Electronic Offsets Calibration¶
new electronic offsets calibration
2230
Basic Usage¶
## Import electronic_offsets_calibration
from jii_multispeq_protocols.protocols.calibrations import electronic_offsets_calibration as _electronic_offsets_calibration
Sequence¶
%%{
init: {
"theme": "base",
"themeVariables": {"primaryColor": "#49e06d", "primaryTextColor": "#005e5e", "primaryBorderColor": "#005e5e", "lineColor": "#fff381", "secondaryColor": "#afd7f4", "tertiaryColor": "#D7EBF9"}
}
}%%
flowchart TD
START((Start))
A0["`**test**`"]:::protocol
START ==> A0
A1["`**test**
Runs only during *first* repeat`"]:::protocol
A0 ==> A1
A2["`**Protocol**`"]:::protocol
A1 ==> A2
A3["`**card_1**
*Detector:*
• 700nm - 1150nm
• 400nm - 700nm (BG18)
*Pulsed LEDs:*
• 530nm (Main)
• 950nm (Clamp)
*Non Pulsed LED:* 655nm (Main)`"]:::protocol
A2 ==> A3
A4["`**test**`"]:::protocol
A3 ==> A4
A5["`**card_9**
*Detector:*
• 700nm - 1150nm
• 400nm - 700nm (BG18)
*Pulsed LEDs:*
• 530nm (Main)
• 950nm (Clamp)
*Non Pulsed LED:* 655nm (Main)`"]:::protocol
A4 ==> A5
A6["`**test**`"]:::protocol
A5 ==> A6
A7["`**cards_1_9**
*Detector:*
• 700nm - 1150nm
• 400nm - 700nm (BG18)
*Pulsed LEDs:*
• 530nm (Main)
• 950nm (Clamp)
*Non Pulsed LED:* 655nm (Main)`"]:::protocol
A6 ==> A7
A7 ==> END
A7 -.-> |1x| A0
linkStyle 9 stroke-width:3px
END(( End ))
classDef protocol text-align:left,white-space:pre;
Details¶
Code¶
[ { '_protocol_set_': [ {'label': 'test'},
{ 'alert': 'Clamp panel #1 (white) of the '
'Chlorophyll calibration cards',
'bleed_correction': 0,
'do_once': 1,
'label': 'test',
'set_detector_offsets': [[1, 0], [3, 0]]},
{ 'autogain': [ [1, 6, 1, 10, 10000],
[2, 6, 1, 20, 20000],
[3, 6, 1, 20, 30000],
[4, 6, 1, 40, 40000],
[5, 1, 3, 40, 5000],
[6, 1, 3, 40, 10000],
[7, 1, 3, 40, 15000],
[8, 1, 3, 40, 20000]]},
{ 'detectors': [[1, 3], [1, 3], [1, 3], [1, 3]],
'label': 'card_1',
'nonpulsed_lights': [[2], [2], [2], [2]],
'nonpulsed_lights_brightness': [ [0],
[0],
[0],
[0]],
'protocol_averages': 1,
'protocol_repeats': 1,
'pulse_distance': [4000, 4000, 4000, 4000],
'pulse_length': [ ['a_d1', 'a_d5'],
['a_d2', 'a_d6'],
['a_d3', 'a_d7'],
['a_d4', 'a_d8']],
'pulsed_lights': [[6, 1], [6, 1], [6, 1], [6, 1]],
'pulsed_lights_brightness': [ ['a_b1', 'a_b5'],
['a_b2', 'a_b6'],
['a_b3', 'a_b7'],
['a_b4', 'a_b8']],
'pulses': [10, 10, 10, 10]},
{ 'alert': 'Clamp panel #9 (white) of the '
'Chlorophyll calibration cards',
'label': 'test'},
{ 'detectors': [[1, 3], [1, 3], [1, 3], [1, 3]],
'label': 'card_9',
'nonpulsed_lights': [[2], [2], [2], [2]],
'nonpulsed_lights_brightness': [ [0],
[0],
[0],
[0]],
'protocol_averages': 1,
'protocol_repeats': 1,
'pulse_distance': [4000, 4000, 4000, 4000],
'pulse_length': [ ['a_d1', 'a_d5'],
['a_d2', 'a_d6'],
['a_d3', 'a_d7'],
['a_d4', 'a_d8']],
'pulsed_lights': [[6, 1], [6, 1], [6, 1], [6, 1]],
'pulsed_lights_brightness': [ ['a_b1', 'a_b5'],
['a_b2', 'a_b6'],
['a_b3', 'a_b7'],
['a_b4', 'a_b8']],
'pulses': [10, 10, 10, 10]},
{ 'alert': 'Clamp panel #1 (white) and #9 (white) '
'of BOTH Chlorophyll calibration cards',
'label': 'test'},
{ 'detectors': [[1, 3], [1, 3], [1, 3], [1, 3]],
'label': 'cards_1_9',
'nonpulsed_lights': [[2], [2], [2], [2]],
'nonpulsed_lights_brightness': [ [0],
[0],
[0],
[0]],
'protocol_averages': 1,
'protocol_repeats': 1,
'pulse_distance': [4000, 4000, 4000, 4000],
'pulse_length': [ ['a_d1', 'a_d5'],
['a_d2', 'a_d6'],
['a_d3', 'a_d7'],
['a_d4', 'a_d8']],
'pulsed_lights': [[6, 1], [6, 1], [6, 1], [6, 1]],
'pulsed_lights_brightness': [ ['a_b1', 'a_b5'],
['a_b2', 'a_b6'],
['a_b3', 'a_b7'],
['a_b4', 'a_b8']],
'pulses': [10, 10, 10, 10]}],
'set_repeats': 1,
'v_arrays': [ [-120, -150, -180, -200, -300, -400],
[-30, -40, -60, -100, -120]]}]
Analysis¶
Usage¶
JII-MultispeQ package)¶from jii_multispeq import measurement as _measurement
from jii_multispeq_protocols.protocols.calibrations import electronic_offsets_calibration as _electronic_offsets_calibration
## Take a measurement using the MultispeQ
data, crc32 = _measurement.measure(port="<Selected Port>", protocol=_electronic_offsets_calibration, filename=None, notes="")
## The analyze function of JII-MultispeQ helps to provide the correct format
output = _measurement.analyze( data, _electronic_offsets_calibration._analyze )
## View Analysis output (as table)
_measurement.view( output )
Function Details¶
- _analyze(_data)[source]
Macro for data evaluation on PhotosynQ.org
by: David M. Kramer
created: May 31, 2020 9:31 AM
This protocol tests for offsets in detectors 1 and 3 by comparing measured transmission values usingtaken with the same settings, but with three different transmission card setups. Plotting these against the first should give a series of lines that intersect at the data offset point.
The protocol sends the offset values back to the toDevice to be used in subtracting off offsets.
Example Data¶
Parameter |
Value |
|---|---|
det3 |
[[4991, 4991, 4993, 4991, 4983, 4982, 4989, 4996, 5001, 4989, 9078, 9085, 9075, 9077, 9082, 9081, 9079, 9081, 9081, 9070, 14447, 14445, 14441, 14450, 14461, 14455, 14447, 14451, 14446, 14454, 19610, 19599, 19611, 19615, 19606, 19607, 19614, 19609, 19605, 19616], [883, 879, 883, 880, 883, 877, 879, 885, 880, 879, 1654, 1653, 1655, 1650, 1650, 1652, 1649, 1655, 1651, 1655, 2685, 2682, 2683, 2682, 2681, 2685, 2686, 2682, 2683, 2681, 3685, 3686, 3689, 3685, 3682, 3688, 3685, 3690, 3687, 3687], [271, 274, 270, 271, 275, 273, 270, 275, 270, 271, 539, 544, 538, 541, 542, 538, 539, 543, 538, 539, 899, 903, 905, 903, 899, 898, 900, 899, 902, 900, 1252, 1251, 1251, 1251, 1255, 1249, 1252, 1255, 1251, 1251]] |
device_battery |
100 |
device_firmware |
2.3433 |
device_id |
52:00:06:f0 |
device_name |
MultispeQ |
device_version |
2 |
offset_det_1 |
33.0 |
offset_det_3 |
148.0 |
r2_det_1_1_v_1_9 |
0.747668 |
r2_det_1_1_v_9 |
0.7302349 |
r2_det_3_1_v_1_9 |
0.9999111 |
r2_det_3_1_v_9 |
0.9999567 |
time |
1600105494848 |
toDevice |
set_detector_offset+1+33.0+set_detector_offset+3+148.0+ |
Figure: Recorded or calculated trace for card_1_data_det_1.¶
Figure: Recorded or calculated trace for card_1_data_det_3.¶
Figure: Recorded or calculated trace for card_9_data_det_1.¶