Photosynthesis (RIDES)¶
Measures the same photosynthesis-related parameters in <15 seconds as ‘Leaf Photosynthesis MutlispeQ v2.0’ plus additional PS1 and P700 measurements.
Chlorophll Fluorescence: Phi2, PhiNPQ, PhiNO, NPQt, qL, LEF
Relative Chlorophyll
ATP synthase conductivity, proton motive force parameters through DIRK(ECS): ECSt mAU, vH+, gH+
Saturation pulse estimation of PSI parameters: PS1 active centers, PS1 open, PS1 oxidized and PS1 over reduced
Absorbance at: 450, 535, 605, 650, 730, 850, 880, and 940nm.
The rate of turnover of the cytochrome b6f complex through DIRKP(700)
Leaf Thickness (in mm), angle, and cardinal direction
Leaf Temperature and differential from ambient temperature
Environmental conditions: PAR and ambient temperature/pressure/humidity
Important
Supports MultispeQ V1 and V2 with Firmware 2.34 and higher
Basic Usage¶
Example: Import statement for the rides protocol¶
## Import rides
from jii_multispeq_protocols.protocols import rides as _rides
Sequence¶
%%{
init: {
"theme": "base",
"themeVariables": {"primaryColor": "#49e06d", "primaryTextColor": "#005e5e", "primaryBorderColor": "#005e5e", "lineColor": "#fff381", "secondaryColor": "#afd7f4", "tertiaryColor": "#D7EBF9"}
}
}%%
flowchart TD
START((Start))
A0["`**no_leaf_baseline**
*Sensors:*
• Accelerometer & Magnetometer
• Ambient Temperature, Humidity, Pressure
• Contactless Temperature
• PAR light sensor`"]:::protocol
START ==>|"`**Waits until**: Clamp opened
655nm (Main)`"| A0
A1["`**DIRK_ECS**
*Detector:*
• 700nm - 1150nm
• 400nm - 700nm (BG18)
*Pulsed LEDs:*
• 530nm (Main)
• 590nm (Main)
*Non Pulsed LED:* 655nm (Main)
*Sensors:*
• Ambient Temperature, Humidity, Pressure
• Contactless Temperature
• Hall Effect Sensor
• PAR light sensor`"]:::protocol
A0 ==>|"`**Waits until**: Clamp closed
655nm (Main)`"| A1
A2["`**DIRK_P700**
*Detector:* 700nm - 1150nm
*Pulsed LED:* 850nm (Clamp)
*Non Pulsed LED:* 655nm (Main)
*Sensors:*
• Accelerometer & Magnetometer
• Ambient Temperature, Humidity, Pressure
• Contactless Temperature
• PAR light sensor`"]:::protocol
A1 ==> A2
A3["`**PAM**
*Detector:*
• 700nm - 1150nm
*Pulsed LEDs:*
• 590nm (Main)
• 850nm (Clamp)
*Non Pulsed LEDs:*
• 655nm (Main)
• 730nm (Clamp)
*Sensors:*
• Accelerometer & Magnetometer
• Ambient Temperature, Humidity, Pressure
• Contactless Temperature
• Hall Effect Sensor
• PAR light sensor`"]:::protocol
A2 ==> A3
A4["`**SPAD**
*Sensors:*
• Accelerometer & Magnetometer
• Ambient Temperature, Humidity, Pressure
• Contactless Temperature
• Hall Effect Sensor
• PAR light sensor`"]:::protocol
A3 ==> A4
A4 ==> END
END(( End ))
classDef protocol text-align:left,white-space:pre;
Details¶
Code¶
Protocol Code¶
[ { '_protocol_set_': [ { 'averages': 1,
'energy_min_wake_time': 7000,
'energy_save_timeout': 300000,
'environmental': [ ['light_intensity'],
[ 'temperature_humidity_pressure'],
[ 'temperature_humidity_pressure2'],
['contactless_temp'],
['compass_and_angle']],
'label': 'no_leaf_baseline',
'par_led_start_on_open': 2},
{ 'autogain': [ [2, 1, 3, 12, 50000],
[3, 8, 1, 80, 50000]],
'averages': 1,
'detectors': [ [3],
[3],
[3],
[3],
[3],
[3],
[3],
[3],
[3],
[3],
[3],
[3],
[3],
[3],
[3],
[3],
[3],
[3],
[3],
[1],
[1],
[1]],
'environmental': [ ['light_intensity'],
[ 'temperature_humidity_pressure'],
[ 'temperature_humidity_pressure2'],
['contactless_temp'],
['thickness']],
'label': 'DIRK_ECS',
'nonpulsed_lights': [ [2],
[2],
[2],
[2],
[2],
[2],
[2],
[2],
[2],
[2],
[2],
[2],
[2],
[2],
[2],
[2],
[2],
[2],
[2],
[2],
[2],
[2]],
'nonpulsed_lights_brightness': [ [ 'light_intensity'],
[ 'light_intensity'],
[0],
[ 'light_intensity'],
[ 'light_intensity'],
[0],
[ 'light_intensity'],
[ 'light_intensity'],
[0],
[ 'light_intensity'],
[ 'light_intensity'],
[0],
[ 'light_intensity'],
[ 'light_intensity'],
[0],
[ 'light_intensity'],
[ 'light_intensity'],
[0],
[ 'light_intensity'],
[ 'light_intensity'],
[0],
[ 'light_intensity']],
'par_led_start_on_close': 2,
'protocols_delay': 10,
'pulse_distance': [ 1500,
1500,
1500,
1500,
1500,
1500,
1500,
1500,
1500,
1500,
1500,
1500,
1500,
1500,
1500,
1500,
1500,
1500,
1500,
1500,
1500,
1500],
'pulse_length': [ ['a_d2'],
['a_d2'],
['a_d2'],
['a_d2'],
['a_d2'],
['a_d2'],
['a_d2'],
['a_d2'],
['a_d2'],
['a_d2'],
['a_d2'],
['a_d2'],
['a_d2'],
['a_d2'],
['a_d2'],
['a_d2'],
['a_d2'],
['a_d2'],
['a_d2'],
['a_d2'],
['a_d2'],
['a_d2']],
'pulsed_lights': [ [1],
[1],
[1],
[1],
[1],
[1],
[1],
[1],
[1],
[1],
[1],
[1],
[1],
[1],
[1],
[1],
[1],
[1],
[1],
[3],
[3],
[3]],
'pulsed_lights_brightness': [ ['a_b2'],
['a_b2'],
['a_b2'],
['a_b2'],
['a_b2'],
['a_b2'],
['a_b2'],
['a_b2'],
['a_b2'],
['a_b2'],
['a_b2'],
['a_b2'],
['a_b2'],
['a_b2'],
['a_b2'],
['a_b2'],
['a_b2'],
['a_b2'],
['a_b2'],
['a_b2'],
['a_b2'],
['a_b2']],
'pulses': [ 100,
100,
20,
100,
100,
20,
100,
100,
20,
100,
100,
20,
100,
100,
20,
100,
100,
20,
100,
20,
20,
100]},
{ 'averages': 1,
'detectors': [ [1],
[1],
[1],
[1],
[1],
[1],
[1],
[1],
[1],
[1],
[1],
[1],
[1],
[1],
[1],
[1],
[1],
[1],
[1],
[1],
[1],
[1]],
'environmental': [ ['previous_light_intensity'],
[ 'temperature_humidity_pressure'],
[ 'temperature_humidity_pressure2'],
['contactless_temp'],
['compass_and_angle']],
'label': 'DIRK_P700',
'nonpulsed_lights': [ [2],
[2],
[2],
[2],
[2],
[2],
[2],
[2],
[2],
[2],
[2],
[2],
[2],
[2],
[2],
[2],
[2],
[2],
[2],
[2],
[2],
[2]],
'nonpulsed_lights_brightness': [ [ 'light_intensity'],
[ 'light_intensity'],
[0],
[ 'light_intensity'],
[ 'light_intensity'],
[0],
[ 'light_intensity'],
[ 'light_intensity'],
[0],
[ 'light_intensity'],
[ 'light_intensity'],
[0],
[ 'light_intensity'],
[ 'light_intensity'],
[0],
[ 'light_intensity'],
[ 'light_intensity'],
[0],
[ 'light_intensity'],
[ 'light_intensity'],
[0],
[ 'light_intensity']],
'protocols_delay': 1,
'pulse_distance': [ 1500,
1500,
1500,
1500,
1500,
1500,
1500,
1500,
1500,
1500,
1500,
1500,
1500,
1500,
1500,
1500,
1500,
1500,
1500,
1500,
1500,
1500],
'pulse_length': [ ['a_d3'],
['a_d3'],
['a_d3'],
['a_d3'],
['a_d3'],
['a_d3'],
['a_d3'],
['a_d3'],
['a_d3'],
['a_d3'],
['a_d3'],
['a_d3'],
['a_d3'],
['a_d3'],
['a_d3'],
['a_d3'],
['a_d3'],
['a_d3'],
['a_d3'],
['a_d3'],
['a_d3'],
['a_d3']],
'pulsed_lights': [ [8],
[8],
[8],
[8],
[8],
[8],
[8],
[8],
[8],
[8],
[8],
[8],
[8],
[8],
[8],
[8],
[8],
[8],
[8],
[8],
[8],
[8]],
'pulsed_lights_brightness': [ ['a_b3'],
['a_b3'],
['a_b3'],
['a_b3'],
['a_b3'],
['a_b3'],
['a_b3'],
['a_b3'],
['a_b3'],
['a_b3'],
['a_b3'],
['a_b3'],
['a_b3'],
['a_b3'],
['a_b3'],
['a_b3'],
['a_b3'],
['a_b3'],
['a_b3'],
['a_b3'],
['a_b3'],
['a_b3']],
'pulses': [ 100,
100,
20,
100,
100,
20,
100,
100,
20,
100,
100,
20,
100,
100,
20,
100,
100,
20,
100,
100,
20,
100]},
{ 'averages': 1,
'detectors': [ [1, 1],
[1, 1],
[1, 1],
[1, 1],
[1, 1],
[1, 1],
[1, 1],
[0],
[1, 1],
[1, 1],
[1, 1],
[1, 1],
[1, 1],
[1, 1]],
'environmental': [ ['previous_light_intensity'],
[ 'temperature_humidity_pressure'],
[ 'temperature_humidity_pressure2'],
['contactless_temp'],
['thickness'],
['compass_and_angle']],
'label': 'PAM',
'nonpulsed_lights': [ [2],
[2],
[2],
[2],
[2],
[2],
[2],
[9],
[0],
[2],
[2],
[2],
[2],
[2]],
'nonpulsed_lights_brightness': [ [ 'light_intensity'],
[8000],
[7000],
[6000],
[5000],
[4000],
[0],
[2090],
[0],
[8000],
[6000],
[4000],
[3000],
[ 'light_intensity']],
'pulse_distance': [ 5000,
5000,
5000,
5000,
5000,
5000,
5000,
5000,
5000,
5000,
5000,
5000,
5000],
'pulse_length': [ [30, 'a_d3'],
[30, 'a_d3'],
[30, 'a_d3'],
[30, 'a_d3'],
[30, 'a_d3'],
[30, 'a_d3'],
[30, 'a_d3'],
[0],
[30, 'a_d3'],
[30, 'a_d3'],
[30, 'a_d3'],
[30, 'a_d3'],
[30, 'a_d3'],
[30, 'a_d3']],
'pulsed_lights': [ [3, 8],
[3, 8],
[3, 8],
[3, 8],
[3, 8],
[3, 8],
[3, 8],
[0],
[3, 8],
[3, 8],
[3, 8],
[3, 8],
[3, 8],
[3, 8]],
'pulsed_lights_brightness': [ [ 400,
'auto_bright3'],
[ 400,
'auto_bright3'],
[ 400,
'auto_bright3'],
[ 400,
'auto_bright3'],
[ 400,
'auto_bright3'],
[ 400,
'auto_bright3'],
[ 400,
'auto_bright3'],
[0],
[ 400,
'auto_bright3'],
[ 400,
'auto_bright3'],
[ 400,
'auto_bright3'],
[ 400,
'auto_bright3'],
[ 400,
'auto_bright3'],
[ 400,
'auto_bright3']],
'pulses': [ 100,
30,
15,
15,
15,
15,
15,
600,
15,
30,
15,
15,
15,
15]},
{ 'averages': 1,
'environmental': [ ['light_intensity'],
[ 'temperature_humidity_pressure'],
[ 'temperature_humidity_pressure2'],
['contactless_temp'],
['thickness'],
['compass_and_angle']],
'label': 'SPAD',
'spad': [1]}]}]
Analysis¶
Usage¶
Analysis Example (requires
JII-MultispeQ package)¶from jii_multispeq import measurement as _measurement
from jii_multispeq_protocols.protocols import rides as _rides
## Take a measurement using the MultispeQ
data, crc32 = _measurement.measure(port="<Selected Port>", protocol=_rides, filename=None, notes="")
## The analyze function of JII-MultispeQ helps to provide the correct format
output = _measurement.analyze( data, _rides._analyze )
## View Analysis output (as table)
_measurement.view( output )
Function Details¶
- _analyze(_data)[source]
Data evaluation of RIDES
by: David M. Kramer created: 2017-05-09 @ 18:15:27
Example Data¶
Parameter |
Value |
|---|---|
Ambient Humidity |
35.835 |
Ambient Pressure |
979.568 |
Ambient Temperature |
23.7 |
device_battery |
93 |
device_firmware |
2.21 |
device_id |
00:00:04:32 |
device_name |
MultispeQ |
device_version |
2 |
FmPrime |
3805.0 |
FoPrime |
1265 |
Fs |
1261.67 |
FvP_over_FmP |
0.668 |
kP700 |
129653.6993 |
Leaf Temperature |
25.53 |
Leaf Temperature Differenial |
1.83 |
Leaf Temperature Differential |
1.83 |
leaf_thickness |
0.3 |
LEF |
4.33 |
Light Intensity (PAR) |
14.403 |
NPQt |
1.43 |
P700_DIRK_ampl |
0.00029 |
Phi2 |
0.668 |
PhiNO |
0.136 |
PhiNPQ |
0.195 |
PS1 Active Centers |
6.64 |
PS1 Open Centers |
0.922 |
PS1 Over Reduced Centers |
0.184 |
PS1 Oxidized Centers |
-0.106 |
qL |
1.004 |
SPAD |
42.726 |
tP700 |
0.0 |
v_initial_P700 |
37.5995728 |
Figure: Recorded or calculated trace for air_temp_kinetics.¶
Figure: Recorded or calculated trace for data_raw_PAM.¶
Figure: Recorded or calculated trace for humidity2_K.¶
Figure: Recorded or calculated trace for humidity_K.¶
Figure: Recorded or calculated trace for LEAF_temp.¶
Figure: Recorded or calculated trace for LEFd_trace.¶
Figure: Recorded or calculated trace for P700_fitinput.¶
Figure: Recorded or calculated trace for P700_outdata.¶
Figure: Recorded or calculated trace for PSI_data_absorbance.¶