Add Horizontal Streamfunction plots + Subpolar North Atlantic projection #898

anirban89 · 2022-09-23T17:52:39Z

Summary :
Config option (climatologyMapBSF) for plotting climatological depth integrated transport streamfunction

either full depth (Barotropic) or up to a specified depth (task file = ocean/climatology_map_bsf.py)
option to add arrows to contourlines: config option arrowsOnContour<suffix> in default.cfg, files updated shared/plot/climatology_map.py, shared/plot/colormap.py
Subpolar North Atlantic projection to visualize sub polar gyre.
subpolar North Atlantic projection added to shared/projection/__init__.py, shared/climatology/comparison_descriptors.py and shared/climatology/remap_mpas_climatology_subtask.py
doctoring updated in shared/climatology/comparison_descriptors.py

anirban89 · 2022-09-26T15:22:43Z

Hi, Can you all please review this pull request? Maybe test this functionality with other E3SM runs. I only tested with a Southern Ocean refined run: /lcrc/group/e3sm/ac.abarthel/E3SMv2/20220808.v2.cryo.Bcase.submesoscale.ne30pg2_SOwISC12to60E2r4.chrysalis.

anirban89 · 2022-09-26T15:57:40Z

I changed the figsize of some of the projections (North Pacific, North Atlantic, Antarctic) to help formatting (reduce whitespace etc.) in the default config file, but I only looked at single panel plots and didn't check any of the 3 panel plots. We would need to check how the figures get formatted with the 3 panel plot

xylar

@anirban89, this is really fantastic! Here are a few comments. Some are changes I noticed on a quick look through the code. Some are notes that will need to be followed up on once I've run the full analysis on a typical cryosphere simulation so we can see the effects on our usual plots.

xylar · 2022-09-24T17:49:50Z

mpas_analysis/default.cfg

@@ -245,6 +245,11 @@ comparisonNorthPacificWidth = 15000.
 comparisonNorthPacificHeight = 5000.
 comparisonNorthPacificResolution = 20.

+# The comparison North Atlantic grid size and resolution in km


Suggested change

# The comparison North Atlantic grid size and resolution in km

# The comparison Subpolar North Atlantic grid size and resolution in km

xylar · 2022-09-24T17:50:49Z

mpas_analysis/default.cfg

-onePanelFigSize = (8, 7.5)
+onePanelFigSize = (7, 7.5)
 threePanelVertFigSize = (8, 22)
-threePanelHorizFigSize = (22, 7.5)
+threePanelHorizFigSize = (20, 7.5)


We will have to see what kind of an effect this has on other Antarctic plots, since it will affect all of them.

Arctic plots will likely need tweaks. See overlapping titles:

xylar · 2022-09-24T17:51:54Z

mpas_analysis/default.cfg

-comparisonGrids = ['latlon']
+comparisonGrids = ['latlon', 'subpolar_north_atlantic']


I'm guessing this was just for testing and we don't want this by default?

Yes this was for testing, you are right

xylar · 2022-09-24T17:53:30Z

mpas_analysis/default.cfg

-colormapTypeResult = indexed
+colormapTypeResult = continuous
+# the type of norm used in the colormap
+normTypeResult = linear
+# A dictionary with keywords for the norm
+normArgsResult = {'vmin': -12., 'vmax': 12.}
 # color indices into colormapName for filled contours
 colormapIndicesResult = numpy.array(numpy.linspace(0, 255, 38), int)
 # colormap levels/values for contour boundaries
 colorbarLevelsResult = numpy.linspace(-12., 12., 37)
 # colormap levels/values for ticks (defaults to same as levels)
 colorbarTicksResult = numpy.linspace(-12., 12., 9)
-
+# Adding contour lines to the figure
+contourLevelsResult = np.arange(-12., 12., 1.)
+contourThicknessResult = 0.5
+contourColorResult = black
 # colormap for differences


We may want to change these but it shouldn't be done in this PR.

xylar · 2022-09-24T17:53:50Z

mpas_analysis/default.cfg

-comparisonGrids = ['latlon']
+comparisonGrids = ['latlon','subpolar_north_atlantic']


Same here, this doesn't belong in this PR.

Sorry you are right

mpas_analysis/shared/plot/climatology_map.py

xylar · 2022-09-24T17:57:41Z

mpas_analysis/shared/plot/climatology_map.py

-        ax.set_title(title, y=1.06, **plottitle_font)
+        ax.set_title(title,**plottitle_font)


We will have to see what the effects of this change are on other plots. It could have a positive effect on the BSF plots but be a problem for other plots.

xylar · 2022-09-24T17:58:39Z

mpas_analysis/shared/plot/climatology_map.py

@@ -597,7 +634,7 @@ def plot_panel(ax, title, array, colormap, norm, levels, ticks, contours,
    else:
        figsize = config.getexpression(section, 'threePanelHorizFigSize')
        subplots = [131, 132, 133]
-
+    aspectratio = figsize[0]/figsize[1]


I don't think you ended up using this so I'd remove it again.

yes, we can remove this for now

mpas_analysis/shared/plot/colormap.py

mpas_analysis/shared/projection/__init__.py

mpas_analysis/default.cfg

xylar

A few more comments.

mpas_analysis/ocean/climatology_map_bsf.py

mpas_analysis/polar_regions.cfg

mpas_analysis/default.cfg

xylar · 2022-09-26T23:00:20Z

mpas_analysis/default.cfg

-onePanelFigSize = (8, 7.5)
+onePanelFigSize = (7, 7.5)
 threePanelVertFigSize = (8, 22)
-threePanelHorizFigSize = (22, 7.5)
+threePanelHorizFigSize = (20, 7.5)


Arctic plots will likely need tweaks. See overlapping titles:

xylar · 2022-09-26T23:57:25Z

Hi, Can you all please review this pull request?

@anirban89, I think if you don't @ people, they won't notice this.

@milenaveneziani, @alicebarthel, could you have a look?

We should also ask LeAnn for feedback before we merge.

milenaveneziani · 2022-09-27T01:26:15Z

This looks great! Thanks @anirban89, @xylar.
I will test this PR on one of the ARRM simulations.

milenaveneziani · 2022-09-27T16:49:36Z

This worked great for me, @anirban89!
Here is the full analysis link: https://portal.nersc.gov/project/m1199/milena/20220810.WCYCL1950.arcticx4v1pg2_ARRM10to60E2r1.baseline_bdvslat/Years11-20/ocean/index.html

And here is the full barotropic SF for the Subpolar gyre:

milenaveneziani

I understand that Anirban wants to change a few aesthetic details, but this is already great for me.

xylar · 2022-09-27T21:11:10Z

@anirban89, this is really fantastic! I'm going to post some figures where the formatting needs a little work. Let's talk about how to fix these so we can get this merged.

Here's the full analysis:
https://web.lcrc.anl.gov/public/e3sm/diagnostic_output/ac.xylar/analysis_testing/bsf_vertices2/v2.cryo.Bcase.submesoscale.ne30pg2_SOwISC12to60E2r4.chrysalis/clim_0001-0020_ts_0001-0020/ocean/index.html

Here is a fake main vs. control analysis (with the same run as main and control) so we can look at the 3-panel plots:

https://web.lcrc.anl.gov/public/e3sm/diagnostic_output/ac.xylar/analysis_testing/bsf_main_vs_ctrl/main/clim_0001-0020_ts_0001-0020/ocean/index.html

Too much whitespace between title and panel titles. Probably, just need to shorten the height of the 3-panel Antarctic figure:

Same with Arctic 3-panel:

The title font in the Subpolar North Atlantic plots seems a lot bigger than in other plots:

This seems to be leading to undesirable whitespace to the left.

We don't plot North Atlantic and North Pacific regions by default but it might be worth doing a test with those regions (both 1 and 3 panel plots) to make sure your modifications here are appropriate. I'm not super worried about those until we start using them by default, though.

xylar · 2022-09-28T21:39:05Z

@anirban89, it would be good to rebase this branch onto the latest develop now that #906 has gone in. It would be important to make sure the 3 commits from that PR no longer appear here. We can chat about this tomorrow.

anirban89 · 2022-09-28T21:42:29Z

Yes lets reconvene tomorrow

mpas_analysis/__main__.py

We remap directly from vertices to the comparison grid.

anirban89 · 2022-09-29T19:22:08Z

@xylar I am not saying it has to be part of this PR, but I noticed that EKE is being plotted on a linear scale with units in cm^2s^-2, whereas surface speed is plotted in linear scale with units in ms^-1. I have always seen EKE being plotted on a logarithmic scale. Is there any specific reason to not have SI units for this one plot? I would expect EKE to be plotted in m^2s^-2 with a logarithmic scale and a different colormap. That will definitely make for a better visualization. Thoughts?

xylar · 2022-09-29T19:37:59Z

@xylar I am not saying it has to be part of this PR, but I noticed that EKE is being plotted on a linear scale with units in cm^2s^-2, whereas surface speed is plotted in linear scale with units in ms^-1. I have always seen EKE being plotted on a logarithmic scale. Is there any specific reason to not have SI units for this one plot? I would expect EKE to be plotted in m^2s^-2 with a logarithmic scale and a different colormap. That will definitely make for a better visualization. Thoughts?

A separate PR to address these things would be very welcome. The analysis was added by a summer student many years ago. It hasn't received much attention since then, in part because we don't always even include it in our output. I agree with all your suggestions: log scale, SI units and a different colormap. What colormap did you have in mind? Is there a typical choice that the community expects?

anirban89 · 2022-09-29T20:22:43Z

I was thinking something on the lines of this. This is a pretty commonly used colormap for speed and EKE. This is named as Black Blue and White in Paraview.

It doesn't appear to match with any of the available maps under MPAS-Tools sciviz color maps.

But I have a python recipe for a custom colormap like this which could work

xylar

@anirban89, this is excellent work! Further tweaks can be made in follow-up PRs if we find anything that needs it but this looks like exactly what I was hoping for!

xylar · 2022-09-29T20:29:47Z

@anirban89, let's move the discussion on EKE to a separate issue. I don't want this PR to be confused with an unrelated issue.

xylar · 2022-09-29T20:35:51Z

@lconlon, are you okay with this plot of the subpolar gyre?

We'd welcome feedback. As I said, we can also tweak it to your liking later if this is okay as a first pass.

(It's duplicated twice in this plot just to test model vs. model comparison. You can ignore that.)

xylar · 2022-10-10T20:57:15Z

@anirban89, would you have time to add a documentation page for this task?
Here's an example to work from:
https://github.com/MPAS-Dev/MPAS-Analysis/blob/develop/docs/users_guide/tasks/climatologyMapEKE.rst
They're pretty formulaic but still I think it would be great if you take care of this rather than me since you put in the effort on this task.

xylar · 2022-10-10T20:57:39Z

You can make a new PR just for that.

milenaveneziani requested review from xylar, milenaveneziani and alicebarthel September 24, 2022 16:33

milenaveneziani added enhancement work in progress labels Sep 24, 2022

anirban89 removed the work in progress label Sep 26, 2022

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anirban89 force-pushed the add_climatology_map_bsf branch from 02acebd to 67e972d Compare September 27, 2022 15:43

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xylar mentioned this pull request Sep 28, 2022

Add support for remapping from MPAS vertices #906

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Fix config file on the webpage #913

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xylar and others added 8 commits September 29, 2022 12:49

Add a new task climatologyMapBSF

e9bb44d

Add config options for climatologyMapBSF

fa7c3c7

Add ClimatologyMapBSF to list of analysis tasks

2767a58

changes to default config for depth integrated streamfunction

94d9ad2

changes to climatology_map_bsf to add depth integrated streamfunction

b1ae4fc

changes to comparison_descriptors to add subpolar north atlantic

909cf2f

changes to remap_mpas_climatology_subtask to add subpolar north atlantic

8bd90e1

update available projections to include subpolar north atlantic

990481e

anirban89 and others added 14 commits September 29, 2022 12:49

Add arrow option for contours

6b73380

Change plot titles to Horizontal Streamfunction

5a87844

capitalize() -> string.capwords() for gallery-group names

5ba5997

modify docstring generalize for projections

9ebb43a

add arrows to contour plot

7fcb5ac

add read config option for arrows on contours

058cdf5

fix typo in north pacific projection in previous iteration

46de04a

Switch to computing BSF only on vertices

46afde2

We remap directly from vertices to the comparison grid.

unsetting config options for nonBSF revert to original

a7b463c

add subpolar north atlantic projection in polar regions config

b58cb79

change max depth switch to 6000 m for BSF

25b95ab

adjust formatting

34c1d4c

adjust formatting

71a4d08

adjust figure formatting 3 panels for projections

45ee0db

anirban89 force-pushed the add_climatology_map_bsf branch from 934cc4c to 45ee0db Compare September 29, 2022 17:52

Fix typo

5b18091

xylar approved these changes Sep 29, 2022

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xylar mentioned this pull request Sep 29, 2022

Change colormap and units for EKE #916

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xylar removed the request for review from alicebarthel September 29, 2022 20:33

xylar merged commit 1447f4a into MPAS-Dev:develop Sep 29, 2022

xylar mentioned this pull request Oct 5, 2022

Fixes to formatting and config options for climatologyMapBSF #918

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Add Horizontal Streamfunction plots + Subpolar North Atlantic projection #898

Add Horizontal Streamfunction plots + Subpolar North Atlantic projection #898

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	# The comparison North Atlantic grid size and resolution in km
	# The comparison Subpolar North Atlantic grid size and resolution in km

		comparisonGrids = ['latlon']
		comparisonGrids = ['latlon', 'subpolar_north_atlantic']

		comparisonGrids = ['latlon']
		comparisonGrids = ['latlon','subpolar_north_atlantic']

		ax.set_title(title, y=1.06, **plottitle_font)
		ax.set_title(title,**plottitle_font)

Add Horizontal Streamfunction plots + Subpolar North Atlantic projection #898

Add Horizontal Streamfunction plots + Subpolar North Atlantic projection #898

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