Automate v-grid generation

[saeed-moghimi-noaa]

No description provided.

[saeed-moghimi-noaa]

Perhaps connecting to our colleagues from Portugal regarding their work.

[felicio93]

INFO:
lsc2 script: vgrid_lsc2

Tasks:
1 - Reduce the dependence on pylib
2 - Coordinate implementation under PYSCHISM
3 - ...

[felicio93]

I updated the vgrid_lsc2 notebook.
Now it only uses numpy and pyschism (no pylib dependencies)

[felicio93]

Slip the script into functions. Will coordinate with Soroosh on how to proceed.

[felicio93]

Created:
set_m_grid(self) # set master grid
set_lsc2_att(self, gr3, crs=None) # set lsc2 attributes
write(self, path, overwrite=False) # write vgrid.in lsc2 file

as part of the Vgrid class (child class LSC2) on PySCHISM.

The user can now:

1. create a LSC2 object:
   lsc2_obj = pyschism.mesh.vgrid.LSC2(hsm, nv, h_c, theta_b, theta_f)

2. set a master grid:
   lsc2_obj.set_m_grid()

3. set a lsc2 grid by passing the hgrid:
   lsc2_obj.set_lsc2_att({PATH_TO_gr3})

4. set a lsc2 grid by passing the hgrid:
   lsc2_obj.write({PATH})

Next:
Meet with Soroosh to discuss pull request

[saeed-moghimi-noaa]

Hi @felicio93
Please consider doc string and possible additions for read the doc if it applies to pyschism. Thanks

[felicio93]

@SorooshMani-NOAA,

I made the changes we discussed on our last meetings, including:

1. Change the name of the functions from "set" to "calc"
2. Allow calc_lsc2_att to take either a gr3 file or gr3 object
3. I also added a new function make_m_plot, for allowing quick master grid visualization

I then added test to a preexisting test file (pyschism\tests_mesh\test_vgrid). I added the following tests:

1. setUp # for setting up a dummy hgrid, and the lsc2 attributes
2. test_LSC2
3. test_calc_m_grid
4. test_make_m_plot
5. test_calc_lsc2_att
6. test_lsc2_write

vgrid.py
test_vgrid.py

Please let me know if you think we are ready to include Fei in the discussion and make the pull request.

[felicio93]

Pull request initiated: schism-dev/pyschism#127

[felicio93]

Pull request accepted by VIMS. @saeed-moghimi-noaa, should we close this ticket?