Added ROMS ocean model example notebook #3116
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| name: xarray-tests | ||
| dependencies: | ||
| - python=3.5.0 | ||
| - pytest | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| name: xarray-tests | ||
| channels: | ||
| - conda-forge | ||
| dependencies: | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| name: xarray-tests | ||
| channels: | ||
| - conda-forge | ||
| dependencies: | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| name: xarray-tests | ||
| channels: | ||
| - conda-forge | ||
| dependencies: | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| name: xarray-tests | ||
| channels: | ||
| - conda-forge | ||
| dependencies: | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change | ||||
|---|---|---|---|---|---|---|
| @@ -0,0 +1,223 @@ | ||||||
| { | ||||||
| "cells": [ | ||||||
| { | ||||||
| "cell_type": "markdown", | ||||||
| "metadata": {}, | ||||||
| "source": [ | ||||||
| "# ROMS Ocean Model Example" | ||||||
| ] | ||||||
| }, | ||||||
| { | ||||||
| "cell_type": "code", | ||||||
| "execution_count": null, | ||||||
| "metadata": {}, | ||||||
| "outputs": [], | ||||||
| "source": [ | ||||||
| "import numpy as np\n", | ||||||
| "import cartopy.crs as ccrs\n", | ||||||
| "import cartopy.feature as cfeature\n", | ||||||
| "import matplotlib.pyplot as plt\n", | ||||||
| "%matplotlib inline\n", | ||||||
| "# import cmocean # TODO: Add this dependency to the docs\n", | ||||||
| "\n", | ||||||
| "import xarray as xr" | ||||||
| ] | ||||||
| }, | ||||||
| { | ||||||
| "cell_type": "markdown", | ||||||
| "metadata": {}, | ||||||
| "source": [ | ||||||
| "Load a sample ROMS file. This is a subset of a full model available at \n", | ||||||
| "\n", | ||||||
| " http://barataria.tamu.edu/thredds/catalog.html?dataset=txla_hindcast_agg\n", | ||||||
| " \n", | ||||||
| "The subsetting was done using the following command on one of the output files:\n", | ||||||
| "\n", | ||||||
| " #open dataset\n", | ||||||
| " ds = xr.open_dataset('/d2/shared/TXLA_ROMS/output_20yr_obc/2001/ocean_his_0015.nc')\n", | ||||||
| " \n", | ||||||
| " # Turn on chunking to activate dask and parallelize read/write.\n", | ||||||
| " ds = ds.chunk({'ocean_time': 1})\n", | ||||||
| " \n", | ||||||
| " # Pick out some of the variables that will be included as coordinates\n", | ||||||
| " ds = ds.set_coords(['Cs_r', 'Cs_w', 'hc', 'h', 'Vtransform'])\n", | ||||||
| " \n", | ||||||
| " # Select a a subset of variables. Salt will be visualized, zeta is used to \n", | ||||||
| " # calculate the vertical coordinate\n", | ||||||
| " variables = ['salt', 'zeta']\n", | ||||||
| " ds[variables].isel(ocean_time=slice(47, None, 7*24), \n", | ||||||
| " xi_rho=slice(300, None)).to_netcdf('ROMS_example.nc', mode='w')\n", | ||||||
| "\n", | ||||||
| "So, the `ROMS_example.nc` file contains a subset of the grid, one 3D variable, and two time steps." | ||||||
| ] | ||||||
| }, | ||||||
| { | ||||||
| "cell_type": "markdown", | ||||||
| "metadata": {}, | ||||||
| "source": [ | ||||||
| "### Load in ROMS dataset as an xarray object" | ||||||
| ] | ||||||
| }, | ||||||
| { | ||||||
| "cell_type": "code", | ||||||
| "execution_count": null, | ||||||
| "metadata": {}, | ||||||
| "outputs": [], | ||||||
| "source": [ | ||||||
| "# load in the file\n", | ||||||
| "ds = xr.tutorial.open_dataset('ROMS_example.nc', chunks={'ocean_time': 1})\n", | ||||||
| "\n", | ||||||
| "# This is a way to turn on chunking and lazy evaluation. Opening with mfdataset, or \n", | ||||||
| "# setting the chunking in the open_dataset would also achive this.\n", | ||||||
|
There was a problem hiding this comment.
Suggested change
|
||||||
| "ds" | ||||||
| ] | ||||||
| }, | ||||||
| { | ||||||
| "cell_type": "markdown", | ||||||
| "metadata": {}, | ||||||
| "source": [ | ||||||
| "### Add a lazilly calculated vertical coordinates\n", | ||||||
| "\n", | ||||||
| "Write equations to calculate the vertical coordinate. These will be only evaluated when data is requested. Information about the ROMS vertical coordinate can be found (here)[https://www.myroms.org/wiki/Vertical_S-coordinate]\n", | ||||||
| "\n", | ||||||
| "In short, for `Vtransform==2` as used in this example, \n", | ||||||
| "\n", | ||||||
| "$Z_0 = (h_c \\, S + h \\,C) / (h_c + h)$\n", | ||||||
| "\n", | ||||||
| "$z = Z_0 (\\zeta + h) + \\zeta$\n", | ||||||
| "\n", | ||||||
| "where the variables are defined as in the link above." | ||||||
| ] | ||||||
| }, | ||||||
| { | ||||||
| "cell_type": "code", | ||||||
| "execution_count": null, | ||||||
| "metadata": {}, | ||||||
| "outputs": [], | ||||||
| "source": [ | ||||||
| "if ds.Vtransform == 1:\n", | ||||||
| " Zo_rho = ds.hc * (ds.s_rho - ds.Cs_r) + ds.Cs_r * ds.h\n", | ||||||
| " z_rho = Zo_rho + ds.zeta * (1 + Zo_rho/ds.h)\n", | ||||||
| "# Zo_w = ds.hc * (ds.s_w - ds.Cs_w) + ds.Cs_w * ds.h\n", | ||||||
| "# z_w = Zo_w + ds.zeta * (1 + Zo_w/ds.h)\n", | ||||||
| "elif ds.Vtransform == 2:\n", | ||||||
| " Zo_rho = (ds.hc * ds.s_rho + ds.Cs_r * ds.h) / (ds.hc + ds.h)\n", | ||||||
| " z_rho = ds.zeta + (ds.zeta + ds.h) * Zo_rho\n", | ||||||
| "# Zo_w = (ds.hc * ds.s_w + ds.Cs_w * ds.h) / (ds.hc + ds.h)\n", | ||||||
| "# z_w = ds.zeta + (ds.zeta + ds.h) * Zo_w\n", | ||||||
| "\n", | ||||||
| "ds.coords['z_rho'] = z_rho.transpose() # needing transpose seems to be an xarray bug\n", | ||||||
| "# ds.coords['z_w'] = z_w.transpose()\n", | ||||||
| "ds.salt" | ||||||
| ] | ||||||
| }, | ||||||
| { | ||||||
| "cell_type": "markdown", | ||||||
| "metadata": {}, | ||||||
| "source": [ | ||||||
| "### A naive vertical slice\n", | ||||||
| "\n", | ||||||
| "Create a slice using the s-coordinate as the vertical dimension is typically not very informative." | ||||||
| ] | ||||||
| }, | ||||||
| { | ||||||
| "cell_type": "code", | ||||||
| "execution_count": null, | ||||||
| "metadata": { | ||||||
| "scrolled": false | ||||||
| }, | ||||||
| "outputs": [], | ||||||
| "source": [ | ||||||
| "ds.salt.isel(xi_rho=50, ocean_time=0).plot()" | ||||||
| ] | ||||||
| }, | ||||||
| { | ||||||
| "cell_type": "markdown", | ||||||
| "metadata": {}, | ||||||
| "source": [ | ||||||
| "We can feed coordinate information to the plot method to give a more informative cross-section that uses the depths. Note that we did not need to slice the depth or longitude information separately, this was done automatically as the variable was sliced." | ||||||
| ] | ||||||
| }, | ||||||
| { | ||||||
| "cell_type": "code", | ||||||
| "execution_count": null, | ||||||
| "metadata": {}, | ||||||
| "outputs": [], | ||||||
| "source": [ | ||||||
| "section = ds.salt.isel(xi_rho=50, eta_rho=slice(0, 167), ocean_time=0)\n", | ||||||
| "section.plot(x='lon_rho', y='z_rho', figsize=(15, 6), cmap=cmocean.cm.haline, clim=(25, 35))\n", | ||||||
|
There was a problem hiding this comment. Lets just use a standard matplotlib colormap |
||||||
| "plt.ylim([-100, 1]);" | ||||||
| ] | ||||||
| }, | ||||||
| { | ||||||
| "cell_type": "markdown", | ||||||
| "metadata": {}, | ||||||
| "source": [ | ||||||
| "### A plan view\n", | ||||||
| "\n", | ||||||
| "Now make a naive plan view, without any projection information, just using lon/lat as x/y. This looks OK, but will appear compressed because lon and lat do not have an aspect constrained by the projection." | ||||||
| ] | ||||||
| }, | ||||||
| { | ||||||
| "cell_type": "code", | ||||||
| "execution_count": null, | ||||||
| "metadata": {}, | ||||||
| "outputs": [], | ||||||
| "source": [ | ||||||
| "ds.salt.isel(s_rho=-1, ocean_time=0).plot(x='lon_rho', y='lat_rho')" | ||||||
| ] | ||||||
| }, | ||||||
| { | ||||||
| "cell_type": "markdown", | ||||||
| "metadata": {}, | ||||||
| "source": [ | ||||||
| "And let's use a projection to make it nicer, and add a coast." | ||||||
| ] | ||||||
| }, | ||||||
| { | ||||||
| "cell_type": "code", | ||||||
| "execution_count": null, | ||||||
| "metadata": {}, | ||||||
| "outputs": [], | ||||||
| "source": [ | ||||||
| "proj = ccrs.LambertConformal(central_longitude=-92, central_latitude=29)\n", | ||||||
| "fig = plt.figure(figsize=(15, 5))\n", | ||||||
| "ax = plt.axes(projection=proj)\n", | ||||||
| "ds.salt.isel(s_rho=-1, ocean_time=0).plot(x='lon_rho', y='lat_rho', \n", | ||||||
| " cmap=cmocean.cm.haline, transform=ccrs.PlateCarree())\n", | ||||||
| "\n", | ||||||
| "coast_10m = cfeature.NaturalEarthFeature('physical', 'land', '10m',\n", | ||||||
| " edgecolor='k', facecolor='0.8')\n", | ||||||
| "ax.add_feature(coast_10m)" | ||||||
| ] | ||||||
| }, | ||||||
| { | ||||||
| "cell_type": "code", | ||||||
| "execution_count": null, | ||||||
| "metadata": {}, | ||||||
| "outputs": [], | ||||||
| "source": [] | ||||||
| } | ||||||
| ], | ||||||
| "metadata": { | ||||||
| "kernelspec": { | ||||||
| "display_name": "Python 3", | ||||||
| "language": "python", | ||||||
| "name": "python3" | ||||||
| }, | ||||||
| "language_info": { | ||||||
| "codemirror_mode": { | ||||||
| "name": "ipython", | ||||||
| "version": 3 | ||||||
| }, | ||||||
| "file_extension": ".py", | ||||||
| "mimetype": "text/x-python", | ||||||
| "name": "python", | ||||||
| "nbconvert_exporter": "python", | ||||||
| "pygments_lexer": "ipython3", | ||||||
| "version": "3.6.7" | ||||||
| } | ||||||
| }, | ||||||
| "nbformat": 4, | ||||||
| "nbformat_minor": 2 | ||||||
| } | ||||||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Let's keep
cmoceanout since it isn't strictly necessary for the example.