Mercurial > repos > ecology > copernicusmarine
annotate argo_getdata.py @ 2:c07f11d8e49a draft default tip
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit fa49586ecc02936c00015c4368a3b5699295203c
author | ecology |
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date | Mon, 18 Nov 2024 10:39:18 +0000 (2 weeks ago) |
parents | 4de886e6300d |
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rev | line source |
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4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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1 # author: Marie Jossé |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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2 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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3 # Python script |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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4 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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5 ############################# |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
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6 # Argo data access # |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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7 ############################# |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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8 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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9 # Packages : argopy |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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10 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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11 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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12 # Load arguments |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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13 import argparse |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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14 import sys |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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15 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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16 import argopy |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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17 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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18 command_line_args = sys.argv[1:] |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
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19 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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20 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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21 parser = argparse.ArgumentParser(description="Retrieve argo Data") |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
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22 # Add arguments |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
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23 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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24 parser.add_argument("--user", type=str, |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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25 help="User mode : standard, expert or research") |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
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changeset
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26 parser.add_argument("--cardinal_1", type=float, help="Longitude min") |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
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27 parser.add_argument("--cardinal_2", type=float, help="Longitude max") |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
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28 parser.add_argument("--cardinal_3", type=float, help="Latitude min") |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
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29 parser.add_argument("--cardinal_4", type=float, help="Latitude max") |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
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30 parser.add_argument("--pressure_1", type=float, help="Pressure min") |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
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changeset
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31 parser.add_argument("--pressure_2", type=float, help="Pressure max") |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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32 parser.add_argument("--date_1", type=str, help="Starting date") |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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33 parser.add_argument("--date_2", type=str, help="Ending date.") |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
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34 parser.add_argument("--wmo", type=str, help="WMO: argo's identifier") |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
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35 parser.add_argument("--profile", type=str, help="Number of profiles") |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
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36 parser.add_argument("--params", type=str, help="List of bgc parameters") |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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37 parser.add_argument("--measured", type=str, help="List of bgc parameters") |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
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38 parser.add_argument("--output_argo", type=str, help="Output data from argo") |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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39 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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40 args = parser.parse_args(command_line_args) |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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41 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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42 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
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43 # Parse the command line arguments |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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44 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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45 print(args) |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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46 # Import data |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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47 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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48 user = args.user |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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49 cardinal_1 = args.cardinal_1 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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50 cardinal_2 = args.cardinal_2 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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51 cardinal_3 = args.cardinal_3 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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52 cardinal_4 = args.cardinal_4 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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53 pressure_1 = args.pressure_1 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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54 pressure_2 = args.pressure_2 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
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55 date_1 = args.date_1 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
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56 date_2 = args.date_2 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
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57 wmo = args.wmo |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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diff
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58 if wmo is not None: |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
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59 wmo = list(map(int, wmo.split(","))) |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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60 profile = args.profile |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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61 if profile is not None: |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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62 profile = list(map(int, profile.split(","))) |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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63 params = args.params |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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64 if params is not None: |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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65 params = params.split(",") |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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66 if len(params) == 83: |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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67 params = "all" |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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68 measured = args.measured |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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69 if measured is not None: |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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70 measured = measured.split(",") |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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71 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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72 # Let’s import the argopy data fetcher: |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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73 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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74 ###################### |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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75 # User mode # |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
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76 ###################### |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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77 # By default, |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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78 # all argopy data fetchers are set to work with a standard user mode. |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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79 # To change that |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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80 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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81 argopy.set_options(mode=user) |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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82 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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83 ###################### |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
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84 # Fetching Argo data # |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
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85 ###################### |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
86 # Data selection # |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
87 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
88 # To access Argo data with a DataFetcher, |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
89 # you need to define how to select your data of interest. |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
90 # argopy provides 3 different data selection methods: |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
91 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
92 argo_data = argopy.DataFetcher() |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
93 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
94 # 🗺 For a space/time domain # |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
95 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
96 if (cardinal_1 is not None): |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
97 mode = "region" |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
98 argo_data = argo_data.region([cardinal_1, cardinal_2, |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
99 cardinal_3, cardinal_4, |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
100 pressure_1, pressure_2, |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
101 date_1, date_2]) |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
102 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
103 # ⚓ For one or more profiles # |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
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104 # Use the fetcher access point argopy.DataFetcher.profile() |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
105 # to specify the float WMO platform number |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
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106 # and the profile cycle number(s) to retrieve profiles for. |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
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107 elif (wmo is not None and profile is not None): |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
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108 argo_data = argo_data.profile(wmo, profile) |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
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109 # can also be argo_data = argo_data.profile(6902755, [3, 12]) |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
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110 mode = "profile" |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
111 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
112 # 🤖 For one or more floats # |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
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113 # If you know the Argo float unique identifier number called a WMO number |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
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114 # you can use the fetcher access point DataFetcher.float() |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
115 # to specify one or more float WMO platform numbers to select. |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
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|
116 else: |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
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117 argo_data = argo_data.float(wmo) |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
118 # can also be argo_data = argo_data.float([6902746, 6902755]) |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
119 mode = "float" |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
120 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
121 # Data sources # |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
122 # Let’s start with standard import: |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
123 # argopy.reset_options() |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
124 # Specify data source erddap, gdac or argovis |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
125 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
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126 # if (ftp != "") : |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
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127 # argopy.set_options(src = "gdac", ftp = ftp) |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
128 # else : |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
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129 # argopy.set_options(src = "erddap") |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
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|
130 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
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131 # With remote, online data sources, |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
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132 # it may happens that the data server is experiencing down time. |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
133 print(argopy.status()) |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
134 |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
135 # Dataset # |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
136 # Argo data are distributed as a single dataset. |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
137 # It is referenced at https://doi.org/10.17882/42182. |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
138 # But they are several Argo missions with specific files and parameters |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
139 # that need special handling by argopy, namely: |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
140 # - the core Argo Mission: from floats that measure temperature, |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
141 # salinity, pressure down to 2000m, |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
142 # - the Deep Argo Mission: from floats that measure temperature, |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
143 # salinity, pressure down to 6000m, |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
144 # - and the BGC-Argo Mission: from floats that measure temperature, |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
145 # salinity, pressure and oxygen, pH, nitrate, chlorophyll, |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
146 # backscatter, irradiance down to 2000m. |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
147 # You can choose between phy or bgc |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
148 if (params is None): |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
149 argopy.set_options(dataset="phy") |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
150 else: |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
151 argopy.set_options(dataset="bgc") |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
152 if (measured != ['None'] and measured is not None): |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
153 argo_data = argopy.DataFetcher(params=params, measured=measured) |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
154 if (mode == "region"): |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
155 argo_data = argo_data.region([cardinal_1, cardinal_2, |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
156 cardinal_3, cardinal_4, |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
157 pressure_1, pressure_2, |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
158 date_1, date_2]) |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
159 elif (mode == "profile"): |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
160 argo_data = argo_data.profile(wmo, profile) |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
161 else: |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
162 argo_data = argo_data.float(wmo) |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
163 else: |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
164 argo_data = argopy.DataFetcher(params=params, measured=None) |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
165 if (mode == "region"): |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
166 argo_data = argo_data.region([cardinal_1, cardinal_2, |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
167 cardinal_3, cardinal_4, |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
168 pressure_1, pressure_2, |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
169 date_1, date_2]) |
4de886e6300d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
ecology
parents:
diff
changeset
|
170 elif (mode == "profile"): |
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171 argo_data = argo_data.profile(wmo, profile) |
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172 else: |
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173 argo_data = argo_data.float(wmo) |
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174 |
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175 # Data fetching # |
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176 # To fetch (i.e. access, download, format) Argo data, |
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177 # argopy provides the DataFetcher class. |
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178 # Several DataFetcher arguments exist to help you select the dataset, |
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179 # the data source and the user mode the most suited for your applications; |
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180 # and also to improve performances. |
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181 |
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182 # You define the selection of data you want to fetch |
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183 # with one of the DataFetcher methods: region, float or profile. |
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184 # 2 lines to download Argo data: import and fetch ! |
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185 |
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186 argo_data = argo_data.load().data |
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187 argo_data.to_netcdf("argo_data.nc") |
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188 |
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189 # argo_metadata = argo_data.to_index() |
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190 |
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191 print(argo_data) |