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Add inline example for xyz2grd #1719

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Merged
weiji14 merged 14 commits into from
Mar 14, 2022
Merged

Add inline example for xyz2grd #1719

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223f84f
add inline example for xyz2grd.py
willschlitzer Feb 2, 2022
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Apply suggestions from code review
willschlitzer Feb 14, 2022
4fc7997
run make format
willschlitzer Feb 14, 2022
63da308
update inline example
willschlitzer Mar 11, 2022
f041309
Fix linting issue
seisman Mar 11, 2022
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seisman Mar 11, 2022
3522401
Fix formatting
seisman Mar 11, 2022
0a3f8bb
Merge branch 'main' into inline-example/xyz2grd
seisman Mar 11, 2022
0b0f471
Merge branch 'main' into inline-example/xyz2grd
willschlitzer Mar 12, 2022
21ee099
add I to sequence in kwargs_to_strings, add region for xyz2grd docstr…
willschlitzer Mar 12, 2022
03877b9
fix use of GMT alias in PyGMT docstring
willschlitzer Mar 12, 2022
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Merge branch 'main' into inline-example/xyz2grd
seisman Mar 12, 2022
7209ecb
Update pygmt/src/xyz2grd.py
willschlitzer Mar 14, 2022
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Merge branch 'main' into inline-example/xyz2grd
willschlitzer Mar 14, 2022
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13 changes: 13 additions & 0 deletions pygmt/src/xyz2grd.py
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Original file line number Diff line number Diff line change
Expand Up @@ -131,6 +131,19 @@ def xyz2grd(data=None, x=None, y=None, z=None, **kwargs):
- :class:`xarray.DataArray`: if ``outgrid`` is not set
- None if ``outgrid`` is set (grid output will be stored in file set by
``outgrid``)

Example
-------
>>> import pygmt # doctest: +SKIP
>>> # Load a sample bathymetry file
>>> sample_bathymetry = pygmt.datasets.load_sample_data(
... name="bathymetry"
... ) # doctest: +SKIP
>>> # Create a new grid from the xyz input, set the x-range to 245-255 and
>>> # the y-range to 20-30, and the spacing to 5 degrees
>>> new_grid = pygmt.xyz2grd(
... data=sample_bathymetry, spacing=5, region=[245, 255, 20, 30]
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@seisman seisman Feb 26, 2022

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As I understand it, xyz2grd doesn't do interpolations, so for densely sampled data like the bathymetry data, calling xyz2grd with a coarse spacing (spacing=5) produces a grid that cannot reflect the original data. Thus, I think this is not a good example for xyz2grd which may mislead users.

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@willschlitzer willschlitzer Feb 27, 2022

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What would you recommend instead?

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@seisman seisman Mar 5, 2022 •
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Perhaps passing a 2D numpy array is a more useful example, for example:

import numpy as np
import pygmt
# prepare input arrays
x, y = np.meshgrid([0, 1, 2, 3], [10.5, 11.0, 11.5, 12.0, 12.5])
z = x**2 + y**2
xx, yy, zz = x.flatten(), y.flatten(), z.flatten()

grid = pygmt.xyz2grd(x=xx, y=yy, z=zz, spacing=(1.0, 0.5))

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@willschlitzer willschlitzer Mar 6, 2022

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I'm not a geoscientist, so I'm not sure how realistic this example is. But this seems confusing, because it uses numpy functions outside of simple math operations. Would be be easier to just pass a numpy array of data?

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@seisman seisman Mar 7, 2022

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The equivalent 2d numpy array would be like this:

array([[  0.  ,  10.5 , 110.25],
       [  1.  ,  10.5 , 111.25],
       [  2.  ,  10.5 , 114.25],
       [  3.  ,  10.5 , 119.25],
       [  0.  ,  11.  , 121.  ],
       [  1.  ,  11.  , 122.  ],
       [  2.  ,  11.  , 125.  ],
       [  3.  ,  11.  , 130.  ],
       [  0.  ,  11.5 , 132.25],
       [  1.  ,  11.5 , 133.25],
       [  2.  ,  11.5 , 136.25],
       [  3.  ,  11.5 , 141.25],
       [  0.  ,  12.  , 144.  ],
       [  1.  ,  12.  , 145.  ],
       [  2.  ,  12.  , 148.  ],
       [  3.  ,  12.  , 153.  ],
       [  0.  ,  12.5 , 156.25],
       [  1.  ,  12.5 , 157.25],
       [  2.  ,  12.5 , 160.25],
       [  3.  ,  12.5 , 165.25]])

People usually know the X range and Y range of the grid, but may don't know how to prepare a 2D numpy array for PyGMT.

Here is a similar example in matplotlib: https://matplotlib.org/stable/plot_types/arrays/pcolormesh.html.

The main difference is that, we have to call the array.flatten() method before passing to xyz2grd.

... ) # doctest: +SKIP
"""
with GMTTempFile(suffix=".nc") as tmpfile:
with Session() as lib:
Expand Down