pelagos_py.steps.processing.chla#

class pelagos_py.steps.processing.chla.chla_deep_correction(name, parameters=None, diagnostics=False, context=None)[source]#

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()[source]#

Example

- name: "Chla Deep Correction"
  parameters:
    apply_to: "CHLA"
    dark_value: null
    depth_threshold: 200
  diagnostics: true
compute_dark_value()[source]#

Compute dark value for chlorophyll-a correction.

The dark value represents the sensor’s baseline reading in the absence of chlorophyll fluorescence. Computed as the median of minimum CHLA values from deep profiles (>= depth_threshold).

Parameters:

  • ds (xarray.Dataset) – Glider dataset with variables: CHLA, DEPTH (or PRES), PROFILE_NUMBER

  • depth_threshold (float, optional) – Minimum depth [m] for dark value calculation (default: 200)

  • n_profiles (int, optional) – Number of deep profiles to use (default: 5)

  • config_path (str or Path, optional) – Path to config file to check for existing dark value

Returns:

  • dark_value (float) – Computed dark value

  • profile_data (dict) – Dictionary containing profile information used in calculation Keys are profile numbers, values are dicts with ‘depth’, ‘chla’, ‘min_value’, ‘min_depth’

apply_dark_correction()[source]#

Apply dark value correction to CHLA data.

class pelagos_py.steps.processing.chla.chla_quenching_correction(name, parameters=None, diagnostics=False, context=None)[source]#

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()[source]#

Example

- name: "Chla Quenching Correction"
  parameters:
    method: "Argo"
    apply_to: "CHLA"
    mld_settings: {
      "threshold_on": "TEMP",
      "reference_depth": 10,
      "threshold": 0.2
      }
    plot_profiles: []
  diagnostics: true
apply_xing2012_quenching_correction(profile)[source]#

Apply non-photochemical quenching (NPQ) correction following Xing et al. (2012, JGR–Oceans, 117:C01019).

The maximum fluorescence within the mixed-layer depth (MLD) is taken as the non-quenched reference. All shallower (PRES < z_qd) values are adjusted upward to that maximum. Correction is only applied when solar elevation > 0°.

Parameters:

  • chlf (array-like of shape (N,)) – Uncorrected chlorophyll fluorescence profile F_Chl(PRES).

  • pres (array-like of shape (N,)) – Pressure (dbar), increasing with depth.

  • mld (float) – Mixed-layer depth (m or dbar).

  • sun_angle (float) – Solar elevation angle (degrees). NPQ correction is applied only if sun_angle > 0.

Returns:

  • chl_corr (ndarray of shape (N,)) – NPQ-corrected fluorescence profile.

  • npq (ndarray of shape (N,)) – NPQ index = (chl_corr − chlf) / chlf.

  • z_qd (float) – Quenching depth (dbar): pressure of maximum fluorescence within the MLD. NaN if not computable or if night-time.

Notes

  • No correction is applied if solar elevation ≤ 0° (nighttime).

  • Shallower than z_qd → fluorescence set to Fmax (non-quenched reference).

  • Below MLD → unchanged.