Feature request: function to fill bathymetry below a certain depth level

[DaniJonesOcean]

Hi Kaitlin,

For my domain, I effectively want to fill in a couple kilometres of the South Sandwich Trench. Is there a function that will allow me to fill the bathymetry below a chosen depth level (e.g. 6000 m)? I didn't see one, but perhaps I missed it.

Could that be added? Where would it fit in the workflow of this code?

Thanks! Dan

[knaughten]

Hi Dan,

I would recommend adding a new "key" to the function edit_mask in make_domain.py, to make custom changes for your domain. Within the if statement for that key, add the line

bathy = np.amax(bathy, -6000)

that should fill everything deeper than 6000m.

I'd be happy to have your key in the master branch if that's easiest for you, just submit a pull request. And the python3 update will be coming soon(ish) - it's on my list! but there are many other things on my list!

[DaniJonesOcean]

That's a good suggestion, thanks! :)

I will do that. If we could leave this issue open for now please, I'll link it to the pull request once I create it. You can "assign" this issue to me, if you want.

[DaniJonesOcean]

Apologies for the delay on this - I hope to get back to it soon!

[DaniJonesOcean]

Hi @knaughten. For some reason, when I add my key and run this function, nothing changes. Here's what I added to the make_domain.py file:

elif key == 'SO-WISE-GYRE':
# SO-WISE (gyre configuration)
# Block out everything west of South America
omask = mask_box(omask, lon_2d, lat_2d, xmin=-85.0, xmax=-70.0, ymin=-45.0, ymax=-30.0)
# Fill in everything deeper than 6000 m
bathy = np.amax(bathy, -6000) 

And I run the command: edit_mask('topo_v02/sowise_gyre_bathy.nc', 'topo_v02/sowise_gyre_bathy_edited.nc', key='SO-WISE-GYRE') It returns

Fields updated successfully. The deepest bathymetry is now 7933.9877905 m.

And there is no difference between the edited and non-edited files. I'm running this in iPython on BAS HPC. Any idea what could be going on?

EDIT: Update. Just needed to restart my iPython kernel, apparently.

[DaniJonesOcean]

A small update: the np.amax command above returns an error, but this function works:

bathy[bathy<-6000] = -6000

I've noticed that if you pass the edit_mask function a nonsense key, it still executes. It doesn't use the default mask in that instance. I might suggest a little error-catching statement that warns you if the key wasn't recognised, if that's okay?

Oh! And I just needed to restart my iPython kernel to incorporate the changes. It seems like the file editing is working now. (That still confuses me about Python - you have to restart the kernel to change your functions and things? Am I missing something?)

[knaughten]

Oh good, glad you figured it out. I think instead of np.amax, np.maximum is what you want. But your fix is just as good.

Python is annoying that way, I think there is a way to re-import all your modules but I usually don't bother - I copy and paste the modified function or block of code using %paste in ipython, and then work interactively for testing purposes.

Dr Kaitlin Naughten | Ocean-Ice Modeller | British Antarctic Survey

High Cross, Madingley Road, Cambridge CB3 0ET

Email: @.**@.>

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From: Dan Jones @.> Sent: 19 March 2021 10:59 To: knaughten/mitgcm_python @.> Cc: Kaitlin Naughten - UKRI BAS @.>; Mention @.> Subject: Re: [knaughten/mitgcm_python] Feature request: function to fill bathymetry below a certain depth level (#4)

A small update: the np.amax command above returns an error, but this function works:

bathy[bathy<-6000] = -6000

I've noticed that if you pass the edit_mask function a nonsense key, it still executes. It doesn't use the default mask in that instance. I might suggest a little error-catching statement that warns you if the key wasn't recognised, if that's okay?

Oh! And I just needed to restart my iPython kernel to incorporate the changes. It seems like the file editing is working now. (That still confuses me about Python - you have to restart the kernel to change your functions and things? Am I missing something?)

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[DaniJonesOcean]

Done! Issue closed with this pull request:

https://github.com/knaughten/mitgcm_python/pull/5