plotly / plotly/plotly.py

go.Scatter3d doesn't display a given tensor

Open
#4,507 3 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

bug P3 sev-2
Dominant language
Python
Stars
18.8k
Forks
2.8k
Avg merge
16h 26m
Merged PRs (30d)
21

Description

Issue

While plotting an np.ndarray of type fp64, it is not displayed.
It is so funny that we could reproduce it only for one specific array.

Thigs that make the script work:

  • If we add epsilon (as in the commented line), then the pointcloud is displayed properly.
  • If we cast to fp32 it works.
  • If we add a small value (0.000000000001 for example), it works.

Things that doesn't work:

  • If we add or substract big values, like 0.4, 1 or 2, it doesn't work
  • If we substract epsilon, it doesn't work
  • if we add numbers larger than 0.000000000001, it doesnt' work even if tehy are small (0.000001 for example)

Environment

We tried this (and reproduced in at least 2 computers) with numpy 1.26.3 and plotly 5.18.0 on ubuntu 22

import numpy as np
import plotly.graph_objects as go

init = np.array(
    [
        [
            -0.063,
            -0.063,
            0.0,
        ],
        [
            -0.063,
            -0.021,
            0.0,
        ],
        [
            -0.063,
            0.021,
            0.0,
        ],
        [
            -0.063,
            0.063,
            0.0,
        ],
        [
            -0.021,
            -0.021,
            0.0,
        ],
        [
            -0.021,
            -0.063,
            0.0,
        ],
        [
            -0.021,
            0.021,
            0.0,
        ],
        [
            -0.021,
            0.063,
            0.0,
        ],
        [
            0.021,
            -0.063,
            0.0,
        ],
        [
            0.021,
            -0.021,
            0.0,
        ],
        [
            0.021,
            0.021,
            0.0,
        ],
        [
            0.021,
            0.063,
            0.0,
        ],
        [
            0.063,
            -0.063,
            0.0,
        ],
        [
            0.063,
            -0.021,
            0.0,
        ],
        [
            0.063,
            0.021,
            0.0,
        ],
        [
            0.063,
            0.063,
            0.0,
        ],
    ]
)

rot_mat = [
    [4.93038066e-32, -1.00000000e00, 2.22044605e-16],
    [2.22044605e-16, 2.22044605e-16, 1.00000000e00],
    [-1.00000000e00, 0.00000000e00, 2.22044605e-16],
]

transformed = (rot_mat @ init.T).T + np.array([0.5, 0.5, 0.5])


x, y, z = 0, 1, 2
idx = list(transformed.shape).index(3)
if idx < 0:
    raise ValueError("Array must be [X,Y,Z] x N")
elif idx == 1:
    array = transformed.transpose()

default_kwargs = dict(
    mode="markers",
    marker=dict(size=3, color="black"),
)

print(array.dtype)

# array[y]+=np.finfo(np.float64).eps
print(array.dtype)
print(array)
plot = go.Scatter3d(x=array[x], y=array[y], z=array[z], **default_kwargs)

default_kwargs = dict(
    scene=dict(
        xaxis=dict(title="X", range=[0, 2]),
        yaxis=dict(title="Y", range=[0, 2]),
        zaxis=dict(title="Z", range=[0, 2]),
    ),
)
layout = go.Layout(**default_kwargs)

fig = go.Figure(data=plot, layout=layout)

fig.show()

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Use the supplied reproduction script as the entry point and run it with numpy 1.26.3 and plotly 5.18.0 on Ubuntu 22. Compare the failing fp64 array with the working epsilon and fp32 variants, then trace the go.Scatter3d rendering path. Done means identifying the cause and adding a regression check showing that the given tensor is displayed.

Written by the indexing model from the issue text.

Assessment

Tech stack
numpy, plotly, python
Domain
data-visualization
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
38/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.