YAML tracking

[Mrvy29]

Hi Antoine,
I am unfamiliar with how to run YAML files but I have been reading, am I correct in just creating a regular text file in editor and save as the conf.yaml ?
Am I correct that this conf.yaml has to run through the terminal?
thank you !

[AntSimi]

Correct

[Mrvy29]

OK perfect ,
I get a traceback error, how do I specify where the file is located?
FileNotFoundError: [Errno 2] No such file or directory: 'conf.yaml'

[AntSimi]

How did you run?

[Mrvy29]

(base) ~% EddyTracking conf.yaml -v DEBUG /Users/py eddy detection/conf.yaml -v DEBUG    
usage: Tool to use identification step to compute tracking [-h] [-v LOGGING_LEVEL] [--correspondance_in CORRESPONDANCE_IN] [--correspondance_out CORRESPONDANCE_OUT] [--save_correspondance_and_stop]
                                                           [--zarr] [--unraw] [--blank_period BLANK_PERIOD] [--memory]
                                                           yaml_file
Tool to use identification step to compute tracking: error: unrecognized arguments: /Users/py eddy detection/conf.yaml

I am sure this wrong, I have just never tried it so going in blindly

[AntSimi]

White space in filename is to avoid

[Mrvy29]

(base) ~ % Eddytracking /Users/Documents/PhD/track/Eddy_ID/Anticyclonic/tracking/conf.yaml -v DEBUG
Traceback (most recent call last):
  File "/Users/opt/anaconda3/bin/Eddytracking", line 8, in <module>
    sys.exit(eddies_tracking())
  File "/Users/opt/anaconda3/lib/python3.9/site-packages/py_eddy_tracker/appli/eddies.py", line 182, in eddies_tracking
    config = safe_load(stream)
  File "/Users/opt/anaconda3/lib/python3.9/site-packages/yaml/__init__.py", line 125, in safe_load
    return load(stream, SafeLoader)
  File "/Users/opt/anaconda3/lib/python3.9/site-packages/yaml/__init__.py", line 81, in load
    return loader.get_single_data()
  File "/Users/opt/anaconda3/lib/python3.9/site-packages/yaml/constructor.py", line 49, in get_single_data
    node = self.get_single_node()
  File "/Users/opt/anaconda3/lib/python3.9/site-packages/yaml/composer.py", line 39, in get_single_node
    if not self.check_event(StreamEndEvent):
  File "/Users/opt/anaconda3/lib/python3.9/site-packages/yaml/parser.py", line 98, in check_event
    self.current_event = self.state()
  File "/Users/opt/anaconda3/lib/python3.9/site-packages/yaml/parser.py", line 171, in parse_document_start
    raise ParserError(None, None,
yaml.parser.ParserError: expected '<document start>', but found '<block mapping start>'
  in "/Users/Documents/PhD/track/Eddy_ID/Anticyclonic/tracking/conf.yaml", line 6, column 1

I've deleted all spaces from directories - any clues to the errors here?

[AntSimi]

could you share your yaml file?

[Mrvy29]

Sure

  # Files produces with EddyIdentification
  FILES_PATTERN: /Users/Documents/PhD/track/Eddy_ID/Anticyclonic*.nc
  SAVE_DIR: /Users/Documents/PhD/track/Eddy_ID/tracking

# Number of consecutive timesteps with missing detection allowed
VIRTUAL_LENGTH_MAX: 3
# Minimal number of timesteps to considered as a long trajectory
TRACK_DURATION_MIN: 7

[AntSimi]

you have done a partial copy of the yaml