Add inline example for xyz2grd #1719

willschlitzer · 2022-02-02T16:21:57Z

This PR adds an inline code example to the docstring for xyz2grd.

Addresses #1686

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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 wrapping a new module, open a 'Wrap new GMT module' issue and submit reasonably-sized PRs.
If adding new functionality, add an example to docstrings or tutorials.

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pygmt/src/xyz2grd.py

Co-authored-by: Michael Grund <23025878+michaelgrund@users.noreply.github.com>

seisman · 2022-02-26T14:00:41Z

pygmt/src/xyz2grd.py

+    >>> # 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]


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.

What would you recommend instead?

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))

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?

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.

seisman · 2022-03-11T13:42:20Z

/format

pygmt/src/xyz2grd.py

seisman · 2022-03-11T14:19:06Z

The doctest example fails with the following error message:

??? >>> grid = pygmt.xyz2grd(x=xx, y=yy, z=zz, spacing=(1.0, 0.5))
UNEXPECTED EXCEPTION: GMTCLibError("Module 'xyz2grd' failed with status code 72:\nxyz2grd [ERROR]: Option -I: Given more than once (offending option is -I1.0)\nxyz2grd [ERROR]: Must specify -R option")
Traceback (most recent call last):
  File "/Users/seisman/opt/miniconda/lib/python3.9/doctest.py", line 1336, in __run
    exec(compile(example.source, filename, "single",
  File "<doctest pygmt.src.xyz2grd.xyz2grd[5]>", line 1, in <module>
  File "/Users/seisman/OSS/gmt/pygmt/pygmt/helpers/decorators.py", line 585, in new_module
    return module_func(*args, **kwargs)
  File "/Users/seisman/OSS/gmt/pygmt/pygmt/helpers/decorators.py", line 725, in new_module
    return module_func(*args, **kwargs)
  File "/Users/seisman/OSS/gmt/pygmt/pygmt/src/xyz2grd.py", line 158, in xyz2grd
    lib.call_module("xyz2grd", arg_str)
  File "/Users/seisman/OSS/gmt/pygmt/pygmt/clib/session.py", line 502, in call_module
    raise GMTCLibError(
pygmt.exceptions.GMTCLibError: Module 'xyz2grd' failed with status code 72:
xyz2grd [ERROR]: Option -I: Given more than once (offending option is -I1.0)
xyz2grd [ERROR]: Must specify -R option

There are two problems here:

-R option is always required for xyz2grd
Need to add I="sequence" in @kwargs_to_strings to make spacing=(1.0, 0.5) work.

seisman · 2022-03-11T14:27:44Z

The doctest example fails with the following error message:

??? >>> grid = pygmt.xyz2grd(x=xx, y=yy, z=zz, spacing=(1.0, 0.5))
UNEXPECTED EXCEPTION: GMTCLibError("Module 'xyz2grd' failed with status code 72:\nxyz2grd [ERROR]: Option -I: Given more than once (offending option is -I1.0)\nxyz2grd [ERROR]: Must specify -R option")
Traceback (most recent call last):
  File "/Users/seisman/opt/miniconda/lib/python3.9/doctest.py", line 1336, in __run
    exec(compile(example.source, filename, "single",
  File "<doctest pygmt.src.xyz2grd.xyz2grd[5]>", line 1, in <module>
  File "/Users/seisman/OSS/gmt/pygmt/pygmt/helpers/decorators.py", line 585, in new_module
    return module_func(*args, **kwargs)
  File "/Users/seisman/OSS/gmt/pygmt/pygmt/helpers/decorators.py", line 725, in new_module
    return module_func(*args, **kwargs)
  File "/Users/seisman/OSS/gmt/pygmt/pygmt/src/xyz2grd.py", line 158, in xyz2grd
    lib.call_module("xyz2grd", arg_str)
  File "/Users/seisman/OSS/gmt/pygmt/pygmt/clib/session.py", line 502, in call_module
    raise GMTCLibError(
pygmt.exceptions.GMTCLibError: Module 'xyz2grd' failed with status code 72:
xyz2grd [ERROR]: Option -I: Given more than once (offending option is -I1.0)
xyz2grd [ERROR]: Must specify -R option

There are two problems here:

-R option is always required for xyz2grd
Need to add I="sequence" in @kwargs_to_strings to make spacing=(1.0, 0.5) work.

Addressed in #1804.

…ing inline example

weiji14

@willschlitzer, for the sake of Pi-Day, I can only approve either this xyz2grd PR or the grdvolume PR at #1299 for v0.6.0 (see #1808 (comment)). So which will it be?

pygmt/src/xyz2grd.py

Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com>

willschlitzer · 2022-03-14T10:41:54Z

@willschlitzer, for the sake of Pi-Day, I can only approve either this xyz2grd PR or the grdvolume PR at #1299 for v0.6.0 (see #1808 (comment)). So which will it be?

Doesn't matter to me

weiji14

Let's do this one then

Example turning an xyz table into a grid. * add I to sequence in kwargs_to_strings, add region for xyz2grd docstring inline example * fix use of GMT alias in PyGMT docstring Co-authored-by: Michael Grund <23025878+michaelgrund@users.noreply.github.com> Co-authored-by: Dongdong Tian <seisman.info@gmail.com> Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com>

add inline example for xyz2grd.py

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willschlitzer added the documentation Improvements or additions to documentation label Feb 2, 2022

willschlitzer added this to the 0.6.0 milestone Feb 2, 2022

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willschlitzer mentioned this pull request Feb 2, 2022

Add inline code examples in data processing module docstrings #1686

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Co-authored-by: Michael Grund <23025878+michaelgrund@users.noreply.github.com>

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run make format

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update inline example

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Merge branch 'main' into inline-example/xyz2grd

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Fix the spacing parameter and check required parameters in xyz2grd #1804

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Merge branch 'main' into inline-example/xyz2grd

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add I to sequence in kwargs_to_strings, add region for xyz2grd docstr…

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fix use of GMT alias in PyGMT docstring

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Merge branch 'main' into inline-example/xyz2grd

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Changelog entry for v0.6.0 #1808

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Format and test-gmt-dev slash commands not working properly #1816

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Update pygmt/src/xyz2grd.py

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Release PyGMT v0.6.0 #1801

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Add inline example for xyz2grd #1719

Add inline example for xyz2grd #1719

willschlitzer commented Feb 2, 2022

seisman Feb 26, 2022

willschlitzer Feb 27, 2022

seisman Mar 5, 2022 •

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Add inline example for xyz2grd #1719

Add inline example for xyz2grd #1719

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