Photic Zone: CTD and other low data rate sensors¶

If we shadows have offended,
Think but this, and all is mended,
That you have but slumber’d here
While these visions did appear.

The ‘photic zone’ is the upper layer of the ocean regularly illuminated by sunlight. This set of photic zone notebooks concerns sensor data from the surface to about 200 meters depth. Data are acquired from two to nine times per day by shallow profilers. This notebook covers CTD (salinity and temperature), dissolved oxygen, nitrate, pH, spectral irradiance, fluorometry and photosynthetically available radiation (PAR).

Data are first taken from the Regional Cabled Array shallow profilers and platforms. A word of explanation here: The profilers rise and then fall over the course of about 80 minutes, nine times per day, from a depth of 200 meters to within about 10 meters of the surface. As the ascend and descend they record data. The resting location in between these excursions is a platform 200 meters below the surface that is anchored to the see floor. The platform also carries sensors that measure basic ocean water properties.

Research ship Revelle in the southern ocean: 100 meters in length. Note: Ninety percent of this iceberg is beneath the surface.

More on the Regional Cabled Array oceanography program here.

Study site locations¶

We begin with three sites in the northeast Pacific:

Site name               Lat               Lon
------------------      ---               ---
Oregon Offshore         44.37415          -124.95648
Oregon Slope Base       44.52897          -125.38966 
Axial Base              45.83049          -129.75326

import os, sys, time, glob, warnings
from pathlib import Path
from IPython.display import clear_output             # use inside loop with clear_output(wait = True) followed by print(i)
warnings.filterwarnings('ignore')
data_dir = Path('../_static/data')

from matplotlib import pyplot as plt
from matplotlib import colors as mplcolors
import numpy as np, pandas as pd, xarray as xr
from numpy import datetime64 as dt64, timedelta64 as td64

# convenience functions abbreviating 'datetime64' and so on
def doy(theDatetime): return 1 + int((theDatetime - dt64(str(theDatetime)[0:4] + '-01-01')) / td64(1, 'D'))
def dt64_from_doy(year, doy): return dt64(str(year) + '-01-01') + td64(doy-1, 'D')
def day_of_month_to_string(d): return str(d) if d > 9 else '0' + str(d)

print('\nJupyter Notebook running Python {}'.format(sys.version_info[0]))

Jupyter Notebook running Python 3

pCO2¶

This seems to be only 2600 observations from June 23 to September 27, 2019. These data are otherwise dubious as well. No charting attempted.

# pCO2_source = '/data/rca/pCO2/'
# pCO2_data = 'depl*PCO2*.nc'
# ds_pCO2 = xr.open_mfdataset(pCO2_source + pCO2_data)   # example of multi-file
# ds_pCO2

# print('pCO2 time range: ' + str(ds_pCO2.time[0].values) + ' to ' + str(ds_pCO2.time[-1].values))
#
# produces:
#
# pCO2 time range: 2019-06-23T06:35:03.680657408 to 2019-09-27T17:35:22.647006208

Spectral Irradiance¶

The data variable is spkir_downwelling_vector x 7 wavelengths per below
9 months continuous operation at about 4 samples per second gives 91 million samples
DataSet includes int_ctd_pressure and time Coordinates; Dimensions are spectra (0–6) and time
Oregon Slope Base node : SF01A, id : RS01SBPS-SF01A-3D-SPKIRA101-streamed-spkir_data_record
Correct would be to plot these as a sequence of rainbow plots with depth, etc

See Interactive Oceans:

The Spectral Irradiance sensor (Satlantic OCR-507 multispectral radiometer) measures the amount of downwelling radiation (light energy) per unit area that reaches a surface. Radiation is measured and reported separately for a series of seven wavelength bands (412, 443, 490, 510, 555, 620, and 683 nm), each between 10-20 nm wide. These measurements depend on the natural illumination conditions of sunlight and measure apparent optical properties. These measurements also are used as proxy measurements of important biogeochemical variables in the ocean.

Spectral Irradiance sensors are installed on the Science Pods on the Shallow Profiler Moorings at Axial Base (SF01A), Slope Base (SF01A), and at the Endurance Array Offshore (SF01B) sites. Instruments on the Cabled Array are provided by Satlantic – OCR-507.

spectral_irradiance_source = data_dir / 'rca/irradiance'
ds_irradiance = [xr.open_dataset(spectral_irradiance_source / ('osb_sp_irr_spec' + str(i) + '.nc')) for i in range(7)]

# Early attempt at using log crashed the kernel

spectral_irradiance_upper_bound = 10.
spectral_irradiance_lower_bound = 0.
ds_irr_time_slice = [ds_irradiance[i].sel(time = slice(time0, time1)) for i in range(7)]

fig, axs = plt.subplots(figsize=(12,8), tight_layout=True)
colorwheel = ['k', 'r', 'y', 'g', 'c', 'b', 'm']
for i in range(1,3):
    axs.plot(ds_irr_time_slice[i].spkir_downwelling_vector, \
                ds_irr_time_slice[i].int_ctd_pressure, marker='.', markersize = 4., color=colorwheel[i])
axs.set(xlim = (spectral_irradiance_lower_bound, spectral_irradiance_upper_bound), \
        ylim = (60., 0.), title='multiple profiles: spectral irradiance')
print('...')

...

../_images/Ocean 01 A Photic Zone CTD_22_1.png

Interactive Oceans Resources

Photic Zone: CTD and other low data rate sensors

Contents

Photic Zone: CTD and other low data rate sensors¶

Study site locations¶

CTD including Dissolved Oxygen¶

pCO2¶

Nitrate¶

pH¶

Fluorometer¶

Spectral Irradiance¶

Photosynthetically Available Radiation¶