Vector plots 2 #3120

pp-mo · 2018-07-31T18:09:55Z

WIP : not yet ready

Followon work from #3096

more review issues : see Outstanding review issues from #3096 (gridcell rotations) #3114
PLUS : tidy up + add some proper tests

~~PLEASE NOTE~~
~~contents of ...tests/unit/analysis/cartography/test_gridcell_angles.py are still mostly junk~~
~~Please await more commits before commenting !~~
(now more sensible, though more tests still wanted)

lbdreyer · 2018-08-01T09:15:29Z

@pp-mo I think you also pushed this branch directly to upstream as we have a upstream/vector_plots_2d branch. I assume this was a mistake?

pp-mo · 2018-08-03T10:31:58Z

I think you also pushed this branch directly to upstream as we have a upstream/vector_plots_2d branch. I assume this was a mistake?

@lbdreyer I was hoping you wouldn't notice that !
I did that when testing the auto-build of docs.
It actually wasn't this branch but something different with the same name !
(now removed).

So, not relevant to this.

pp-mo · 2018-08-03T18:54:31Z

Note: now rebased onto 'pin_dask', so we can hopefully have working tests (for now!).

@lbdreyer hopefully, this should be looking a lot more sensible.

However, it is still lacking some tests of the grid_angles method, like failure methods and some features.
In principle, it can use a grid with a rotated or even non-latlon coord system, but that quite possibly does not even work yet, and could even instead be removed ? Undecided.

Also, no tests yet for rotate_grid_vectors function.

stickler-ci · 2018-08-13T10:00:22Z

lib/iris/tests/unit/analysis/cartography/test_gridcell_angles.py

+        angles_expected = (angles_expected + 360.) % 360.
+
+        # Assert (toleranced) equality, and return results.
+        ok = np.allclose(angles_calculated, angles_expected,


F841 local variable 'ok' is assigned to but never used

…utine.

pp-mo · 2018-08-15T10:01:55Z

hi @lbdreyer tests now passing : ready for a look-over ?

lbdreyer · 2018-08-15T14:49:51Z

lib/iris/analysis/_grid_angles.py

@@ -24,6 +24,7 @@

 import numpy as np

+import cartopy.crs as ccrs
 import iris




Potential changes to the _3d_xyz_from_latlon function

Returns: xyz : (array, dtype=float64) cartesian coordinates on a unit sphere. Dimension 0 maps x,y,z.

Clarify the last sentence? Dimension 0 maps x,y,z

lon1 and lat1 -> lon_rad and lat_rad? seems a little more informative

lbdreyer · 2018-08-15T14:50:40Z

lib/iris/analysis/_grid_angles.py

@@ -65,13 +66,13 @@ def _latlon_from_xyz(xyz):
    Returns:

        lonlat : (array)
-            spherical angles, of dims (2, <others>), in radians.
+            spherical angles, of dims (2, <others>), in degrees.
            Dim 0 maps longitude, latitude.


Here's this Dim 0 maps longitude, latitde again. I don't know what that means?

lbdreyer · 2018-08-15T14:58:54Z

lib/iris/analysis/_grid_angles.py

@@ -65,13 +66,13 @@ def _latlon_from_xyz(xyz):
    Returns:

        lonlat : (array)
-            spherical angles, of dims (2, <others>), in radians.
+            spherical angles, of dims (2, <others>), in degrees.


I do prefer that this is working in degrees to be consistent with the _3d_xyz_from_latlon function

hi @lbdreyer
I'll look into these now if you like,
but in principle I had already deferred these "comments on the comments" to a follow-on : #3109, also linked from #3114.

I have been working on the follow-up (tentatively titled "vector_plots_3" !), to address those remaining issues + add missing tests ...

pp-mo · 2018-08-15T16:01:42Z

Latest tries to improve docstrings,
Is probably overkill (!)

stickler-ci · 2018-08-16T10:56:00Z

lib/iris/analysis/_grid_angles.py

+            # Transform points into true lats + lons.
+            crs_src = cs.as_cartopy_crs()
+            crs_pc = ccrs.PlateCarree()
+            def transform_xy_arrays(x, y):


E306 expected 1 blank line before a nested definition, found 0

stickler-ci · 2018-08-16T10:56:00Z

lib/iris/tests/unit/analysis/cartography/test_gridcell_angles.py

+
+
+
+if __name__ == "__main__":


E303 too many blank lines (3)

lbdreyer

Goodness, this was a challenging PR to review! I was familiar with the code from previously having looked at, but this time I took the time to give it a much more thorough review.

It looks like most of the changes are good (and really well done for getting the code for this very complex problem together!! 👏 👏 👏), but I just have a couple of comments before I merge this in.

My only big issue is that I'm not overly keen on the supporting calculations based on points rather than bounds as there are a number of caveats with it, but as long as the user is aware of them I suppose it is okay.

lbdreyer · 2018-08-24T09:28:17Z

lib/iris/analysis/_grid_angles.py

    axial_radii = np.sqrt(xyz[0] * xyz[0] + xyz[1] * xyz[1])
-    lats = np.arctan2(xyz[2], axial_radii)
+    lats = np.rad2deg(np.arctan2(xyz[2], axial_radii))


Should this not be asin rather than atan2?
lats = np.rad2deg(np.asin(xyz[2], axial_radii))
See wikipedia article

Also, why don't you calculate the axial radii with z?, i.e.
axial_radii = np.sqrt(xyz[0] * xyz[0] + xyz[1] * xyz[1] + xyz[2] * xyz[2])

(a) Should this not be asin rather than atan2 ... (b) why don't you calculate the axial radii with z?

(b) explains (a) : so the calc is actually the same !
But I agree that 'full radius + arcsin' is clearer, so I will change it.

lbdreyer · 2018-08-24T12:35:27Z

lib/iris/analysis/_grid_angles.py

+                standard_name='longitude', units='degrees')
+            x_coord = iris.coords.AuxCoord(
+                points=xpts, bounds=xbds,
+                standard_name='longitude', units='degrees')


It may worth mentioning this (that the output cube may contain transformed coordinates) in the doc string

Currently, in the Returns section of the docstring it says that the coordinates will be identical:

"Cube of angles of grid-x vector from true Eastward direction for
each gridcell, in degrees.
It also has longitude and latitude coordinates. If coordinates
were input the output has identical ones : If the input was 2d
arrays, the output coords have no bounds; or, if the input was 3d
arrays, the output coords have bounds and centrepoints which are
the average of the 4 bounds."

Also note that you've set x_coord twice (lines 276 and 279) rather than setting x_coord and y_coord

output cube may contain transformed coordinates

Agreed, I will fix that.

you've set x_coord twice

Ouch! Will fix, and also add something to test_nonlatlon_coord_system which "would have caught" this goof !

lbdreyer · 2018-08-24T15:34:33Z

lib/iris/tests/unit/analysis/cartography/test_gridcell_angles.py

+        # In this case, the match is actually rather poor (!).
+        self.assertArrayAllClose(result.data,
+                                 global_cube_results,
+                                 atol=7.5)


This is the problem with the points based calculation!

lbdreyer · 2018-08-24T15:55:18Z

lib/iris/analysis/_grid_angles.py

+    psi = np.arccos(cosine) * np.sign(r[1] - p[1])
+    psi[index] = np.nan
+
+    return np.rad2deg(psi)


Well this has melted my brain! 😵
I'm going to need a little more time to get my head around why the lines 125 and 130 give the right answer! I'm almost there!

Until then, I did do a quick test but get slightly off answers.

>>> p,q,r = [0,0],[10,10],[20,20] >>> mid_lons = np.deg2rad(q[0]) >>> pr = xyz_latlon(r[0], r[1]) - xyz_latlon(p[0], p[1]) >>> pr_norm = np.sqrt(np.sum(pr**2, axis=0)) >>> pr_top = pr[1] * np.cos(mid_lons) - pr[0] * np.sin(mid_lons) >>> cosine = np.maximum(np.minimum(pr_top / pr_norm, 1), -1) >>> psi = np.arccos(cosine) * np.sign(r[1] - p[1]) >>> np.rad2deg(psi) 45.863970536175245

Where I would expect 45

pp-mo · 2018-08-28T16:30:47Z

Hi @lbdreyer 💐 🍾 for checking the trigonometry code !
I'm hoping my latest addresses all your outstanding points.

lbdreyer · 2018-08-29T09:35:01Z

@pp-mo Thanks for this! The changes you've added all look fine so I'll squash and merge this in

@corinnebosley

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This is mentioned in the Iris Check List in pulls.rst list, but would be good to have it here as well (useful for new contributors like me). * Add link to developer guide. (SciTools#3093) * Combine identical test routines for pcolor + pcolormesh. * Test 'contiguity_tolerance' use in iris.plot.pcolor and pcolormesh. * Unpin dask * Handle printing bounds of long time interval coords (SciTools#3140) * Handle printing time bounds * Whatsnew, whitespace fix for test result * iris.util.reverse on cubes (SciTools#3155) * make cube reversing official * review: test conventions, etc. * review: enable coord specification * add whatsnew * review: AssertRaises --> AssertRaisesRegexp * cube error handling * Improved Aux factory error handling: better message, delivered earlier (SciTools#3182) * Tests for expected behaviour * Raise error if aux factory relies on a coordinate external to cube * Include coordinate name in error message * Don't check whether dependencies that are "None" are in the coords. * Review changes: check cube name in error and variable rename * Truncated variable for flake8 * Correct cube collapse code * Provide info on pp-field indices in the file for structured um loads. (SciTools#2977) * Field locations for structured um loads. * Remove unused import. * Fix test for new implementation. * Added whatsnew. * Review changes. * simplify dev guide * Integration test for iris.plot.contour with 2d coords. (SciTools#3189) * Integration test for iris.plot.contour with 2d coords. * Review changes. * pinned numpy to not 1.15.2 in core requirements * Public contiguity checking (SciTools#3144) :champagne: :1st_place_medal: for sticking with it @corinnebosley * Populate whatsnew 2.2 (SciTools#3192) * started adding entries to whatsnew * more updates to whatsnew * first complete draft of 2.2 whatsnew * some small corrections * made corrections suggested in review * Update version str * Update CF standard name table to v59 * Fix docstring re structured text warnings (SciTools#3073) (SciTools#3197) * updated version string to 2.3.0dev0 * add contact options to README removed gitter from contact list * Add stash mapping changes to v2.1.0 changelog replaced list with link of stash mappings * expanded name of dev group * added an n for better flow * Fix broken link to dask docs (SciTools#3204)

* Small improvements; first sensible tests. * Enhanced testing; better checking and crs awareness in grid_angles routine. * Remove crud from test_gridcell_angles. * Use degree units for everything in _grid_angles. * Make assertArrayAllClose print details when it fails. * Rework and extend testing for gridcell_angles. * Fix assertArrayAllClose; remove debug code from test_gridcell_angles. * Remove obsolete assignments. * Remove obsolete code. * Small comment improvements. * Attempt to clarify docstrings of low-level routines. * More tests, and some functional fixes. * Codestyle fixes. * Review changes + fixes. * Avoid using sample data.

pp-mo added the 2d_coords label Jul 31, 2018

pp-mo force-pushed the vector_plots_2 branch from 7e96863 to 9052bf0 Compare August 3, 2018 18:48

stickler-ci reviewed Aug 13, 2018

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pp-mo force-pushed the 2d_coords branch from d340037 to e3e82e4 Compare August 14, 2018 13:59

pp-mo force-pushed the vector_plots_2 branch from 4b3469b to 5a017a5 Compare August 14, 2018 14:38

pp-mo added 10 commits August 14, 2018 16:18

Small improvements; first sensible tests.

ebfc4c1

Enhanced testing; better checking and crs awareness in grid_angles ro…

670982e

…utine.

Remove crud from test_gridcell_angles.

fdb693b

Use degree units for everything in _grid_angles.

e832fe3

Make assertArrayAllClose print details when it fails.

56944df

Rework and extend testing for gridcell_angles.

f149341

Fix assertArrayAllClose; remove debug code from test_gridcell_angles.

dff7750

Remove obsolete assignments.

fd14631

Remove obsolete code.

d19f3d9

Small comment improvements.

330c71e

pp-mo force-pushed the vector_plots_2 branch from fec9716 to 330c71e Compare August 14, 2018 15:19

lbdreyer reviewed Aug 15, 2018

View reviewed changes

Attempt to clarify docstrings of low-level routines.

995864d

pp-mo force-pushed the vector_plots_2 branch from cd986fb to 995864d Compare August 15, 2018 16:04

More tests, and some functional fixes.

4820572

stickler-ci reviewed Aug 16, 2018

View reviewed changes

Codestyle fixes.

605ef0c

pp-mo mentioned this pull request Aug 16, 2018

Outstanding review issues from #3096 (gridcell rotations) #3114

Closed

lbdreyer requested changes Aug 24, 2018

View reviewed changes

Review changes + fixes.

1d37367

pp-mo closed this Aug 28, 2018

pp-mo reopened this Aug 28, 2018

Avoid using sample data.

5a047a6

lbdreyer approved these changes Aug 29, 2018

View reviewed changes

lbdreyer merged commit 5de040f into SciTools:2d_coords Aug 29, 2018

QuLogic added this to the v2.2.0 milestone Aug 29, 2018

pp-mo mentioned this pull request Aug 29, 2018

Improve comments describing calculation in iris.analysis.cartography.grid_angles #3109

Closed

pp-mo deleted the vector_plots_2 branch January 8, 2019 12:58

Vector plots 2 #3120

Vector plots 2 #3120

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