Add inline example for xyz2grd by willschlitzer · Pull Request #1719 · GenericMappingTools/pygmt

willschlitzer · 2022-02-02T16:21:57Z

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

Addresses #1686

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 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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specific operations. Supported slash commands are:

/format: automatically format and lint the code
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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

willschlitzer self-assigned this Feb 2, 2022

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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…ing inline example

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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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