How to extract data from matplotlib plot

Question

I have a wxPython program which reads from different datasets, performs various types of simple on-the-fly analysis on the data and plots various combinations of the datasets to matplotlib canvas. I would like to have the opportunity to dump currently plotted data to file for more sophisticated analysis later on.

The question is: are there any methods in matplotlib that allow access to the data currently plotted in matplotlib.Figure?

score 37 · Accepted Answer · answered Jan 20 '12 at 09:12

37

Jakub is right about modifying the Python script to write out the data directly from the source from which it was sent into the plot; that's the way I'd prefer to do this. But for reference, if you do need to get data out of a plot, I think this should do it

gca().get_lines()[n].get_xydata()

Alternatively you can get the x and y data sets separately:

line = gca().get_lines()[n]
xd = line.get_xdata()
yd = line.get_ydata()

answered Jan 20 '12 at 09:12

David Z

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Thanks, I think that should do it. If you want to know the reasons why I prefer dumping data from plot to messing with data sources, please see my comment to @Jacub. – Andrey Sobolev Jan 20 '12 at 09:42
1

Why doesn't a `mpl_toolkits.mplot3d.art3d.Line3D object` have `get_zdata()`? I can't extract the z values. :-( – Sibbs Gambling Jan 12 '18 at 01:35
@SibbsGambling That you'd have to take up with the developers of matplotlib. – David Z Jan 12 '18 at 02:28

score 9 · Answer 2 · answered Nov 20 '18 at 17:01

The matplotlib.pyplot.gca can be used to extract data from matplotlib plots. Here is a simple example:

import matplotlib.pyplot as plt
plt.plot([1,2,3],[4,5,6])
ax = plt.gca()
line = ax.lines[0]
line.get_xydata()

On running this, you will see 2 outputs - the plot and the data:

array([[1., 4.],
   [2., 5.],
   [3., 6.]])

You can also get the x data and y data seperately. On running line.get_xdata(), you will get:

array([1, 2, 3])

And on running line.get_ydata(), you will get:

array([4, 5, 6])

Note: gca stands for get current axis

mobiuscreek · Answer 3 · 2021-06-16T13:50:20.963

To sum up, for future reference:

If plotting with plt.plot() or plt.stem() or plt.step() you can get a list of Line2D objects with:

ax = plt.gca() # to get the axis
ax.get_lines()

For plt.pie(), plt.bar() or plt.barh() you can get a list of wedge or rectangle objects with:

ax = plt.gca() # to get the axis
ax.patches()

Then, depending on the situation you can get the data by running get_xdata(), get_ydata() (see Line2D) for more info.

or i.e get_height() for a bar plot (see Rectangle) for more info.

In general for all basic plotting functions, you can find what you are looking for by running ax.get_children()

that returns a list of the children Artists (the base class the includes all of the figure's elements).

score 1 · Answer 4 · answered Jan 04 '19 at 04:21

1

I know this is an old question, but I feel there is a solution better than the ones offered here so I decided to write this answer.

You can use unittest.mock.patch to temporarily replace the matplotlib.axes.Axes.plot function:

from unittest.mock import patch

def save_data(self, *args, **kwargs):
    # save the data that was passed into the plot function
    print(args)

with patch('matplotlib.axes.Axes.plot', new=save_data):
    # some code that will eventually plot data
    a_function_that_plots()

Once you exit the with block, Axes.plot will resume normal behavior.

answered Jan 04 '19 at 04:21

uclatommy

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Brilliant, just brilliant! Should be the accepted answer in 2021 – jtlz2 Nov 16 '21 at 09:19
How do I get the data into memory without writing to file? The `with` kills it. `global`? :\ – jtlz2 Nov 16 '21 at 09:21

score 1 · Answer 5 · answered Jan 20 '12 at 08:55

1

Its Python, so you can modify the source script directly so the data is dumped before it is plotted

answered Jan 20 '12 at 08:55

Jakub M.

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I know that's the most pythonic way :) But first, the data is sent to plot from many places and is modified while on the plot; I would need to keep track of every modification of the plotted data. And second - I don't need to dump the data *every time* it is plotted. I would like first to find something interesting and then press a button on NavigationToolbar to export it to file. NavigationToolbar is linked to FigureCanvas, so the buttons have seamless access to Figure properties and methods. That's why I asked how to dump the data from plot. – Andrey Sobolev Jan 20 '12 at 09:35
2

This would only work if the user knows beforehand that they want to export the data and the data is static. Rare I would say. – Oliver Sep 25 '14 at 19:56
while this answer is a general good advice, it is not a good answer to the question – LudvigH Mar 29 '23 at 07:57

score 0 · Answer 6 · answered Mar 22 '23 at 11:34

As pointed out in the answer by @mobiuscreek, the way to extract data from axis depends on the function used for plotting: e.g., ax.get_lines() would work for a plot created via ax.plot(), but it gives an empty array, if the lines were created, e.g., using matplotlib.collections.LineCollection. (It is likely to be more of a problem when the figures are created by a third-party code.)

The general approach is then using ax.get_children() and parsing it as needed. See, e.g., this answer.

How to extract data from matplotlib plot

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