Add function to load Blue Marble dataset #2235

willschlitzer · 2022-12-07T13:02:39Z

This PR (hopefully) adds a function to load the Blue Marble image dataset.

Official documentation: https://www.generic-mapping-tools.org/remote-datasets/earth-daynight.html
Recipe: https://github.com/GenericMappingTools/gmtserver-admin/blob/master/recipes/earth_day.recipe
Preview: https://pygmt-dev--2235.org.readthedocs.build/en/2235/api/generated/pygmt.datasets.load_blue_marble.html

Addresses #1442

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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/format: automatically format and lint the code
/test-gmt-dev: run full tests on the latest GMT development version

weiji14 · 2024-02-17T02:50:53Z

Gonna push some commits here to get the load_blue_marble function in for PyGMT v0.12.0.

Need modify arguments into the Resolution class.

A short doctest to test loading the Blue Marble dataset, and rename grid to image since a 3-band RGB image is returned.

weiji14 · 2024-02-18T05:30:01Z

pygmt/io.py

+    if kwargs.get("engine") == "rasterio":
+        import rioxarray
+
+        open_dataarray_func = rioxarray.open_rasterio
+        kwargs.pop("engine")
+    else:
+        open_dataarray_func = xr.open_dataarray
+
+    with open_dataarray_func(filename_or_obj, **kwargs) as dataarray:
        result = dataarray.load()
        _ = result.gmt  # load GMTDataArray accessor information


There is a segfault when loading the RGB image, see https://github.com/GenericMappingTools/pygmt/actions/runs/7939085789/job/21678737828?pr=2235#step:8:415:

Fatal Python error: Segmentation fault Current thread 0x00007f0a18438740 (most recent call first): File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/xarray/backends/file_manager.py", line 234 in close File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/xarray/core/common.py", line 1205 in close File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/xarray/core/common.py", line 1422 in __exit__ File "/home/runner/work/pygmt/pygmt/pygmt/io.py", line 50 in load_dataarray File "/home/runner/work/pygmt/pygmt/pygmt/datasets/load_remote_dataset.py", line 439 in _load_remote_dataset File "/home/runner/work/pygmt/pygmt/pygmt/helpers/decorators.py", line 776 in new_module File "/home/runner/work/pygmt/pygmt/pygmt/datasets/earth_daynight.py", line 57 in load_blue_marble File "/home/runner/work/pygmt/pygmt/pygmt/tests/test_grdimage_image.py", line 17 in fixture_xr_image File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/_pytest/fixtures.py", line 902 in call_fixture_func File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/_pytest/fixtures.py", line 1123 in pytest_fixture_setup File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/pluggy/_callers.py", line 77 in _multicall File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/pluggy/_manager.py", line 115 in _hookexec File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/pluggy/_hooks.py", line 493 in __call__ File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/_pytest/fixtures.py", line 1069 in execute File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/_pytest/fixtures.py", line 693 in _compute_fixture_value File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/_pytest/fixtures.py", line 607 in _get_active_fixturedef File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/_pytest/fixtures.py", line 585 in getfixturevalue File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/_pytest/fixtures.py", line 566 in _fillfixtures File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/_pytest/python.py", line 1795 in setup File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/_pytest/runner.py", line 494 in setup File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/_pytest/runner.py", line 157 in pytest_runtest_setup File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/pluggy/_callers.py", line 77 in _multicall File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/pluggy/_manager.py", line 115 in _hookexec File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/pluggy/_hooks.py", line 493 in __call__ File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/_pytest/runner.py", line 262 in <lambda> File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/_pytest/runner.py", line 341 in from_call File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/_pytest/runner.py", line 261 in call_runtest_hook File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/_pytest/runner.py", line 222 in call_and_report File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/_pytest/runner.py", line 127 in runtestprotocol File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/_pytest/runner.py", line 114 in pytest_runtest_protocol File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/pluggy/_callers.py", line 77 in _multicall File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/pluggy/_manager.py", line 115 in _hookexec File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/pluggy/_hooks.py", line 493 in __call__ File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/_pytest/main.py", line 350 in pytest_runtestloop File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/pluggy/_callers.py", line 77 in _multicall File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/pluggy/_manager.py", line 115 in _hookexec File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/pluggy/_hooks.py", line 493 in __call__ File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/_pytest/main.py", line 325 in _main File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/_pytest/main.py", line 271 in wrap_session File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/_pytest/main.py", line 318 in pytest_cmdline_main File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/pluggy/_callers.py", line 77 in _multicall File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/pluggy/_manager.py", line 115 in _hookexec File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/pluggy/_hooks.py", line 493 in __call__ File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/_pytest/config/__init__.py", line 169 in main File "/home/runner/micromamba/envs/pygmt/lib/python3.12/site-packages/_pytest/config/__init__.py", line 192 in console_main File "/home/runner/micromamba/envs/pygmt/bin/pytest", line 10 in <module> Extension modules: markupsafe._speedups, yaml._yaml, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, matplotlib._c_internal_utils, PIL._imaging, matplotlib._path, kiwisolver._cext, pyarrow.lib, pyarrow._hdfsio, pandas._libs.tslibs.np_datetime, pandas._libs.tslibs.dtypes, pandas._libs.tslibs.base, pandas._libs.tslibs.nattype, pandas._libs.tslibs.timezones, pandas._libs.tslibs.ccalendar, pandas._libs.tslibs.fields, pandas._libs.tslibs.timedeltas, pandas._libs.tslibs.tzconversion, pandas._libs.tslibs.timestamps, pandas._libs.properties, pandas._libs.tslibs.offsets, pandas._libs.tslibs.strptime, pandas._libs.tslibs.parsing, pandas._libs.tslibs.conversion, pandas._libs.tslibs.period, pandas._libs.tslibs.vectorized, pandas._libs.ops_dispatch, pandas._libs.missing, pandas._libs.hashtable, pandas._libs.algos, pandas._libs.interval, pandas._libs.lib, pandas._libs.ops, pyarrow._compute, pandas._libs.arrays, pandas._libs.tslib, pandas._libs.sparse, pandas._libs.indexing, pandas._libs.index, pandas._libs.internals, pandas._libs.join, pandas._libs.writers, pandas._libs.window.aggregations, pandas._libs.window.indexers, pandas._libs.reshape, pandas._libs.groupby, pandas._libs.json, pandas._libs.parsers, pandas._libs.testing, cftime._cftime, _brotli, multidict._multidict, yarl._quoting_c, aiohttp._helpers, aiohttp._http_writer, aiohttp._http_parser, aiohttp._websocket, frozenlist._frozenlist, matplotlib._image, rasterio._version, rasterio._err, rasterio._filepath, rasterio._env, rasterio._transform, rasterio._base, rasterio.crs, rasterio._features, rasterio._warp, rasterio._io, psutil._psutil_linux, psutil._psutil_posix, pyproj._compat, pyproj._datadir, pyproj._network, pyproj._geod, pyproj.list, pyproj._crs, pyproj.database, pyproj._transformer, pyproj._sync, shapely.lib, shapely._geos, shapely._geometry_helpers, netCDF4._netCDF4, PIL._imagingmath, fiona._err, fiona._env, fiona.crs, fiona._geometry, fiona.schema, fiona.ogrext (total: 103) Segmentation fault (core dumped) make: *** [Makefile:38: _runtest] Error 139 ../pygmt/tests/test_grdimage_image.py::test_grdimage_image_dataarray

If I comment out the _ = result.gmt line locally, the test_grdimage_image_dataarray check will pass, but there will be a segfault later at test_grdimage_image_dataarray_unsupported_dtype. Not sure why.

If I comment out the _ = result.gmt line locally, the test_grdimage_image_dataarray check will pass, but there will be a segfault later at test_grdimage_image_dataarray_unsupported_dtype. Not sure why.

Hmm, so I removed the GMTAccessor loading in fc060ea when the Blue Marble GeoTIFF is loaded using rioxarray.open_rasterio, and it seems like the segfault disappears on CI, though I still get a segfault if I run just test_grdimage_image_dataarray locally...

Note to self: using GMT_OUT|GMT_IS_REFERENCE for images seems to help to avoid the segfault. See commit 6eabbf4, c01d6ab (#3338) and 003383d (#3115) where this has been applied.

Prevent segfault when loading accessor info from an xarray.Datarray loaded using rioxarray.open_rasterio.

Also set units=None, and renamed 'grid' to 'image' in the docstrings.

Also added some failing unit tests, since grdcut doesn't allow cropping GeoTIFFs yet.

This reverts commit aa8a474.

GMT can automatically uses -JQ15c for `@earth_day_01d`, but not the xarray.DataArray, so need to set `-Rd` here.

weiji14

I think this is ready for review! I can approve this since I didn't open the PR, but would appreciate someone else to take a look too.

weiji14 · 2024-09-29T21:16:45Z

pygmt/tests/test_grdimage_image.py

@@ -39,7 +37,7 @@ def test_grdimage_image_dataarray(xr_image):
    Plot a 3-band RGB image using xarray.DataArray input.
    """
    fig = Figure()
-    fig.grdimage(grid=xr_image)
+    fig.grdimage(grid=xr_image, region="d")


Need to set region="d" here, because fig.grdimage(grid="@earth_day_01d") plots using projection="Q15c" by default, whereas fig.grdimage(grid=xr_image) uses projection="X15c/15c".

Baseline (@earth_day_01d) Result (xr_image without region="d")

Currently, we write the 3-band xarray.DataArray into a temporary GeoTIFF file. Is it because we don't set the CRS?

Oh yes, good point! I've set the projection in commit 471c6e8, and grdimage now plots both of them the same way.

seisman · 2024-09-29T23:39:23Z

pygmt/datasets/earth_daynight.py

+    >>> # load the default image (pixel-registered 1 arc-degree image)
+    >>> image = load_blue_marble()
+    """
+    image = _load_remote_dataset(


Are you going to support earth_night in this function?

I'll open a separate PR for load_black_marble after this one is done.

Sorry for the confusion. I meant whether you plan to add the load_black_marble function in this file pygmt/datasets/earth_daynight.py or have load_blue_marble/load_black_marble in two separate files.

I'd put them in the same file, and in pygmt/datasets/__init__.py, have a line like:

from pygmt.datasets.earth_daynight import load_blue_marble, load_black_marble

Does that sound ok?

I prefer to having them in separate files. The two files are almost identical, except the differences in the dataset name.

Ok, renamed in 5b6bb42.

pygmt/datasets/load_remote_dataset.py

seisman · 2024-09-29T23:41:59Z

pygmt/tests/test_grdimage_image.py

@@ -39,7 +37,7 @@ def test_grdimage_image_dataarray(xr_image):
    Plot a 3-band RGB image using xarray.DataArray input.
    """
    fig = Figure()
-    fig.grdimage(grid=xr_image)
+    fig.grdimage(grid=xr_image, region="d")


Currently, we write the 3-band xarray.DataArray into a temporary GeoTIFF file. Is it because we don't set the CRS?

seisman · 2024-09-29T23:43:03Z

pygmt/tests/test_grdimage_image.py

@@ -3,7 +3,8 @@
 """

 import pytest
-from pygmt import Figure, which
+from pygmt import Figure
+from pygmt.datasets import load_blue_marble

 rioxarray = pytest.importorskip("rioxarray")


Can this line be removed?

Suggested change

rioxarray = pytest.importorskip("rioxarray")

Not yet, because we are still using tempfile_from_image to convert xarray.DataArray to a GeoTIFF before passing into grdimage. But see #3468.

Co-authored-by: Dongdong Tian <[email protected]>

Set the projection system so that the xarray.DataArray image is plotted as a Geographic image rather than a Cartesian image by GMT.

seisman · 2024-09-30T00:15:45Z

pygmt/tests/test_datasets_earth_daynight.py

+    Test that the grid returned by default for the 1 arc-minute resolution has
+    a "pixel" registration.
+    """
+    data = load_blue_marble(resolution="01m", region=[-10, -9, 3, 5])


Need to cache this earth_day_01m tile in pygmt/helpers/caching.py.

I just looked at my ~/.gmt/server/earth/earth_day/earth_day_01m_p.tif file and it is 179.6MB 😅 Are they not meant to be tiled?

You are right. They're not tiled due to technical difficulties.

Yeah, earth_day files are not tiled at https://oceania.generic-mapping-tools.org/server/earth/earth_day/. And actually, there are only pixel-registered grids so can probably just remove this test.

Xref #2384.

The earth_day images are always pixel-registered anyway.

The earth_day images are not tiled, but come as a single GeoTIFF file for all resolutions.

seisman · 2024-09-30T01:44:41Z

pygmt/datasets/earth_day.py

+    # If rioxarray is installed, set the coordinate reference system
+    if hasattr(image, "rio"):
+        image = image.rio.write_crs(input_crs="OGC:CRS84")


In GMT_IMAGE.to_dataarray(), perhaps we should parse the header->ProjRefPROJ4 and set the correct CRS to the 3-band xarray.DataArray. If done, then we probably don't need to set the CRS here.

Yeah, I was thinking of parsing the projection information from the header when you mentioned this ProjRefPROJ4 field at #3128 (comment). But ideally we'll need to handle PROJ4/WKT/EPSG:

pygmt/pygmt/datatypes/header.py

Lines 138 to 143 in f97c3a4

# Referencing system string in PROJ.4 format

("ProjRefPROJ4", ctp.c_char_p),

# Referencing system string in WKT format

("ProjRefWKT", ctp.c_char_p),

# Referencing system EPSG code

("ProjRefEPSG", ctp.c_int),

Something to consider for a separate PR, because we might need to use pyproj for this.

pygmt/datasets/load_remote_dataset.py

pygmt/tests/test_datasets_earth_day.py

Co-Authored-By: Dongdong Tian <[email protected]>

seisman

Looks good to me except one minor comment.

pygmt/datasets/load_remote_dataset.py

Co-authored-by: Dongdong Tian <[email protected]>

weiji14

Approving for fun ✔️. Thanks @willschlitzer for starting this almost two years ago (hope you're doing well), and @seisman for reviewing! Let's get this in for PyGMT v0.14.0!

willschlitzer added 2 commits December 7, 2022 07:59

initial commit for blue_marble dataset

9bde7f7

update docstring

d8c8759

willschlitzer added the feature Brand new feature label Dec 7, 2022

willschlitzer added this to the 0.8.0 milestone Dec 7, 2022

willschlitzer self-assigned this Dec 7, 2022

seisman modified the milestones: 0.8.0, 0.9.0 Dec 11, 2022

seisman modified the milestones: 0.9.0, 0.10.0 Mar 16, 2023

seisman modified the milestones: 0.10.0, 0.11.0 Jun 28, 2023

weiji14 mentioned this pull request Jul 4, 2023

Allow passing RGB xarray.DataArray images into grdimage #2590

Merged

11 tasks

seisman modified the milestones: 0.11.0, 0.12.0 Dec 11, 2023

weiji14 added 3 commits February 17, 2024 15:31

Merge branch 'main' into load-remote-dataset/blue-marble

c6bd235

Rename load_blue_marble.py to earth_daynight.py and update docs

093fc26

Add load_blue_marble funtion to doc/api/index.rst

2f29458

weiji14 added 4 commits February 17, 2024 15:58

Fix mypy errors in load_remote_dataset.py

1c99f21

Need modify arguments into the Resolution class.

Add doctest and rename returned output from grid to image

e839ef7

A short doctest to test loading the Blue Marble dataset, and rename grid to image since a 3-band RGB image is returned.

Use rioxarray.open_rasterio to open earth_day images

aa8a474

Refactor fixture_xr_image to use load_blue_marble function

cd4cab6

weiji14 reviewed Feb 18, 2024

View reviewed changes

Only load GMTDataArray accessor info when engine!=rasterio

fc060ea

Prevent segfault when loading accessor info from an xarray.Datarray loaded using rioxarray.open_rasterio.

weiji14 self-assigned this Feb 18, 2024

weiji14 added 4 commits February 18, 2024 10:40

Set tiled=True for spatial resolutions 05m and higher

c3017d5

Also set units=None, and renamed 'grid' to 'image' in the docstrings.

Add unit test to load_blue_marble 01d

c3e2e66

Skip test_datasets_load_earth_daynight if rioxarray not installed

a2a18a9

Add region parameter for load_blue_marble

7c38754

Also added some failing unit tests, since grdcut doesn't allow cropping GeoTIFFs yet.

seisman removed this from the 0.12.0 milestone Feb 26, 2024

weiji14 added 3 commits September 30, 2024 08:57

Revert "Use rioxarray.open_rasterio to open earth_day images"

0ca210a

This reverts commit aa8a474.

Use npt.assert_allclose in test_blue_marble_01m_default_registration

28d668d

Plot xr_image in same fashion as @earth_day_01d using region="d"

a6a08e3

GMT can automatically uses -JQ15c for `@earth_day_01d`, but not the xarray.DataArray, so need to set `-Rd` here.

weiji14 reviewed Sep 29, 2024

View reviewed changes

weiji14 added this to the 0.14.0 milestone Sep 29, 2024

weiji14 marked this pull request as ready for review September 29, 2024 21:18

weiji14 added the needs review This PR has higher priority and needs review. label Sep 29, 2024

weiji14 mentioned this pull request Sep 29, 2024

Function to load NASA Blue and Black marble mosaic images #1442

Closed

seisman reviewed Sep 29, 2024

View reviewed changes

weiji14 and others added 2 commits September 30, 2024 12:54

Delete comment about images not being supported

f13d12b

Co-authored-by: Dongdong Tian <[email protected]>

Set OGC:CRS84 projection on blue_marble image

471c6e8

Set the projection system so that the xarray.DataArray image is plotted as a Geographic image rather than a Cartesian image by GMT.

seisman reviewed Sep 30, 2024

View reviewed changes

weiji14 added 4 commits September 30, 2024 14:22

Add note on registration/gtype

e886408

Xref #2384.

Rename earth_daynight to earth_day

5b6bb42

Remove test_blue_marble_01m_default_registration

755275e

The earth_day images are always pixel-registered anyway.

Remove mention of tiled images for 5 arc-min or higher

f7e381e

The earth_day images are not tiled, but come as a single GeoTIFF file for all resolutions.

seisman reviewed Sep 30, 2024

View reviewed changes

Apply suggestions from code review

9a5e36b

Co-Authored-By: Dongdong Tian <[email protected]>

seisman approved these changes Sep 30, 2024

View reviewed changes

pygmt/datasets/load_remote_dataset.py Outdated Show resolved Hide resolved

weiji14 and others added 2 commits September 30, 2024 15:14

Create kwdict with R and T keys once

a0fa29b

Co-authored-by: Dongdong Tian <[email protected]>

Lint

70f6041

weiji14 added final review call This PR requires final review and approval from a second reviewer and removed needs review This PR has higher priority and needs review. labels Sep 30, 2024

weiji14 approved these changes Sep 30, 2024

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weiji14 merged commit 66f258a into main Sep 30, 2024
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weiji14 deleted the load-remote-dataset/blue-marble branch September 30, 2024 02:25

weiji14 removed the final review call This PR requires final review and approval from a second reviewer label Sep 30, 2024

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Add function to load Black Marble dataset #3469

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Get projection/crs from GMT_GRID_HEADER #3470

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Add function to load Blue Marble dataset #2235

Add function to load Blue Marble dataset #2235

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	# Referencing system string in PROJ.4 format
	("ProjRefPROJ4", ctp.c_char_p),
	# Referencing system string in WKT format
	("ProjRefWKT", ctp.c_char_p),
	# Referencing system EPSG code
	("ProjRefEPSG", ctp.c_int),

Add function to load Blue Marble dataset #2235

Add function to load Blue Marble dataset #2235

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willschlitzer commented Dec 7, 2022 •

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