggle_parallel_proj = pn.widgets.Toggle(name='Parallel Projection', value=False)
def update_camera_projection(*evts):
    volume.camera['parallelProjection'] = evts[0].new
    volume.param.trigger('camera')
toggle_parallel_proj.param.watch(update_camera_projection, ['value'], onlychanged=True)



stream_i = hv.streams.Params(volume, parameters=['slice_i'], rename={'slice_i':'si'})
stream_j = hv.streams.Params(volume, parameters=['slice_j'], rename={'slice_j':'sj'})
stream_k = hv.streams.Params(volume, parameters=['slice_k'], rename={'slice_k':'sk'})
stream_mapper = hv.streams.Params(volume, parameters=['mapper'])
smoother = ImageSmoother()
stream_smooth = smoother.stream

arr = vol.active_scalar.reshape(vol.dimensions, order='F')

def image_slice_i(si, mapper, smooth_fun):
    low = mapper['low'] if mapper else arr.min()
    high = mapper['high'] if mapper else arr.max()
    cmap = mapper['palette'] if mapper else 'fire'
    lbrt = vol.extent[4], vol.extent[2], vol.extent[5], vol.extent[3]
    im_i = hv.Image(smooth_fun(arr[si,::-1,:]), bounds=lbrt, kdims=['z','y'], vdims='Intensity')
    frame_width = 500
    frame_height = int(frame_width * (lbrt[2]-lbrt[0])/(lbrt[3]-lbrt[1]))
    return im_i.opts(hv.opts.Image(clim=(low, high), cmap=cmap, frame_width=frame_width, frame_height=frame_height))
    
def image_slice_j(sj, mapper, smooth_fun):
    low = mapper['low'] if mapper else arr.min()
    high = mapper['high'] if mapper else arr.max()
    cmap = mapper['palette'] if mapper else 'fire'
    lbrt = vol.extent[4], vol.extent[0], vol.extent[5], vol.extent[1]
    im_j = hv.Image(smooth_fun(arr[::-1,sj,:]), bounds=lbrt, kdims=['z','x'], vdims='Intensity')
    frame_width = 500
    frame_height = int(frame_width * (lbrt[2]-lbrt[0])/(lbrt[3]-lbrt[1]))
    return im_j.opts(hv.opts.Image(clim=(low, high), cmap=cmap, frame_width=frame_width, frame_height=frame_height))
                     
def image_slice_k(sk, mapper, smooth_fun):
    low = mapper['low'] if mapper else arr.min()
    high = mapper['high'] if mapper else arr.max()
    cmap = mapper['palette'] if mapper else 'fire'
    lbrt = vol.extent[2], vol.extent[0], vol.extent[3], vol.extent[1]
    im_k = hv.Image(smooth_fun(arr[::-1,:,sk]), bounds=lbrt, kdims=['y','x'], vdims='Intensity')
    frame_width = 500
    frame_height = int(frame_width * (lbrt[2]-lbrt[0])/(lbrt[3]-lbrt[1]))
    return im_k.opts(hv.opts.Image(clim=(low, high), cmap=cmap, frame_width=frame_width, frame_height=frame_height))

hv.opts.defaults(hv.opts.Image(invert_axes=True, data_aspect=1))
dmap_i = hv.DynamicMap(image_slice_i, streams=[stream_i, stream_mapper, stream_smooth])
dmap_j = hv.DynamicMap(image_slice_j, streams=[stream_j, stream_mapper, stream_smooth])
dmap_k = hv.DynamicMap(image_slice_k, streams=[stream_k, stream_mapper, stream_smooth])


controller = pn.WidgetBox(toggle_parallel_proj, *volume_controls[1:], pn.Param(smoother, parameters=['zoom', 'order']))
pn.Row(pn.Column(pn.Row(controller, volume), pn.Row(dmap_i, dmap_j)), dmap_k, sizing_mode='stretch_height').show()

codecov · 2020-02-06T17:16:38Z

Codecov Report

Merging #1073 into master will decrease coverage by 0.32%.
The diff coverage is 84.37%.

@@            Coverage Diff             @@
##           master    #1073      +/-   ##
==========================================
- Coverage    88.1%   87.77%   -0.33%     
==========================================
  Files         105      105              
  Lines       12380    12590     +210     
==========================================
+ Hits        10907    11051     +144     
- Misses       1473     1539      +66

Impacted Files	Coverage Δ
panel/pane/vtk/__init__.py	`100% <ø> (ø)`	⬆️
panel/models/vtk.py	`100% <100%> (ø)`	⬆️
panel/pane/vtk/vtk.py	`86.45% <80%> (-3.77%)`	⬇️
panel/util.py	`86.16% <0%> (-3.15%)`	⬇️
panel/interact.py	`73.57% <0%> (-2.5%)`	⬇️
panel/tests/test_reactive.py	`98.76% <0%> (-1.24%)`	⬇️
panel/io/notebook.py	`61.13% <0%> (-1.22%)`	⬇️
panel/pane/vtk/vtkjs_serializer.py	`82.05% <0%> (-0.65%)`	⬇️
panel/viewable.py	`83.42% <0%> (+0.94%)`	⬆️
... and 1 more

Continue to review full report at Codecov.

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xavArtley · 2020-02-06T17:17:44Z

philippjfr · 2020-02-06T17:19:46Z

Wow, how did you do the draggable layout?

xavArtley · 2020-02-06T17:21:04Z

I used http://golden-layout.com/
In the ipynb you can view the template.
It was not to difficult to learn it (just for the purpose of this example)

philippjfr · 2020-02-06T17:27:36Z

Very cool, you used it as a custom template?

xavArtley · 2020-02-06T17:30:02Z

Yes i tried to mix different aspects of panel Le jeu. 6 févr. 2020 à 18:27, Philipp Rudiger <notifications@github.com> a écrit :

…

Very cool, you used it as a custom template? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1073?email_source=notifications&email_token=AENMGS3ZQCDCZZ2P7IGRXQTRBRCATA5CNFSM4KQMKZE2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELACD4Y#issuecomment-583016947>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AENMGS7ND3FPL7QO2GQOQYDRBRCATANCNFSM4KQMKZEQ> .

panel/models/vtk/vtk_layout.ts

philippjfr · 2020-02-07T18:43:12Z

Going to merge and get this in 0.8.1 pretending it's a simple enhancement 😄

philippjfr · 2020-02-07T23:51:42Z

@xavArtley The VTKVolume.mapper isn't syncing for me in the notebook, any idea what's going on there?

xavArtley · 2020-02-08T07:13:57Z

Actually for me it's not sync too in the notebook but only when I use the tempate. If I use panel Row and Columns it works as expected. Le sam. 8 févr. 2020 à 00:51, Philipp Rudiger <notifications@github.com> a écrit :

…

@xavArtley <https://github.com/xavArtley> The VTKVolume.mapper isn't syncing for me in the notebook, any idea what's going on there? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1073?email_source=notifications&email_token=AENMGSY3PHSCYHK34LUBOO3RBXXY5A5CNFSM4KQMKZE2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELFAGAA#issuecomment-583664384>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AENMGSZ5OE4ZCO57GSD3QM3RBXXY5ANCNFSM4KQMKZEQ> .

examples/gallery/demos/VTKSlicer.ipynb

xavArtley · 2020-02-08T11:31:51Z

I haven't read all the template documentation to handle template in notebook. I will make some modifications instead of testing the document title

xavArtley · 2020-02-08T12:16:48Z

@xavArtley The VTKVolume.mapper isn't syncing for me in the notebook, any idea what's going on there?

I found something strange when looking at volume.model after displaying the template there is 2 reférences

philippjfr · 2020-02-10T15:38:57Z

I found something strange when looking at volume.model after displaying the template there is 2 reférences

This is in fact expected, templates have to do some funny stuff to linking set up.

xavArtley · 2020-02-13T10:48:23Z

@philippjfr Do you think it should be possible to set data_aspect=1 to images while keeping layout responsivness?

philippjfr · 2020-02-15T23:53:34Z

@philippjfr Do you think it should be possible to set data_aspect=1 to images while keeping layout responsivness?

Would definitely need some special handling I think only bokeh figures currently support aspect handling out of the box.

xavArtley · 2020-02-16T06:35:12Z

@philippjfr Python 2 failed on master because the property .active_scalars was introduced on pyvista 0.23.1 and for the python 2 build the version 0.22.4 seems to be installed.
2 solutions to correct it:

use the old property (trigger deprection warnings) .active_scalar
update pyvista version to >= 0.23for python 2 build however I don't know why it's not the same version on python 3 and python 2.

philippjfr · 2020-02-17T18:46:44Z

@xavArtley I'm happy to defer to your judgement here. Given that we are dropping python 2 support in about a week and there will be only one more release, I'm happy to skip this test for py2 if pyvista>=0.23 doesn't support py2.

JeffreyWardman · 2020-10-20T05:54:21Z

The notebook for this (VTKSlicer.ipynb) does not successfully link the controls with the image. E.g. slicing does not work, neither does selecting the background.

xavArtley · 2020-10-20T08:27:56Z

Are you talking about it in the panel documentation or when you run the notebook locally?
It is not working in the documentation because it needs a server
however locally I tested it and it seems ok:

JeffreyWardman · 2020-10-20T22:55:03Z

@xavArtley I was testing locally. It had to do with the Jupyter extensions. It didn't return anything in Jupyter notebook. In Jupyter lab it showed the window but didn't have any interactivity. Turns out the reason was because I hadn't installed the pyviz extension. Problem solved! Thanks for your help.

xavArtley force-pushed the xav/export_colormap branch from 49edbd2 to 1172866 Compare February 5, 2020 14:53

xavArtley mentioned this pull request Feb 6, 2020

Enable orientation widget and camera control for vtkvolume #1068

Closed

xavArtley added status: ready status: WIP and removed status: ready labels Feb 6, 2020

xavArtley force-pushed the xav/export_colormap branch from ffbf0ac to 88f0526 Compare February 7, 2020 17:47

xavArtley added status: ready and removed status: WIP labels Feb 7, 2020

xavArtley requested review from philippjfr and jbednar February 7, 2020 18:25

philippjfr reviewed Feb 7, 2020

View reviewed changes

panel/models/vtk/vtk_layout.ts Outdated Show resolved Hide resolved

xavArtley added 9 commits February 7, 2020 20:09

vtk models code factorisation

4ae4eed

Enable orientation widget for vtk volume

4984e03

Factorize vtk camera code

8c50181

Add camera control to VTK volume

fe88741

lut converter

a86f99f

Add demo of VTKSlicer to gallery

994eda5

update reference vtvolume ipynb

360ca4d

Fix number of palettes color to 255

d970aa6

slice params was wrong when data are subsamples

34f0835

xavArtley added 4 commits February 7, 2020 20:09

Improve and correct slicer example

25abd1a

Correction on None data

e010363

Py2...

6d9bfa4

Correct visibility misspelled

033ce54

xavArtley force-pushed the xav/export_colormap branch from 6636f8a to 033ce54 Compare February 7, 2020 19:20

philippjfr added 2 commits February 7, 2020 13:50

Simplified VTKSlicer

f6b1d20

Further simplified VTKSlicer

f05b2b9

Remove duplicate hook function

a0b2751

xavArtley commented Feb 8, 2020

View reviewed changes

examples/gallery/demos/VTKSlicer.ipynb Outdated Show resolved Hide resolved

Automatic rescale plots when ranges changed

1512fcf

xavArtley added 2 commits February 8, 2020 20:16

Better handling notebook and server context

aa5d10c

time_ns was specific to py3.7

e402daa

Minor cleanup

b3ce0ff

xavArtley added 2 commits February 13, 2020 15:15

active_scalar deprecated and use bounds instead of extent

4f86879

Update VTKSlicer.ipynb

5577a2b

philippjfr merged commit 25a734c into master Feb 15, 2020

xavArtley deleted the xav/export_colormap branch February 21, 2020 16:00

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VTK volume viewer export color mapper informations to python side #1073

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VTK volume viewer export color mapper informations to python side #1073

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