Syntax¶

Automatically Generated

This part of the documentation is automatically generated from the schema file used for validating protocols following the 2020-12 draft. For more detailed information on protocols, please refer the documentation by PhotosynQ, Inc.

_protocol_set_¶

Treating protocols as integrated sets

## Code Example
_protocol_set_: [
  {
    "label": "PAM"
  },
  {
    "label": "ECS"
  }
]

Array
- Object
- Protocol within the protocol set

adc_show¶

ADC (analog to digital converter) values are outputted in data_raw instead of the regular output

## Code Example
adc_show: 0

Integer
Values: 0, 1

autogain¶

Automatic gain control. Multiple gain functions can be added.

## Code Example
autogain: [
  [
    2,
    1,
    3,
    12,
    50000
  ],
  [
    3,
    8,
    1,
    80,
    50000
  ]
]

Array (Up to 10 items)
- Array (Exactly 5 items)
- Order and type for first 5 items (Required)
  - Integer
  - Minimum: 0
  - Maximum: 9
  - Index for storing gain settings
  - Integer
  - Minimum: 1
  - Maximum: 10
  - Select pulsed LED to test
  - Integer
  - Minimum: 1
  - Maximum: 3
  - Select detector to use
  - Number
  - Minimum: 1
  - Maximum: 65535
  - Duration in microseconds
  - Number
  - Minimum: 0
  - Maximum: 65535
  - Target Value, recommended: 40000-50000
- Automatic gain control settings

averages¶

Number of times to average the protocol (only avarage is returned)

## Code Example
averages: 3

Number
Minimum: 0
Maximum: 10000

averages_delay¶

Delay between protocol averages in ms

## Code Example
averages_delay: 2000

Number
Minimum: 0
Maximum: 999999999999

bleed_correction¶

Set to 0 to disables the application of electronic offsets corrections, otherwise set to 1 or ignore parameter

## Code Example
bleed_correction: 1

Integer
Values: 0, 1

check_battery¶

Set to 1, otherwise set to 0 or ignore parameter. Adds error message “battery low” when active and battery level is below 10%

## Code Example
check_battery: 1

Integer
Values: 0, 1

dac_lights¶

When set to 1, values of ‘pulsed_lights_brightness’ and ‘nonpulsed_lights_brightness’ are interpreted as 12-bit values (0 - 4095) controlling the DAC instead of PAR values.

## Code Example
dac_lights: 0

Integer
Values: 0, 1

detectors¶

Detectors used in measurement, data returned in data_raw

## Code Example
detectors: [
  [
    3
  ],
  [
    3
  ],
  [
    "@s0"
  ],
  [
    3
  ]
]

Array
- Array
  - String, Number
  - Input must be a number, light_intensity, previous_light_intensity, p_light, or a variable reference (@s0, @p0, @n0:1)

do_once¶

Set to 1, to execute a protocol in a repeating set only one time, otherwise set to 0

## Code Example
do_once: 1

Integer
Values: 0, 1

dw¶

Digital write to “digital_write or dw” to a specific pin number

## Code Example
dw: [
  14,
  0
]

Array
Order and type for first 2 items (Required)
- Integer
- Minimum: 0
- Maximum: 34
- Set the pin number (see: Teensy 3.2 pin layout)
- Integer
- Values: 0, 1
- Set to 1, to enable digital_write, otherwise set to 0

e_time¶

When added, returns elapsed time since timer started with (s_time) in [ms]. Value for started timer reflects time elapsed since protocol start. Format: [timer started, elapsed time]

## Code Example
e_time: 1

energy_min_wake_time¶

Adjust time between 5V shutdown and wake up time in ms

## Code Example
energy_min_wake_time: 7000

Number
Minimum: 0
Maximum: 1000000

energy_save_timeout¶

Adjust Energy Save Timeout in ms

## Code Example
energy_save_timeout: 300000

Number
Minimum: 0
Maximum: 1000000

environmental¶

## Code Example
environmental: [
  [
    "light_intensity"
  ],
  [
    "temperature_humidity_pressure"
  ],
  [
    "temperature_humidity_pressure2"
  ],
  [
    "contactless_temp"
  ],
  [
    "thickness"
  ],
  [
    "compass_and_angle"
  ]
]

Array
- Array
- Order and type for first 5 items (Required)
  - String
  - Any of the following
    - Values: light_intensity, previous_light_intensity, temperature_humidity_pressure, temperature_humidity_pressure2, thp, thp2, thickness, thickness_raw, compass_and_angle, contactless_temp
  - Number
  - Number
  - Number
  - Number
- Environmental measurement configuration

environmental_array¶

## Code Example
environmental_array: [
  [
    1
  ]
]

Array
- Array
- Order and type for first 1 item (Required)
  - Number

indicator¶

Change the color of the indicator Light (MultispeQ v2) defining the color using the channels Red, Green, Blue. The White channel needs to be defined but is ignored. All channels at 0 will turn the light off.

## Code Example #1
indicator: [
  255,
  0,
  0,
  0
]

## Code Example #2
indicator: [
  0,
  128,
  128,
  0
]

## Code Example #3
indicator: [
  0,
  0,
  0,
  0
]

Array (Exactly 4 items)
Order and type for first 4 items (Required)
- Integer
- Minimum: 0
- Maximum: 255
- Red channel
- Integer
- Minimum: 0
- Maximum: 255
- Green channel
- Integer
- Minimum: 0
- Maximum: 2550
- Blue channel
- Integer
- Minimum: 0
- Maximum: 255
- White channel

ir_baseline¶

## Code Example
ir_baseline: <input>

label¶

Provide a label to a sub-protocol

## Code Example #1
label: "PAM"

## Code Example #2
label: "ECS"

String

max_hold_time¶

Set time (in ms) at which the hold commands timeout, default is 15000

## Code Example
max_hold_time: 15000

Number

measurements¶

Number of measurement repeats, which is a set of protocols

## Code Example
measurements: 2

Number

measurements_delay¶

Delay between measurement repeats in ms

## Code Example
measurements_delay: 30

Number

message¶

Send message to user between pulse sets.

## Code Example #1
message: [
  [
    "alert",
    "Measurement noisy"
  ]
]

## Code Example #2
message: [
  [
    "prompt",
    "What is the leaf color"
  ]
]

## Code Example #3
message: [
  [
    "confirm",
    "Is the leaf clamped?"
  ]
]

Array
- Array (Exactly 2 items)
- Order and type for first 2 items (Required)
  - String
  - Values: alert, prompt, confirm
  - Message type
  - String
  - Message content

nonpulsed_lights¶

Select LEDs that are not pulsed during a pulse set

## Code Example
nonpulsed_lights: [
  [
    2,
    2,
    2,
    2
  ]
]

Array
- Array
  - String, Number
  - Input must be a number, light_intensity, previous_light_intensity, p_light, or a variable reference (@s0, @p0, @n0:1)

nonpulsed_lights_brightness¶

LED brightness in µE * s⁻¹ * m⁻² (PAR) for non pulsed lights

## Code Example
nonpulsed_lights_brightness: [
  [
    100,
    100,
    200,
    300
  ]
]

Array
- Array
  - String, Number
  - Input must be a number, light_intensity, previous_light_intensity, p_light, or a variable reference (@s0, @p0, @n0:1)

number_samples¶

Number of samples taken by the ADC (analog to digital converter)

## Code Example
number_samples: 10

Number
Minimum: 0
Maximum: 100

open_close_start¶

## Code Example
open_close_start: 1

Integer
Values: 0, 1

par_led_start_on_close¶

Ambient light intensity is measured and matched by selected LED until the clamp is closed

## Code Example
par_led_start_on_close: 2

Integer
Minimum: 1
Maximum: 10

par_led_start_on_open¶

Ambient light intensity is measured and matched by selected LED when the clamp is opened

## Code Example
par_led_start_on_open: 1

Integer
Minimum: 1
Maximum: 10

par_led_start_on_open_close¶

Ambient light intensity is measured and matched by selected LED until the clamp is closed

## Code Example
par_led_start_on_open_close: 2

Integer
Minimum: 1
Maximum: 10

pre_illumination¶

Sample illumination with a single LED at a set duration and light intensity

## Code Example #1
pre_illumination: [
  2,
  200,
  600000
]

## Code Example #2
pre_illumination: [
  [
    2,
    200,
    600000
  ],
  [
    3,
    400,
    600000
  ]
]

Only One of the following
- Array (Exactly 3 items)
- Order and type for first 3 items (Required)
  - String, Integer
  - Minimum: 1
  - Maximum: 10
  - LED for illumination
  - String, Number
  - Illumination duration in ms
  - String, Number
  - Intensity in µE * s⁻¹ * m⁻² (PAR) - Only for LEDs in the range of 400 nm - 700 nm
- Array
  - Array (Exactly 3 items)
  - Order and type for first 3 items (Required)
    - String, Integer
    - Minimum: 1
    - Maximum: 10
    - LED for illumination
    - String, Number
    - Illumination duration in ms
    - String, Number
    - Intensity in µE * s⁻¹ * m⁻² (PAR) - Only for LEDs in the range of 400 nm - 700 nm

protocol_averages¶

Sets the number of times a sub-protocol is repeated and the results are averaged

## Code Example
protocol_averages: 5

Number
Minimum: 0
Maximum: 1000000

protocol_repeats¶

## Code Example #1
protocol_repeats: 30

## Code Example #2
protocol_repeats: "@n1:1"

String, Number
Minimum: 0
Maximum: 1000000

protocols¶

## Code Example
protocols: 2

Number
Minimum: 0
Maximum: 100

protocols_delay¶

## Code Example
protocols_delay: 2000

Number
Minimum: 0
Maximum: 999999999

pulse_distance¶

## Code Example
pulse_distance: <input>

Array
- String, Number

Dependencies: pulses, pulse_length

pulse_length¶

## Code Example
pulse_length: [
  [
    20,
    20,
    20,
    20
  ]
]

Array
- Array
  - String, Number

Dependencies: pulses, pulse_distance

pulsed_lights¶

## Code Example
pulsed_lights: [
  [
    1,
    1,
    1,
    2
  ]
]

Array
- Array
  - String, Number
  - Input must be a number, light_intensity, previous_light_intensity, p_light, or a variable reference (@s0, @p0, @n0:1)

Dependencies: pulsed_lights_brightness

pulsed_lights_brightness¶

## Code Example
pulsed_lights_brightness: [
  [
    100,
    "auto_bright[1]",
    300,
    100
  ]
]

Array
- Array
  - String, Number

Dependencies: pulsed_lights

pulses¶

Pulses defines sequence the measurement pulses by the LEDs during a measurement

## Code Example
pulses: [
  10,
  10,
  50,
  "@n1:2",
  100
]

Array
- Integer, String

Dependencies: pulse_length, pulse_distance

recall¶

Load value from device memory (EEPROM) or receive device settings (settings) or device modifications (device_mod)

## Code Example #1
recall: [
  "userdef[1]"
]

## Code Example #2
recall: [
  "settings"
]

## Code Example #3
recall: [
  "device_mod"
]

Array
- String

reference¶

Specify another detector to be measured and subtracted from detector.

## Code Example #1
reference: [
  [
    1
  ]
]

## Code Example #2
reference: [
  [
    1,
    2
  ]
]

Array
- Array (Exactly 1 item)
- Order and type for first 1 item (Required)
  - Number
  - Minimum: 1
  - Maximum: 4

s_time¶

When added, starts timer to return elapesed time with (e_time) in [ms]

## Code Example
s_time: 1

save¶

Save value to device memory (EEPROM).

## Code Example
save: [
  [
    1,
    1500
  ]
]

Array
- Array (Exactly 2 items)
- Order and type for first 2 items (Required)
  - Number
  - Storage Location
  - Number
  - Value to be stored in selected location

save_trace_time_scale¶

Set to 1 to save time scale for trace as data_raw_time, otherwise set to 0.

## Code Example
save_trace_time_scale: 1

Integer
Values: 0, 1

set_led_delay¶

Set pre-illumination with a selected LED for a specific amount of time. (Multiple LEDs can be used).

## Code Example
set_led_delay: [
  [
    2,
    20000,
    0
  ],
  [
    2,
    20000,
    100
  ]
]

Array (Between 1 and 10 items)
- Array (Exactly 3 items)
- Order and type for first 3 items (Required)
  - Integer
  - Values: 1, 10
  - LED identification number
  - Number
  - Minimum: 0
  - Illumination duration in ms
  - Number
  - Values: 0, 2500
  - Light intensity in µE * s⁻¹ * m⁻² (PAR)

set_light_intensity¶

Set a constant actinic background light intensity.

## Code Example
set_light_intensity: 1500

Number
Minimum: 0
Maximum: 2500

spad¶

Measure relative Chlorophyll content (SPAD - Special Products Analysis Division)

## Code Example #1
spad: 1

## Code Example #2
spad: [
  1
]

Only One of the following
- Integer
- Values: 0, 1
- Array (Exactly 1 item)
- Order and type for first 1 item (Required)
  - Integer
  - Values: 0, 1

start_on_close¶

Set to 1, to wait for the protocol to run until clamp is closed, otherwise set to 0

## Code Example
start_on_close: 1

Integer
Values: 0, 1

start_on_open¶

Set to 1, to wait for the protocol to run until clamp is opened, otherwise set to 0

## Code Example
start_on_open: 1

Integer
Values: 0, 1

start_on_open_close¶

## Code Example
start_on_open_close: 1

Integer
Values: 0, 1

v_arrays¶

Storing variables in arrays available within the protocol

## Code Example
v_arrays: [
  [
    1,
    2
  ],
  [
    100,
    200
  ]
]

Array (Up to 10 items)
- Array (Up to 10 items)
  - String, Number
  - Input must be a number, light_intensity, previous_light_intensity, p_light, or a variable reference (@s0, @p0, @n0:1)

Definitions¶

Array: In Python, “array” is analogous to the list or tuple type, depending on usage.
Boolean: In Python, “boolean” is analogous to bool. Note that in JSON, true and false are lower case, whereas in Python they are capitalized (True and False).
Integer: In Python, “integer” is analogous to the int type.
Dependencies: When a command has dependencies, all dependent commands have to be used as well for a valid protocol and to ensure proper function.
Null: In Python, null is analogous to None.
Number: The number type is used for any numeric type, either integers or floating point numbers (int or float in Python).
Object: In Python, “objects” are analogous to the dict type. An important difference, however, is that while Python dictionaries may use anything hashable as a key, in JSON all the keys must be strings.
String: The string type, in Python str is used for strings of text. It may contain Unicode characters.