Matplotlib: `pcolormesh.get_array()` returns flattened array - how to get 2D data back?

Question

I'm trying to get the data values along a line (like in this hint). That example uses imshow(), but I'm currently using pcolormesh() to plot.

I'm finding that the get_array() function, to grab plotted data from pcolormesh() is returning a 1-D, flattened array of my data, instead of the original (or truncated) 2-D data.

For example:

D = np.genfromtxt(DataFilePath, skip_header=4, delimiter=',', unpack=True)
print( D.shape )
: (500, 500)

...more code...

img = ax[0].pcolormesh( np.arange( len(D[0,:]) ), np.arange(len(D[:,0])), D)

>>> D
: array([[ 42.38,  41.93,  41.92, ...,  41.73,  41.74,  41.51],
       [ 41.88,  42.24,  42.21, ...,  41.88,  41.67,  41.64],
       [ 42.4 ,  41.47,  41.49, ...,  41.92,  42.07,  41.49],
       ..., 
       [ 44.24,  44.14,  44.17, ...,  40.2 ,  40.68,  40.67],
       [ 44.59,  44.24,  44.3 , ...,  40.91,  40.92,  40.95],
       [ 44.2 ,  44.27,  44.27, ...,  40.82,  40.91,  40.94]])
>>> img.get_array()
: array([ 42.38,  41.93,  41.92, ...,  40.85,  40.91,  40.92])

Since I'm trying to grab user-clicks on the plot and then re-plot using the clicked data values (like in this hint), I would like to use a function/class which won't have global access to the original data, but does have access to the img object.

Any idea how I get the 2D data from pcolormesh() using only the img(QuadMesh) object? It doesn't even seem to have the x/y length/shape values, for me to reconstruct the data from the 1-D get_array().

Thanks!

It's like pcolormesh ran np.ravel() on the data and stroed it in get_array() - any way to unravel? — Demis
– Demis, Commented Jan 17, 2016 at 16:07
Just want to get the plotted data values along a line between the points the user clicked & then let go - this will occur inside the event-handler class that only gets access to the img (QuadMesh) object, but can't access the original Data array. — Demis
– Demis, Commented Jan 17, 2016 at 22:24
Then the img attributes the @unutbu mentions are the way go. — hpaulj
– hpaulj, Commented Jan 17, 2016 at 23:56
posted the whole function here: stackoverflow.com/questions/7878398/… — Demis
– Demis, Commented Jan 20, 2016 at 15:22

unutbu · Accepted Answer · 2016-01-17 18:44:45Z

4

The shape of the array in stored in private attributes, _meshWidth and _meshHeight. Nevertheless, since these attributes are not part of the public API, it would be better to save the shape of the original data than to rely on these if possible.

import matplotlib.pyplot as plt
import numpy as np

D = np.random.uniform(0, 100, size=(5, 5))
fig, ax = plt.subplots()
h, w = D.shape
img = ax.pcolormesh( np.arange(h+1), np.arange(w+1), D)

D2 = img.get_array().reshape(img._meshWidth, img._meshHeight)
assert  np.array_equal(D, D2)

Note also that if you wish to recover the original array D, then the coordinate arrays, np.arange(h+1), np.arange(w+1) must have lengths one bigger than the shape of D. Otherwise, img.get_array() returns an array of shape (499, 499) when D has shape (500, 500).

answered Jan 17, 2016 at 18:44

unutbu

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3 Comments

hpaulj Over a year ago

From _pcolorargs it looks like pcolor will lop off points from C if needed to match x and y.

Demis Over a year ago

ah, the _meshWidth & _meshHeight values are what I needed to reproduce something like the original array. Unfortunately, coding these attributes makes my function now only work for pcolormesh - if there was a general API call (like get_width()/get_height()), my function would work for pcolor, pcolormesh, and maybe also contourf and others. Maybe should submit a feature request...

hpaulj Over a year ago

I added some notes on what pcolor produces - it divides the mesh into many simple quadrilaterals, so it's img does not have any notion of mesh height or width.

hpaulj · Accepted Answer · 2016-01-18 18:06:42Z

3

Yes, it does ravel the inputs:

https://github.com/matplotlib/matplotlib/blob/master/lib/matplotlib/axes/_axes.py

    # convert to one dimensional arrays
    C = C.ravel()
    X = X.ravel()
    Y = Y.ravel()

If you know the desired 2d shape, you can unravel with a simple reshape call.

If the result should have the same shape as D use:

img.get_array().reshape(D.shape)

If the size of the raveled C can change, then this won't work.

If I make a D array that is (10,20), and plot it

img = pyplot.pcolormesh(D)

img._A is (200,), the array that img.get_array() returns.

img._meshHeight, img._meshWidth
# 10, 20

So the array can be reshaped with:

img._A.reshape(img._meshHeight, img._meshWidth)

img._coordinates is a (11,21,2) array, the coordinates in the x and y direction, plus one point. So you could get the C reshaping information from _coordinates as well. I don't see any public API method for retrieving these attributes, but that doesn't stop 'serious' Python programmers. In this test case, it generated the coordinates from the shape of D.

This Quadmesh was created with:

    coords = np.zeros(((Nx * Ny), 2), dtype=float)
    coords[:, 0] = X
    coords[:, 1] = Y

    collection = QuadMesh(
        Nx - 1, Ny - 1, coords, ...)
    ....
    collection.set_array(C)

A search for get_array in the matplotlib github repository does not get many hits.

I dug into the pcolor code a bit. It returns a PolyCollections img rather than a Quadmesh. It contains the information for drawing a collection of quadrilaterals.

For example in my test case with a 10x20 input, img._paths is a list of 200 Path objects

In [486]: img1._paths[0]
Out[486]: 
Path(array([[ 0.,  0.],
       [ 0.,  1.],
       [ 1.,  1.],
       [ 1.,  0.],
       [ 0.,  0.],
       [ 0.,  0.]]), array([ 1,  2,  2,  2,  2, 79], dtype=uint8))

It has five coordinate pairs, the xy points needed to draw the boundary of the quad, which will have a color value corresponding to C[0] (in the raveled form).

So all the X Y grid information is now coded in these Path objects. Instead of plotting a mesh it plots 200 colored squares (quads). The PolyCollections code does not assume that the squares are in any order or even touching each other. The big picture has been replaced with a bunch of independent small pictures.

You might be able reassemble those quads into a mesh, looking for matching vertices, etc. But it would be a lot of work.

edited Jan 18, 2016 at 18:06

answered Jan 17, 2016 at 18:16

hpaulj

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3 Comments

Demis Over a year ago

My function won't have access to the original data D unfortunately.

Demis Over a year ago

Thanks, that is really interesting. Have you, in your research, come across a way that would work for the various types of surface/2D plotting? I haven't tried it yet, but I am wondering if the '_coordinates' method could work for not just 'Pcolormesh', but also 'Pcolor', or 'ContorF'.

hpaulj Over a year ago

The pcolor img doesn't have a _coordinates attribute. The only place I could find the xy values was in ._paths. I looked in both the code and a sample img object (via ipython).

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