Plotting

phyto_photo_utils._plot.plot_fluorescence_light_curve(par, etr, etrmax=None, alpha=None, rmse=None, sigma=None, phi=False)
Parameters:
  • par (np.array, dtype=float) – The actinic light data from the fluorescence light curve.
  • etr (np.array, dtype=float) – The electron transport rate data.
  • etrmax (float, default=None) – The maximum electron transport rate.
  • alpha (float, default=None) – The light limited slope of electron transport.
  • rmse (float, default=None) – The RMSE value of the fit.
  • sigma (float, default=None) – The effective absorption-cross section.
  • phi (bool, default=False) – If True, etr data is phi and the modified Webb et al. (1974) fit is used.
Returns:

ax – A matplotlib figure object.

Return type:

object

Example

>>> ppu.plot_fluorescence_light_curve(par, etr, etrmax=etr_max, alpha=alpha, rsq=rsq, sigma=sigma, phi=True)
phyto_photo_utils._plot.plot_relaxation_data(fyield, seq_time, fo_relax=None, fm_relax=None, tau=None, alpha=None, rmse=None)
Parameters:
  • fyield (np.array, dtype=float, shape=[n,]) – The raw fluorescence yield data.
  • seq_time (np.array, dtype=float, shape=[n,]) – The time of the flashlet measurements.
  • fo_relax (float, default=None) – The minimum fluorescence value in the relaxation phase.
  • fm_relax (float, default=None) – The maximum fluorescence value in the relaxation phase.
  • tau (float, default=None) – The rate of reoxidation in μs.
  • alpha (float, default=None) – The ratio of reoxidisation components.
  • rmse (float, default=None) – The RMSE value of the fit.
Returns:

ax – A matplotlib figure object.

Return type:

object

Example

>>> ppu.plot_relaxation_data(fyield, seq_time, fo_relax=fo_r, fm_relax=fm_r, tau=(tau1, tau2, tau3), alpha=(alpha1, alpha2, alpha3), rsq=rsq)
phyto_photo_utils._plot.plot_saturation_data(fyield, pfd, fo=None, fm=None, sigma=None, ro=None, rmse=None)
Parameters:
  • fyield (np.array, dtype=float, shape=[n,]) – The raw fluorescence yield data.
  • pfd (np.array, dtype=float, shape=[n,]) – The photon flux density.
  • fo (float, default=None) – The minimum fluorescence value.
  • fm (float, default=None) – The maximum fluorescence value.
  • sigma (float, default=None) – The effective absorption cross-section value in Å2.
  • ro (float, default=None) – The connectivity coefficient.
  • rmse (float, default=None) – The RMSE value of the fit.
Returns:

ax – A matplotlib figure object.

Return type:

object

Example

>>> plot_saturation_data(fyield, pfd, fo=fo, fm=fm, sigma=sigma, ro=None, rmse=rmse)