`euler_pole`: add PMM plotting functions #935

yuankailiu · 2022-12-23T19:59:13Z

add plate boundary files from GSRMv2.1 and MORVEL56
functions to read the boundary files and plot

Check here for the usage: https://github.com/yuankailiu/utils/blob/main/notebooks/PMM_plot.ipynb

Description of proposed changes

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+ add plate boundary files from GSRMv2.1 and MORVEL56 + functions to read the boundary files and plot

+ Consistent NNR model file: - src/mintpy/data/plate_boundary/GSRMv2.1/nnr.csv - src/mintpy/data/plate_boundary/MRVL56/nnr.csv - use camelCase plate names (but caplitalize the first character) + Consistent plate boundary file: - src/mintpy/data/plate_boundary/GSRMv2.1/plate_outlines.txt - src/mintpy/data/plate_boundary/MRVL56/plate_outlines.txt - use '> ' before plate abbv. names, good for GMT - use longitude, latitude for the columns, good for GMT + remove useless script: src/mintpy/data/plate_boundary/GSRMv2.1/split_bnds.py + update full reference in README.md under src/mintpy/data/plate_boundary/ + euler_pole.py: update read_plate_attributes() read_plate_outlines()

yuankailiu · 2023-01-06T22:39:23Z

Checks seem to fail at testing /root/tools/MintPy/tests/objects/ionex.py

But I did not change this file.

attempt to fix the unit test error below: ``` Testing /root/tools/MintPy/tests/objects/ionex.py Traceback (most recent call last): File "/root/tools/MintPy/tests/objects/ionex.py", line 110, in <module> test_get_ionex_value() File "/root/tools/MintPy/tests/objects/ionex.py", line 93, in test_get_ionex_value tec_val = ionex.get_ionex_value( File "/root/tools/miniconda3/lib/python3.10/site-packages/mintpy/objects/ionex.py", line 102, in get_ionex_value tec_val = interp_3d_maps( File "/root/tools/miniconda3/lib/python3.10/site-packages/mintpy/objects/ionex.py", line 184, in interp_3d_maps tec_val = interpolate.interpn( File "/root/tools/miniconda3/lib/python3.10/site-packages/scipy/interpolate/_rgi.py", line 654, in interpn return interp(xi) File "/root/tools/miniconda3/lib/python3.10/site-packages/scipy/interpolate/_rgi.py", line 331, in __call__ indices, norm_distances = self._find_indices(xi.T) File "/root/tools/miniconda3/lib/python3.10/site-packages/scipy/interpolate/_rgi.py", line 499, in _find_indices return find_indices(self.grid, xi) File "_rgi_cython.pyx", line 95, in scipy.interpolate._rgi_cython.find_indices File "stringsource", line 660, in View.MemoryView.memoryview_cwrapper File "stringsource", line 350, in View.MemoryView.memoryview.__cinit__ ValueError: ndarray is not C-contiguous ```

This reverts commit b62d748.

This reverts commit 22f88ba.

This reverts commit 5e491ab.

yunjunz · 2023-01-07T02:43:43Z

Checks seem to fail at testing /root/tools/MintPy/tests/objects/ionex.py

But I did not change this file.

The same test works well locally on my laptop, and I could not find out the reason on circle CI. As you said, this PR did not touch this part of the code, let's ignore this error.

Update: this is a bug in scipy (scipy/scipy#17717) affecting its interpolate sub-module. Hopefully the next patch release of scipy will include the fix and we don't need to do anything on our side except for waiting.

src/mintpy/objects/euler_pole.py

yunjunz · 2023-01-07T03:06:34Z

For the NNR PMM value/tables, maybe it's easier to use if we write them in Python, similar to what we have for ITRM2014-PMM, instead of a data file, which requires extra reading?

If so, we could move these variable definitions from mintpy.cli.plate_motion into mintpy.plate_motion, for easier usage.

Update: I am done with changes on my side for this round of PR review. Please feel free to pull the changes and work on them.

yuankailiu · 2023-01-09T19:06:13Z

For the NNR PMM value/tables, maybe it's easier to use if we write them in Python, similar to what we have for ITRM2014-PMM, instead of a data file, which requires extra reading?

If so, we could move these variable definitions from mintpy.cli.plate_motion into mintpy.plate_motion, for easier usage.

Yes, I can do that. Now those files have different units compared with our ITRF2014 dictionary.
The files are in the format of Lat, Lon, and the rotation rate in degrees per Ma.
I can just create dictionaries for them without converting the units. Anyway, these parameters are not supposed to be used in computing the plate motion.

These files still exist just because I need the abbreviated names for the plate polygons.

+ read GSRM and MORVEL56 model parameters (abbrev) from built-in dictionary + GSRM and MORVEL56 PMM files (csv) are not in used, but keep them for bookkeeping + folder names hosting plate boundaries are modified + use original file names for plate boundaries files (consistent with the source)

yuankailiu · 2023-01-09T20:24:42Z

Please take a look at the new updates.

If so, we could move these variable definitions from mintpy.cli.plate_motion into mintpy.plate_motion, for easier usage.

But I don't see why we will need to put those dict() in mintpy.plate_motion? Also where should we put the PLATE_BOUNDARY_FILE ? Right now, it is under the euler_pole.py.

refer to: https://github.com/insarlab/MintPy/wiki/plate-motion-package + euler_pole.py: put pmm definitions here, plate abbv are upper case + cli/plate_motion.py: remove pmm definitions + plate_boundary/*/nnr.csv: delete them + to-do: move --plate to --om-cart from mintpy.cli.plate_motion to mintpy.plate_motion

src/mintpy/cli/plate_motion.py will not need this dictionary

from mintpy.objects.euler_pole import ITRF2014_PMM

+ use `MORVEL` instead of `MORVEL56` for the folder name, as it's generic for MORVEL and NNR-MORVEL56, to be consistent of using GSRM, instead of GSRMv2.1 + rename both data files as `plate_outlines.gmt` with shell commands in the README for easy produce + euler_pole: - update data file path from above changes - use `GSRM_V21_PMM` and `NNR_MORVEL56_PMM` for more precise info

yuankailiu · 2023-01-12T17:10:29Z

src/mintpy/objects/euler_pole.py

+    elif 'MORVEL' in pmm_name:
+        pmm_name = 'MORVEL'
+        pmm_dict = NNR_MORVEL56_PMM
+        coord_order = 'lalo'


This place should be 'lola' as well.

Because I also flip the order in the file from the original All_boundary in MORVEL_56.

So we can just set the default as coord_order='lola' and keep the file as it is (and it also makes sense since it has .gmt extension.).

But this way, we no longer keep the original downloaded file untouched. But anyway, I already added those > signs in the file.

As we discussed offline:

let's keep the original downloaded file content untouched, for reproducibility.

use .lonlat and .latlon as file extensions, instead of .gmt, to be more informative.

update the data/plate_boundary/README.md file to be consistent with the above changes.

+ use center_lalo to replace center_lat/lon + use satellite_height directly, instead of zoom + map center priority: direct input arg > pts_lalo > polygon centroid + remove vu as it's not used

yunjunz

Thank you @yuankailiu for the nice PR. I went through everything and am able to produce a nice plot as below. All looks good to me, pending the above comments as we discussed offline.

from matplotlib import pyplot as plt
from mintpy.objects import euler_pole
from shapely import geometry

plate_pmm = euler_pole.ITRF2014_PMM['Arabia']
epole_obj = euler_pole.EulerPole(wx=plate_pmm.omega_x, wy=plate_pmm.omega_y, wz=plate_pmm.omega_z, unit='mas/yr')

plate_boundary = geometry.Polygon(euler_pole.read_plate_outline('GSRM')['Arabia'])

fig, ax = euler_pole.plot_plate_motion(plate_boundary, epole_obj)
plt.show()

+ use the original downloaded files + extensions as .lalo or .lola + modify euler_pole.py accordingly

yuankailiu · 2023-01-15T23:19:47Z

Thanks @yunjunz for testing. I finish my changes for this PR as we discussed.

By the way, now you can do the following to read the dictionary in your notebook:

plate_boundary = geometry.Polygon(euler_pole.read_plate_outline('GSRM', 'Arabia'))

yunjunz · 2023-01-15T23:47:33Z

Thank you @yuankailiu for the changes. Built on top of yours, the commit above further simplify the read_plate_outline() call as below. Everything looks good to me now! Merged it when you got a chance please.

plate_boundary = euler_pole.read_plate_outline('GSRM', 'Arabia')

+ dependency: add shapely to requirements.txt and setup.py file, as it's used in `objects.euler_pole.py` to plot plate motion since insarlab#935. Note that shapely is the dependency for cartopy already, so this won't really affect the mintpy installation.

+ dependency: add shapely to requirements.txt and setup.py file, as it's used in `objects.euler_pole.py` to plot plate motion since insarlab#935. Note that shapely is the dependency for cartopy already, so this won't really affect the mintpy installation. + docs/installation/argcomplete: replace conda with brew for bash installation, so that the bash is independent from the conda directory, which can removed more easily/frequently than /usr/local directory from brew.

+ `dependency`: add `shapely` to `requirements.txt` and `setup.py` file, as it's used in `objects.euler_pole.py` to plot plate motion since #935. Note that 1) shapely is already a dependency for cartopy, so this won't really affect the mintpy installation; 2) shapely has been added explicitly to the dependency on conda-forge for mintpy (conda-forge/mintpy-feedstock#10) + `docs/installation/argcomplete`: replace `conda` with `brew` for bash installation, so that the bash is independent of the conda directory, which can be removed more easily/frequently than `/usr/local directory` from brew.

euler_pole.py: add PMM plotting functions

c1eb0d8

+ add plate boundary files from GSRMv2.1 and MORVEL56 + functions to read the boundary files and plot

yuankailiu force-pushed the dev.pmm_plot branch from 42bf86e to c1eb0d8 Compare January 5, 2023 19:54

yuankailiu added 3 commits January 6, 2023 08:43

updates

fa16079

bugfix for codacy and unit_test checks

ed9f4dd

yuankailiu requested a review from yunjunz January 6, 2023 22:38

yunjunz added 6 commits January 6, 2023 15:48

ionex: bugfix attempt no. 2

22f88ba

test git rename via jupyter

b62d748

Revert "test git rename via jupyter"

217c914

This reverts commit b62d748.

Revert "ionex: bugfix attempt no. 2"

e5f3057

This reverts commit 22f88ba.

Revert "ionex: attempt to fix the unit test"

5eed6d6

This reverts commit 5e491ab.

yunjunz reviewed Jan 7, 2023

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src/mintpy/objects/euler_pole.py Show resolved Hide resolved

remove the unnecessary plate name abbreviation in plate_motion.py -h

c92a02d

yuankailiu and others added 8 commits January 9, 2023 21:12

move ITRF2014_PMM dependent codes to src/mintpy/plate_motion.py

2722779

src/mintpy/cli/plate_motion.py will not need this dictionary

src/mintpy/plate_motion.py

bd365f4

from mintpy.objects.euler_pole import ITRF2014_PMM

fix import in tests/objects/euler_pole.py

c0024a3

codacy fix

f460c3e

euler_pole refactor - part 1

866a7f6

codacy fix

1ff55c3

yuankailiu commented Jan 12, 2023

View reviewed changes

euler_pole refactor part 2

0509ac5

+ use center_lalo to replace center_lat/lon + use satellite_height directly, instead of zoom + map center priority: direct input arg > pts_lalo > polygon centroid + remove vu as it's not used

yunjunz approved these changes Jan 12, 2023

View reviewed changes

yuankailiu added 2 commits January 15, 2023 15:14

updates to the plate boundary files:

7ca596f

+ use the original downloaded files + extensions as .lalo or .lola + modify euler_pole.py accordingly

update

d008dcc

read_plate_outline: return as shapely object

975f9d8

yunjunz changed the title ~~euler_pole.py: add PMM plotting functions~~ euler_pole: add PMM plotting functions Jan 15, 2023

yuankailiu merged commit ce1aed0 into insarlab:main Jan 15, 2023

yuankailiu deleted the dev.pmm_plot branch January 15, 2023 23:55

yunjunz mentioned this pull request Aug 10, 2023

dep: add shapely #1069

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`euler_pole`: add PMM plotting functions #935

`euler_pole`: add PMM plotting functions #935

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euler_pole: add PMM plotting functions #935

euler_pole: add PMM plotting functions #935

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`euler_pole`: add PMM plotting functions #935

`euler_pole`: add PMM plotting functions #935

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