Allow passing an array as intensity for plot

[core-man]

Description of proposed changes

Pass a NumPy array to intensity (similar to the x, y, size parameters) for the plot method when we use x/y as the input. (See #891 for details)

Currently, we can have two ways to specify an intensity/intensities.

• Simply give a constant intensity like intensity=0.5, which works for both x/y and data input. This is similar to -I0.5 in the GMT command line.
• Set intensity=True, and read intensities from an input file or from a 2D NumPy array, which is only for the data parameter. This is similar to -I in the GMT command line.

So, when we want to change the intensities for different points, we can only use the data parameter now. This PR tries to pass an array to intensity so that we can set different intensities when we use x/y as point input. This way will not work for data input.

Related to #891

Reminders

• Run make format and make check to make sure the code follows the style guide.
• Add tests for new features or tests that would have caught the bug that you're fixing.
• Add new public functions/methods/classes to doc/api/index.rst.
• Write detailed docstrings for all functions/methods.
• If adding new functionality, add an example to docstrings or tutorials.

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[seisman]

I haven't reviewed your codes, but please do plot and plot3d in two PRs.

[core-man]

I haven't reviewed your codes, but please do plot and plot3d in two PRs.

Okay. BTW, I only added a NumPy array support for intensity now to test if it works (it works). More work need to be done (e.g., add test).

[weiji14]

Just one comment for now :)

Okay. BTW, I only added a NumPy array support for intensity now to test if it works (it works). More work need to be done (e.g., add test).

Yes, time for you to pick up unit testing! I'm currently revamping the plot testing ways at #1036 but you can start first and we'll refactor later. The PyGMT guidelines are at https://github.com/GenericMappingTools/pygmt/blob/v0.3.1/CONTRIBUTING.md#testing-plots, but if you're new to (or need a refresher on) testing, I found https://automationpanda.com/python/ to be a good resource to understand the 'why' and 'how' of testing.

[core-man]

A test with an array intensity is added (9adf272), referring to test_plot_varying_transparency().

pygmt/pygmt/tests/test_plot.py

Line 264 in 1a2289a

def test_plot_varying_transparency():

[core-man]

Two related questions:

1. The documentation for color parameter needs a revision in the API page of plot (also plot3d)?

color (str) – Select color or pattern for filling of symbols or polygons. Default is no fill.

color can also be a 1D array just like the sizes parameter when we use x/y parameters. See the last example in Plotting data points.

2. We can now input array-like sizes, color, intensity. Shall we support array-like symbols?

The format of the input file of plot is (-S and -I):

x y [ z ] [ size ] [ symbol-parameters ] [ intensity ] [ symbol ]

See an example with x y z size intensity symbol

gmt begin symbols png
gmt makecpt -Chot -T0/3/1
gmt plot -R0/5/0/1 -JX5c/1c -BWSne -Bxa1 -Bya0.5 -S -C -I -W1p,black << EOF
1  0.5   0   0.3  1  c
2  0.5   1   0.8 -1  t
3  0.5   2   0.5  0  i
EOF
gmt end show

[seisman]

1. We can now input array-like sizes, color, intensity. Shall we support array-like symbols?

Yes, please open a new feature request.

[seisman]

This PR looks good to me. We will merge this PR if others have no objections.

[maxrjones]

Nice work!