EddiesObservations cannot be imported from py_eddy_tracker.observations

[evanmason]

The Wiki needs to be updated.

The section for creating a tracking recipe presently fails as follows:

In [7]: from py_eddy_tracker.observations import EddiesObservations as Model                                                                                                                                      
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-7-77527e386807> in <module>
----> 1 from py_eddy_tracker.observations import EddiesObservations as Model

ImportError: cannot import name 'EddiesObservations' from 'py_eddy_tracker.observations' (/home/emason/VENVP3/lib/python3.7/site-packages/pyEddyTracker-3.0.0-py3.7.egg/py_eddy_tracker/observations/__init__.py)

This seems to work:
In [2]: from py_eddy_tracker.observations.observation import EddiesObservations as Model but I then get the following when trying to follow the Wiki:

(VENVP3) [emason@marula global4eddytracking]$ EddyTracking my_tracking.py my_tracking.yaml
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]
                                                           [--blank_period BLANK_PERIOD]
                                                           yaml_file
Tool to use identification step to compute tracking: error: unrecognized arguments: my_tracking.yaml
(VENVP3) [emason@marula global4eddytracking]$

[AntSimi]

The correct command is EddyTracking yamlfile Le ven. 27 déc. 2019 à 13:03, evanmason <notifications@github.com> a écrit :

…

The Wiki needs to be updated. The section for creating a tracking recipe presently fails as follows: In [7]: from py_eddy_tracker.observations import EddiesObservations as Model --------------------------------------------------------------------------- ImportError Traceback (most recent call last) <ipython-input-7-77527e386807> in <module> ----> 1 from py_eddy_tracker.observations import EddiesObservations as Model ImportError: cannot import name 'EddiesObservations' from 'py_eddy_tracker.observations' (/home/emason/VENVP3/lib/python3.7/site-packages/pyEddyTracker-3.0.0-py3.7.egg/py_eddy_tracker/observations/__init__.py) This seems to work: In [2]: from py_eddy_tracker.observations.observation import EddiesObservations as Model but I then get the following when trying to follow the Wiki: (VENVP3) ***@***.*** global4eddytracking]$ EddyTracking my_tracking.py my_tracking.yaml 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] [--blank_period BLANK_PERIOD] yaml_file Tool to use identification step to compute tracking: error: unrecognized arguments: my_tracking.yaml (VENVP3) ***@***.*** global4eddytracking]$ — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#3?email_source=notifications&email_token=AIS7AZJBHKOPJSKA2ULOV6DQ2XVIPA5CNFSM4J73DSJ2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IC3I7YQ>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AIS7AZIXZEQ3TIG5FHTJU2TQ2XVIPANCNFSM4J73DSJQ> .

[evanmason]

Ok, so the Wiki should be updated to reflect that. Is it no longer possible to add a 'tracking recipe', or is that now done within the yaml?

[evanmason]

Is it the file 'tracking.yaml' in share? That is 2 years old.

Using that I get the following error:

(VENVP3) [emason@marula global4eddytracking]$ EddyTracking my_tracking.yaml
/home/emason/VENVP3/lib/python3.7/site-packages/pyEddyTracker-3.0.0-py3.7.egg/EGG-INFO/scripts/EddyTracking:109: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
  config = yaml_load(stream)
/home/emason/VENVP3/lib/python3.7/site-packages/pyEddyTracker-3.0.0-py3.7.egg/py_eddy_tracker/observations/observation.py:692: RuntimeWarning: invalid value encountered in less
  return distance < 125
/home/emason/VENVP3/lib/python3.7/site-packages/numpy/ma/core.py:4008: RuntimeWarning: invalid value encountered in equal
  check = compare(sdata, odata)
/home/emason/VENVP3/lib/python3.7/site-packages/pyEddyTracker-3.0.0-py3.7.egg/py_eddy_tracker/tracking.py:400: RuntimeWarning: invalid value encountered in equal
  h_v.min = h_v[:].min()
/home/emason/VENVP3/lib/python3.7/site-packages/pyEddyTracker-3.0.0-py3.7.egg/py_eddy_tracker/tracking.py:401: RuntimeWarning: invalid value encountered in equal
  h_v.max = h_v[:].max()
Traceback (most recent call last):
  File "/home/emason/VENVP3/bin/EddyTracking", line 4, in <module>
    __import__('pkg_resources').run_script('pyEddyTracker==3.0.0', 'EddyTracking')
  File "/home/emason/VENVP3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/home/emason/VENVP3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1462, in run_script
    exec(code, namespace, namespace)
  File "/home/emason/VENVP3/lib/python3.7/site-packages/pyEddyTracker-3.0.0-py3.7.egg/EGG-INFO/scripts/EddyTracking", line 190, in <module>
    SHORT_CORRESPONDANCES.shorter_than(size_max=NB_OBS_MIN)
  File "/home/emason/VENVP3/lib/python3.7/site-packages/pyEddyTracker-3.0.0-py3.7.egg/py_eddy_tracker/tracking.py", line 513, in shorter_than
    translate = empty(i_keep_track.max() + 1, dtype='u4')
  File "/home/emason/VENVP3/lib/python3.7/site-packages/numpy/core/_methods.py", line 30, in _amax
    return umr_maximum(a, axis, None, out, keepdims, initial, where)
ValueError: zero-size array to reduction operation maximum which has no identity
(VENVP3) [emason@marula global4eddytracking]$

Two files are produced:
148 -rw-rw-r-- 1 emason emason 148224 Dec 28 17:43 Cyclonic_correspondances.nc
28 -rw-rw-r-- 1 emason emason 25888 Dec 28 17:43 Cyclonic_untracked.nc
but no Cyclonic.nc.

My yaml file contains:

#DIAGNOSTIC_TYPE: 'SLA'
#DIAGNOSTIC_TYPE: 'ADT'

PATHS:
  # Files produces with EddyIdentification
  FILES_PATTERN: /marula/emason/data/Copernicus/GLOBAL_REANALYSIS_PHY_001_030/global4eddytracking/Cyclonic_20061*.nc
  # Path and filename of Chelton et al (1998) Rossby radius data
  # Obtain file from:
  # http://www-po.coas.oregonstate.edu/research/po/research/rossby_radius/
  RW_PATH: '/home/emason/Dropbox/rossrad.dat'
  # Path for saving of outputs
  SAVE_DIR: '/marula/emason/data/Copernicus/GLOBAL_REANALYSIS_PHY_001_030/global4eddytracking/'

# Minimum number of observations to store eddy
TRACK_DURATION_MIN: 10
VIRTUAL_LENGTH_MAX: 0

[evanmason]

So I updated all PET dependencies and that solved the issue for the missing Cyclonic.nc. I don't know which dependency was the culprit.