Define a marine habitat

History | Updated Sep 2023 ## Background The TurtleWatch project investigated the overlap between loggerhead sea turtles habitat and fishing effort of the Hawaii-based shallow-set longline fishery in the Pacific Ocean north of the Hawaiian Islands. That fishery, which targets swordfish, used to experience high levels of bycatch of loggerhead turtles. Considerable changes in gear and operations lowered bycatch rate and TurtleWatch was designed as a tool to advise fishermen on areas to avoid to limit bycatch.

Research results indicated that 50% of interactions occurred between 17.5°C and 18.5°C.

Objective

Here we will draw the 17.5 and 18.5ºC temperature contours on a map of satellite sea surface temperature.

The exercise demonstrates the following techniques:

• Subsetting and loading data from an ERDDAP server using xarray
  
• Set flag values for features of interest
  
• Plotting maps

Datasets used

CoralTemp Sea Surface Temperature product from the NOAA Coral Reef Watch program. The NOAA Coral Reef Watch (CRW) daily global 5km Sea Surface Temperature (SST) product, also known as CoralTemp, shows the nighttime ocean temperature measured at the surface. The SST scale ranges from -2 to 35 °C. The CoralTemp SST data product was developed from two related reanalysis (reprocessed) SST products and a near real-time SST product. Spanning January 1, 1985 to the present, the CoralTemp SST is one of the best and most internally consistent daily global 5km SST products available. More information about the product: https://coralreefwatch.noaa.gov/product/5km/index_5km_sst.php

Install required packages

import xarray as xr    
import matplotlib.pyplot as plt
import matplotlib as mpl

Download the SST data

Select a geographical range

• Select an area of the central North Pacific where the fishery operates: longitude range of 185 to 235 east and latitude range of 20 to 45 north

Select a date

• Select a date in the first quarter of the year when bycatch typically occurs: 2023-01-06

Set variables for the habitat temperature range

# Longitude range
lon_min = 185
lon_max = 235

# Latitude range
lat_min = 20
lat_max = 45

date_for_sat_data = '2023-01-06'

# Turtle habitat temperature range
hab_temp_min = 17.5
hab_temp_max = 18.5

Open the netCDF file to create an xarray dataset object

url = "https://oceanwatch.pifsc.noaa.gov/erddap/griddap/CRW_sst_v3_1"
ds = xr.open_dataset(url)
ds

<xarray.Dataset>
Dimensions:           (time: 14130, latitude: 3600, longitude: 7200)
Coordinates:
  * time              (time) datetime64[ns] 1985-01-01T12:00:00 ... 2023-09-0...
  * latitude          (latitude) float32 -89.97 -89.93 -89.88 ... 89.93 89.97
  * longitude         (longitude) float32 0.025 0.075 0.125 ... 359.9 360.0
Data variables:
    analysed_sst      (time, latitude, longitude) float64 ...
    sea_ice_fraction  (time, latitude, longitude) float64 ...
Attributes: (12/68)
    acknowledgement:                  NOAA Coral Reef Watch Program
    cdm_data_type:                    Grid
    comment:                          This product is designed to improve on ...
    contributor_name:                 NOAA Coral Reef Watch Program
    contributor_role:                 Collecting source data and deriving pro...
    Conventions:                      CF-1.6, ACDD-1.3, COARDS
    ...                               ...
    time_coverage_duration:           P1D
    time_coverage_end:                2023-09-09T12:00:00Z
    time_coverage_resolution:         P1D
    time_coverage_start:              1985-01-01T12:00:00Z
    title:                            Sea Surface Temperature, Coral Reef Wat...
    Westernmost_Easting:              0.025

xarray.Dataset

• Dimensions:
  • time: 14130
  • latitude: 3600
  • longitude: 7200
• Coordinates: (3)
  • time
    (time)
    datetime64[ns]
    1985-01-01T12:00:00 ... 2023-09-...

    _CoordinateAxisType :

    Time

    actual_range :

    [4.7342880e+08 1.6942608e+09]

    axis :

    T

    coverage_content_type :

    coordinate

    ioos_category :

    Time

    long_name :

    reference time of the sst field

    standard_name :

    time

    time_origin :

    01-JAN-1970 00:00:00

    array(['1985-01-01T12:00:00.000000000', '1985-01-02T12:00:00.000000000',
           '1985-01-03T12:00:00.000000000', ..., '2023-09-07T12:00:00.000000000',
           '2023-09-08T12:00:00.000000000', '2023-09-09T12:00:00.000000000'],
          dtype='datetime64[ns]')

  • latitude
    (latitude)
    float32
    -89.97 -89.93 ... 89.93 89.97

    _CoordinateAxisType :

    Lat

    actual_range :

    [-89.975 89.975]

    axis :

    Y

    comment :

    equirectangular projection and grid centers

    coverage_content_type :

    coordinate

    ioos_category :

    Location

    long_name :

    Latitude

    standard_name :

    latitude

    units :

    degrees_north

    valid_max :

    89.975

    valid_min :

    -89.975

    array([-89.975, -89.925, -89.875, ...,  89.875,  89.925,  89.975],
          dtype=float32)

  • longitude
    (longitude)
    float32
    0.025 0.075 0.125 ... 359.9 360.0

    _CoordinateAxisType :

    Lon

    actual_range :

    [2.50000e-02 3.59975e+02]

    axis :

    X

    comment :

    equirectangular projection and grid centers

    coverage_content_type :

    coordinate

    ioos_category :

    Location

    long_name :

    Longitude

    standard_name :

    longitude

    units :

    degrees_east

    valid_max :

    359.975

    valid_min :

    0.025

    array([2.50000e-02, 7.50000e-02, 1.25000e-01, ..., 3.59875e+02, 3.59925e+02,
           3.59975e+02], dtype=float32)

• Data variables: (2)
  • analysed_sst
    (time, latitude, longitude)
    float64
    ...

    colorBarMaximum :

    32.0

    colorBarMinimum :

    0.0

    coverage_content_type :

    physicalMeasurement

    ioos_category :

    Temperature

    long_name :

    analysed sea surface temperature

    standard_name :

    sea_surface_temperature

    units :

    degree_C

    valid_max :

    50.0

    valid_min :

    -2.0

    [366249600000 values with dtype=float64]

  • sea_ice_fraction
    (time, latitude, longitude)
    float64
    ...

    colorBarMaximum :

    1.0

    colorBarMinimum :

    0.0

    comment :

    0 is 0% ice, 1 is 100% ice

    coverage_content_type :

    physicalMeasurement

    ioos_category :

    Ice Distribution

    long_name :

    Sea Ice Fraction

    standard_name :

    sea_ice_area_fraction

    units :

    1

    valid_max :

    1.0

    valid_min :

    0.0

    [366249600000 values with dtype=float64]

• Indexes: (3)
  • time
    PandasIndex

    PandasIndex(DatetimeIndex(['1985-01-01 12:00:00', '1985-01-02 12:00:00',
                   '1985-01-03 12:00:00', '1985-01-04 12:00:00',
                   '1985-01-05 12:00:00', '1985-01-06 12:00:00',
                   '1985-01-07 12:00:00', '1985-01-08 12:00:00',
                   '1985-01-09 12:00:00', '1985-01-10 12:00:00',
                   ...
                   '2023-08-31 12:00:00', '2023-09-01 12:00:00',
                   '2023-09-02 12:00:00', '2023-09-03 12:00:00',
                   '2023-09-04 12:00:00', '2023-09-05 12:00:00',
                   '2023-09-06 12:00:00', '2023-09-07 12:00:00',
                   '2023-09-08 12:00:00', '2023-09-09 12:00:00'],
                  dtype='datetime64[ns]', name='time', length=14130, freq=None))

  • latitude
    PandasIndex

    PandasIndex(Float64Index([ -89.9749984741211, -89.92500305175781,            -89.875,
                  -89.82499694824219,  -89.7750015258789,  -89.7249984741211,
                  -89.67500305175781,            -89.625, -89.57499694824219,
                   -89.5250015258789,
                  ...
                    89.5250015258789,  89.57499694824219,             89.625,
                   89.67500305175781,   89.7249984741211,   89.7750015258789,
                   89.82499694824219,             89.875,  89.92500305175781,
                    89.9749984741211],
                 dtype='float64', name='latitude', length=3600))

  • longitude
    PandasIndex

    PandasIndex(Float64Index([0.02500000037252903, 0.07500000298023224,               0.125,
                  0.17499999701976776, 0.22499999403953552,  0.2750000059604645,
                  0.32499998807907104,               0.375, 0.42500001192092896,
                   0.4749999940395355,
                  ...
                    359.5249938964844,  359.57501220703125,             359.625,
                   359.67498779296875,   359.7250061035156,   359.7749938964844,
                   359.82501220703125,             359.875,  359.92498779296875,
                    359.9750061035156],
                 dtype='float64', name='longitude', length=7200))

• Attributes: (68)

  acknowledgement :

  NOAA Coral Reef Watch Program

  cdm_data_type :

  Grid

  comment :

  This product is designed to improve on and replace the use of AVHRR Pathfinder SST for use within the Coral Reef Watch Program.

  contributor_name :

  NOAA Coral Reef Watch Program

  contributor_role :

  Collecting source data and deriving products; performing quality control of products; disseminating, storing, and submitting data to archive

  Conventions :

  CF-1.6, ACDD-1.3, COARDS

  creator_email :

  coralreefwatch@noaa.gov

  creator_institution :

  NOAA/NESDIS/STAR Coral Reef Watch Program

  creator_name :

  NOAA Coral Reef Watch Program

  creator_type :

  group

  creator_url :

  https://coralreefwatch.noaa.gov/

  data_source :

  NOAA Daily Global 5km Geo-Polar Blended Night-only Sea Surface Temperature Analysis from the date specified in the global attribute time_coverage_start. Note, if the text of this global attribute begins with "Due to ...", one of the following situations occurred: (1) the source data file for the CoralTemp of data file for the CoralTemp of the day was missing; (2) the sea_ice_fraction data array in the source data was missing, (3) some alternation was made on the source data to derive the CoralTemp data of the day.

  date_created :

  2018-01-01T00:00:00Z

  date_issued :

  2021-04-04T13:40:08Z

  date_metadata_modified :

  2020-11-18T00:00:00Z

  date_modified :

  2018-01-01T00:00:00Z

  Easternmost_Easting :

  359.975

  geospatial_bounds :

  "POLYGON((-90.0 360.0, 90.0 360.0, 90.0 0.0, -90.0 0.0, -90.0 360.0))"

  geospatial_bounds_crs :

  EPSG:4326

  geospatial_lat_max :

  89.975

  geospatial_lat_min :

  -89.975

  geospatial_lat_resolution :

  0.049999999999999996

  geospatial_lat_units :

  degrees_north

  geospatial_lon_max :

  359.975

  geospatial_lon_min :

  0.025

  geospatial_lon_resolution :

  0.05000000000000001

  geospatial_lon_units :

  degrees_east

  grid_mapping_epsg_code :

  EPSG:4326

  grid_mapping_inverse_flattening :

  298.2572

  grid_mapping_name :

  latitude_longitude

  grid_mapping_semi_major_axis :

  6378137.0

  history :

  Sat Sep 9 06:30:11 2023: ncatted -O -a geospatial_bounds,global,o,c,"POLYGON((-90.0 360.0, 90.0 360.0, 90.0 0.0, -90.0 0.0, -90.0 360.0))" coraltemp_v3.1_20230908-0-360.nc Sat Sep 9 06:30:11 2023: ncatted -O -a geospatial_lon_max,global,o,f,359.975 coraltemp_v3.1_20230908-0-360.nc Sat Sep 9 06:30:11 2023: ncatted -O -a geospatial_lon_min,global,o,f,0.025 coraltemp_v3.1_20230908-0-360.nc Sat Sep 9 06:30:11 2023: ncatted -O -a valid_max,lon,o,f,359.975 coraltemp_v3.1_20230908-0-360.nc Sat Sep 9 06:30:11 2023: ncatted -O -a valid_min,lon,o,f,0.025 coraltemp_v3.1_20230908-0-360.nc Sat Sep 9 06:30:10 2023: ncap2 -O -s where(lon<0) lon=lon+360 coraltemp_v3.1_20230908-0-360.nc coraltemp_v3.1_20230908-0-360.nc Sat Sep 9 06:30:08 2023: ncks -O --msa_usr_rdr -d lon,0.0,180.0 -d lon,-180.0,0.0 coraltemp_v3.1_20230908.nc coraltemp_v3.1_20230908-0-360.nc This is the first version of CoralTemp. It was originally called v1.0 and then renamed to v3.1 with no change to the overall product) 2023-09-11T14:46:38Z (local files) 2023-09-11T14:46:38Z https://oceanwatch.pifsc.noaa.gov/erddap/griddap/CRW_sst_v3_1.das

  id :

  CoralTemp-v3.1

  infoUrl :

  https://coralreefwatch.noaa.gov/satellite/bleaching5km

  institution :

  NOAA/NESDIS/STAR Coral Reef Watch Program

  instrument :

  ATSR-1, ATSR-2, AATSR, AVHRR, AVHRR-2, AVHRR-3, VIIRS, GOES Imager, MTSAT Imager, MTSAT 2 Imager, AHI, ABI, SEVIRI, buoy - moored buoy, buoy - drifting buoy, buoy - TAO buoy, surface seawater intake

  instrument_vocabulary :

  NOAA NODC Ocean Archive System Instruments

  keywords :

  5km, analysed, analysed_sst, analysis, area, coral, coraltemp, crw, cryosphere, daily, data, day, distribution, earth, Earth Science > Cryosphere > Sea Ice > Ice Extent, Earth Science > Oceans > Ocean Temperature > Sea Surface Temperature, Earth Science > Oceans > Ocean Temperature > Water Temperature, Earth Science > Oceans > Sea Ice > Ice Extent, Earth Science > Spectral/Engineering > Infrared Wavelengths > Thermal Infrared, engineering, environmental, extent, fraction, global, ice, ice distribution, information, infrared, national, near, nesdis, noaa, nrt, ocean, oceans, operational, ostia, program, real, reef, satellite, science, sea, sea_ice_area_fraction, sea_ice_fraction, sea_surface_temperature, seawater, service, spectral, spectral/engineering, sst, star, surface, temperature, thermal, time, watch, water, wavelengths

  keywords_vocabulary :

  GCMD Science Keywords

  license :

  OSTIA Usage Statement (1985-2002): IMPORTANT usage statement. Unless otherwise agreed in writing, these data may be used for pure academic research only, with no commercial or other application and all usage must meet the Met Office Standard Terms and Conditions, which may be found here: https://www.metoffice.gov.uk/corporate/legal/tandc.html. The data may be used for a maximum period of 5 years. Reproduction of the data is permitted provided the following copyright statement is included: (C) Crown Copyright 2010, published by the Met Office. You must submit a completed reproduction license application form (here https://www.metoffice.gov.uk/corporate/legal/repro_licence.html) before using the data. This only needs to be completed once for each user. WARNING Some applications are unable to properly handle signed byte values. If values are encountered > 127, please subtract 256 from this reported value. GHRSST statement (2002-present): GHRSST protocol describes data use as free and open. Coral Reef Watch program statement: The data produced by Coral Reef Watch are available for use without restriction, but Coral Reef Watch relies on the ethics and integrity of the user to ensure that the source of the data and products is appropriately cited and credited. When using these data and products, credit and courtesy should be given to NOAA Coral Reef Watch. Please include the appropriate DOI associated with this dataset in the citation. For more information, visit the NOAA Coral Reef Watch website: https://coralreefwatch.noaa.gov. Recommendations for citing and providing credit are provided at https://coralreefwatch.noaa.gov/satellite/docs/recommendations_crw_citation.php. Users are referred to the footer section of Coral Reef Watch's website (https://coralreefwatch.noaa.gov/index.php) for disclaimers, policies, notices pertaining to the use of the data.

  metadata_link :

  https://coralreefwatch.noaa.gov/satellite/bleaching5km

  naming_authority :

  gov.noaa.coralreefwatch

  NCO :

  netCDF Operators version 4.7.5 (Homepage = http://nco.sf.net, Code = https://github.com/nco/nco)

  nco_openmp_thread_number :

  1

  Northernmost_Northing :

  89.975

  platform :

  Ships, drifting buoys, moored buoys, TOGA-TAO buoy arrays, GOES-8 satellite, GOES-9 satellite, GOES-10 satellite, GOES-11 satellite, GOES-12 satellite, GOES-13 satellite, GOES-14 satellite, GOES-15 satellite, GOES-16 satellite, MTSAT-1R satellite, MTSAT-2 satellite, Himawari-8 satellite, Meteosat-8 satellite, Meteosat-9 satellite, Meteoset-10 satellite, Meteosat-11 satellite, Suomi NPP, MetOp-A satellite, MetOp-B satellite, NOAA-9 satellite, NOAA-11 satellite, NOAA-12 satellite, NOAA-14 satellite, NOAA-15 satellite, NOAA-16 satellite, NOAA-17 satellite, NOAA-18 satellite, NOAA-19 satellite.

  platform_vocabulary :

  NOAA NODC Ocean Archive System Platforms

  processing_level :

  L4

  product_version :

  3.1

  program :

  NOAA Coral Reef Watch Program

  project :

  NOAA Coral Reef Watch Program

  publisher_email :

  coralreefwatch@noaa.gov

  publisher_institution :

  NOAA/NESDIS/STAR Coral Reef Watch Program

  publisher_name :

  NOAA Coral Reef Watch Program

  publisher_type :

  group

  publisher_url :

  https://coralreefwatch.noaa.gov/

  references :

  Donlon, et al., 2011. The Operational Sea Surface Temperature and Sea Ice analysis (OSTIA). Maturi, et al., 2017. A new high-resolution sea surface temperature analysis. https://coralreefwatch.noaa.gov/satellite/coraltemp.php

  source :

  OSTIA Sea Surface Temperature Reanalysis (night-only), NOAA Geo-Polar Blended Night-only Sea Surface Temperature Reanalysis, NOAA Geo-Polar Blended Night-only Sea Surface Temperature (near real-time)

  sourceUrl :

  (local files)

  Southernmost_Northing :

  -89.975

  standard_name_vocabulary :

  CF Standard Name Table v27

  summary :

  NOAA Coral Reef Watch Daily Global 5km Satellite Sea Surface Temperature (CoralTemp). CoralTemp is derived from three different but related 5km daily gap-free SST data sets and provides an internally consistent SST product that stretches from 1985 to present: Operational Sea Surface Temperature and Sea Ice Analysis (OSTIA) Sea Surface Temperature Reanalysis (1985-2002), Geo-Polar Blended Night-only Sea Surface Temperature Reanalysis (2002-2016), Geo-Polar Blended Night-only Sea Surface Temperature Near Real-Time (2017 to present).

  time_coverage_duration :

  P1D

  time_coverage_end :

  2023-09-09T12:00:00Z

  time_coverage_resolution :

  P1D

  time_coverage_start :

  1985-01-01T12:00:00Z

  title :

  Sea Surface Temperature, Coral Reef Watch, CoralTemp, v3.1 - Daily, 1985-present

  Westernmost_Easting :

  0.025

Subset the ERDDAP dataset

The code below does the following: * Trims the data to include only SST data
* Selects the date. To avoid the need to match the exact date found in the dataset, include method='nearest'. * Slices within the latitude and longitude ranges

ds_subset = ds['analysed_sst'].sel(time=date_for_sat_data, 
                          method='nearest'
                          ).sel(latitude=slice(lat_min, lat_max),
                                longitude=slice(lon_min, lon_max)
                                )

Make a plot to view the data

This may take a few seconds. So far you have only set the parameters for download but not requested that the data be downloaded. However, downloading will be necessary to plot the data, so xarray will download it.

ds_subset.plot.pcolormesh(cmap="gist_rainbow_r",
                          vmin=5,
                          vmax=30,
                          aspect=2,
                          size=4
                          )

Define and mask the TurtleWatch band

• The band is between 17.5°C and 18.5°C.
• Use the “where” function of xarray to flag all pixels in the habitat range by replacing their values with a value that is much smaller than the data range minimum.

ds_masked = xr.where((ds_subset > hab_temp_min) & (ds_subset < hab_temp_max), 
                     -999,  # Set flag value
                     ds_subset  
                     )

Map the masked data

Make some adjustments to the color map:
* Set the palette to be the reverse of the gist_rainbow
* Set missing values (like land..) to gray
* Set the flag value color

# Create the color palette
cmap = mpl.cm.get_cmap("gist_rainbow_r").copy()

# Set the color of the missing or masked data 
cmap.set_bad(color='gray')  # missing values color (like land..)

# Set the color of flag value (-999)
cmap.set_under(color='firebrick')  # flag value color

# Plot the data
ds_masked.plot.pcolormesh(cmap=cmap,
                          vmin=5,
                          vmax=30,
                          aspect=2,
                          size=4
                          )

# Add plot annotation
plt.title('TurtleWatch band - ' + date_for_sat_data)
plt.ylabel('Latitude')
plt.xlabel('Longitude')

Text(0.5, 0, 'Longitude')

References

• TurtleWatch: https://oceanwatch.pifsc.noaa.gov/turtlewatch.html

• Several CoastWatch Node websites have data catalogs containing documentation and links to all the datasets available:

  • https://oceanwatch.pifsc.noaa.gov/doc.html
  • https://coastwatch.pfeg.noaa.gov/data.html
  • https://polarwatch.noaa.gov/catalog/