pelagos_py.steps.processing.oxygen

pelagos_py.steps.processing.oxygen.check_config(self, expected_params)

Runtime checks beyond the parameter schema.

Parameter presence and defaults are handled by parameter_schema; this additionally (a) catches method-dependent parameters left unset (None) and (b) verifies that any *_name parameter points at a variable that actually exists in the dataset.

class pelagos_py.steps.processing.oxygen.DeriveUncalibratedPhase(name, parameters=None, diagnostics=False, context=None)

Bases: pelagos_py.steps.base_step.BaseStep, pelagos_py.utils.qc_handling.QCHandlingMixin

Base class for pipeline steps with config-mirroring support. Every concrete subclass (registered via @register_step) inherits this.

run()

Example

- name: "Derive Uncalibrated Phase"
  parameters:
    #  <MANDATORY>
    blue_phase_name: "BPHASE_DOXY"
    # <OPTIONAL>
    red_phase_name: "RPHASE_DOXY"
  diagnostics: false

class pelagos_py.steps.processing.oxygen.DeriveOptodeTemperature(name, parameters=None, diagnostics=False, context=None)

Bases: pelagos_py.steps.base_step.BaseStep, pelagos_py.utils.qc_handling.QCHandlingMixin

Base class for pipeline steps with config-mirroring support. Every concrete subclass (registered via @register_step) inherits this.

run()

Example

- name: "Derive Optode Temperature"
  parameters:
    temp_voltage_name: "TEMP_VOLTAGE_DOXY"
    calib_coefficients: [0, 1, 0, 0, 0, 0]
  diagnostics: false

class pelagos_py.steps.processing.oxygen.PhasePressureCorrection(name, parameters=None, diagnostics=False, context=None)

Bases: pelagos_py.steps.base_step.BaseStep, pelagos_py.utils.qc_handling.QCHandlingMixin

Base class for pipeline steps with config-mirroring support. Every concrete subclass (registered via @register_step) inherits this.

run()

Example

- name: "Phase Pressure Correction"
  parameters:
    optode_pressure_name: "PRES"
    correction_coefficient: 0.1
  diagnostics: false

class pelagos_py.steps.processing.oxygen.DeriveCalibratedPhase(name, parameters=None, diagnostics=False, context=None)

Bases: pelagos_py.steps.base_step.BaseStep, pelagos_py.utils.qc_handling.QCHandlingMixin

Base class for pipeline steps with config-mirroring support. Every concrete subclass (registered via @register_step) inherits this.

run()

Example

- name: "Derive Calibrated Phase"
  parameters:
    uncalibrated_phase_name: "UNCAL_PHASE_DOXY"
    calib_coefficients: [0, 1, 0, 0]
  diagnostics: false

class pelagos_py.steps.processing.oxygen.DeriveOxygenConcentration(name, parameters=None, diagnostics=False, context=None)

Bases: pelagos_py.steps.base_step.BaseStep, pelagos_py.utils.qc_handling.QCHandlingMixin

Base class for pipeline steps with config-mirroring support. Every concrete subclass (registered via @register_step) inherits this.

run()

Example

- name: "Derive Oxygen Concentration"
  parameters:
    # <MANDATORY>
    method: "poly"
    # <METHOD DEPENDENT>
    # The following params are for "poly" method
    temperature_name: "TEMP"
    calib_coefficient_matrix: [
      [0, 1, 0, 0],
      [0, 1, 0, 0],
      [0, 1, 0, 0],
      [0, 1, 0, 0],
      [0, 1, 0, 0]
    ]
  diagnostics: false

class pelagos_py.steps.processing.oxygen.MolarDOXYSalinityCorrection(name, parameters=None, diagnostics=False, context=None)

Bases: pelagos_py.steps.base_step.BaseStep, pelagos_py.utils.qc_handling.QCHandlingMixin

Base class for pipeline steps with config-mirroring support. Every concrete subclass (registered via @register_step) inherits this.

run()

Example

- name: "Molar DOXY Salinity Correction"
  parameters:
    # <MANDATORY>
    salinity_name: "PRAC_SALINITY"
    temperature_name: "TEMP"
    # <OPTIONAL>
    reference_salinity: 0
  diagnostics: false

class pelagos_py.steps.processing.oxygen.MolarDOXYPressureCorrection(name, parameters=None, diagnostics=False, context=None)

Bases: pelagos_py.steps.base_step.BaseStep, pelagos_py.utils.qc_handling.QCHandlingMixin

Base class for pipeline steps with config-mirroring support. Every concrete subclass (registered via @register_step) inherits this.

run()

Example

- name: "Molar DOXY Pressure Correction"
  parameters:
    # <MANDATORY>
    pressure_name: "PRES"
    temperature_name: "TEMP"
    molar_doxy_name: "MOLAR_DOXY_PSAL"
    uncalibrated_phase_correction_applied: true
  diagnostics: false