Jupyter Book and GitHub repo.
GLODAP: Global Ocean Data Analysis Project#
This notebook is a viewer for global ocean chemistry. It depends upon downloading local copies of five data files. The data are organized as depth-sorted layers of the global ocean (where the depths are predetermined). The data files are not part of this Jupyter Book due to size limits.
The GLODAP global ocean dataset compiles several decades of observation. It is a ‘geological instant’ snapshot of the state of the entire ocean.
Moving the sliders for each chart selects for depth, as shown at the bottom left.
GLODAP data used here is the 2016 version; 2021 v2 available
Color map cmocean
Make a subset intrinsic, show by default e.g. Atlantic / Caribbean / Amazon
This sequence of download commands gets five global ocean state datasets.
!mkdir glodap
!wget -q https://kilroybackup.s3.us-west-2.amazonaws.com/glodap/NO3.nc -O glodap/NO3.nc
!wget -q https://kilroybackup.s3.us-west-2.amazonaws.com/glodap/TCO2.nc -O glodap/TCO2.nc
!wget -q https://kilroybackup.s3.us-west-2.amazonaws.com/glodap/oxygen.nc -O glodap/oxygen.nc
!wget -q https://kilroybackup.s3.us-west-2.amazonaws.com/glodap/salinity.nc -O glodap/salinity.nc
!wget -q https://kilroybackup.s3.us-west-2.amazonaws.com/glodap/temperature.nc -O glodap/temperature.nc
Artifact: configuration#
import os, sys, time, glob, warnings, cmocean
from IPython.display import clear_output
warnings.filterwarnings('ignore')
this_dir = os.getcwd()
from matplotlib import animation, rc
from numpy import datetime64 as dt64, timedelta64 as td64
from matplotlib import pyplot as plt, colors as mplcolors
import numpy as np, pandas as pd, xarray as xr
from ipywidgets import *
from traitlets import dlink
glodapdir = '../../../data/oceanography/glodap/' # this is a location outside of the repository
temperatureFnm = glodapdir + 'temperature.nc'
salinityFnm = glodapdir + 'salinity.nc'
oxygenFnm = glodapdir + 'oxygen.nc'
NO3Fnm = glodapdir + 'NO3.nc'
TCO2Fnm = glodapdir + 'TCO2.nc'
glodap = {}
glodap['S'] = xr.open_dataset(salinityFnm)
glodap['T'] = xr.open_dataset(temperatureFnm)
glodap['O'] = xr.open_dataset(oxygenFnm)
glodap['N'] = xr.open_dataset(NO3Fnm)
glodap['R'] = xr.open_dataset(TCO2Fnm)
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
File ~/micromamba/envs/geosmart-template/lib/python3.12/site-packages/xarray/backends/file_manager.py:211, in CachingFileManager._acquire_with_cache_info(self, needs_lock)
210 try:
--> 211 file = self._cache[self._key]
212 except KeyError:
File ~/micromamba/envs/geosmart-template/lib/python3.12/site-packages/xarray/backends/lru_cache.py:56, in LRUCache.__getitem__(self, key)
55 with self._lock:
---> 56 value = self._cache[key]
57 self._cache.move_to_end(key)
KeyError: [<class 'netCDF4._netCDF4.Dataset'>, ('/home/runner/work/oceanography/data/oceanography/glodap/salinity.nc',), 'r', (('clobber', True), ('diskless', False), ('format', 'NETCDF4'), ('persist', False)), '42cafba4-114f-4875-970a-d9fd325e17ae']
During handling of the above exception, another exception occurred:
FileNotFoundError Traceback (most recent call last)
Cell In[2], line 10
7 TCO2Fnm = glodapdir + 'TCO2.nc'
9 glodap = {}
---> 10 glodap['S'] = xr.open_dataset(salinityFnm)
11 glodap['T'] = xr.open_dataset(temperatureFnm)
12 glodap['O'] = xr.open_dataset(oxygenFnm)
File ~/micromamba/envs/geosmart-template/lib/python3.12/site-packages/xarray/backends/api.py:686, in open_dataset(filename_or_obj, engine, chunks, cache, decode_cf, mask_and_scale, decode_times, decode_timedelta, use_cftime, concat_characters, decode_coords, drop_variables, inline_array, chunked_array_type, from_array_kwargs, backend_kwargs, **kwargs)
674 decoders = _resolve_decoders_kwargs(
675 decode_cf,
676 open_backend_dataset_parameters=backend.open_dataset_parameters,
(...) 682 decode_coords=decode_coords,
683 )
685 overwrite_encoded_chunks = kwargs.pop("overwrite_encoded_chunks", None)
--> 686 backend_ds = backend.open_dataset(
687 filename_or_obj,
688 drop_variables=drop_variables,
689 **decoders,
690 **kwargs,
691 )
692 ds = _dataset_from_backend_dataset(
693 backend_ds,
694 filename_or_obj,
(...) 704 **kwargs,
705 )
706 return ds
File ~/micromamba/envs/geosmart-template/lib/python3.12/site-packages/xarray/backends/netCDF4_.py:666, in NetCDF4BackendEntrypoint.open_dataset(self, filename_or_obj, mask_and_scale, decode_times, concat_characters, decode_coords, drop_variables, use_cftime, decode_timedelta, group, mode, format, clobber, diskless, persist, auto_complex, lock, autoclose)
644 def open_dataset(
645 self,
646 filename_or_obj: str | os.PathLike[Any] | ReadBuffer | AbstractDataStore,
(...) 663 autoclose=False,
664 ) -> Dataset:
665 filename_or_obj = _normalize_path(filename_or_obj)
--> 666 store = NetCDF4DataStore.open(
667 filename_or_obj,
668 mode=mode,
669 format=format,
670 group=group,
671 clobber=clobber,
672 diskless=diskless,
673 persist=persist,
674 auto_complex=auto_complex,
675 lock=lock,
676 autoclose=autoclose,
677 )
679 store_entrypoint = StoreBackendEntrypoint()
680 with close_on_error(store):
File ~/micromamba/envs/geosmart-template/lib/python3.12/site-packages/xarray/backends/netCDF4_.py:452, in NetCDF4DataStore.open(cls, filename, mode, format, group, clobber, diskless, persist, auto_complex, lock, lock_maker, autoclose)
448 kwargs["auto_complex"] = auto_complex
449 manager = CachingFileManager(
450 netCDF4.Dataset, filename, mode=mode, kwargs=kwargs
451 )
--> 452 return cls(manager, group=group, mode=mode, lock=lock, autoclose=autoclose)
File ~/micromamba/envs/geosmart-template/lib/python3.12/site-packages/xarray/backends/netCDF4_.py:393, in NetCDF4DataStore.__init__(self, manager, group, mode, lock, autoclose)
391 self._group = group
392 self._mode = mode
--> 393 self.format = self.ds.data_model
394 self._filename = self.ds.filepath()
395 self.is_remote = is_remote_uri(self._filename)
File ~/micromamba/envs/geosmart-template/lib/python3.12/site-packages/xarray/backends/netCDF4_.py:461, in NetCDF4DataStore.ds(self)
459 @property
460 def ds(self):
--> 461 return self._acquire()
File ~/micromamba/envs/geosmart-template/lib/python3.12/site-packages/xarray/backends/netCDF4_.py:455, in NetCDF4DataStore._acquire(self, needs_lock)
454 def _acquire(self, needs_lock=True):
--> 455 with self._manager.acquire_context(needs_lock) as root:
456 ds = _nc4_require_group(root, self._group, self._mode)
457 return ds
File ~/micromamba/envs/geosmart-template/lib/python3.12/contextlib.py:137, in _GeneratorContextManager.__enter__(self)
135 del self.args, self.kwds, self.func
136 try:
--> 137 return next(self.gen)
138 except StopIteration:
139 raise RuntimeError("generator didn't yield") from None
File ~/micromamba/envs/geosmart-template/lib/python3.12/site-packages/xarray/backends/file_manager.py:199, in CachingFileManager.acquire_context(self, needs_lock)
196 @contextlib.contextmanager
197 def acquire_context(self, needs_lock=True):
198 """Context manager for acquiring a file."""
--> 199 file, cached = self._acquire_with_cache_info(needs_lock)
200 try:
201 yield file
File ~/micromamba/envs/geosmart-template/lib/python3.12/site-packages/xarray/backends/file_manager.py:217, in CachingFileManager._acquire_with_cache_info(self, needs_lock)
215 kwargs = kwargs.copy()
216 kwargs["mode"] = self._mode
--> 217 file = self._opener(*self._args, **kwargs)
218 if self._mode == "w":
219 # ensure file doesn't get overridden when opened again
220 self._mode = "a"
File src/netCDF4/_netCDF4.pyx:2521, in netCDF4._netCDF4.Dataset.__init__()
File src/netCDF4/_netCDF4.pyx:2158, in netCDF4._netCDF4._ensure_nc_success()
FileNotFoundError: [Errno 2] No such file or directory: '/home/runner/work/oceanography/data/oceanography/glodap/salinity.nc'
for ds in glodap: print(ds)
# should print S T O N R respectively Salinity, Temperature, Oxygen, Nitrate, CO2
S
T
O
N
R
def oxygen(depth_index):
glodap['O']['oxygen'].sel(depth_surface = depth_index).plot(figsize=(11, 7),cmap='viridis',vmin=150, vmax=350) # original: cmocean.cm.oxy
plt.ylabel(None); plt.xlabel(None)
if depth_index == 0: msg = 'This is for surface water'
else: msg = 'This is for water at ' + str(int(glodap['O']['Depth'].values[depth_index])) + ' meters depth'
plt.text(25, -87, msg); plt.text(28, 50, 'oxygen dissolved in'); plt.text(28, 42, ' ocean water ')
interact(oxygen, depth_index=widgets.IntSlider(min=0, max=32, step=1, value=0, continuous_update=False, description='O depth'))
<function __main__.oxygen(depth_index)>
plt.rcParams.update({'font.size': 16})
# return to cmocean.cm.oxy, haline, thermal, algae, delta
def oxygen(depth_index):
glodap['O']['oxygen'].sel(depth_surface = depth_index).plot(figsize=(11, 7),cmap='viridis', vmin=150, vmax=350)
plt.ylabel(None); plt.xlabel(None)
if depth_index == 0: msg = 'This is for surface water'
else: msg = 'This is for water at ' + str(int(glodap['O']['Depth'].values[depth_index])) + ' meters depth'
plt.text(25, -87, msg); plt.text(28, 50, 'oxygen dissolved in'); plt.text(28, 42, ' ocean water ')
def salinity(depth_index):
glodap['S']['salinity'].sel(depth_surface = depth_index).plot(figsize=(11, 7),cmap='plasma',vmin=33, vmax=36)
plt.ylabel(None); plt.xlabel(None)
if depth_index == 0: msg = 'This is for surface water'
else: msg = 'This is for water at ' + str(int(glodap['S']['Depth'].values[depth_index])) + ' meters depth'
plt.text(25, -87, msg); plt.text(47, 50, 'salinity of'); plt.text(47, 42, 'ocean water')
def temperature(depth_index):
glodap['T']['temperature'].sel(depth_surface = depth_index).plot(figsize=(11, 7),cmap='inferno',vmin=2., vmax=12.)
plt.ylabel(None); plt.xlabel(None)
if depth_index == 0: msg = 'This is for surface water'
else: msg = 'This is for water at ' + str(int(glodap['T']['Depth'].values[depth_index])) + ' meters depth'
plt.text(25, -87, msg); plt.text(47, 50, 'temperature of'); plt.text(47, 42, 'ocean water')
def nitrate(depth_index):
glodap['N']['NO3'].sel(depth_surface = depth_index).plot(figsize=(11, 7),cmap='magma', vmin=2., vmax=40.)
plt.ylabel(None); plt.xlabel(None)
if depth_index == 0: msg = 'This is for surface water'
else: msg = 'This is for water at ' + str(int(glodap['N']['Depth'].values[depth_index])) + ' meters depth'
plt.text(25, -87, msg); plt.text(47, 50, 'nitrate in'); plt.text(47, 42, 'ocean water')
def carbonate(depth_index):
glodap['R']['TCO2'].sel(depth_surface = depth_index).plot(figsize=(11, 7), cmap='cividis', vmin=2000., vmax=2500.)
plt.ylabel(None); plt.xlabel(None)
if depth_index == 0: msg = 'This is for surface water'
else: msg = 'This is for water at ' + str(int(glodap['R']['Depth'].values[depth_index])) + ' meters depth'
plt.text(25, -87, msg); plt.text(47, 50, 'carbon dioxide in'); plt.text(47, 42, 'ocean water')
interact(oxygen, depth_index=widgets.IntSlider(min=0, max=32, step=1, value=0, continuous_update=False, description='O depth'))
interact(salinity, depth_index=widgets.IntSlider(min=0, max=32, step=1, value=0, continuous_update=False, description='S depth'))
interact(temperature, depth_index=widgets.IntSlider(min=0, max=32, step=1, value=0, continuous_update=False, description='T depth'))
interact(nitrate, depth_index=widgets.IntSlider(min=0, max=32, step=1, value=0, continuous_update=False, description='NO3 depth'))
interact(carbonate, depth_index=widgets.IntSlider(min=0, max=32, step=1, value=0, continuous_update=False, description='CO2 depth'))
<function __main__.carbonate(depth_index)>
Set the slider above to 28#
Compare with the mid-ocean ridges shown here.
