Switch to pyproj for projection to CF NetCDF grid mapping #1038

djhoese · 2020-01-09T03:20:52Z

This is the long term solution for fixing #1029 (FYI @RickKohrs).

This switches the CF writer to depend on pyproj 2.0+ for converting the PROJ information to a CF compatible set of attributes. This is a no brainer in the long run as it lets the projection-specific library handling the projection logic (and people who are much more up to date on changes in CF and PROJ).

However, this has some important changes and this PR is kind of 50/50 on deciding how it handles them. I'm not sure whether we want to completely switch to depending on pyproj and remove all previous methods for "unknown" projections or not. Pyproj also doesn't provide any default way of "naming" the grid_mapping variable. I made it default to the same name as the grid_mapping_name attribute.

I think I might make a short term solution for a 0.19.1 release of Satpy to fix #1029 but wanted to make this for now so people could see it and discuss.

Closes NetCDF (CF) writer doesn't include semi_minor_axis/semi_major_axis for new versions of pyproj #1029
Tests added and test suite added to parent suite
Tests passed
Passes flake8 satpy
Fully documented

coveralls · 2020-01-09T03:42:38Z

Coverage increased (+0.06%) to 89.535% when pulling 11ae112 on djhoese:bugfix-cf-projections into 8853aac on pytroll:master.

mraspaud · 2020-01-09T07:40:38Z

I'd like to use the opportunity to add an oblique mercator test. I'll try to provide something during the day.

djhoese · 2020-01-09T13:39:29Z

I learned while working on the short term solution last night that I'm pretty sure the projection tests aren't actually comparing any of the .attrs for the grid mapping variable. Meaning, they basically don't test anything.

mraspaud · 2020-01-09T14:01:32Z

I'll have a look now

mraspaud · 2020-01-09T14:44:42Z

you're right, the attrs weren't checked...

codecov · 2020-01-09T14:45:52Z

Codecov Report

Merging #1038 into master will increase coverage by 0.05%.
The diff coverage is 98.92%.

@@            Coverage Diff             @@
##           master    #1038      +/-   ##
==========================================
+ Coverage   89.47%   89.53%   +0.05%     
==========================================
  Files         198      200       +2     
  Lines       29210    29356     +146     
==========================================
+ Hits        26136    26284     +148     
+ Misses       3074     3072       -2

Impacted Files	Coverage Δ
satpy/writers/cf_writer.py	`93.79% <96.42%> (+1.14%)`	⬆️
satpy/tests/writer_tests/test_cf.py	`98.53% <100.00%> (ø)`
satpy/tests/test_scene.py	`99.71% <0.00%> (-0.14%)`	⬇️
satpy/readers/hy2_scat_l2b_h5.py	`98.00% <0.00%> (ø)`
satpy/tests/reader_tests/test_hy2_scat_l2b_h5.py	`100.00% <0.00%> (ø)`
satpy/scene.py	`90.19% <0.00%> (+0.01%)`	⬆️

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djhoese · 2020-01-23T17:40:30Z

So I've just rebased this on to master and I have a few things I think we need to decide on before merging this:

Do we completely depend on pyproj for all CF projection conversions? Would make the code nice but could delay updates/fixes for our users if we need to wait for a pyproj release (although they come pretty quickly, faster than satpy usually).
Whoever is using the omerc stuff really needs to test what their clients can accept for the grid mapping? There was some stuff that was not CF compliant in the previous conversion functions.
I think we should remove the name handling stuff that is based on the projection definition and instead use the area.area_id as the name of the variable in the NetCDF file. This should make it unique for NetCDF files with multiple areas in the same file (if possible or in the future).

Edit: Also see pyproj4/pyproj#515

mraspaud · 2020-01-24T13:01:58Z

If we can delegate it to pyproj, I'm good with it. But we need thorough tests to make things don't break with future releases.
I'm using omerc, I'll check
Fine by me.

mraspaud · 2020-02-14T14:01:45Z

Here is the result of a before/after comparison with omerc:

Before

	int64 omerc ;
		omerc:azimuth_of_central_line = 8.14048957652079 ;
		omerc:false_easting = 0. ;
		omerc:false_northing = 0. ;
		omerc:gamma = 0LL ;
		omerc:geographic_crs_name = "unknown" ;
		omerc:grid_mapping_name = "oblique_mercator" ;
		omerc:horizontal_datum_name = "unknown" ;
		omerc:latitude_of_projection_origin = 0LL ;
		omerc:long_name = "omerc" ;
		omerc:longitude_of_projection_origin = 33.8226584093497 ;
		omerc:prime_meridian_name = "Greenwich" ;
		omerc:reference_ellipsoid_name = "sphere" ;

After

	int64 oblique_mercator ;
		oblique_mercator:azimuth_of_central_line = 8.14048957652079 ;
		oblique_mercator:crs_wkt = "PROJCRS[\"unknown\",BASEGEOGCRS[\"unknown\",DATUM[\"Unknown based on Normal Sphere (r=6370997) ellipsoid\",ELLIPSOID[\"Normal Sphere (r=6370997)\",6370997,0,LENGTHUNIT[\"metre\",1,ID[\"EPSG\",9001]]]],PRIMEM[\"Greenwich\",0,ANGLEUNIT[\"degree\",0.0174532925199433],ID[\"EPSG\",8901]]],CONVERSION[\"unknown\",METHOD[\"Hotine Oblique Mercator (variant B)\",ID[\"EPSG\",9815]],PARAMETER[\"Latitude of projection centre\",0,ANGLEUNIT[\"degree\",0.0174532925199433],ID[\"EPSG\",8811]],PARAMETER[\"Longitude of projection centre\",33.8226584093497,ANGLEUNIT[\"degree\",0.0174532925199433],ID[\"EPSG\",8812]],PARAMETER[\"Azimuth of initial line\",8.14048957652079,ANGLEUNIT[\"degree\",0.0174532925199433],ID[\"EPSG\",8813]],PARAMETER[\"Angle from Rectified to Skew Grid\",0,ANGLEUNIT[\"degree\",0.0174532925199433],ID[\"EPSG\",8814]],PARAMETER[\"Scale factor on initial line\",1,SCALEUNIT[\"unity\",1],ID[\"EPSG\",8815]],PARAMETER[\"Easting at projection centre\",0,LENGTHUNIT[\"metre\",1],ID[\"EPSG\",8816]],PARAMETER[\"Northing at projection centre\",0,LENGTHUNIT[\"metre\",1],ID[\"EPSG\",8817]]],CS[Cartesian,2],AXIS[\"(E)\",east,ORDER[1],LENGTHUNIT[\"metre\",1,ID[\"EPSG\",9001]]],AXIS[\"(N)\",north,ORDER[2],LENGTHUNIT[\"metre\",1,ID[\"EPSG\",9001]]]]" ;
		oblique_mercator:false_easting = 0LL ;
		oblique_mercator:false_northing = 0LL ;
		oblique_mercator:grid_mapping_name = "oblique_mercator" ;
		oblique_mercator:latitude_of_projection_origin = 0LL ;
		oblique_mercator:long_name = "oblique_mercator" ;
		oblique_mercator:longitude_of_projection_origin = 33.8226584093497 ;
		oblique_mercator:reference_ellipsoid_name = "sphere" ;
		oblique_mercator:unit = "m" ;

It's basically fine, but there are some parameters missing (both in the before and after), since CF 1.8 says:

reference_ellipsoid_name, prime_meridian_name, horizontal_datum_name and geographic_crs_name must be all defined if any one is defined, and if projected_crs_name is defined then geographic_crs_name must be also.

mraspaud · 2020-02-14T14:26:32Z

It's better with pyproj master, but geographic_crs_name is still missing

	int64 oblique_mercator ;
		oblique_mercator:azimuth_of_central_line = 8.14048957652079 ;
		oblique_mercator:crs_wkt = "PROJCRS[\"unknown\",BASEGEOGCRS[\"unknown\",DATUM[\"Unknown based on Normal Sphere (r=6370997) ellipsoid\",ELLIPSOID[\"Normal Sphere (r=6370997)\",6370997,0,LENGTHUNIT[\"metre\",1,ID[\"EPSG\",9001]]]],PRIMEM[\"Greenwich\",0,ANGLEUNIT[\"degree\",0.0174532925199433],ID[\"EPSG\",8901]]],CONVERSION[\"unknown\",METHOD[\"Hotine Oblique Mercator (variant B)\",ID[\"EPSG\",9815]],PARAMETER[\"Latitude of projection centre\",0,ANGLEUNIT[\"degree\",0.0174532925199433],ID[\"EPSG\",8811]],PARAMETER[\"Longitude of projection centre\",33.8226584093497,ANGLEUNIT[\"degree\",0.0174532925199433],ID[\"EPSG\",8812]],PARAMETER[\"Azimuth of initial line\",8.14048957652079,ANGLEUNIT[\"degree\",0.0174532925199433],ID[\"EPSG\",8813]],PARAMETER[\"Angle from Rectified to Skew Grid\",0,ANGLEUNIT[\"degree\",0.0174532925199433],ID[\"EPSG\",8814]],PARAMETER[\"Scale factor on initial line\",1,SCALEUNIT[\"unity\",1],ID[\"EPSG\",8815]],PARAMETER[\"Easting at projection centre\",0,LENGTHUNIT[\"metre\",1],ID[\"EPSG\",8816]],PARAMETER[\"Northing at projection centre\",0,LENGTHUNIT[\"metre\",1],ID[\"EPSG\",8817]]],CS[Cartesian,2],AXIS[\"(E)\",east,ORDER[1],LENGTHUNIT[\"metre\",1,ID[\"EPSG\",9001]]],AXIS[\"(N)\",north,ORDER[2],LENGTHUNIT[\"metre\",1,ID[\"EPSG\",9001]]]]" ;
		oblique_mercator:false_easting = 0. ;
		oblique_mercator:false_northing = 0. ;
		oblique_mercator:grid_mapping_name = "oblique_mercator" ;
		oblique_mercator:horizontal_datum_name = "Unknown based on Normal Sphere (r=6370997) ellipsoid" ;
		oblique_mercator:inverse_flattening = 0. ;
		oblique_mercator:latitude_of_projection_origin = -0. ;
		oblique_mercator:long_name = "oblique_mercator" ;
		oblique_mercator:longitude_of_prime_meridian = 0. ;
		oblique_mercator:longitude_of_projection_origin = 33.8226584093497 ;
		oblique_mercator:prime_meridian_name = "Greenwich" ;
		oblique_mercator:reference_ellipsoid_name = "Normal Sphere (r=6370997)" ;
		oblique_mercator:scale_factor_at_projection_origin = 1. ;
		oblique_mercator:semi_major_axis = 6370997. ;
		oblique_mercator:semi_minor_axis = 6370997. ;

djhoese · 2020-02-14T14:28:20Z

geographic_crs_name isn't CF though. Does your application need that for some reason? Even though it is "unknown"?

mraspaud · 2020-02-14T14:33:49Z

http://cfconventions.org/Data/cf-conventions/cf-conventions-1.8/cf-conventions.html

it is there, in table F.1

djhoese · 2020-02-14T14:47:36Z

Hm, but for your projection it isn't defined by the OGC WKT spec, so maybe that's ok? The CF docs don't say anything about "unknown" when it isn't defined. I assume that means you just don't include it if it isn't defined which is what pyproj is doing here.

What if you do have a OGC WKT GEOGCS defined? Does pyproj include it then?

sfinkens

Very nice development! And thanks for getting in touch with the pyproj developers.

Agree with Martin.
Never used that projection.
See my comment.

sfinkens · 2020-02-25T10:50:43Z

satpy/writers/cf_writer.py

+            grid_mapping['name'] = grid_mapping['grid_mapping_name']
+        except AttributeError:
+            grid_mapping = mappings[area.proj_dict['proj']](area)
+            grid_mapping['name'] = area.proj_dict['proj']


Does that mean that the name attribute would depend on the pyproj version? If so, should we align those names?

My suggestion for 3 is not implemented. Right now this does not depend on the pyproj version because proj is statically defined and unchanging (merc, geos, etc). However, the name attribute is not required by CF for the grid mapping variable so we can remove this portion and instead use area.area_id as the name of the variable.

Ok, I see. Using area.area_id sounds good!

mraspaud · 2020-03-25T11:46:41Z

@djhoese I don't think there is much more to do here, I'm glad with the result of this actually. If there are improvements to make, I suppose they should go in pyproj, no here, right ?

djhoese · 2020-03-25T12:46:04Z

There still need to be some changes for what area.area_id is and to use it as the variable name in the NetCDF. Also, I would like to drop the old functions completely and depend on pyproj 2.1+ (I think that's it at least). We could do it during the import of the module and raise an import error if the version isn't new enough. Thoughts?

mraspaud · 2020-03-25T13:05:09Z

I'm good with depending in a new pyproj. But maybe we skip this PR for v0.21 then.

djhoese · 2020-03-25T13:14:32Z

But maybe we skip this PR for v0.21 then.

I'm OK with that. Are you saying that due to the time it would take me to finish this or because you don't want this writer to depend on pyproj 2+?

mraspaud · 2020-03-25T14:20:06Z

I was thinking time constraints, I'd like a release within a week.

# Conflicts: # .travis.yml # appveyor.yml # satpy/tests/writer_tests/test_cf.py

ghost · 2020-03-30T01:40:20Z

DeepCode's analysis on #11ae11 found:

1 minor issue. ✔️ 1 issue were fixed.

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djhoese · 2020-03-30T02:21:35Z

@mraspaud This is ready for re-review. The big change is that the CRS conversion now completely depends on pyproj. The biggest change here on the user side is that there is no longer a warning if a CRS can't be converted "properly". This is because pyproj follows what the current CF standard is (not sure it is fully documented but I saw it on the mailing list) which is to provide a crs_wkt attribute in the grid mapping variable and no other attributes. I believe this is meant as a fallback for clients who say they can read any CF file but data providers' data is not in a CF CRS.

@sfinkens This also implements the grid mapping variable naming talked about above. Basically, it now names the grid mapping variable to area.area_id.

mraspaud

This looks good to me as afaics, but we need to check how this performs against the cf-checker.
Moreover, @sfinkens are you going to be affected by these changes ?

mraspaud · 2020-03-30T11:20:43Z

satpy/tests/writer_tests/test_cf.py

-        with mock.patch('satpy.writers.cf_writer.warnings.warn') as warn:
-            res, grid_mapping = area2gridmapping(ds)
-            warn.assert_called()
-            proj_dict = pyresample.geometry.proj4_str_to_dict(res.attrs['grid_proj4'])
-            self.assertEqual(proj_dict['lon_0'], 4.535)
-            self.assertEqual(proj_dict['lat_0'], 46.0)
-            self.assertEqual(proj_dict['o_lon_p'], -5.465)
-            self.assertEqual(proj_dict['o_lat_p'], 90.0)
-            self.assertEqual(proj_dict['proj'], 'ob_tran')
-            self.assertEqual(proj_dict['o_proj'], 'stere')
-            self.assertEqual(proj_dict['ellps'], 'WGS84')
-            self.assertEqual(grid_mapping.attrs['name'], 'proj4')
+        # with mock.patch('satpy.writers.cf_writer.warnings.warn') as warn:
+        res, grid_mapping = area2gridmapping(ds)
+        # warn.assert_called()
+        # proj_dict = pyresample.geometry.proj4_str_to_dict(res.attrs['grid_proj4'])
+        # self.assertEqual(proj_dict['lon_0'], 4.535)
+        # self.assertEqual(proj_dict['lat_0'], 46.0)
+        # self.assertEqual(proj_dict['o_lon_p'], -5.465)
+        # self.assertEqual(proj_dict['o_lat_p'], 90.0)
+        # self.assertEqual(proj_dict['proj'], 'ob_tran')
+        # self.assertEqual(proj_dict['o_proj'], 'stere')
+        # self.assertEqual(proj_dict['ellps'], 'WGS84')
+        self.assertIn('crs_wkt', grid_mapping.attrs)
+        self.assertEqual(res.attrs['grid_mapping'], 'cosmo7')


@loreclem I believe you implemented this, would you mind checking if you are ok with this ?

satpy/tests/writer_tests/test_cf.py

djhoese · 2020-03-30T15:53:55Z

The tests were failing previously because reference_ellipsoid_name for pyproj 2.5+ seems to add a space (ex. WGS 84) where it didn't before. I've asked on gitter about this. If it is intended I may need to add a special case to the test to handle this.

See travis-ci/travis-ci#8920

djhoese · 2020-03-30T20:46:35Z

Ok I just pushed a commit with some more big changes after @peters77 pointed out that this PR wasn't actually working in a real world case. Turns out the tests weren't actually testing very much. The lesson from us (the developers) should be "just because you can mock something in a test, doesn't mean you should". There are ways with mocks to declare them with wraps=original_function so that you still call the original code while also being able to check how many calls there were and what the arguments were. However, these tests were also using these checks if a function was called or what arguments it was called with instead of checking the actual result for what that function should be doing. This most recent commit should fix all of this based on what I saw in the tests.

The other big change in this last commit: the da2cf method now removes the .attrs['name'] attribute and instead renames the xarray DataArray's Variable object. This means that my_data_array.name is the name of the Variable and that .attrs['name'] is no longer available after things have been CF-ified.

Lastly, long_name now only defaults to my_var.name if standard_name is not provided instead of always being set. This should go along with the CF conventions based on what @mraspaud told me on slack.

mraspaud · 2020-03-31T06:48:10Z

Regarding my comment on geographic_crs_name, an issue has been opened in pyproj:
pyproj4/pyproj#585

mraspaud

Ok, this looks quite good now. I still have a few comments, but nothing serious.

mraspaud · 2020-03-31T07:39:13Z

satpy/tests/writer_tests/test_cf.py

@@ -759,14 +754,14 @@ def _gm_matches(gmapping, expected):
                                            'grid_mapping_name': 'geostationary',
                                            'semi_major_axis': a,
                                            'semi_minor_axis': b,
-                                            'sweep_axis': None,
-                                            'name': 'geos'})
+                                            # 'sweep_angle_axis': None,


In my offline test, I get 'sweep_angle_axis': 'y'. Should this be added ?

I think sweep angle axis is only guaranteed with pyproj 2.5+ since that version now bases the CF output on the WKT version of the CRS instead of the PROJ string. Ok with requiring pyproj 2.5+ for this writer?

I'm fine with it, but it might be too recent. Could we just check that sweep_angle_axis is y if it is there ?

mraspaud · 2020-03-31T07:46:35Z

satpy/tests/writer_tests/test_cf.py

+        # warn.assert_called()
+        # proj_dict = pyresample.geometry.proj4_str_to_dict(res.attrs['grid_proj4'])
+        # self.assertEqual(proj_dict['lon_0'], 4.535)
+        # self.assertEqual(proj_dict['lat_0'], 46.0)
+        # self.assertEqual(proj_dict['o_lon_p'], -5.465)
+        # self.assertEqual(proj_dict['o_lat_p'], 90.0)
+        # self.assertEqual(proj_dict['proj'], 'ob_tran')
+        # self.assertEqual(proj_dict['o_proj'], 'stere')
+        # self.assertEqual(proj_dict['ellps'], 'WGS84')


This isn't useful anymore and should be removed

Yes, I just wanted to make sure it was obvious that this is no longer being done. I can remove it.

mraspaud · 2020-03-31T07:47:37Z

satpy/tests/writer_tests/test_cf.py

+        # self.assertEqual(proj_dict['proj'], 'ob_tran')
+        # self.assertEqual(proj_dict['o_proj'], 'stere')
+        # self.assertEqual(proj_dict['ellps'], 'WGS84')
+        self.assertIn('crs_wkt', grid_mapping.attrs)


Should we copy the generated wkt and test against it ?

Maybe not the whole string but I'd be comfortable with checking if certain parts are there. Just in case the WKT changes a bit I don't want to have to update these tests every time.

mraspaud · 2020-03-31T08:01:56Z

satpy/writers/cf_writer.py

+        # modifies dataarray in-place
+        area2lonlat(dataarray)


For style, I'd rather avoid in-place modifications. Can we make this return a modified copy of the array and do:

Suggested change

# modifies dataarray in-place

area2lonlat(dataarray)

dataarray = area2lonlat(dataarray)

?

I know we had this before, but since we're changing this anyway...

Sure. The way this is set up is that area2lonlat and area2gridmapping are given a copy by area2cf. So these two functions are in-place but are only called with a copy. Still want the change? Not a big deal.

yes, I'd rather have each function make a copy.

In the lonlat case we add coordinates, does that still only need a shallow copy?

I think so, but don't take my word for it.

mraspaud · 2020-03-31T08:12:29Z

satpy/writers/cf_writer.py

-        res.extend(area2gridmapping(dataarray))
+        res.append(area2gridmapping(dataarray))


Same here, can we have area2gridmapping also return a modified copy of the array ? In this case we probably just need a shallow copy as we just add an attribute.

mraspaud

LGTM

sfinkens · 2020-04-01T09:21:39Z

Very nice, good work!
@martin I don't think this affects us, because PPS uses the lons/lats directly.
Good point about the tests @djhoese. I tend to patch too much.

djhoese added bug component:writers labels Jan 9, 2020

djhoese requested review from mraspaud and sfinkens January 9, 2020 03:20

djhoese self-assigned this Jan 9, 2020

djhoese mentioned this pull request Jan 9, 2020

Fix geostationary axis handling in CF writer #1040

Merged

4 tasks

djhoese and others added 4 commits January 23, 2020 10:44

Switch to pyproj for projection to CF NetCDF grid mapping

3610c26

Add cf test for projection with no a/b

3a897a8

Add cf test for omerc grid mapping

5d4d265

Update CF conversion to use pyproj 2.0+

10337c1

djhoese force-pushed the bugfix-cf-projections branch from 02986d1 to 10337c1 Compare January 23, 2020 17:30

sfinkens reviewed Feb 25, 2020

View reviewed changes

mraspaud added this to the v0.21.0 milestone Mar 25, 2020

mraspaud removed this from the v0.21.0 milestone Mar 26, 2020

Merge branch 'master' into bugfix-cf-projections

2663ac9

# Conflicts: # .travis.yml # appveyor.yml # satpy/tests/writer_tests/test_cf.py

Switch to only using pyproj for CF CRS conversion

f92fbee

mraspaud reviewed Mar 30, 2020

View reviewed changes

djhoese added 2 commits March 30, 2020 08:11

Remove redundant CF omerc test

1078dea

Remove pyproj restriction on travis environments

1218d21

Add travis workaround for long logs

be98fe2

See travis-ci/travis-ci#8920

mraspaud added this to the v0.21.0 milestone Mar 30, 2020

Fix CF writer tests to be more thorough and remove extra name attr

26a93a4

djhoese requested review from mraspaud and sfinkens March 30, 2020 20:46

mraspaud reviewed Mar 31, 2020

View reviewed changes

djhoese added 2 commits March 31, 2020 09:29

Refactor area2X functions to copy instead of doing things in-place

641bc86

Move CF DataArray deep copy to be more obvious

11ae112

mraspaud approved these changes Mar 31, 2020

View reviewed changes

mraspaud merged commit d12bb7a into pytroll:master Apr 1, 2020

	# modifies dataarray in-place
	area2lonlat(dataarray)
	dataarray = area2lonlat(dataarray)

		res.extend(area2gridmapping(dataarray))
		res.append(area2gridmapping(dataarray))

Switch to pyproj for projection to CF NetCDF grid mapping #1038

Switch to pyproj for projection to CF NetCDF grid mapping #1038

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