"""
Photosystem II efficiency (ϕₗₗ)
===============================
Basic protocol to measure the Photosystem II efficiency called phi2 or :math:`\Phi_{II}`.
From the fluorescence trace several more values are produced, including
:math:`F_{S}`, the steady state fluorescence, :math:`F_{M}`, the maximum fluorescence, and LEF,
the linear electron flow, based on phi2 and the ambient light intensity.
"""
import numpy as np
_protocol = [
{
"pulses": [
20, 50, 20
],
"pulse_distance": [
10000, 10000, 10000
],
"pulse_length": [
[ 30 ], [ 30 ], [ 30 ]
],
"pulsed_lights": [
[ 3 ], [ 3 ], [ 3 ]
],
"pulsed_lights_brightness": [
[ 2000 ], [ 2000 ], [ 2000 ]
],
"nonpulsed_lights": [
[ 2 ], [ 2 ], [ 2 ]
],
"nonpulsed_lights_brightness": [
[ "light_intensity" ], [ 4500 ], [ "light_intensity" ]
],
"detectors": [
[ 1 ], [ 1 ], [ 1 ]
],
"environmental": [
[ "light_intensity" ]
],
"open_close_start": 1
}
]
[docs]
def _analyze ( _data ):
"""
Macro for data evaluation on PhotosynQ.org
by: John Doe
created: June 4, 2018 4:00 PM
"""
# Define the output dictionary here
output = {}
fs = np.mean(_data['data_raw'][1:5])
fmp = np.mean( _data['data_raw'][63:68])
phi2 = (fmp-fs)/fmp
lef = phi2 * _data['light_intensity'] * 0.45
output['Fs'] = fs
output['Fmp'] = fmp
output['Phi2'] = phi2
output['LEF'] = lef
output['PAR'] = _data['light_intensity']
output['Fluorescence Trace'] = _data['data_raw']
# Return data
return output
_example = {
"time": 1501283341143,
"device_name": "MultispeQ",
"device_version": "1",
"device_id": "00:00:00:01",
"device_battery": 100,
"device_firmware": 1.2,
"sample": [
[
{
"time": 1501283341154,
"label": "",
"light_intensity": 17.95,
"r": 15,
"g": 7,
"b": 4,
"light_intensity_raw": 26,
"data_raw": [
15064,
15232,
15307,
15334,
15353,
15351,
15350,
15341,
15330,
15331,
15317,
15315,
15310,
15298,
15298,
15290,
15293,
15289,
15279,
15280,
20357,
20671,
20781,
20838,
20870,
20894,
20910,
20924,
20935,
20953,
20957,
20958,
20966,
20974,
20975,
20978,
20983,
20986,
20987,
20992,
20990,
20996,
20996,
20991,
20988,
20991,
20996,
20993,
20991,
20985,
20985,
20983,
20981,
20977,
20974,
20971,
20966,
20965,
20961,
20960,
20954,
20951,
20943,
20943,
20933,
20931,
20930,
20922,
20921,
20912,
19360,
18530,
18110,
17863,
17695,
17565,
17448,
17349,
17263,
17171,
17082,
17006,
16932,
16851,
16786,
16715,
16649,
16594,
16534,
16471
]
}
]
]
}