Loading¶
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phyto_photo_utils._load.
load_FASTTrackaI_files
(file_, append=False, save_files=False, res_path=None, seq_len=120, irrad=None) Process the raw data file and convert to a csv with standard formatting.
Parameters: - file (str) – The path directory to the .000 data file from benchtop SAtlantic FIRe.
- append (bool, default=False) – If True, multiple files will be concatenated together.
- save_files (bool, default=False) – If True, files will be saved as .csv.
- res_path (dir, default=None) – The path directory where to save files, only required if save_files = True.
- seq_len (int, default=120) – The number of flashlets in the protocol.
- irrad (int, default=None) – The light/dark chamber photons per count from the calibration file.
Returns: - df (pandas.DataFrame, shape=[n,8]) – A dataframe of the raw fluorescence data with columns as below:
- flashlet_number (np.array, dtype=int, shape=[n,]) – A sequential number from 1 to
seq_len
- flevel (np.array, dtype=float, shape=[n,]) – The raw fluorescence data.
- datetime (np.array, dtype=datetime64, shape=[n,]) – The date and time of measurement.
- seq (np.array, dtype=int, shape=[n,]) – The sample measurement number.
- seq_time (np.array, dtype=float, shape=[n,]) – The measurement sequence time in μs.
- pfd (np.array, dype=float, shape=[n,]) – The photon flux density in μmol photons m2 s-1.
- channel (np.array, dtype=str, shape=[n,]) – The chamber used for measurements, A = light chamber, B = dark chamber.
- gain (np.array, dtype=int, shape=[n,]) – The gain settings of the instrument.
Example
>>> fname = './data/raw/instrument/fasttrackai/FASTTrackaI_example.csv' >>> output = './data/raw/ppu/fasttrackai/' >>> df = ppu.load_FASTTrackaI_files(fname, append=False, save_files=True, res_path=output, seq_len=120, irrad=545.62e10)
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phyto_photo_utils._load.
load_FIRe_files
(file_, append=False, save_files=False, res_path=None, seq_len=160, gain_value=None, flen=1e-06, irrad=None, continuous=False, light_step=False, single_turnover=True) Process the raw data file (.000 format) and convert to a csv with standard formatting.
Parameters: - file (str) – The path directory to the data file from benchtop SAtlantic FIRe.
- append (bool, default=False) – If True, multiple files will be concatenated together.
- save_files (bool, default=False) – If True, files will be saved as .csv.
- res_path (str, default=None) – The path directory where to save files, only required if save_files = True.
- seq_len (int , default=160) – The number of flashlets in the protocol. Only required if continuous = True.
- gain (int, default=None) – The gain value set when performing measurements. Only required if continous = True. Discrete Gain values are recorded in raw data files.
- flen (float, default=1e-6) – The flashlet length in seconds.
- irrad (int, default=None) – The LED output in μE m2 s-1. Only required if continuous = True.
- continuous (bool, default=False) – If True, will load files from the continuous format. If False, will load the discrete file format.
- light_step (bool, default=False) – If True, will load files from a discrete format FLC file. If False, will load the discrete file format with no light steps.
- single_turnover (bool, default=True) – If True, will load the saturation and relaxation from the single turnover measurement. If False, will load the multiple turnover measurement.
Returns: - df (pandas.DataFrame, shape=[n,6]) – A dataframe of the raw fluorescence data with columns as below:
- flashlet_number (np.array, dtype=int, shape=[n,]) – A sequential number from 1 to
seq_len
- flevel (np.array, dtype=float, shape=[n,]) – The raw fluorescence data.
- datetime (np.array, dtype=datetime64, shape=[n,]) – The date and time of measurement.
- seq (np.array, dtype=int, shape=[n,]) – The sample measurement number.
- seq_time (np.array, dtype=float, shape=[n,]) – The measurement sequence time in μs.
- pfd (np.array, dype=float, shape=[n,]) – The photon flux density in μmol photons m2 s-1.
Example
>>> fname = './data/raw/instrument/fire/FIRe_example.000' >>> output = './data/raw/ppu/fire/' >>> df = ppu.load_FIRe_files(fname, append=False, save_files=True, res_path=output, seq_len=160, flen=1e-6, irrad=47248)
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phyto_photo_utils._load.
load_FastOcean_files
(file_, append=False, save_files=False, led_separate=False, res_path=None, seq_len=125, seq_reps=None, flen=1e-06, delimiter=', ', FastAct1=True, Single_Acq=False) Process the raw data file and convert to a csv with standard formatting.
Parameters: - file (dir) – The path directory to the .csv data file from the FastOcean with either the FastAct11 or FastAct12 laboratory system.
- append (bool, default=False) – If True, multiple files will be concatenated together. Not applicable if Single_Acq = True.
- save_files (bool, default=False) – If True, files will be saved as .csv.
- led_separate (bool, default=False) – If True, the protocols will be separated dependent upon the LED sequence.
- res_path (dir) – The path directory where to save files, only required if save_files = True.
- seq_len (int, default=125) – The number of flashlets in the protocol.
- seq_reps (int, default=None) – The number of sequences per acquisition or in FastAct2 multiple acquisition files the number of light steps.
- flen (float, default=1e-6) – The flashlet length in seconds.
- delimiter (str, default=',') – Specify the delimiter to be used by Pandas.read_csv for loading the raw files.
- FastAct1 (bool, default=True) – If True, will load data from FastAct1 laboratory system format. If False, will load data from FastAct2 laboratory system format.
- Single_Acq (bool, default=False) – If True, will load a single acquisition data from either the FastAct1 or FastAct2 laboratory system, dependent upon whether FastAct1 is True of False.
Returns: - df (pandas.DataFrame, shape=[n,7]) – A dataframe of the raw fluorescence data with columns as below:
- flashlet_number (np.array, dtype=int, shape=[n,]) – A sequential number from 1 to
seq_len
- flevel (np.array, dtype=float, shape=[n,]) – The raw fluorescence data.
- datetime (np.array, dtype=datetime64, shape=[n,]) – The date and time of measurement.
- seq (np.array, dtype=int, shape=[n,]) – The sample measurement number.
- seq_time (np.array, dtype=float, shape=[n,]) – The measurement sequence time in μs.
- pfd (np.array, dype=float, shape=[n,]) – The photon flux density in μmol photons m2 s-1.
- led_sequence (np.array, dtype=int, shape=[n,]) – The LED combination using during the measurement, see example below.
Example
>>> fname = './data/raw/instrument/fire/FastOcean_example.csv' >>> output = './data/raw/ppu/fastocean/' >>> df = ppu.load_FastOcean_files(fname, append=False, save_files=True, led_separate=False, res_path=output, seq_len=125, flen=1e-6) >>> led_sequence == 1, LED 450 nm >>> led_sequence == 2, LED 450 nm + LED 530 nm >>> led_sequence == 3, LED 450 nm + LED 624 nm >>> led_sequence == 4, LED 450 nm + LED 530 nm + LED 624 nm >>> led_sequence == 5, LED 530 nm + LED 624 nm >>> led_sequence == 6, LED 530 nm >>> led_sequence == 7, LED 624 nm
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phyto_photo_utils._load.
load_LIFT_FRR_files
(file_, append=False, save_files=False, res_path=None, seq_len=228) Process the raw data file from the Soliense LIFT FRR and convert to a csv with standard formatting.
Parameters: - file (dir) – The path directory to the .000 data file from benchtop SAtlantic FIRe.
- append (bool, default=False) – If True, multiple files will be concatenated together.
- save_files (bool, default=False) – If True, files will be saved as .csv.
- res_path (dir) – The path directory where to save files, only required if save_files = True.
- seq_len (int, default=228) – The number of flashlets in the protocol.
Returns: - df (pandas.DataFrame, shape=[n,7]) – A dataframe of the raw fluorescence data with columns as below:
- flashlet_number (np.array, dtype=int, shape=[n,]) – A sequential number from 1 to
seq_len
- flevel (np.array, dtype=float, shape=[n,]) – The raw fluorescence data.
- datetime (np.array, dtype=datetime64, shape=[n,]) – The date and time of measurement.
- seq (np.array, dtype=int, shape=[n,]) – The sample measurement number.
- seq_time (np.array, dtype=float, shape=[n,]) – The measurement sequence time in μs.
- pfd (np.array, dype=float, shape=[n,]) – The photon flux density in μmol photons m2 s-1.