IOOS provides an API for getting information on all the glider deployments available in the Glider DAC.
The raw JSON can be accessed at https://data.ioos.us/gliders/providers/api/deployment and it is quite simple to parse it with Python.
First, lets check how many glider deployments exist in the Glider DAC.
In [1]:
import requests
url = "http://data.ioos.us/gliders/providers/api/deployment"
response = requests.get(url)
res = response.json()
print("Found {0} deployments!".format(res["num_results"]))
And here is the JSON of the last deployment found in the list.
In [2]:
deployments = res["results"]
deployment = deployments[-1]
deployment
Out[2]:
The metadata is very rich and informative. A quick way to get to the data is to read dap endpoint with iris.
In [3]:
import iris
iris.FUTURE.netcdf_promote = True
# Get this specific glider because it looks cool ;-)
for deployment in deployments:
if deployment["name"] == "sp064-20161214T1913":
url = deployment["dap"]
# See https://github.com/Unidata/netcdf-c/issues/1299 for the explanation of `#fillmismatch`.
cubes = iris.load_raw("".join([url, "#fillmismatch"]))
print(cubes)
In order to plot, for example sea water temperature data, one must clean the data first for missing values
In [4]:
import matplotlib.pyplot as plt
import numpy as np
import numpy.ma as ma
import seawater as sw
from mpl_toolkits.axes_grid1.inset_locator import inset_axes
def distance(x, y, units="km"):
if ma.isMaskedArray(x):
x = x.filled(fill_value=np.NaN)
if ma.isMaskedArray(y):
y = y.filled(fill_value=np.NaN)
dist, pha = sw.dist(x, y, units=units)
return np.r_[0, np.cumsum(dist)]
def apply_range(cube_coord):
if isinstance(cube_coord, iris.cube.Cube):
data = cube_coord.data.squeeze()
elif isinstance(cube_coord, (iris.coords.AuxCoord, iris.coords.Coord)):
data = cube_coord.points.squeeze()
actual_range = cube_coord.attributes.get("actual_range")
if actual_range is not None:
vmin, vmax = actual_range
data = ma.masked_outside(data, vmin, vmax)
return data
def plot_glider(cube, cmap=plt.cm.viridis, figsize=(9, 3.75), track_inset=False):
data = apply_range(cube)
x = apply_range(cube.coord(axis="X"))
y = apply_range(cube.coord(axis="Y"))
z = apply_range(cube.coord(axis="Z"))
t = cube.coord(axis="T")
t = t.units.num2date(t.points.squeeze())
fig, ax = plt.subplots(figsize=figsize)
dist = distance(x, y)
z = ma.abs(z)
dist, _ = np.broadcast_arrays(dist[..., np.newaxis], z.filled(fill_value=np.NaN))
dist, z = map(ma.masked_invalid, (dist, z))
cs = ax.pcolor(dist, z, data, cmap=cmap, snap=True)
kw = dict(orientation="horizontal", extend="both", shrink=0.65)
cbar = fig.colorbar(cs, **kw)
if track_inset:
axin = inset_axes(
ax,
width=2,
height=2,
loc=4,
bbox_to_anchor=(1.15, 0.35),
bbox_transform=ax.figure.transFigure,
)
axin.plot(x, y, "k.")
start, end = (x[0], y[0]), (x[-1], y[-1])
kw = dict(marker="o", linestyle="none")
axin.plot(*start, color="g", **kw)
axin.plot(*end, color="r", **kw)
axin.axis("off")
ax.invert_yaxis()
ax.invert_xaxis()
ax.set_xlabel("Distance (km)")
ax.set_ylabel("Depth (m)")
return fig, ax, cbar
The functions above apply the actual_range metadata to the data, mask the invalid/bad values, and prepare the parameters for plotting.
The figure below shows the temperature slice (left), and glider track (right) with start and end points marked with green and red respectively.
Note: This glider was deployed off the west of the U.S.
In [5]:
%matplotlib inline
temp = cubes.extract_strict("sea_water_temperature")
fig, ax, cbar = plot_glider(
temp, cmap=plt.cm.viridis, figsize=(9, 4.25), track_inset=True
)
There are many things the user can do with the API. Here is another example that finds all glider deployments within a boundary box.
In [6]:
bbox = [[-125.72, 32.60], [-117.57, 36.93]]
The cell below defines two helper functions to parse the geometry from the JSON and convert the trajectory to a shapely LineString to prepare the data for GIS operations later.
In [7]:
from shapely.geometry import LineString
def parse_geometry(geometry):
"""
Filters out potentially bad coordinate pairs as returned from
GliderDAC. Returns a safe geometry object.
:param dict geometry: A GeoJSON Geometry object
"""
coords = []
for lon, lat in geometry["coordinates"]:
if lon is None or lat is None:
continue
coords.append([lon, lat])
return {"coordinates": coords}
def fetch_trajectory(deployment):
"""
Downloads the track as GeoJSON from GliderDAC
:param dict deployment: The deployment object as returned from GliderDAC
"""
track_url = "http://data.ioos.us/gliders/status/api/track/{}".format
response = requests.get(track_url(deployment["deployment_dir"]))
if response.status_code != 200:
raise IOError(
"Failed to get Glider Track for %s" % deployment["deployment_dir"]
)
geometry = parse_geometry(response.json())
coords = LineString(geometry["coordinates"])
return coords
Now it is easy to check which tracks lie inside the box.
In [8]:
res = response.json()["results"]
len(res[-100:])
Out[8]:
In [9]:
from shapely.geometry import box
search_box = box(bbox[0][0], bbox[0][1], bbox[1][0], bbox[1][1])
inside = dict()
# Getting only the 10 deployments.
for deployment in response.json()["results"][-10:]:
try:
coords = fetch_trajectory(deployment)
except IOError:
continue
if search_box.intersects(coords):
inside.update({deployment["name"]: coords})
Finally, we can create an interactive map displaying the tracks found in the bounding box.
In [10]:
def plot_track(coords, name, color="orange"):
x, y = coords.xy
locations = list(zip(y.tolist(), x.tolist()))
kw = {"fill": True, "radius": 10, "stroke": False}
folium.CircleMarker(locations[0], color="green", **kw).add_to(m)
folium.CircleMarker(locations[-1], color="red", **kw).add_to(m)
folium.PolyLine(
locations=locations, color=color, weight=8, opacity=0.2, popup=name
).add_to(m)
In [11]:
import folium
tiles = (
"http://services.arcgisonline.com/arcgis/rest/services/"
"World_Topo_Map/MapServer/MapServer/tile/{z}/{y}/{x}"
)
location = [search_box.centroid.y, search_box.centroid.x]
m = folium.Map(location=location, zoom_start=5, tiles=tiles, attr="ESRI")
for name, coords in inside.items():
plot_track(coords, name, color="orange")
m
Out[11]: