Add scatter3d

[nvaytet]

Can now make 3d scatter plots using

import plopp as pp
import scipp as sc
import numpy as np

nclusters = 100
npercluster = 1000

position = np.zeros((nclusters, npercluster, 3))
values = np.zeros((nclusters, npercluster))

for n in range(nclusters):
    center = 500.0 * (np.random.random(3) - 0.5)
    r = 20.0 * np.random.normal(size=[npercluster, 3])
    position[n, :] = r + center
    values[n, :] = np.linalg.norm(r, axis=1) + n

da = sc.DataArray(
    data=sc.array(dims=['row'], values=values.flatten(), unit='K'),
    coords={
        'position': sc.vectors(dims=['row'], unit='m',
                               values=position.reshape(nclusters*npercluster, 3))
    })

pp.scatter3d(da, pos='position')

You can also use 3 separate coordinates instead of a vector3 coord:

time = np.linspace(0, 10, 50)
x = np.cos(time)
y = np.sin(time)

da = sc.DataArray(
    data=sc.array(dims=['row'], values=time),
    coords={
        'x': sc.array(dims=['row'], unit='m', values=x),
        'y': sc.array(dims=['row'], unit='m', values=y),
        'time': sc.array(dims=['row'], unit='s', values=time)
    })

pp.scatter3d(da, x='x', y='y', z='time', pixel_size=0.2)

Additional notes / things to check:

• Camera buttons should work
• Added tests for most things
• Made common ColorMapper class for 2d images and 3d scatter plots
• For now, Scene3d only makes PointClouds but in principle, it could accept more in the future? (meshes or other).

Fixes #13

[jl-wynen]

The camera buttons in the first plot don't work exactly correctly. The camera is almost but not quite aligned with the axis you are looking along. This might just be a problem with numerical precision.

[nvaytet]

I think it might be because they are lining up with the center of the box, not the origin of the rgb axes. Because the data is random, the center of the box is close to zero but not exactly zero.

[jl-wynen]

How do we make sure that plots look ok on different machines given that there are so many hard coded values. I assume, you picked them based on how things look on your machine?

[jl-wynen]

Why is this not needed here anymore?

[nvaytet]

I moved the requirement to the docs.in. We decided pythreejs should be a soft requirement for plopp.

[jl-wynen]

But isn't it needed in the tests as well? Are these requirement files meant for users as well?

[nvaytet]

Good point about the tests.... how did the CI even pass?

[jl-wynen]

Where do these numbers come from?

[nvaytet]

The same as in Scipp. It is 1% of the range spanned by the data for the near value. It's basically to say at what distance from the camera do the objects start to disappear, so it makes sense to have it as a fraction of the extent of the data points.
The same does for the far which means when objects start disappearing when they are far away.
Those numbers have worked well for Scipp users, I think.

[jl-wynen]

Is this a left over from debugging?

[nvaytet]

Yes and no. There is no config in plopp yet. I didn't want to mess with the pixel_ratio just now, so I just set it to 1, and left the commented code as a reminder. I will change to a TODO.

[jl-wynen]

How does this interact with user chosen dpi for the rest of the figure?

[nvaytet]

There is no other dpi for the rest of the figure. Pythreejs uses pixels for figure size, no dpi.

[jl-wynen]

Same issue as scipp/scipp#2824

[nvaytet]

Yes.

[nvaytet]

I changed it to match scipp

[jl-wynen]

Uncomment?

[nvaytet]

Again, no config yet.

[nvaytet]

I changed it to a TODO

[jl-wynen]

dim is not a good name. Maybe coord?

[nvaytet]

Yeah, dim is not the best. Maybe pos, or positions, or vectors ?