diff argo_getdata.py @ 0:055a934a380f draft

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit d3171d27d35f51b8e7464082610431642f1e4660

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/argo_getdata.py	Thu Dec 21 13:21:21 2023 +0000
@@ -0,0 +1,191 @@
+# author: Marie Jossé
+
+# Python script
+
+#############################
+#      Argo data access     #
+#############################
+
+# Packages : argopy
+
+
+# Load arguments
+import argparse
+import sys
+
+import argopy
+
+command_line_args = sys.argv[1:]
+
+
+parser = argparse.ArgumentParser(description="Retrieve argo Data")
+# Add arguments
+
+parser.add_argument("--user", type=str,
+                    help="User mode : standard, expert or research")
+parser.add_argument("--cardinal_1", type=float, help="Longitude min")
+parser.add_argument("--cardinal_2", type=float, help="Longitude max")
+parser.add_argument("--cardinal_3", type=float, help="Latitude min")
+parser.add_argument("--cardinal_4", type=float, help="Latitude max")
+parser.add_argument("--pressure_1", type=float, help="Pressure min")
+parser.add_argument("--pressure_2", type=float, help="Pressure max")
+parser.add_argument("--date_1", type=str, help="Starting date")
+parser.add_argument("--date_2", type=str, help="Ending date.")
+parser.add_argument("--wmo", type=str, help="WMO: argo's identifier")
+parser.add_argument("--profile", type=str, help="Number of profiles")
+parser.add_argument("--params", type=str, help="List of bgc parameters")
+parser.add_argument("--measured", type=str, help="List of bgc parameters")
+parser.add_argument("--output_argo", type=str, help="Output data from argo")
+
+args = parser.parse_args(command_line_args)
+
+
+# Parse the command line arguments
+
+print(args)
+# Import data
+
+user = args.user
+cardinal_1 = args.cardinal_1
+cardinal_2 = args.cardinal_2
+cardinal_3 = args.cardinal_3
+cardinal_4 = args.cardinal_4
+pressure_1 = args.pressure_1
+pressure_2 = args.pressure_2
+date_1 = args.date_1
+date_2 = args.date_2
+wmo = args.wmo
+if wmo is not None:
+    wmo = list(map(int, wmo.split(",")))
+profile = args.profile
+if profile is not None:
+    profile = list(map(int, profile.split(",")))
+params = args.params
+if params is not None:
+    params = params.split(",")
+    if len(params) == 83:
+        params = "all"
+measured = args.measured
+if measured is not None:
+    measured = measured.split(",")
+
+# Let’s import the argopy data fetcher:
+
+######################
+#       User mode    #
+######################
+# By default,
+# all argopy data fetchers are set to work with a standard user mode.
+# To change that
+
+argopy.set_options(mode=user)
+
+######################
+# Fetching Argo data #
+######################
+# Data selection #
+
+# To access Argo data with a DataFetcher,
+# you need to define how to select your data of interest.
+# argopy provides 3 different data selection methods:
+
+argo_data = argopy.DataFetcher()
+
+# 🗺 For a space/time domain #
+
+if (cardinal_1 is not None):
+    mode = "region"
+    argo_data = argo_data.region([cardinal_1, cardinal_2,
+                                  cardinal_3, cardinal_4,
+                                  pressure_1, pressure_2,
+                                  date_1, date_2])
+
+# ⚓ For one or more profiles #
+# Use the fetcher access point argopy.DataFetcher.profile()
+# to specify the float WMO platform number
+# and the profile cycle number(s) to retrieve profiles for.
+elif (wmo is not None and profile is not None):
+    argo_data = argo_data.profile(wmo, profile)
+    # can also be argo_data = argo_data.profile(6902755, [3, 12])
+    mode = "profile"
+
+# 🤖 For one or more floats #
+# If you know the Argo float unique identifier number called a WMO number
+# you can use the fetcher access point DataFetcher.float()
+# to specify one or more float WMO platform numbers to select.
+else:
+    argo_data = argo_data.float(wmo)
+    # can also be argo_data = argo_data.float([6902746, 6902755])
+    mode = "float"
+
+# Data sources #
+# Let’s start with standard import:
+# argopy.reset_options()
+# Specify data source erddap, gdac or argovis
+
+# if (ftp != "") :
+    # argopy.set_options(src = "gdac", ftp = ftp)
+# else :
+    # argopy.set_options(src = "erddap")
+
+# With remote, online data sources,
+# it may happens that the data server is experiencing down time.
+print(argopy.status())
+
+# Dataset #
+# Argo data are distributed as a single dataset.
+# It is referenced at https://doi.org/10.17882/42182.
+# But they are several Argo missions with specific files and parameters
+# that need special handling by argopy, namely:
+#   - the core Argo Mission: from floats that measure temperature,
+#     salinity, pressure down to 2000m,
+#   - the Deep Argo Mission: from floats that measure temperature,
+#     salinity, pressure down to 6000m,
+#   - and the BGC-Argo Mission: from floats that measure temperature,
+#     salinity, pressure and oxygen, pH, nitrate, chlorophyll,
+#     backscatter, irradiance down to 2000m.
+# You can choose between phy or bgc
+if (params is None):
+    argopy.set_options(dataset="phy")
+else:
+    argopy.set_options(dataset="bgc")
+    if (measured != ['None'] and measured is not None):
+        argo_data = argopy.DataFetcher(params=params, measured=measured)
+        if (mode == "region"):
+            argo_data = argo_data.region([cardinal_1, cardinal_2,
+                                          cardinal_3, cardinal_4,
+                                          pressure_1, pressure_2,
+                                          date_1, date_2])
+        elif (mode == "profile"):
+            argo_data = argo_data.profile(wmo, profile)
+        else:
+            argo_data = argo_data.float(wmo)
+    else:
+        argo_data = argopy.DataFetcher(params=params, measured=None)
+        if (mode == "region"):
+            argo_data = argo_data.region([cardinal_1, cardinal_2,
+                                          cardinal_3, cardinal_4,
+                                          pressure_1, pressure_2,
+                                          date_1, date_2])
+        elif (mode == "profile"):
+            argo_data = argo_data.profile(wmo, profile)
+        else:
+            argo_data = argo_data.float(wmo)
+
+# Data fetching #
+# To fetch (i.e. access, download, format) Argo data,
+# argopy provides the DataFetcher class.
+# Several DataFetcher arguments exist to help you select the dataset,
+# the data source and the user mode the most suited for your applications;
+# and also to improve performances.
+
+# You define the selection of data you want to fetch
+# with one of the DataFetcher methods: region, float or profile.
+# 2 lines to download Argo data: import and fetch !
+
+argo_data = argo_data.load().data
+argo_data.to_netcdf("argo_data.nc")
+
+# argo_metadata = argo_data.to_index()
+
+print(argo_data)