Visualizing Hypoxia Cruise Sampling Locations in the Gulf of Mexico¶

In [1]:

# %pip install -U openpyxl hypercoast

# %pip install -U openpyxl hypercoast

In [2]:

import pandas as pd
import hypercoast

import pandas as pd import hypercoast

In [3]:

url = "https://github.com/opengeos/datasets/releases/download/hypercoast/Hypoxia_Data_Sheet.xlsx"
xls_path = "data/Hypoxia_Data_Sheet.xlsx"
hypercoast.download_file(url, xls_path, overwrite=True)

url = "https://github.com/opengeos/datasets/releases/download/hypercoast/Hypoxia_Data_Sheet.xlsx" xls_path = "data/Hypoxia_Data_Sheet.xlsx" hypercoast.download_file(url, xls_path, overwrite=True)

Out[3]:

'/home/runner/work/HyperCoast/HyperCoast/docs/examples/data/Hypoxia_Data_Sheet.xlsx'

In [4]:

df = pd.read_excel(xls_path)
df.head()

df = pd.read_excel(xls_path) df.head()

Out[4]:

	Station	Station.1	Time	Date	Lon	Lat	Depth (m)	Secchi (m)	Salinity	Water Temp	...	Absorption	CDOM	LISST	Nano	Surface \npH	Sufface \nO2	Bottom \nO2	FL-ECO	FL-CDOM	Notes
0	River stations	NaN	NaN	NaT	NaN	NaN	NaN	NaN	NaN	NaN	...	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN
1	R1	St1	09:39:00	2024-07-21	-89.45114	28.89887	NaN	2	28.71	30.74161	...	125ml	yes	yes	no	NaN	NaN	NaN	NaN	NaN	River Mouth
2	R2	St2	09:47:00	2024-07-21	-89.45306	28.90001	NaN	2	25.91325	30.91475	...	150ml	yes	yes	yes	NaN	NaN	NaN	NaN	NaN	River plume, seaside
3	R3	St3	09:59:00	2024-07-21	-89.43833	28.89487	NaN	0.75	24.44862	30.59565	...	100ml	yes	yes	yes	NaN	NaN	NaN	NaN	NaN	NaN
4	R4	St4	10:13:00	2024-07-21	-89.43162	28.90630	NaN	0.5	8.34838	30.13989	...	100ml	yes	yes	yes	NaN	NaN	NaN	NaN	NaN	NaN

5 rows × 22 columns

In [5]:

df_filtered = df.dropna(subset=["Lon", "Lat"]).reset_index(drop=True)
df_filtered.head()

df_filtered = df.dropna(subset=["Lon", "Lat"]).reset_index(drop=True) df_filtered.head()

Out[5]:

	Station	Station.1	Time	Date	Lon	Lat	Depth (m)	Secchi (m)	Salinity	Water Temp	...	Absorption	CDOM	LISST	Nano	Surface \npH	Sufface \nO2	Bottom \nO2	FL-ECO	FL-CDOM	Notes
0	R1	St1	09:39:00	2024-07-21	-89.45114	28.89887	NaN	2	28.71	30.74161	...	125ml	yes	yes	no	NaN	NaN	NaN	NaN	NaN	River Mouth
1	R2	St2	09:47:00	2024-07-21	-89.45306	28.90001	NaN	2	25.91325	30.91475	...	150ml	yes	yes	yes	NaN	NaN	NaN	NaN	NaN	River plume, seaside
2	R3	St3	09:59:00	2024-07-21	-89.43833	28.89487	NaN	0.75	24.44862	30.59565	...	100ml	yes	yes	yes	NaN	NaN	NaN	NaN	NaN	NaN
3	R4	St4	10:13:00	2024-07-21	-89.43162	28.90630	NaN	0.5	8.34838	30.13989	...	100ml	yes	yes	yes	NaN	NaN	NaN	NaN	NaN	NaN
4	R5	St5	10:58:00	2024-07-21	-89.37324	28.98095	NaN	0.5	2.4625	30.3054	...	100ml	yes	yes	yes	NaN	NaN	NaN	NaN	NaN	NaN

5 rows × 22 columns

In [6]:

url = (
    "https://github.com/opengeos/datasets/releases/download/hypercoast/Hypoxia_Path.kml"
)
kml_path = "data/Hypoxia_Path.kml"
hypercoast.download_file(url, kml_path)

url = ( "https://github.com/opengeos/datasets/releases/download/hypercoast/Hypoxia_Path.kml" ) kml_path = "data/Hypoxia_Path.kml" hypercoast.download_file(url, kml_path)

Out[6]:

'/home/runner/work/HyperCoast/HyperCoast/docs/examples/data/Hypoxia_Path.kml'

In [7]:

url = "https://github.com/opengeos/datasets/releases/download/hypercoast/PACE_OCI.20240730T181157.L2.OC_AOP.V2_0.NRT.nc"
filepath = "data/PACE_OCI.20240730T181157.L2.OC_AOP.V2_0.NRT.nc"
hypercoast.download_file(url, filepath)

url = "https://github.com/opengeos/datasets/releases/download/hypercoast/PACE_OCI.20240730T181157.L2.OC_AOP.V2_0.NRT.nc" filepath = "data/PACE_OCI.20240730T181157.L2.OC_AOP.V2_0.NRT.nc" hypercoast.download_file(url, filepath)

data/PACE_OCI.20240730T181157.L2.OC_AOP.V2_0.NRT.nc already exists. Skip downloading. Set overwrite=True to overwrite.

Out[7]:

'/home/runner/work/HyperCoast/HyperCoast/docs/examples/data/PACE_OCI.20240730T181157.L2.OC_AOP.V2_0.NRT.nc'

In [8]:

dataset = hypercoast.read_pace(filepath)
# dataset

dataset = hypercoast.read_pace(filepath) # dataset

In [9]:

m = hypercoast.Map()
m.add_basemap("Hybrid")
wavelengths = [450, 550, 650]
m.add_pace(
    dataset, wavelengths, indexes=[3, 2, 1], vmin=0, vmax=0.02, layer_name="PACE"
)
m.add("spectral")
style = {"weight": 2, "color": "red"}
m.add_kml(kml_path, style=style, layer_name="Hypoxia Path", info_mode=None)
m.add_points_from_xy(
    df_filtered,
    x="Lon",
    y="Lat",
    max_cluster_radius=50,
    layer_name="Hypoxia Data Points",
)
m.set_center(-91.46118, 28.89758, zoom=8)
m

m = hypercoast.Map() m.add_basemap("Hybrid") wavelengths = [450, 550, 650] m.add_pace( dataset, wavelengths, indexes=[3, 2, 1], vmin=0, vmax=0.02, layer_name="PACE" ) m.add("spectral") style = {"weight": 2, "color": "red"} m.add_kml(kml_path, style=style, layer_name="Hypoxia Path", info_mode=None) m.add_points_from_xy( df_filtered, x="Lon", y="Lat", max_cluster_radius=50, layer_name="Hypoxia Data Points", ) m.set_center(-91.46118, 28.89758, zoom=8) m

Out[9]: