[FIXED] Matplotlib scatter plot without line PDF export error: `ValueError: zero-size array to reduction operation maximum which has no identity`

Issue

MPL throws a weird error when I want to export a scatter plot as PDF format. When creating the MWE, I could reduce the error to one line.

import numpy as np
import matplotlib.pyplot as plt

x = np.linspace(0, 2 * np.pi, 1000)
y = np.sin(x)

plt.plot(  # works just fine
    x,
    y,
    ls="",
    marker="x",
)
plt.savefig("test_fig_plot", format='pdf')
plt.close()

plt.scatter(
    x,
    y,
    ls="",  # <== PROBLEM
    marker="x",
)
plt.savefig("test_fig_scatter", format='pdf')

This is the error:

Traceback (most recent call last):
  File "/home/user/miniconda3/envs/gis2/lib/python3.11/site-packages/IPython/core/interactiveshell.py", line 3553, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "<ipython-input-2-7465ebbcb267>", line 1, in <module>
    runfile('/mnt/c/Users/erit/AppData/Roaming/JetBrains/PyCharm2023.3/scratches/scratch_2.py', wdir='/mnt/c/Users/erit/AppData/Roaming/JetBrains/PyCharm2023.3/scratches')
  File "/home/user/.pycharm_helpers/pydev/_pydev_bundle/pydev_umd.py", line 197, in runfile
    pydev_imports.execfile(filename, global_vars, local_vars)  # execute the script
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/user/.pycharm_helpers/pydev/_pydev_imps/_pydev_execfile.py", line 18, in execfile
    exec(compile(contents+"\n", file, 'exec'), glob, loc)
  File "/mnt/c/Users/erit/AppData/Roaming/JetBrains/PyCharm2023.3/scratches/scratch_2.py", line 24, in <module>
    plt.savefig("test_fig_scatter", format='pdf')
  File "/home/user/miniconda3/envs/gis2/lib/python3.11/site-packages/matplotlib/pyplot.py", line 1119, in savefig
    res = fig.savefig(*args, **kwargs)  # type: ignore[func-returns-value]
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/user/miniconda3/envs/gis2/lib/python3.11/site-packages/matplotlib/figure.py", line 3390, in savefig
    self.canvas.print_figure(fname, **kwargs)
  File "/home/user/miniconda3/envs/gis2/lib/python3.11/site-packages/matplotlib/backend_bases.py", line 2187, in print_figure
    result = print_method(
             ^^^^^^^^^^^^^
  File "/home/user/miniconda3/envs/gis2/lib/python3.11/site-packages/matplotlib/backend_bases.py", line 2043, in <lambda>
    print_method = functools.wraps(meth)(lambda *args, **kwargs: meth(
                                                                 ^^^^^
  File "/home/user/miniconda3/envs/gis2/lib/python3.11/site-packages/matplotlib/backends/backend_pdf.py", line 2807, in print_pdf
    self.figure.draw(renderer)
  File "/home/user/miniconda3/envs/gis2/lib/python3.11/site-packages/matplotlib/artist.py", line 95, in draw_wrapper
    result = draw(artist, renderer, *args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/user/miniconda3/envs/gis2/lib/python3.11/site-packages/matplotlib/artist.py", line 72, in draw_wrapper
    return draw(artist, renderer)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/home/user/miniconda3/envs/gis2/lib/python3.11/site-packages/matplotlib/figure.py", line 3154, in draw
    mimage._draw_list_compositing_images(
  File "/home/user/miniconda3/envs/gis2/lib/python3.11/site-packages/matplotlib/image.py", line 132, in _draw_list_compositing_images
    a.draw(renderer)
  File "/home/user/miniconda3/envs/gis2/lib/python3.11/site-packages/matplotlib/artist.py", line 72, in draw_wrapper
    return draw(artist, renderer)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/home/user/miniconda3/envs/gis2/lib/python3.11/site-packages/matplotlib/axes/_base.py", line 3070, in draw
    mimage._draw_list_compositing_images(
  File "/home/user/miniconda3/envs/gis2/lib/python3.11/site-packages/matplotlib/image.py", line 132, in _draw_list_compositing_images
    a.draw(renderer)
  File "/home/user/miniconda3/envs/gis2/lib/python3.11/site-packages/matplotlib/artist.py", line 72, in draw_wrapper
    return draw(artist, renderer)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/home/user/miniconda3/envs/gis2/lib/python3.11/site-packages/matplotlib/collections.py", line 1005, in draw
    super().draw(renderer)
  File "/home/user/miniconda3/envs/gis2/lib/python3.11/site-packages/matplotlib/artist.py", line 72, in draw_wrapper
    return draw(artist, renderer)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/home/user/miniconda3/envs/gis2/lib/python3.11/site-packages/matplotlib/collections.py", line 423, in draw
    renderer.draw_path_collection(
  File "/home/user/miniconda3/envs/gis2/lib/python3.11/site-packages/matplotlib/backends/backend_pdf.py", line 2074, in draw_path_collection
    padding = np.max(linewidths)
              ^^^^^^^^^^^^^^^^^^
  File "/home/user/miniconda3/envs/gis2/lib/python3.11/site-packages/numpy/core/fromnumeric.py", line 2810, in max
    return _wrapreduction(a, np.maximum, 'max', axis, None, out,
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/user/miniconda3/envs/gis2/lib/python3.11/site-packages/numpy/core/fromnumeric.py", line 88, in _wrapreduction
    return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: zero-size array to reduction operation maximum which has no identity

I am using:

• python 3.11.7
• matplotlib 3.8.0
• on WSL Debian 12

I need scatter plots to color my data but I don't want to have a line, just markers. Markers with line is working as plt.plot with the desired settings (but no color map) is. PNG export is also fine.
I really cannot uderstand the error...

Thanks already for helping!

Solution

plt.scatter does not have a ls kwarg since there is no line (that's what it means for it to be a scatter plot). Remove that argument and the code works fine.

import numpy as np
import matplotlib.pyplot as plt

x = np.linspace(0, 2*np.pi, 1000)
y = np.sin(x)

plt.figure()
plt.scatter(x, y, marker="x")
plt.savefig("test_fig_scatter.pdf", format="pdf")

Answered By - jared