Package: phyto-photo-utils
Phytoplankton Photophysiology UtilsThis is a tool to read and process active chlorophyll fluorescence data from raw format and apply the biophysical model of Kolber et al. (1998).
For more information see the documentation and demo file, below is a short example of how to use the data to read in and process variables.EXAMPLE USAGEThis package is meant to be used in an interactive environment - ideally JuPyTer Notebookimportphyto_photo_utilsasppufname='/path_to_data/data'output='/output_path'# Load all variables needed for fitting saturation and relaxation modelsdf=ppu.load_FASTTrackaI_files(fname,append=False,save_files=True,res_path=output,seq_len=120,irrad=545.62e10)# Perform a calculate ro saturation model fit on the datasat=ppu.fit_saturation(pfd,flevel,seq,datetime,blank=0,sat_len=100,skip=0,model_type='calc_ro',bounds=True,ro_lims=[0.01,1.0],sig_lims=[100,2200])# Perform a single decay relaxation model fit on the datarel=ppu.fit_relaxation(flevel,seq_time,seq,datetime,blank=0,sat_len=100,rel_len=40,model_type='single',bounds=True,tau1_lims=[100,50000])# Perform time averaging (5 minute averages) on raw transients, including the removal of outliers (mean + stdev * 3)dfm=ppu.remove_outlier_from_time_average(df,time=5,multiplier=3)# Correct for FIRe instrument detector biasdfb=ppu.correct_fire_instrument_bias(df,sat=False,pos=1,sat_len=100)# See the demo file for more infoABOUTThis work was funded by the CSIR. This research was partially supported by the Australian Government through the Australian Research Council's Discovery Projects funding scheme (DP160103387).Version: 1.6.4Author:  Thomas Ryan-Keogh, Charlotte RobinsonEmail:   tjryankeogh(at)gmail.comDate:    2018-12-06Institution: Council for Scientific and Industrial Research, Curtin UniversityResearch group: Southern Ocean Carbon - Climate Observatory (SOCCO), Remote Sensing and Satellite Research GroupPlease use the guidlines given onhttps://integrity.mit.edu/handbook/writing-codeto cite this code.Example citation:Source: phyto_photo_utils [https://gitlab.com/tjryankeogh/phytophotoutils] retrieved on 30 May 2019.PACKAGE STRUCTURENOTE: This package structure is defined by the__init__.pyfileloadload_FIRe_filesload_FASTTrackaI_filesload_FastOcean_filesload_LIFT_FRR_filessaturationfit_saturationrelaxationfit_relaxationtoolsremove_outlier_from_time_averagecorrect_fire_instrument_biascalculate_blank_FastOcean
_ calculate_blank_FIRespectral_correctioncalculate_chl_specific_absorptioncalculate_instrument_led_correctionetrcalculate_amplitude_etrplotplot_saturation_dataplot_relaxation_dataplot_fluorescence_light_curveequationsfit_kolber_nopcalculatate_residual_saturation_nopfit_kolber_pcalculate_residual_saturation_pfit_single_relaxationcalculate_residual_single_relaxationfit_triple_relaxationcalculate_residual_triple_relaxationcalculate_alpha_modelcalculate_residual_etrcalculate_modified_alpha_modelcalculate_residual_phicalculate_beta_modelcalculate_residual_betacalculate_modified_beta_modelcalculate_residual_mbetacalculate_biascalculate_rmsecalculate_nrmsecalculate_fit_errorsfittingfit_kpf_saturationfit_kpf_relaxationACKNOWLEDGEMENTSKevin Oxborough (Chelsea Technology Groups) for linear methods to estimate Fo and FmTO DOAdd a_PSII calculation. PFD (micromol quanta m-2 s-1) * sigmaPSII (m-2 PSII-1).Add in function to read FastTracka I binary filesAdd deconvolution method for triple decay relaxationAdd additional load method for CTG LabSTAFAdd function to fit saturation and relaxation togetherCheck fit definitions match SOP terminology.