Holoviews; timeseries plot does not show

[IvanTImo]

Good day. I am trying to plot timeseries with large data 2 billions of points and embed this plot into PyQt5 using QtWebEngineWidgets.

The Holoviews manual has the whole section on working with large data Working with large data using datashader. I am using the timeseries example from this chapter but when I run it the plot does not show. I tried python from VS Code and run python from Jupyter notebook. I am missing something…

Thanks.

The code snippet and list of installed packages are included

import datashader as ds
import numpy as np
import holoviews as hv
import pandas as pd

from holoviews import opts
from holoviews.operation.datashader import datashade, shade, dynspread, spread, rasterize
from holoviews.operation import decimate

hv.extension(‘bokeh’,‘matplotlib’)

def time_series(T = 1, N = 100, mu = 0.1, sigma = 0.1, S0 = 20):
“”“Parameterized noisy time series”""
dt = float(T)/N
t = np.linspace(0, T, N)
W = np.random.standard_normal(size = N)
W = np.cumsum(W)np.sqrt(dt) # standard brownian motion
X = (mu-0.5sigma**2)t + sigmaW
S = S0*np.exp(X) # geometric brownian motion
return S

points = [(0.1i, np.sin(0.1i)) for i in range(100)]
hv.Curve(points)

hv.HoloMap({i: hv.Curve([1, 2, 3-i], group=‘Group’, label=‘Label’) for i in range(3)}, ‘Value’)

dates = pd.date_range(start=“2014-01-01”, end=“2016-01-01”, freq=‘1D’) # or ‘1min’
curve = hv.Curve((dates, time_series(N=len(dates), sigma = 1)))
rasterize(curve, width=800).opts(width=800, cmap=[‘blue’])

Package                   Version
------------------------- ---------
altgraph                  0.17
aplus                     0.11.0
argon2-cffi               20.1.0
astropy                   4.2
async-generator           1.10
attrs                     20.3.0
autopep8                  1.5.4
backcall                  0.2.0
bleach                    3.2.1
bokeh                     2.2.3
boto3                     1.16.30
botocore                  1.19.30
bqplot                    0.12.19
branca                    0.4.1
cachetools                4.1.1
certifi                   2020.12.5
cffi                      1.14.4
chardet                   3.0.4
click                     7.1.2
cloudpickle               1.6.0
colorama                  0.4.4
colorcet                  2.0.2
cycler                    0.10.0
dask                      2.30.0
datashader                0.11.1
datashape                 0.5.2
decorator                 4.4.2
defusedxml                0.6.0
distributed               2.30.1
entrypoints               0.3
fsspec                    0.8.4
future                    0.18.2
h5py                      3.1.0
HeapDict                  1.0.1
holoviews                 1.14.0
idna                      2.10
ipydatawidgets            4.1.0
ipykernel                 5.3.4
ipyleaflet                0.13.3
ipympl                    0.5.8
ipython                   7.19.0
ipython-genutils          0.2.0
ipyvolume                 0.5.2
ipyvue                    1.4.1
ipyvuetify                1.5.1
ipywebrtc                 0.5.0
ipywidgets                7.5.1
jedi                      0.17.2
Jinja2                    2.11.2
jmespath                  0.10.0
jsonschema                3.2.0
jupyter                   1.0.0
jupyter-client            6.1.7
jupyter-console           6.2.0
jupyter-core              4.7.0
jupyterlab-pygments       0.1.2
kiwisolver                1.3.1
llvmlite                  0.35.0
locket                    0.2.0
Markdown                  3.3.3
MarkupSafe                1.1.1
matplotlib                3.3.3
mistune                   0.8.4
msgpack                   1.0.1
multipledispatch          0.6.0
nbclient                  0.5.1
nbconvert                 6.0.7
nbformat                  5.0.8
nest-asyncio              1.4.3
notebook                  6.1.5
numba                     0.52.0
numexpr                   2.7.1
numpy                     1.19.4
packaging                 20.7
pandas                    1.2.0
pandocfilters             1.4.3
panel                     0.10.2
param                     1.10.0
parso                     0.7.1
partd                     1.1.0
pefile                    2019.4.18
pickleshare               0.7.5
Pillow                    8.0.1
pip                       21.0.1
progressbar2              3.53.1
prometheus-client         0.9.0
prompt-toolkit            3.0.8
psutil                    5.7.3
pyarrow                   2.0.0
pycodestyle               2.6.0
pycparser                 2.20
pyct                      0.4.6
pyerfa                    1.7.1.1
Pygments                  2.7.3
pyinstaller               4.2
pyinstaller-hooks-contrib 2020.10
PyOpenGL                  3.1.5
pyparsing                 2.4.7
PyQt5                     5.15.2
PyQt5-sip                 12.8.1
pyqtgraph                 0.11.0
PyQtWebEngine             5.15.2
pyrsistent                0.17.3
python-dateutil           2.8.1
python-utils              2.4.0
pythreejs                 2.2.1
pytz                      2020.4
pyviz-comms               0.7.6
pywin32                   300
pywin32-ctypes            0.2.0
pywinpty                  0.5.7
PyYAML                    5.3.1
pyzmq                     20.0.0
qtconsole                 5.0.1
QtPy                      1.9.0
requests                  2.25.0
s3fs                      0.2.2
s3transfer                0.3.3
scipy                     1.5.4
Send2Trash                1.5.0
setuptools                49.2.1
six                       1.15.0
sortedcontainers          2.3.0
tabulate                  0.8.7
tblib                     1.7.0
terminado                 0.9.1
testpath                  0.4.4
toml                      0.10.2
toolz                     0.11.1
tornado                   6.1
tqdm                      4.54.1
traitlets                 5.0.5
traittypes                0.2.1
typing-extensions         3.7.4.3
urllib3                   1.26.2
wcwidth                   0.2.5
webencodings              0.5.1
widgetsnbextension        3.5.1
xarray                    0.16.2
zict                      2.0.0

[fmfreeze]

Hi!
If you share code, please do it in a proper markdown way for better readability. How to do it is e.g. described here:
https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet#code-and-syntax-highlighting

Copying lines like X = (mu-0.5 sigma**2) t + sigma W is not python anymore, as for example the * character is a markup formatter. In a code block it looks like it should I guess X = (mu-0.5* sigma**2) *t + sigma* W

Further the code you shared is not fully python code.
It seems you are using the wrong character for specifying string objects:
E.g. hv.extension(‘bokeh’,‘matplotlib’) throws the error message SyntaxError: invalid character in identifier. This happens throughout your whole code example. Fix it, so it is easier to help you.

[IvanTImo]

I am new to this. I could not find how to edit the original post. I would like to output a graph into a qWebEngineWidgets of PyQt5. When I am running this code fragment from VS code nothing shows up. I am missing something.

import datashader as ds
import numpy as np
import holoviews as hv
import pandas as pd

from holoviews import opts
from holoviews.operation.datashader import datashade, shade, dynspread, spread, rasterize
from holoviews.operation import decimate

hv.extension('bokeh','matplotlib')

def time_series(T = 1, N = 100, mu = 0.1, sigma = 0.1, S0 = 20):  
    """Parameterized noisy time series"""
    dt = float(T)/N
    t = np.linspace(0, T, N)
    W = np.random.standard_normal(size = N) 
    W = np.cumsum(W)*np.sqrt(dt) # standard brownian motion
    X = (mu-0.5*sigma**2)*t + sigma*W 
    S = S0*np.exp(X) # geometric brownian motion
    return S

points = [(0.1*i, np.sin(0.1*i)) for i in range(100)]
hv.Curve(points)

hv.HoloMap({i: hv.Curve([1, 2, 3-i], group='Group', label='Label') for i in range(3)}, 'Value')

dates = pd.date_range(start="2014-01-01", end="2016-01-01", freq='1D') # or '1min'
curve = hv.Curve((dates, time_series(N=len(dates), sigma = 1)))
rasterize(curve, width=800).opts(width=800, cmap=['blue'])

Thanks

[fmfreeze]

I have no experience with qWebEngineWidgets, sorry.

But the code itself I guess is producing what you want.Running it in a Jupyter notebook it outputs this plot:

[Marc]

Hi @IvanTImo

Thanks welcome to the community and sharing your question.

Here are my observations

Edit Post

You can edit your original post (if needed) by clicking the pencil.

VS Code

I could get your code working in VS Code

Things to try

Try creating a new virtual environment and install the dependencies. Make sure you have the latest version of HoloViews and DataShader. And then try again.

If that does not work. Try to provide us more information.

• Check the “console” of the browser. There might be errors. You find it via CTRL+SHIFT+I (at least for me on Windows).

• Create a small video or .gif of what you are doing. Maybe you are doing something wrong that we cannot see from our side.

[IvanTImo]

Thanks for your help!
The code works if I cut and paste it directly to the Jupyter Notebook.
If I run it as an external file the plot does not appear. It cannot find the browser to display.

Marc, you run the code in the VS code studio and the plot appeared in the Jupyter?

I need to start the web engine in the PyQt and find a way to bind it to Holoviews.

Thanks for you help.

[Marc]

Hi @IvanTImo

In order for me to understand the problems you are facing you would have to come up with some code that gives me a better understanding of the problem and something from where I can reproduce the problems and start exploring solutions. This would include some Qt code. And include screenshot, videos and/ or errors messages. Is that possible?