Wrap grdtrack #308

weiji14 · 2019-05-22T12:34:45Z

Description of proposed changes

Wrapping the grdtrack sampling function. Also added new tutorial function load_ocean_ridge_points() to use in test cases.

Fixes #307

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.

Initial commit for #307. Implement GMT grdtrack function under sampling.py. Test cases checking proper pandas.DataFrame and xarray.DataArray inputs stored in test_grdtrack.py. Sample datasets for tests uses newly created load_east_pacific_rise_grid and load_ocean_ridge_points functions in datasets/tutorial.py. GMT grdtrack documentation can be found at https://gmt.soest.hawaii.edu/doc/latest/grdtrack. Originally, grdtrack should take in an xyfile and -Ggridfile as parameters, and pass the output table to stdout. Here, the implementation (currently) takes in a pandas.DataFrame table and xarray.DataArray grid instead as input, and returns a pandas.DataFrame with an extra column for the sampled grid data.

Enable passing in netcdf file as input into grdtrack, instead of just xarray.DataArray. Also fix bug with kwargs being overwritten instead of appended to...

leouieda

Hi @weiji14 thanks for taking the time to implement this! I left a few minor comments. It would be great to have a gallery example of grdtrack and the new data sets as well (as simple as possible).

One thing I'm considering is if we need the East Pacific Rise grid. We can recreate that by slicing the Earth relief grids. This way we have one less function to test.

What do you think?

pygmt/sampling.py

Rename 'table' parameter to 'points', remove default 'newcolname' parameter (require it to be explicitly set) and change the output 'ret' to 'track' in docstring. Unit tests updated accordingly.

weiji14 · 2019-05-23T19:08:40Z

Hi @weiji14 thanks for taking the time to implement this! I left a few minor comments. It would be great to have a gallery example of grdtrack and the new data sets as well (as simple as possible).

I'll see if I have time over the weekend for making the examples (most likely in a separate pull request though). Is the sphinx gallery stable again?

One thing I'm considering is if we need the East Pacific Rise grid. We can recreate that by slicing the Earth relief grids. This way we have one less function to test.

What do you think?

That's actually a brilliant idea! ~~I'll have a think about how to implement that in code. Hopefully I don't need to implement grdcut first~~ 😆 Edit: Ok I've found I can do something like load_earth_relief().sel(lat=slice(-49, -42), lon=slice(-118, -107)) to get the same area.

One less dataset to test by replacing the east_pacific_rise_grid with the earth_relief 60m grid (sliced to the same area). Also add tests for loading the ocean_ridge_points dataset.

PyGMT grdtrack added under "Operations on grids" (though it does require a tabular data input). Also added the ocean_ridge_points tutorial dataset used in grdtrack's unit tests and reordered the tutorial datasets alphabetically.

Enable passing in ascii file inputs (csv, txt, etc) into grdtrack's 'points' parameter instead of just pandas.DataFrame. This requires a new 'outfile' parameter to be set. The type of 'points' input determines the type of 'track' returned, i.e. pd.DataFrame in, pd.DataFrame out; filename in, filename out. Extra unit tests created to test the various new input combinations and associated outputs.

New raster grid gallery example for grdtrack! Plotting bathymetry sampled along ocean ridge points around the globe. As this 'grid' subsection is new to the gallery, I've added it to the ExplicitOrder part within the sphinx conf.py file.

weiji14 · 2019-05-30T20:03:46Z

@leouieda, when you have time, please review some of the changes I've made to grdtrack. I've removed the East Pacific Rise grid with the earth relief one as requested, and also enabled passing in an ASCII file input to points as requested by @seisman. Plus you'll be happy to see that there's a new gallery example! 🎉

It's been a while since I used gmt to do any plotting, and my first time using sphinx-gallery, so I really welcome any comments on how this gallery example might be improved 😄

leouieda

@weiji14 the gallery plot looks great! Thanks for all this work 🎉

I left a few comments and suggestions. Overall, this just needs a few tweaks and should be good to merge.

examples/gallery/grid/README.txt

examples/gallery/grid/track_sampling.py

pygmt/tests/test_grdtrack.py

examples/gallery/grid/track_sampling.py

Using numpy.testing.assert_allclose in test_grdtrack.py unit tests and make some cosmetic changes to docs and gallery example. To make the gallery example plot clearer, grid background colormap was changed from 'ocean' to 'gray', and the points are made slightly bigger. Also changed map to be Pacific-centered!

weiji14 · 2019-06-09T14:23:46Z

Ok, I've made the requested tweaks and it should be good to merge 🔀! There was a small timeout issue on the Travis CI MacOS build failing to download the earth relief 60m resolution grid 🌐, but I've restarted it and the automated checks have all passed now 🎉.

leouieda · 2019-06-19T22:52:05Z

@weiji14 sorry I let this sit here for so long. We're working on a release candidate for GMT 6 and need to get #311 merged before we can merge this one. I'll merge it in as soon as I can.

weiji14 · 2019-06-20T04:08:58Z

Please don't apologize, I'd rather have GMT6 released properly more than anything now! I see #311 has been merged so I'm gonna install 6.0.0rc1 on my linux system as well and run some tests to see if there's any issues.

Let me know once everything settles and I can merge in the changes from PyGMT master into this Pull Request :)

weiji14 · 2019-10-02T20:30:20Z

Just checking in here 👋. I've merged in the latest 6.0.0rc4 stuff and the tests have passed. Would love to get this PR merged in soon as there's the "ocean ridge points" dataset that will be great from testing some of the other wrappers. Plus grdtrack will be super helpful for some of the transect/cross-section work I'm doing now.

weiji14 · 2019-10-15T21:14:10Z

Right, the documentation preview (from #344) is awesome! You can see the new gallery example at https://pygmt-git-fork-weiji14-sampling-grdtrack.gmt.now.sh/gallery/grid/track_sampling.html. However, there's a yellow box called 'Out' printing the stdout that comes from downloading the earth relief grid 🤦‍♂️ ...

Something to do with the sphinx extension?

leouieda · 2019-10-16T07:54:56Z

@weiji14 nice! I’ll have a look at this soon. The Out box is captured by Sphinx-gallery so you can print variables etc to show values. That is fine and nothing to worry about.

Due to new SRTM15+V2 grids, see also #350.

weiji14 · 2020-03-11T21:30:57Z

@leouieda, did you have anything extra to add here? It's been more than half a year and I'd like to get on with merging this pull request (and maybe some of the other 'Wrapper' code I wrote).

Make tests pass again, by fixing the test bathymetry values, and cutting our docstrings to 79 characters instead of 88.

weiji14 · 2020-03-25T22:24:19Z

Status checks for Travis not being updated properly (see https://travis-ci.community/t/github-status-not-posted-on-commits-on-repositories-using-legacy-service-integration/7798). I think we need to migrate to using the Travis Github Apps Integration. Issue opened at #403.

weiji14 added 2 commits May 22, 2019 14:28

Enable netcdf file input for grdtrack

97c2b4a

Enable passing in netcdf file as input into grdtrack, instead of just xarray.DataArray. Also fix bug with kwargs being overwritten instead of appended to...

leouieda requested changes May 22, 2019

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Modify grdtrack parameter names according to code review

bcfab7f

Rename 'table' parameter to 'points', remove default 'newcolname' parameter (require it to be explicitly set) and change the output 'ret' to 'track' in docstring. Unit tests updated accordingly.

weiji14 added 2 commits May 23, 2019 21:55

Remove east_pacific_rise_grid, add test for load_ocean_ridge_points

028b55a

One less dataset to test by replacing the east_pacific_rise_grid with the earth_relief 60m grid (sliced to the same area). Also add tests for loading the ocean_ridge_points dataset.

weiji14 marked this pull request as ready for review May 23, 2019 20:19

weiji14 added 2 commits May 27, 2019 21:45

leouieda reviewed Jun 5, 2019

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weiji14 mentioned this pull request Aug 23, 2019

How to handle one or more file inputs #322

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Merge branch 'master' into sampling/grdtrack

421e10d

weiji14 force-pushed the sampling/grdtrack branch from 29220bd to 421e10d Compare September 7, 2019 00:23

Merge branch 'master' into sampling/grdtrack

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weiji14 added this to the 0.1.0 milestone Oct 4, 2019

weiji14 requested a review from leouieda October 7, 2019 01:52

Merge branch 'master' into sampling/grdtrack

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vercel bot temporarily deployed to staging October 15, 2019 20:29 Inactive

weiji14 mentioned this pull request Oct 20, 2019

Wrapper for blockmedian #348

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Merge branch 'master' into sampling/grdtrack

b737684

vercel bot temporarily deployed to staging November 1, 2019 04:32 Inactive

Fix bathymetry values in test_grdtrack

afb4382

Due to new SRTM15+V2 grids, see also #350.

vercel bot temporarily deployed to staging November 1, 2019 04:46 Inactive

Merge branch 'master' into sampling/grdtrack

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Merge branch 'master' into sampling/grdtrack

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Fix test values and truncate docstrings to 79 char

0ed8eb4

Make tests pass again, by fixing the test bathymetry values, and cutting our docstrings to 79 characters instead of 88.

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vercel bot temporarily deployed to Preview March 24, 2020 23:14 Inactive

Minor formatting fix

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weiji14 force-pushed the sampling/grdtrack branch from 1cb310e to f0b6de3 Compare March 25, 2020 21:50

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weiji14 merged commit 16f5a10 into GenericMappingTools:master Mar 26, 2020

weiji14 mentioned this pull request Mar 22, 2021

Improve input/output options for blockm* and grdtrack #1099

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seisman mentioned this pull request Dec 28, 2022

Add colorbars to plots of gallery and tutorial examples #2190

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Missing colorbars in examples #2030

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Rewrite gallery example "track_sampling.py" #2282

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This was referenced Nov 11, 2023

Wrap GMT's standard data type GMT_DATASET for table inputs #2729

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Support Type Hints #2794

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Wrap grdtrack #308

Wrap grdtrack #308

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Wrap grdtrack #308

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