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comparison argo_getdata.py @ 0:055a934a380f draft

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit d3171d27d35f51b8e7464082610431642f1e4660
author ecology
date Thu, 21 Dec 2023 13:21:21 +0000
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-1:000000000000 0:055a934a380f
1 # author: Marie Jossé
2
3 # Python script
4
5 #############################
6 # Argo data access #
7 #############################
8
9 # Packages : argopy
10
11
12 # Load arguments
13 import argparse
14 import sys
15
16 import argopy
17
18 command_line_args = sys.argv[1:]
19
20
21 parser = argparse.ArgumentParser(description="Retrieve argo Data")
22 # Add arguments
23
24 parser.add_argument("--user", type=str,
25 help="User mode : standard, expert or research")
26 parser.add_argument("--cardinal_1", type=float, help="Longitude min")
27 parser.add_argument("--cardinal_2", type=float, help="Longitude max")
28 parser.add_argument("--cardinal_3", type=float, help="Latitude min")
29 parser.add_argument("--cardinal_4", type=float, help="Latitude max")
30 parser.add_argument("--pressure_1", type=float, help="Pressure min")
31 parser.add_argument("--pressure_2", type=float, help="Pressure max")
32 parser.add_argument("--date_1", type=str, help="Starting date")
33 parser.add_argument("--date_2", type=str, help="Ending date.")
34 parser.add_argument("--wmo", type=str, help="WMO: argo's identifier")
35 parser.add_argument("--profile", type=str, help="Number of profiles")
36 parser.add_argument("--params", type=str, help="List of bgc parameters")
37 parser.add_argument("--measured", type=str, help="List of bgc parameters")
38 parser.add_argument("--output_argo", type=str, help="Output data from argo")
39
40 args = parser.parse_args(command_line_args)
41
42
43 # Parse the command line arguments
44
45 print(args)
46 # Import data
47
48 user = args.user
49 cardinal_1 = args.cardinal_1
50 cardinal_2 = args.cardinal_2
51 cardinal_3 = args.cardinal_3
52 cardinal_4 = args.cardinal_4
53 pressure_1 = args.pressure_1
54 pressure_2 = args.pressure_2
55 date_1 = args.date_1
56 date_2 = args.date_2
57 wmo = args.wmo
58 if wmo is not None:
59 wmo = list(map(int, wmo.split(",")))
60 profile = args.profile
61 if profile is not None:
62 profile = list(map(int, profile.split(",")))
63 params = args.params
64 if params is not None:
65 params = params.split(",")
66 if len(params) == 83:
67 params = "all"
68 measured = args.measured
69 if measured is not None:
70 measured = measured.split(",")
71
72 # Let’s import the argopy data fetcher:
73
74 ######################
75 # User mode #
76 ######################
77 # By default,
78 # all argopy data fetchers are set to work with a standard user mode.
79 # To change that
80
81 argopy.set_options(mode=user)
82
83 ######################
84 # Fetching Argo data #
85 ######################
86 # Data selection #
87
88 # To access Argo data with a DataFetcher,
89 # you need to define how to select your data of interest.
90 # argopy provides 3 different data selection methods:
91
92 argo_data = argopy.DataFetcher()
93
94 # 🗺 For a space/time domain #
95
96 if (cardinal_1 is not None):
97 mode = "region"
98 argo_data = argo_data.region([cardinal_1, cardinal_2,
99 cardinal_3, cardinal_4,
100 pressure_1, pressure_2,
101 date_1, date_2])
102
103 # ⚓ For one or more profiles #
104 # Use the fetcher access point argopy.DataFetcher.profile()
105 # to specify the float WMO platform number
106 # and the profile cycle number(s) to retrieve profiles for.
107 elif (wmo is not None and profile is not None):
108 argo_data = argo_data.profile(wmo, profile)
109 # can also be argo_data = argo_data.profile(6902755, [3, 12])
110 mode = "profile"
111
112 # 🤖 For one or more floats #
113 # If you know the Argo float unique identifier number called a WMO number
114 # you can use the fetcher access point DataFetcher.float()
115 # to specify one or more float WMO platform numbers to select.
116 else:
117 argo_data = argo_data.float(wmo)
118 # can also be argo_data = argo_data.float([6902746, 6902755])
119 mode = "float"
120
121 # Data sources #
122 # Let’s start with standard import:
123 # argopy.reset_options()
124 # Specify data source erddap, gdac or argovis
125
126 # if (ftp != "") :
127 # argopy.set_options(src = "gdac", ftp = ftp)
128 # else :
129 # argopy.set_options(src = "erddap")
130
131 # With remote, online data sources,
132 # it may happens that the data server is experiencing down time.
133 print(argopy.status())
134
135 # Dataset #
136 # Argo data are distributed as a single dataset.
137 # It is referenced at https://doi.org/10.17882/42182.
138 # But they are several Argo missions with specific files and parameters
139 # that need special handling by argopy, namely:
140 # - the core Argo Mission: from floats that measure temperature,
141 # salinity, pressure down to 2000m,
142 # - the Deep Argo Mission: from floats that measure temperature,
143 # salinity, pressure down to 6000m,
144 # - and the BGC-Argo Mission: from floats that measure temperature,
145 # salinity, pressure and oxygen, pH, nitrate, chlorophyll,
146 # backscatter, irradiance down to 2000m.
147 # You can choose between phy or bgc
148 if (params is None):
149 argopy.set_options(dataset="phy")
150 else:
151 argopy.set_options(dataset="bgc")
152 if (measured != ['None'] and measured is not None):
153 argo_data = argopy.DataFetcher(params=params, measured=measured)
154 if (mode == "region"):
155 argo_data = argo_data.region([cardinal_1, cardinal_2,
156 cardinal_3, cardinal_4,
157 pressure_1, pressure_2,
158 date_1, date_2])
159 elif (mode == "profile"):
160 argo_data = argo_data.profile(wmo, profile)
161 else:
162 argo_data = argo_data.float(wmo)
163 else:
164 argo_data = argopy.DataFetcher(params=params, measured=None)
165 if (mode == "region"):
166 argo_data = argo_data.region([cardinal_1, cardinal_2,
167 cardinal_3, cardinal_4,
168 pressure_1, pressure_2,
169 date_1, date_2])
170 elif (mode == "profile"):
171 argo_data = argo_data.profile(wmo, profile)
172 else:
173 argo_data = argo_data.float(wmo)
174
175 # Data fetching #
176 # To fetch (i.e. access, download, format) Argo data,
177 # argopy provides the DataFetcher class.
178 # Several DataFetcher arguments exist to help you select the dataset,
179 # the data source and the user mode the most suited for your applications;
180 # and also to improve performances.
181
182 # You define the selection of data you want to fetch
183 # with one of the DataFetcher methods: region, float or profile.
184 # 2 lines to download Argo data: import and fetch !
185
186 argo_data = argo_data.load().data
187 argo_data.to_netcdf("argo_data.nc")
188
189 # argo_metadata = argo_data.to_index()
190
191 print(argo_data)