question-mark
Stuck on an issue?

Lightrun Answers was designed to reduce the constant googling that comes with debugging 3rd party libraries. It collects links to all the places you might be looking at while hunting down a tough bug.

And, if you’re still stuck at the end, we’re happy to hop on a call to see how we can help out.

`df.my_column.plot(datashade=True)` gives strange graphs when my_column dtype=uint32

See original GitHub issue

ALL software version info

Ubuntu 20.04

name: puma-lab
channels:
  - pyviz
  - conda-forge
  - defaults
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=1_gnu
  - abseil-cpp=20210324.2=h9c3ff4c_0
  - alembic=1.7.3=pyhd8ed1ab_0
  - alsa-lib=1.2.3=h516909a_0
  - anyio=3.3.0=py37h89c1867_0
  - argcomplete=1.12.3=pyhd8ed1ab_2
  - argon2-cffi=20.1.0=py37h5e8e339_2
  - arrow-cpp=5.0.0=py37hdf48254_5_cpu
  - async_generator=1.10=py_0
  - attrs=21.2.0=pyhd8ed1ab_0
  - autopage=0.4.0=pyhd8ed1ab_0
  - aws-c-cal=0.5.11=h95a6274_0
  - aws-c-common=0.6.2=h7f98852_0
  - aws-c-event-stream=0.2.7=h3541f99_13
  - aws-c-io=0.10.5=hfb6a706_0
  - aws-checksums=0.1.11=ha31a3da_7
  - aws-sdk-cpp=1.8.186=hb4091e7_3
  - babel=2.9.1=pyh44b312d_0
  - backcall=0.2.0=pyh9f0ad1d_0
  - backports=1.0=py_2
  - backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0
  - backports.zoneinfo=0.2.1=py37h5e8e339_4
  - bleach=4.1.0=pyhd8ed1ab_0
  - bokeh=2.3.3=py37h89c1867_0
  - brotlipy=0.7.0=py37h5e8e339_1001
  - bzip2=1.0.8=h7f98852_4
  - c-ares=1.17.2=h7f98852_0
  - ca-certificates=2021.10.8=ha878542_0
  - certifi=2021.10.8=py37h89c1867_0
  - cffi=1.14.6=py37hc58025e_0
  - chardet=4.0.0=py37h89c1867_1
  - charset-normalizer=2.0.0=pyhd8ed1ab_0
  - click=8.0.1=py37h89c1867_0
  - clickhouse-cityhash=1.0.2.3=py37h3340039_2
  - clickhouse-driver=0.2.1=py37h5e8e339_0
  - cliff=3.9.0=pyhd8ed1ab_0
  - cloudpickle=2.0.0=pyhd8ed1ab_0
  - cmaes=0.8.2=pyh44b312d_0
  - cmd2=2.2.0=py37h89c1867_0
  - colorama=0.4.4=pyh9f0ad1d_0
  - colorcet=2.0.6=pyhd8ed1ab_0
  - colorlog=6.4.1=py37h89c1867_0
  - conda=4.10.3=py37h89c1867_1
  - conda-package-handling=1.7.3=py37h5e8e339_0
  - cramjam=2.3.1=py37h5e8e339_1
  - cryptography=3.4.7=py37h5d9358c_0
  - cycler=0.10.0=py_2
  - cytoolz=0.11.0=py37h5e8e339_3
  - dask=2021.9.0=pyhd8ed1ab_0
  - dask-core=2021.9.0=pyhd8ed1ab_0
  - datashader=0.13.0=pyh6c4a22f_0
  - datashape=0.5.4=py_1
  - dbus=1.13.6=h48d8840_2
  - debugpy=1.4.1=py37hcd2ae1e_0
  - decorator=5.1.0=pyhd8ed1ab_0
  - defusedxml=0.7.1=pyhd8ed1ab_0
  - distributed=2021.9.0=py37h89c1867_0
  - entrypoints=0.3=py37hc8dfbb8_1002
  - expat=2.4.1=h9c3ff4c_0
  - fastparquet=0.7.1=py37hb1e94ed_0
  - filelock=3.0.12=pyh9f0ad1d_0
  - fontconfig=2.13.1=hba837de_1005
  - freetype=2.10.4=h0708190_1
  - fsspec=2021.8.1=pyhd8ed1ab_0
  - gettext=0.19.8.1=h0b5b191_1005
  - gflags=2.2.2=he1b5a44_1004
  - gitdb=4.0.7=pyhd8ed1ab_0
  - gitpython=3.1.23=pyhd8ed1ab_1
  - glib=2.68.4=h9c3ff4c_0
  - glib-tools=2.68.4=h9c3ff4c_0
  - glog=0.5.0=h48cff8f_0
  - greenlet=1.1.1=py37hcd2ae1e_0
  - grpc-cpp=1.40.0=h850795e_0
  - gst-plugins-base=1.18.5=hf529b03_0
  - gstreamer=1.18.5=h76c114f_0
  - heapdict=1.0.1=py_0
  - holoviews=1.14.5=py_0
  - hvplot=0.7.3=py_0
  - icu=68.1=h58526e2_0
  - idna=3.1=pyhd3deb0d_0
  - importlib-metadata=4.8.1=py37h89c1867_0
  - importlib_metadata=4.8.1=hd8ed1ab_0
  - importlib_resources=5.2.2=pyhd8ed1ab_0
  - ipykernel=6.4.1=py37h6531663_0
  - ipympl=0.7.0=pyhd8ed1ab_0
  - ipython=7.27.0=py37h6531663_0
  - ipython_genutils=0.2.0=py_1
  - ipywidgets=7.6.5=pyhd8ed1ab_0
  - jbig=2.1=h7f98852_2003
  - jedi=0.18.0=py37h89c1867_2
  - jinja2=3.0.1=pyhd8ed1ab_0
  - joblib=1.0.1=pyhd8ed1ab_0
  - jpeg=9d=h36c2ea0_0
  - json5=0.9.5=pyh9f0ad1d_0
  - jsonschema=3.2.0=py37hc8dfbb8_1
  - jupyter-server-mathjax=0.2.3=pyhd8ed1ab_0
  - jupyter_client=7.0.2=pyhd8ed1ab_0
  - jupyter_contrib_core=0.3.3=py_2
  - jupyter_contrib_nbextensions=0.5.1=py37hc8dfbb8_1
  - jupyter_core=4.7.1=py37h89c1867_0
  - jupyter_highlight_selected_word=0.2.0=py37h89c1867_1002
  - jupyter_latex_envs=1.4.6=py37h89c1867_1001
  - jupyter_nbextensions_configurator=0.4.1=py37h89c1867_2
  - jupyter_server=1.11.0=pyhd8ed1ab_0
  - jupyterlab=3.1.11=pyhd8ed1ab_0
  - jupyterlab-git=0.32.2=pyhd8ed1ab_0
  - jupyterlab_pygments=0.1.2=pyh9f0ad1d_0
  - jupyterlab_server=2.8.1=pyhd8ed1ab_0
  - jupyterlab_widgets=1.0.2=pyhd8ed1ab_0
  - kiwisolver=1.3.2=py37h2527ec5_0
  - krb5=1.19.2=hcc1bbae_0
  - lcms2=2.12=hddcbb42_0
  - ld_impl_linux-64=2.36.1=hea4e1c9_2
  - lerc=2.2.1=h9c3ff4c_0
  - libarchive=3.5.2=hccf745f_0
  - libblas=3.9.0=11_linux64_openblas
  - libbrotlicommon=1.0.9=h7f98852_5
  - libbrotlidec=1.0.9=h7f98852_5
  - libbrotlienc=1.0.9=h7f98852_5
  - libcblas=3.9.0=11_linux64_openblas
  - libclang=11.1.0=default_ha53f305_1
  - libcurl=7.78.0=h2574ce0_0
  - libdeflate=1.7=h7f98852_5
  - libedit=3.1.20191231=he28a2e2_2
  - libev=4.33=h516909a_1
  - libevent=2.1.10=hcdb4288_3
  - libffi=3.3=h58526e2_2
  - libgcc-ng=11.1.0=hc902ee8_8
  - libgfortran-ng=11.1.0=h69a702a_8
  - libgfortran5=11.1.0=h6c583b3_8
  - libglib=2.68.4=h3e27bee_0
  - libgomp=11.1.0=hc902ee8_8
  - libiconv=1.16=h516909a_0
  - liblapack=3.9.0=11_linux64_openblas
  - libllvm11=11.1.0=hf817b99_2
  - libnghttp2=1.43.0=h812cca2_0
  - libogg=1.3.4=h7f98852_1
  - libopenblas=0.3.17=pthreads_h8fe5266_1
  - libopus=1.3.1=h7f98852_1
  - libpng=1.6.37=h21135ba_2
  - libpq=13.3=hd57d9b9_0
  - libprotobuf=3.16.0=h780b84a_0
  - libsodium=1.0.18=h36c2ea0_1
  - libsolv=0.7.19=h780b84a_5
  - libssh2=1.10.0=ha56f1ee_0
  - libstdcxx-ng=11.1.0=h56837e0_8
  - libta-lib=0.4.0=h516909a_0
  - libthrift=0.14.2=he6d91bd_1
  - libtiff=4.3.0=hf544144_1
  - libutf8proc=2.6.1=h7f98852_0
  - libuuid=2.32.1=h7f98852_1000
  - libuv=1.42.0=h7f98852_0
  - libvorbis=1.3.7=h9c3ff4c_0
  - libwebp-base=1.2.1=h7f98852_0
  - libxcb=1.13=h7f98852_1003
  - libxkbcommon=1.0.3=he3ba5ed_0
  - libxml2=2.9.12=h72842e0_0
  - libxslt=1.1.33=h15afd5d_2
  - llvmlite=0.37.0=py37h9d7f4d0_0
  - locket=0.2.0=py_2
  - lxml=4.6.3=py37h77fd288_0
  - lz4-c=1.9.3=h9c3ff4c_1
  - lzo=2.10=h516909a_1000
  - mako=1.1.5=pyhd8ed1ab_0
  - mamba=0.15.3=py37h7f483ca_0
  - markdown=3.3.4=pyhd8ed1ab_0
  - markupsafe=2.0.1=py37h5e8e339_0
  - matplotlib=3.4.3=py37h89c1867_0
  - matplotlib-base=3.4.3=py37h1058ff1_0
  - matplotlib-inline=0.1.3=pyhd8ed1ab_0
  - mistune=0.8.4=py37h5e8e339_1004
  - msgpack-python=1.0.2=py37h2527ec5_1
  - multipledispatch=0.6.0=py_0
  - mysql-common=8.0.25=ha770c72_2
  - mysql-libs=8.0.25=hfa10184_2
  - nb_conda_kernels=2.3.1=py37h89c1867_0
  - nbclassic=0.3.1=pyhd8ed1ab_1
  - nbclient=0.5.4=pyhd8ed1ab_0
  - nbconvert=6.1.0=py37h89c1867_0
  - nbdime=3.1.0=pyhd8ed1ab_0
  - nbformat=5.1.3=pyhd8ed1ab_0
  - ncurses=6.2=h58526e2_4
  - nest-asyncio=1.5.1=pyhd8ed1ab_0
  - notebook=6.4.3=pyha770c72_0
  - nspr=4.30=h9c3ff4c_0
  - nss=3.69=hb5efdd6_0
  - numba=0.54.0=py37h2d894fd_0
  - numpy=1.20.3=py37h038b26d_1
  - olefile=0.46=pyh9f0ad1d_1
  - openjpeg=2.4.0=hb52868f_1
  - openssl=1.1.1l=h7f98852_0
  - optuna=2.10.0=pyhd8ed1ab_0
  - orc=1.6.10=h58a87f1_0
  - packaging=21.0=pyhd8ed1ab_0
  - pandas=1.3.2=py37he8f5f7f_0
  - pandoc=2.14.2=h7f98852_0
  - pandocfilters=1.4.2=py_1
  - panel=0.12.1=py_0
  - param=1.11.1=pyh6c4a22f_0
  - parquet-cpp=1.5.1=1
  - parso=0.8.2=pyhd8ed1ab_0
  - partd=1.2.0=pyhd8ed1ab_0
  - patsy=0.5.2=pyhd8ed1ab_0
  - pbr=5.6.0=pyhd8ed1ab_0
  - pcre=8.45=h9c3ff4c_0
  - pexpect=4.8.0=py37hc8dfbb8_1
  - pickle5=0.0.11=py37h5e8e339_0
  - pickleshare=0.7.5=py37hc8dfbb8_1002
  - pillow=8.3.2=py37h0f21c89_0
  - pip=21.2.4=pyhd8ed1ab_0
  - prettytable=2.2.0=pyhd8ed1ab_0
  - prometheus_client=0.11.0=pyhd8ed1ab_0
  - prompt-toolkit=3.0.20=pyha770c72_0
  - psutil=5.8.0=py37h5e8e339_1
  - pthread-stubs=0.4=h36c2ea0_1001
  - ptyprocess=0.7.0=pyhd3deb0d_0
  - pyarrow=5.0.0=py37h58331f5_5_cpu
  - pycosat=0.6.3=py37h5e8e339_1006
  - pycparser=2.20=pyh9f0ad1d_2
  - pyct=0.4.6=py_0
  - pyct-core=0.4.6=py_0
  - pygments=2.10.0=pyhd8ed1ab_0
  - pykalman=0.9.5=py_1
  - pyopenssl=20.0.1=pyhd8ed1ab_0
  - pyparsing=2.4.7=pyh9f0ad1d_0
  - pyperclip=1.8.2=pyhd8ed1ab_2
  - pyqt=5.12.3=py37h89c1867_7
  - pyqt-impl=5.12.3=py37he336c9b_7
  - pyqt5-sip=4.19.18=py37hcd2ae1e_7
  - pyqtchart=5.12=py37he336c9b_7
  - pyqtwebengine=5.12.1=py37he336c9b_7
  - pyrsistent=0.17.3=py37h5e8e339_2
  - pysocks=1.7.1=py37h89c1867_3
  - python=3.7.10=hffdb5ce_100_cpython
  - python-dateutil=2.8.2=pyhd8ed1ab_0
  - python_abi=3.7=2_cp37m
  - pytz=2021.1=pyhd8ed1ab_0
  - pyviz_comms=2.1.0=py_0
  - pyyaml=5.4.1=py37h5e8e339_1
  - pyzmq=22.2.1=py37h336d617_0
  - qt=5.12.9=hda022c4_4
  - re2=2021.09.01=h9c3ff4c_0
  - readline=8.1=h46c0cb4_0
  - redis-py=3.5.3=pyh9f0ad1d_0
  - reproc=14.2.3=h7f98852_0
  - reproc-cpp=14.2.3=h9c3ff4c_0
  - requests=2.26.0=pyhd8ed1ab_0
  - requests-unixsocket=0.2.0=py_0
  - ruamel_yaml=0.15.80=py37h5e8e339_1004
  - s2n=1.0.10=h9b69904_0
  - scikit-learn=0.24.2=py37hf0f1638_1
  - send2trash=1.8.0=pyhd8ed1ab_0
  - setproctitle=1.1.10=py37h5e8e339_1004
  - setuptools=58.0.4=py37h89c1867_0
  - six=1.16.0=pyh6c4a22f_0
  - smmap=3.0.5=pyh44b312d_0
  - snappy=1.1.8=he1b5a44_3
  - sniffio=1.2.0=py37h89c1867_1
  - sortedcontainers=2.4.0=pyhd8ed1ab_0
  - sqlalchemy=1.4.25=py37h5e8e339_0
  - sqlite=3.36.0=h9cd32fc_1
  - statsmodels=0.12.2=py37hb1e94ed_0
  - stevedore=3.4.0=py37h89c1867_0
  - ta-lib=0.4.19=py37ha21ca33_2
  - tabulate=0.8.9=pyhd8ed1ab_0
  - tblib=1.7.0=pyhd8ed1ab_0
  - tensorboardx=2.4=pyhd8ed1ab_0
  - terminado=0.12.1=py37h89c1867_0
  - testpath=0.5.0=pyhd8ed1ab_0
  - threadpoolctl=2.2.0=pyh8a188c0_0
  - thrift=0.13.0=py37hcd2ae1e_2
  - tk=8.6.11=h27826a3_1
  - toolz=0.11.1=py_0
  - tornado=6.1=py37h5e8e339_1
  - tqdm=4.62.2=pyhd8ed1ab_0
  - traitlets=5.1.0=pyhd8ed1ab_0
  - typing_extensions=3.10.0.0=pyha770c72_0
  - tzdata=2021a=he74cb21_1
  - tzlocal=3.0=py37h89c1867_2
  - urllib3=1.26.6=pyhd8ed1ab_0
  - wcwidth=0.2.5=pyh9f0ad1d_2
  - webencodings=0.5.1=py_1
  - websocket-client=0.57.0=py37h89c1867_4
  - wheel=0.37.0=pyhd8ed1ab_1
  - widgetsnbextension=3.5.1=py37h89c1867_4
  - xarray=0.19.0=pyhd8ed1ab_1
  - xeus=2.0.0=h7d0c39e_0
  - xeus-python=0.13.0=py37h4b46df4_1
  - xeus-python-shell=0.1.5=pyhd8ed1ab_0
  - xorg-libxau=1.0.9=h7f98852_0
  - xorg-libxdmcp=1.1.3=h7f98852_0
  - xz=5.2.5=h516909a_1
  - yaml=0.2.5=h516909a_0
  - zeromq=4.3.4=h9c3ff4c_1
  - zict=2.0.0=py_0
  - zipp=3.5.0=pyhd8ed1ab_0
  - zlib=1.2.11=h516909a_1010
  - zstandard=0.15.2=py37h5e8e339_0
  - zstd=1.5.0=ha95c52a_0
  - pip:
    - absl-py==0.13.0
    - aiohttp==3.7.4.post0
    - aiohttp-cors==0.7.0
    - aioredis==1.3.1
    - async-timeout==3.0.1
    - autograd==1.3
    - bayesian-optimization==1.2.0
    - blessed==1.19.0
    - blessings==1.7
    - cachetools==4.2.2
    - cma==2.7.0
    - colorful==0.5.4
    - cython==0.29.24
    - future==0.18.2
    - google-api-core==1.31.2
    - google-auth==1.35.0
    - google-auth-oauthlib==0.4.6
    - googleapis-common-protos==1.53.0
    - gpustat==0.6.0
    - gpy==1.10.0
    - gpytorch==1.5.1
    - grpcio==1.40.0
    - hebo==0.1.0
    - hiredis==2.0.0
    - multidict==5.1.0
    - nevergrad==0.4.3.post8
    - nvidia-ml-py3==7.352.0
    - oauthlib==3.1.1
    - opencensus==0.7.13
    - opencensus-context==0.1.2
    - paramz==0.9.5
    - protobuf==3.17.3
    - psycopg2==2.9.1
    - py-spy==0.3.9
    - pyasn1==0.4.8
    - pyasn1-modules==0.2.8
    - pydantic==1.8.2
    - pymoo==0.4.2.2
    - ray==1.7.1
    - requests-oauthlib==1.3.0
    - rsa==4.7.2
    - scipy==1.5.4
    - sklearn==0.0
    - tensorboard==2.6.0
    - tensorboard-data-server==0.6.1
    - tensorboard-plugin-wit==1.8.0
    - torch==1.9.1
    - werkzeug==2.0.1
    - yarl==1.6.3

Description of expected behavior and the observed behavior

Expected: Screenshot from 2021-10-30 23-48-06

Got: Screenshot from 2021-10-30 23-48-23

The original dtype is numpy.uint32 (which gives the second figure). To get the first figure I have to change type: my_df.my_col = my_df.my_col.astype(np.int32)

Complete, minimal, self-contained example code that reproduces the issue

The only thing I noticed is the difference in dtype of data frame’s column. The original is dtype: uint32. When type is changed to e.g. dtype: int32, it works as expected. When trying to reproduce I get an empty figure instead of a half colored plot (see the picture above). So not sure what else the difference could be.

import numpy as np

# works as intended
test = pd.DataFrame([i for i in range(100)], columns=["my_column"])
test.plot(datashade=True)

# creates an empty figure
test.my_column = test.my_column.astype(np.uint32)
test.plot(datashade=True)

Stack traceback and/or browser JavaScript console output

Only a couple of warnings:

/home/toaster/PROGS/miniconda3/envs/puma-lab/lib/python3.7/site-packages/holoviews/operation/datashader.py:428: FutureWarning: casting datetime64[ns] values to int64 with .astype(...) is deprecated and will raise in a future version. Use .view(...) instead.
  df[d.name] = vals.astype('int64')
/home/toaster/PROGS/miniconda3/envs/puma-lab/lib/python3.7/site-packages/holoviews/operation/datashader.py:428: FutureWarning: casting datetime64[ns] values to int64 with .astype(...) is deprecated and will raise in a future version. Use .view(...) instead.
  df[d.name] = vals.astype('int64')

Issue Analytics

  • State:closed
  • Created 2 years ago
  • Comments:6 (4 by maintainers)

github_iconTop GitHub Comments

1reaction
Hoxbrocommented, Nov 27, 2021

Sorry if I wasn’t clear, the plot I showed was with my fix in it. See the PR above my comment.

1reaction
jbednarcommented, Nov 27, 2021

Someone could investigate, but no one has volunteered yet, so it’s an open challenge. I am not sure it’s a datashader issue, and mostly the same people work on both projects, so here is as good a place as any. For now there is a workaround, but if you’d like to investigate, the first step would be to trace though and see if the data is converted to a new type before calling datashader. Wish I had more details than that, but that’s what needs investigating!

Read more comments on GitHub >

github_iconTop Results From Across the Web

strange graph while plotting two columns of a DataFrame
The problem comes due to the fact that the elements in the x-axis are not sorted. Consider the following example:
Read more >
Chart visualization — pandas 1.5.2 documentation - PyData |
We provide the basics in pandas to easily create decent looking plots. ... On DataFrame, plot() is a convenience to plot all of...
Read more >
Understand df.plot in pandas - Jonathan Soma
Plotting Version 1: .plot plots the index against every column. Let's look at a slice somewhere in the middle of our data. It's...
Read more >
Plot Histograms Using Pandas: hist() Example - Mode Analytics
Calling the dtypes attribute of a dataframe will return information about the data ... column: the specific column(s) you want to create a...
Read more >
Plot With Pandas: Python Data Visualization for Beginners
You'll learn about the different kinds of plots that pandas offers, ... The next plots will give you a general overview of a...
Read more >

github_iconTop Related Medium Post

No results found

github_iconTop Related StackOverflow Question

No results found

github_iconTroubleshoot Live Code

Lightrun enables developers to add logs, metrics and snapshots to live code - no restarts or redeploys required.
Start Free

github_iconTop Related Reddit Thread

No results found

github_iconTop Related Hackernoon Post

No results found

github_iconTop Related Tweet

No results found

github_iconTop Related Dev.to Post

No results found

github_iconTop Related Hashnode Post

No results found