UnicodeDecodeError: 'utf-8' codec can't decode byte 0x89 in position 0: invalid start byte

[justineuro]

Bug summary

plt.scatter gives UnicodeDecodeError: 'utf-8' codec can't decode byte 0x89 in position 0: invalid start byte error with notebook running python3 ipykernel, matplotlib-3.4.3, backend: module://matplotlib_inline.backend_inline.

Works fine when kernel is switched to python2, matplotlib-2.2.3, backend: module://ipykernel.pylab.backend_inline .

Code for reproduction

import matplotlib.pyplot as plt

X = [590,540,740,130,810,300,320,230,470,620,770,250]
Y = [32,36,39,52,61,72,77,75,68,57,48,48]
print(X)
print(Y)

plt.scatter(X,Y)

Actual outcome

[590, 540, 740, 130, 810, 300, 320, 230, 470, 620, 770, 250]
[32, 36, 39, 52, 61, 72, 77, 75, 68, 57, 48, 48]
<matplotlib.collections.PathCollection at 0x7fd16a4d8390>
---------------------------------------------------------------------------
UnicodeDecodeError                        Traceback (most recent call last)
~/.local/lib/python3.7/site-packages/matplotlib_inline/backend_inline.py in show(close, block)
     41             display(
     42                 figure_manager.canvas.figure,
---> 43                 metadata=_fetch_figure_metadata(figure_manager.canvas.figure)
     44             )
     45     finally:

~/.local/lib/python3.7/site-packages/IPython/core/display.py in display(include, exclude, metadata, transient, display_id, *objs, **kwargs)
    325                 # kwarg-specified metadata gets precedence
    326                 _merge(md_dict, metadata)
--> 327             publish_display_data(data=format_dict, metadata=md_dict, **kwargs)
    328     if display_id:
    329         return DisplayHandle(display_id)

~/.local/lib/python3.7/site-packages/IPython/core/display.py in publish_display_data(data, metadata, source, transient, **kwargs)
    120         data=data,
    121         metadata=metadata,
--> 122         **kwargs
    123     )
    124 

~/.local/lib/python3.7/site-packages/ipykernel/zmqshell.py in publish(self, data, metadata, transient, update)
    137 
    138         self.session.send(
--> 139             self.pub_socket, msg, ident=self.topic,
    140         )
    141 

~/.local/lib/python3.7/site-packages/jupyter_client/session.py in send(self, stream, msg_or_type, content, parent, ident, buffers, track, header, metadata)
    828         if self.adapt_version:
    829             msg = adapt(msg, self.adapt_version)
--> 830         to_send = self.serialize(msg, ident)
    831         to_send.extend(buffers)
    832         longest = max([len(s) for s in to_send])

~/.local/lib/python3.7/site-packages/jupyter_client/session.py in serialize(self, msg, ident)
    702             content = self.none
    703         elif isinstance(content, dict):
--> 704             content = self.pack(content)
    705         elif isinstance(content, bytes):
    706             # content is already packed, as in a relayed message

~/.local/lib/python3.7/site-packages/jupyter_client/session.py in json_packer(obj)
     97         default=json_default,
     98         ensure_ascii=False,
---> 99         allow_nan=False,
    100     )
    101 

/usr/lib/python3/dist-packages/zmq/utils/jsonapi.py in dumps(o, **kwargs)
     38         kwargs['separators'] = (',', ':')
     39 
---> 40     s = jsonmod.dumps(o, **kwargs)
     41 
     42     if isinstance(s, unicode):

/usr/lib/python3/dist-packages/simplejson/__init__.py in dumps(obj, skipkeys, ensure_ascii, check_circular, allow_nan, cls, indent, separators, encoding, default, use_decimal, namedtuple_as_object, tuple_as_array, bigint_as_string, sort_keys, item_sort_key, for_json, ignore_nan, int_as_string_bitcount, iterable_as_array, **kw)
    397         ignore_nan=ignore_nan,
    398         int_as_string_bitcount=int_as_string_bitcount,
--> 399         **kw).encode(obj)
    400 
    401 

/usr/lib/python3/dist-packages/simplejson/encoder.py in encode(self, o)
    294         # exceptions aren't as detailed.  The list call should be roughly
    295         # equivalent to the PySequence_Fast that ''.join() would do.
--> 296         chunks = self.iterencode(o, _one_shot=True)
    297         if not isinstance(chunks, (list, tuple)):
    298             chunks = list(chunks)

/usr/lib/python3/dist-packages/simplejson/encoder.py in iterencode(self, o, _one_shot)
    376                 self.iterable_as_array, Decimal=decimal.Decimal)
    377         try:
--> 378             return _iterencode(o, 0)
    379         finally:
    380             key_memo.clear()

/usr/lib/python3/dist-packages/simplejson/encoder.py in encode_basestring(s, _PY3, _q)
     42     if _PY3:
     43         if isinstance(s, bytes):
---> 44             s = str(s, 'utf-8')
     45         elif type(s) is not str:
     46             # convert an str subclass instance to exact str

UnicodeDecodeError: 'utf-8' codec can't decode byte 0x89 in position 0: invalid start byte

Expected outcome

plt.show() right after this should give an image of the plot.

Operating system

Debian 10 (Skolelinux)

Matplotlib Version

3.4.3

Matplotlib Backend

module://matplotlib_inline.backend_inline

Python version

3.7.3

Jupyter version

5.7.8

Other libraries

No response

Installation

pip

Conda channel

No response

[justineuro]

The modified code below does save a PNG file as expected but the previously mentioned error still occurs.

import matplotlib.pyplot as plt

X = [590,540,740,130,810,300,320,230,470,620,770,250]
Y = [32,36,39,52,61,72,77,75,68,57,48,48]
print(X)
print(Y)

plt.scatter(X,Y)
plt.savefig('xy0.png')

Actual outcome in the space below the notebook cell:

[590, 540, 740, 130, 810, 300, 320, 230, 470, 620, 770, 250]
[32, 36, 39, 52, 61, 72, 77, 75, 68, 57, 48, 48]
---------------------------------------------------------------------------
UnicodeDecodeError                        Traceback (most recent call last)
~/.local/lib/python3.7/site-packages/matplotlib_inline/backend_inline.py in show(close, block)
     41             display(
     42                 figure_manager.canvas.figure,
---> 43                 metadata=_fetch_figure_metadata(figure_manager.canvas.figure)
     44             )
     45     finally:

~/.local/lib/python3.7/site-packages/IPython/core/display.py in display(include, exclude, metadata, transient, display_id, *objs, **kwargs)
    325                 # kwarg-specified metadata gets precedence
    326                 _merge(md_dict, metadata)
--> 327             publish_display_data(data=format_dict, metadata=md_dict, **kwargs)
    328     if display_id:
    329         return DisplayHandle(display_id)

~/.local/lib/python3.7/site-packages/IPython/core/display.py in publish_display_data(data, metadata, source, transient, **kwargs)
    120         data=data,
    121         metadata=metadata,
--> 122         **kwargs
    123     )
    124 

~/.local/lib/python3.7/site-packages/ipykernel/zmqshell.py in publish(self, data, metadata, transient, update)
    137 
    138         self.session.send(
--> 139             self.pub_socket, msg, ident=self.topic,
    140         )
    141 

~/.local/lib/python3.7/site-packages/jupyter_client/session.py in send(self, stream, msg_or_type, content, parent, ident, buffers, track, header, metadata)
    828         if self.adapt_version:
    829             msg = adapt(msg, self.adapt_version)
--> 830         to_send = self.serialize(msg, ident)
    831         to_send.extend(buffers)
    832         longest = max([len(s) for s in to_send])

~/.local/lib/python3.7/site-packages/jupyter_client/session.py in serialize(self, msg, ident)
    702             content = self.none
    703         elif isinstance(content, dict):
--> 704             content = self.pack(content)
    705         elif isinstance(content, bytes):
    706             # content is already packed, as in a relayed message

~/.local/lib/python3.7/site-packages/jupyter_client/session.py in json_packer(obj)
     97         default=json_default,
     98         ensure_ascii=False,
---> 99         allow_nan=False,
    100     )
    101 

/usr/lib/python3/dist-packages/zmq/utils/jsonapi.py in dumps(o, **kwargs)
     38         kwargs['separators'] = (',', ':')
     39 
---> 40     s = jsonmod.dumps(o, **kwargs)
     41 
     42     if isinstance(s, unicode):

/usr/lib/python3/dist-packages/simplejson/__init__.py in dumps(obj, skipkeys, ensure_ascii, check_circular, allow_nan, cls, indent, separators, encoding, default, use_decimal, namedtuple_as_object, tuple_as_array, bigint_as_string, sort_keys, item_sort_key, for_json, ignore_nan, int_as_string_bitcount, iterable_as_array, **kw)
    397         ignore_nan=ignore_nan,
    398         int_as_string_bitcount=int_as_string_bitcount,
--> 399         **kw).encode(obj)
    400 
    401 

/usr/lib/python3/dist-packages/simplejson/encoder.py in encode(self, o)
    294         # exceptions aren't as detailed.  The list call should be roughly
    295         # equivalent to the PySequence_Fast that ''.join() would do.
--> 296         chunks = self.iterencode(o, _one_shot=True)
    297         if not isinstance(chunks, (list, tuple)):
    298             chunks = list(chunks)

/usr/lib/python3/dist-packages/simplejson/encoder.py in iterencode(self, o, _one_shot)
    376                 self.iterable_as_array, Decimal=decimal.Decimal)
    377         try:
--> 378             return _iterencode(o, 0)
    379         finally:
    380             key_memo.clear()

/usr/lib/python3/dist-packages/simplejson/encoder.py in encode_basestring(s, _PY3, _q)
     42     if _PY3:
     43         if isinstance(s, bytes):
---> 44             s = str(s, 'utf-8')
     45         elif type(s) is not str:
     46             # convert an str subclass instance to exact str

UnicodeDecodeError: 'utf-8' codec can't decode byte 0x89 in position 0: invalid start byte

[HemingLiao]

Thanks for posting this. Same error here when running command:
import matplotlib.pyplot as plt
fig, ax = plt.subplots()

However, if I run this command in terminal directly, there is no such error. I could provide more info if needed.

[HemingLiao]

Python 3.8.5 (default, Sep 4 2020, 07:30:14)
Type "copyright", "credits" or "license" for more information.

IPython 7.27.0 -- An enhanced Interactive Python.

import matplotlib.pyplot as plt

fig, axes = plt.subplots(nrows=2,ncols=2)
Traceback (most recent call last):

File "/home/heming/.local/lib/python3.8/site-packages/matplotlib_inline/backend_inline.py", line 41, in show
display(

File "/home/heming/anaconda3/envs/gee/lib/python3.8/site-packages/IPython/core/display.py", line 327, in display
publish_display_data(data=format_dict, metadata=md_dict, **kwargs)

File "/home/heming/anaconda3/envs/gee/lib/python3.8/site-packages/IPython/core/display.py", line 119, in publish_display_data
display_pub.publish(

File "/home/heming/.local/lib/python3.8/site-packages/ipykernel/zmqshell.py", line 138, in publish
self.session.send(

File "/home/heming/anaconda3/envs/gee/lib/python3.8/site-packages/jupyter_client/session.py", line 830, in send
to_send = self.serialize(msg, ident)

File "/home/heming/anaconda3/envs/gee/lib/python3.8/site-packages/jupyter_client/session.py", line 704, in serialize
content = self.pack(content)

File "/home/heming/anaconda3/envs/gee/lib/python3.8/site-packages/jupyter_client/session.py", line 95, in json_packer
return jsonapi.dumps(

File "/home/heming/anaconda3/envs/gee/lib/python3.8/site-packages/zmq/utils/jsonapi.py", line 40, in dumps
s = jsonmod.dumps(o, **kwargs)

File "/home/heming/anaconda3/envs/gee/lib/python3.8/site-packages/simplejson/init.py", line 398, in dumps
return cls(

File "/home/heming/anaconda3/envs/gee/lib/python3.8/site-packages/simplejson/encoder.py", line 296, in encode
chunks = self.iterencode(o, _one_shot=True)

File "/home/heming/anaconda3/envs/gee/lib/python3.8/site-packages/simplejson/encoder.py", line 378, in iterencode
return _iterencode(o, 0)

File "/home/heming/anaconda3/envs/gee/lib/python3.8/site-packages/simplejson/encoder.py", line 44, in encode_basestring
s = str(s, 'utf-8')

UnicodeDecodeError: 'utf-8' codec can't decode byte 0x89 in position 0: invalid start byte

[justineuro]

...

However, if I run this command in terminal directly, there is no such error. I could provide more info if needed.

Ditto.

[Cabbache]

I have this exact issue with the following code on a jupyter notebook.

import matplotlib.pyplot
matplotlib.pyplot.plot([1,2,3], [4,5,6])
matplotlib.pyplot.show()

UnicodeDecodeError: 'utf-8' codec can't decode byte 0x89 in position 0: invalid start byte

Output from jupyter --version

Selected Jupyter core packages...
IPython          : 7.27.0
ipykernel        : 6.4.1
ipywidgets       : 7.6.5
jupyter_client   : 7.0.3
jupyter_core     : 4.8.1
jupyter_server   : not installed
jupyterlab       : not installed
nbclient         : 0.5.4
nbconvert        : 6.1.0
nbformat         : 5.1.3
notebook         : 6.4.4
qtconsole        : 5.1.1
traitlets        : 5.1.0

matplotlib version:

>>> import matplotlib
>>> matplotlib.__version__
'3.1.2'

[martinRenou]

Can you try updating jupyter_client to >= 7.0.4

[Cabbache]

I tried updating jupyter_client to version 7.0.4 and I still got the same issue.

However, when I tried to update to version 7.0.5 it worked fine.

In summary my fix was pip3 install jupyter-client==7.0.5

[martinRenou]

Good! Thanks for reporting

[justineuro]

Many thanks @Cabbache and @martinRenou! Updating to jupyter-client v.7.0.5 fixed this error for me.