Change Log

**v1.4.6**(2021-04-12) - Bias metric no longer log transformed. - FIRe loading function includes gain correction and calculations for σPSII in absolute units.

**v1.4.5**(2021-01-23) - Bug fix for separating files when loading FastOcean FastAct1 data

**v1.4.4**(2020-10-21) - Error reporting for ETR calculations cleaned up to reduce redundancy

**v1.4.3**(2020-10-07) - Bug fix to absorption calculations - Error reporting for ETR calculations

**v1.4.2**(2020-09-28) - Bug fix for columns to include normalised RMSE

**v1.4.1**(2020-09-17) - Fo and Fm errors are now reported as percentages. - Model bias is now normalised. - Additional statistical output included in the form of normalised RMSE, where RMSE is normalised to the mean fluorescence level.

**v1.4**(2020-07-01)

  • Added an option to ETR fitting to apply Serodio corrections for samples that have dark relaxation.
  • Added an option for the fit to return Ek and manually calculate ETRmax.
  • Added an option to fit ETRmax using a beta model.

**v1.3.5**(2020-05-22)

  • Bug fix for ETR fitting when the number of measurements per light level is 1.

**v1.3.4**(2020-05-05)

  • Bug fix for fitting with no connectivity model.

**v1.3.3**(2020-04-17)

  • Bug fix for handling single FIRe files
  • Loading FIRe files can now split single turnover and multiple turnover measurements

**v1.3.2**(2020-03-26)

  • Bug fix to tools functions for change in name from fyield to flevel
  • Bug fix for spectral correction to sort wavelengths to always be ascending

**v1.3.1**(2020-03-05)

  • Added functionality to load raw data files of Single Acquisitions from Chelsea FastAct1 laboratory system
  • Added functionality to calculate ETR by only using the last 3 measurements of each time step

**v1.3**(2020-02-20)

  • Added functionality to load raw data files from Soliense LIFT-FRR
  • Added functionality to load raw data files from Chelsea FastAct2 laboratory systems
  • Bug fix to fit triple relaxation

**v1.2.1**(2020-01-08)

  • Bug fix for fixed ro calculation

**v1.2.1**(2020-01-08)

  • Bug fixes for fitting triple relaxation error codes
  • Update to recommend bounds for tau1

**v1.2**(2019-12-09)

  • Update to bias calculation.
  • Update to spectral correction code for correcting for background light and using chlorophyll to calculate Kd.
  • Update to spectral correction code to include FastOcean LED spectra.
  • Update to spectral correction code that allows the user to include their own constants/spectra instead of the pre-included file.
  • Plot functions now close any existing figure objects.
  • Plot functions now include RMSE in the legend.
  • Update to remove outliers code to make the datetime array ‘datetime64’.
  • Statistical metrics returned from FLC fitting procedure no longer include R2, Chi2 or reduced Chi2.

**v1.1**(2019-10-15)

  • Statistical metrics returned from fitting procedure no longer include R2, Chi2 or reduced Chi2.

**v1.0.2**(2019-10-06)

  • Saturation flashlets in relaxation fitting are now included in F:sub:`m`Relax estimation, rather than replacing relaxation flashlets.
  • FIRe instrument relaxation bias now only uses the difference in relaxation flashlets to correct the large difference in flashlets.

**v1.0.1**(2019-10-04)

  • Implementation of code for submission to PyPi. Package now available for installation using pip install phyto_photo_utils.

v1.0 (2019-10-01)

  • Syntax changes to saturation, relaxation and flc. Different models now called with optional arguments instead of separate functions.

v0.9 (2019-10-01)

  • Update to phytoplankton specific absorption code for handling phycobilin content
  • Update to phytoplankton specific absorption code for updated pathlength amplification coefficients
  • Update to phytoplankton specific absorption code for not normalising in the infra-red (750 nm) region

v0.8 (2019-06-28)

  • Bug fix to spectral correction for handling arrays
  • Statistical metrics now outputs RMSE, reduced Chi squared
  • Processing flags now included in output

v0.7 (2019-06-20)

  • Fo and Fm now estimated as intercepts of Huber Regression linear fits
  • Fitting skipped if Fo is greater than Fm
  • Spectral correction now calculates factor as a function of depth

v0.6 (2019-05-30)

  • read the docs formatting applied
  • added warning messages when lower bounds are higher than upper bounds
  • added demo file

v0.5 (2019-05-23)

  • various bug fixes
  • spectral LED correction now estimates in situ light field

v0.4 (2019-05-21)

  • added plot function

v0.3 (2019-05-17)

  • restructured package to avoid nested functions
  • added outlier removal tool to FLC function

v0.2 (2018-12-07)

  • added functionality for FLCs

v0.1 (2018-12-01)

  • Functions compiled in package format