Test devices

PBR

class app.workspace.devices.PSI.test.classes.PBR.PBR(*args, **kwargs)

Bases: Connector

Commands:

  • “1”: self.get_temp_settings,

  • “2”: self.get_temp,

  • “3”: self.set_temp,

  • “4”: self.get_ph,

  • “5”: self.measure_od,

  • “6”: self.get_pump_params,

  • “7”: self.set_pump_params,

  • “8”: self.set_pump_state,

  • “9”: self.get_light_intensity,

  • “10”: self.set_light_intensity,

  • “11”: self.turn_on_light,

  • “12”: self.get_pwm_settings,

  • “13”: self.set_pwm,

  • “14”: self.get_o2,

  • “15”: self.set_thermoregulator_state,

  • “16”: self.measure_ft,

  • “17”: self.get_co2,

  • “18”: self.measure_all,

  • “19”: self.measure_AUX,

  • “20”: self.flash_LED,

  • “21”: self.get_hardware_address,

  • “22”: self.get_cluster_name

disconnect() → None

Terminate the connection between the application and physical device.

flash_LED()

Triggers a flashing sequence and is used to physically identify the PBR.

Returns

True if was successful, False otherwise

get_cluster_name()

The name of the bioreactor array / cluster.

Returns

the cluster name

get_co2(raw=True, repeats=5)

Measure dissolved CO2 concentration.

Parameters

  • raw – True for raw data, False for calibrated data

  • repeats – the number of measurement repeats

Returns

averaged CO2 concentration

get_hardware_address()

Get the MAC address of the PBR.

Returns

the MAC address

get_light_intensity(attribute)

Checks for current (max?) light intensity.

Items:

  • “intensity”: current light intensity (float) in μE,

  • “max”: maximal intensity (float) in μE,

  • “on”: True if light is turned on (bool)

Parameters

attribute – Given attribute ID

Returns

The current settings structured in a dictionary.

get_o2(raw=True, repeats=5, wait=0)

Checks for concentration of dissociated O2.

Items:

  • “pulse”: current stirring in %,

  • “min”: minimal stirring in %,

  • “max”: maximal stirring in %,

  • “on”: True if stirring is turned on (bool)

Parameters

  • raw – True for raw data, False for data calculated according to temperature calibration

  • repeats – the number of measurement repeats

  • wait – waiting time between individual repeats

Returns

The current settings structured in a dictionary.

get_ph(repeats=5, wait=0)

Get current pH (dimensionless.)

Parameters

  • repeats – the number of measurement repeats

  • wait – waiting time between individual repeats

Returns

The current pH.

get_pump_params(pump)

Get parameters for given pump.

Parameters

pump – Given pump

Returns

The current settings structured in a dictionary.

get_pwm_settings()

Checks for current stirring settings.

Items:

  • “pulse”: current stirring in %,

  • “min”: minimal stirring in %,

  • “max”: maximal stirring in %,

  • “on”: True if stirring is turned on (bool)

Returns

The current settings structured in a dictionary.

get_temp()

Get current temperature in Celsius degree.

Returns

The current temperature.

get_temp_settings()

Get information about currently set temperature, maximal and minimal allowed temperature.

Returns

The current settings structured in a dictionary.

get_thermoregulator_settings()

Get current settings of thermoregulator.

Items:

  • “temp”: current temperature in Celsius degrees,

  • “min”: minimal allowed temperature,

  • “max”: maximal allowed temperature,

  • “on”: state of thermoregulator (1 -> on, 0 -> freeze, -1 -> off)

Returns

The current settings structured in a dictionary.

measure_AUX(attribute)

Values of AUX auxiliary input voltage.

Parameters

attribute –

???

Returns

???

measure_all(ft_attribute=5, pump_id=5)

Measures all basic measurable values.

Parameters

  • ft_attribute – attribute for ft_measure

  • pump_id – id of particular pump

Returns

dictionary of all measured values

measure_ft(attribute)

Measure steady-state terminal fluorescence.

Parameters

attribute – 0 -> blue (455 nm) measuring LEDs, 1 -> red (627 nm) measuring LEDs

Returns

fluorescence value in arbitrary units

measure_od(attribute=0, repeats=5)

Measure current Optical Density (OD, dimensionless).

Parameters

  • attribute – which attribute should be measured

  • repeats – the number of measurement repeats

Returns

Measured OD

set_light_intensity(attribute, intensity)

Control LED panel on photobioreactor.

Parameters

  • attribute – Given attribute (0 for red light, 1 for blue light)

  • intensity – Desired intensity

Returns

True if was successful, False otherwise.

set_pump_params(pump, direction, flow)

Set up the rotation direction and flow for given pump.

Parameters

  • pump – Given pump

  • direction – Rotation direction (1 right, -1 left)

  • flow – Desired flow rate

Returns

True if was successful, False otherwise.

set_pump_state(pump, on)

Turns on/off given pump.

Parameters

  • pump – ID of a pump

  • on – True to turn on, False to turn off

Returns

True if was successful, False otherwise.

set_pwm(value, on)

Set stirring settings.

Parameters

  • value – desired stirring pulse

  • on – True turns on, False turns off

Returns

True if was successful, False otherwise.

set_ratio_light_intensity(intensity, ratio=0.5)

Set target light intensity as a sum of red and blue lights, mixed according to given ratio.

Parameters

  • intensity – target light intensity

  • ratio – (red/ratio) == (blue/(1-ratio))

Returns

True if both were successful, False otherwise.

set_temp(temp)

Set desired temperature in Celsius degree.

Parameters

temp – The temperature.

Returns

True if was successful, False otherwise.

set_thermoregulator_state(on)

Set state of thermoregulator.

Parameters

on – 1 -> on, 0 -> freeze, -1 -> off

Returns

True if was successful, False otherwise.

test_connection() → bool

Test the connection between the application and physical device.

turn_on_light(attribute, on)

Turn on/off LED panel on photobioreactor.

Parameters

  • attribute – Given attribute

  • on – True turns on, False turns off

Returns

True if was successful, False otherwise.

app.workspace.devices.PSI.test.classes.PBR.random() → x in the interval [0, 1).

GAS

class app.workspace.devices.PSI.test.classes.GAS.GAS(*args, **kwargs)

Bases: Connector

Commands:

  • “1”: self.get_flow,

  • “2”: self.get_flow_target,

  • “3”: self.set_flow_target,

  • “4”: self.get_flow_max,

  • “5”: self.get_pressure,

  • “6”: self.measure_all,

  • “7”: self.get_co2_air,

  • “8”: self.get_small_valves,

  • “9”: self.set_small_valves,

disconnect() → None

Terminate the connection between the application and physical device.

get_co2_air()

Measures CO2 in air.

Returns

measured CO2 in air

get_flow(repeats)

Actual flow being send from GAS to the PBR.

Parameters

repeats – the number of measurement repeats

Returns

The current flow in L/min.

get_flow_max()

Maximal allowed flow.

Returns

The maximal flow in L/min

get_flow_target()

Actual desired flow.

Returns

The desired flow in L/min.

get_pressure(repeats=5, wait=0)

Current pressure.

Parameters

  • repeats – the number of measurement repeats

  • wait – waiting time between individual repeats

Returns

Current pressure in ???

get_small_valves()

Obtain settings of individual vents of GAS device.

Represented as one byte, where first 6 bits represent vents indexed as in a picture scheme available here: https://i.imgur.com/jSeFFaO.jpg

Returns

byte representation of vents settings.

measure_all()

Measures all basic measurable values.

Returns

dictionary of all measured values

set_flow_target(flow)

Set flow we want to achieve.

Parameters

flow – flow in L/min we want to achieve (max given by get_flow_max)

Returns

True if was successful, False otherwise.

set_small_valves(mode)

Changes settings of individual vents of GAS device.

Can be set by one byte (converted to int), where first 6 bits represent vents indexed as in a picture scheme available here: https://i.imgur.com/jSeFFaO.jpg

Mode 0 - normal mode, output from GMS goes to PBR (255) Mode 1 - reset mode, N2 (nitrogen) goes to PBR (239) Mode 2 - no gas input to PBR (249) Mode 3 - output of PBR goes to input of PBR (246)

Parameters

mode – chosen mode (0 to 3)

Returns

True if was successful, False otherwise.

test_connection() → bool

Test the connection between the application and physical device.

GMS

class app.workspace.devices.PSI.test.classes.GMS.GMS(*args, **kwargs)

Bases: Connector

Commands:

  • “1”: self.get_info,

  • “2”: self.get_valve_flow,

  • “3”: self.set_valve_flow,

disconnect() → None

Terminate the connection between the application and physical device.

get_valve_flow(valve)

Get value (L/min) of current flow in the given valve.

Parameters

valve – ID of the valve (0 for CO2, 1 for Air)

Returns

The current settings of the valve flow and actual value, both in (L/min).

get_valve_info(valve)

Gives information about the valve

Parameters

valve – ID of the valve (0 for CO2, 1 for Air)

Returns

A dictionary with gas type and maximal allowed flow.

set_valve_flow(valve, value)

Set value (L/min) of current flow in the given valve.

Parameters

  • valve – ID of the valve (0 for CO2, 1 for Air)

  • value – desired value for valve flow in (L/min).

Returns

True if was successful, False otherwise.

test_connection() → bool

Test the connection between the application and physical device.