Wrap gmtselect #1429

weiji14 · 2021-08-10T11:23:44Z

Description of proposed changes

Wrapping the gmtselect function which "Selects data table subsets based on multiple spatial criteria". For a GMT example, see https://docs.generic-mapping-tools.org/6.2/gallery/ex24.html.

Preview docs at https://pygmt-git-wrap-gmtselect-gmt.vercel.app/api/generated/pygmt.select.html

Crossref GMT.jl docs at https://www.generic-mapping-tools.org/GMT.jl/v0.31/#GMT.gmtselect.

Parameters/Aliases to wrap:

To keep this PR small, I would prefer implementing only 4 out of 7 of the possible gmtselect filters, specifically -A (once #1426 is done), -R rectangular region subset, -D/-N coastline subset, and -Z z value data subset. These, plus the reverse (-I) and grid subset (-G) option. The others can be done in a follow-up PR.

Other implementation points to consider (may need to be done in other PRs):

GMT's select function supports multiple file inputs, should we support this in PyGMT? See e.g. text at 7a08ebd. Related to this is if we should support multiple table-like inputs (e.g. two geopandas.GeoDataFrame objects in a list).
I've used the long alias z_subregion for -Z (following pygmt.grdcut, xref Wrap grdcut #492). Should we use zsubregion (no underscore) instead, following policy set in https://github.com/GenericMappingTools/pygmt/blame/v0.4.1/doc/contributing.md#L446-L450)?
Using the region -R and -J common aliases here in select doesn't look good since it's not a plotting function. Probably don't need the Required if this is the first plot command part. Edit: Will be resolved by Add region docstring to COMMON_OPTIONS for non-plotting modules #1493/Update region and projection standard docstrings #1510
![image](https://user-images.githubusercontent.com/23487320/128861719-c17dffdb-026e-4d7b-a30d-ff01bf4766d9.png

Addresses first part of #1427.

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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Initial commit for wrapping the gmtselect function for #1427 which selects data table subsets based on multiple spatial criteria. Original GMT `gmtselect` documentation is at https://docs.generic-mapping-tools.org/6.2/gmtselect.html. Aliased non-common optional parameters reverse (I) and z_subregion (Z).

willschlitzer · 2021-10-05T18:35:43Z

@weiji14 Is the intent just to have the output of this as the file or a DataFrame, or should their be an option for a numpy array as well?

weiji14 · 2021-10-05T18:41:26Z

@weiji14 Is the intent just to have the output of this as the file or a DataFrame, or should their be an option for a numpy array as well?

Yeah, maybe just a file or pandas.DataFrame for now, until someone makes a reusable function to handle #1318.

willschlitzer · 2021-10-05T19:21:10Z

pygmt/src/select.py

+        Pass in either a file name to an ASCII data table, a 2D
+        {table-classes}.


Suggested change

Pass in either a file name to an ASCII data table, a 2D

{table-classes}.

Pass in either a file name to an ASCII data table or a 2D

{table-classes}.

I"m not familiar with using gmtselect, but can't it accept 3D tables (as indicated by z_subregion?

This docstring gets rendered like so:

So 2D numpy.array is correct. I don't think it's common to speak of a 3D table (though I did find https://stackoverflow.com/questions/24290495/constructing-3d-pandas-dataframe), but I know what you mean by having a z-column.

Maybe something like "2D or 3D {table-classes}"? I understand that 3D tables aren't the norm, but it doesn't make sense to have a parameter specifically for a 3D table but then say that gmtselect only accepts a 2D table.

This is what I get when I search for 3D data table:

If we are talking about a 3D numpy array, the shape will be something like (1, 2, 3), but in this case, our input cannot be like that. It can only be a 2D shape like (2, 3). The extra z-column isn't considered an extra dimension, more like an extra attribute.

Okay! That makes sense to me; I was thinking a 3D table meant one with data for the third dimension.

willschlitzer · 2021-10-05T19:22:33Z

pygmt/src/select.py

+    {A}
+    reverse : str
+        [**cflrsz**].
+        Reverses the sense of the test for each of the criteria specified:


Suggested change

Reverses the sense of the test for each of the criteria specified:

Reverses the criteria of the test for each of the criteria specified:

The use of "sense" doesn't make much sense to me. I know it's from the GMT docs, but would there be a better way to phrase this?

Yeah, it doesn't sound nice, but I think the following statements ("select records NOT inside/within ...") should (hopefully) make it clear to users what is meant by reverse. So maybe just keep it as with the GMT docs?

If it's easier to keep it in line with the GMT docs, I'm fine with it. But I might open a PR over at GMT; I don't think the current version makes much sense.

willschlitzer · 2021-10-25T08:20:54Z

@weiji14 Are you intending to get this pull request complete for v0.5.0?

weiji14 · 2021-10-25T22:26:47Z

@weiji14 Are you intending to get this pull request complete for v0.5.0?

Yes, I've added this PR to the priority list at #1576 (comment).

pygmt/src/select.py

Specifically, resolution (D), gridmask (G) and mask (N). These aliases are currently undocumented/disabled, but will be implemented/enabled in the future.

pygmt/src/select.py

* Wrap the gmtselect function which selects data table subsets based on multiple spatial criteria. Aliased non-common optional parameters reverse (I) and z_subregion (Z), area_thresh (A), resolution (D), gridmask (G) and mask (N). *Add tests for select *Add imports for select Co-authored-by: Will Schlitzer <schlitzer90@gmail.com>

weiji14 added the feature Brand new feature label Aug 10, 2021

weiji14 added this to the 0.5.0 milestone Aug 10, 2021

weiji14 self-assigned this Aug 10, 2021

weiji14 force-pushed the wrap/gmtselect branch from 253163b to 53ef119 Compare August 10, 2021 11:29

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Merge branch 'main' into wrap/gmtselect

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Alias area_thresh (A) for select

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maxrjones mentioned this pull request Sep 11, 2021

Standardize parameter name for table data inputs #1479

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weiji14 added 2 commits September 27, 2021 21:23

Merge branch 'main' into wrap/gmtselect

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Rename 'table' parameter to 'data'

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Merge branch 'main' into wrap/gmtselect

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Parse incols and outcols arguments using sequence_comma

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Merge branch 'main' into wrap/gmtselect

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Use area_thresh instead of -A in docstring for reverse param

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weiji14 mentioned this pull request Oct 25, 2021

Release PyGMT v0.5.0 #1576

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Use long aliases instead of short param in description of reverse param

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Specifically, resolution (D), gridmask (G) and mask (N). These aliases are currently undocumented/disabled, but will be implemented/enabled in the future.

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Alias resolution (D), gridmask (G) and mask (N) for gmtselect

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Merge branch 'main' into wrap/gmtselect

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seisman mentioned this pull request Mar 9, 2022

Wrapper for gmtselect #1427

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Wrap gmtselect #1429

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weiji14 commented Oct 25, 2021

		Pass in either a file name to an ASCII data table, a 2D
		{table-classes}.

	Reverses the sense of the test for each of the criteria specified:
	Reverses the criteria of the test for each of the criteria specified:

Wrap gmtselect #1429

Wrap gmtselect #1429

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