PSI devices

PBR

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

Bases: app.workspace.devices.PSI.java.abstract.java_device.JavaDevice

Photobioreactors FMT 150 feature a combination of the bench-top cultivator and computer-controlled monitoring device. The product line comprises three instruments that differ in the cultivation vessel capacity - 400 ml, 1 and 3 l. All Photobioreactor models may be supplied with a number of useful accessories that facilitate to meet wide range of special experimental conditions.

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

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=0)

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.

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.

measure_AUX(attribute)

Values of AUX auxiliary input voltage.

Parameters

attribute –

???

Returns

???

measure_all(pump_id=5)

Measures all basic measurable values.

Parameters: pump_id – id of particular pump
Returns: dictionary of all measured values

measure_ft(attribute=0)

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 – Optical path to be measured ()
repeats – The number of measurement repeats

Returns

Measured OD

measure_qy(attribute=0)

Measure steady-state terminal and maximal fluorescence and calculate quantum yield !This measure NOT to be included with measure_all

Parameters: attribute – {int} – measuring light attribute
Returns

qy {real} – quantum yield calculated as (fm-ft)/fm
ft-flash {int} – steady-state terminal fluorescence
ft-background {int} – steady-state terminal fluorescence background signal
fm-flash{int} – maximal fluorescence
fm-background {int} – maximal fluorescence background signal
sp-delay-cycles {int} – ?number of cycles before reaching stable signal?

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. For standard stirrer max (100 %) intensity is 600 rpm.

Parameters

value – desired stirring intensity in %
on – True turns on, False turns off

Returns

True if 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=0)

Set state of thermoregulator.

Parameters: on – 0 - off, 1 - on, 2 - freeze
Returns: True if was successful, False otherwise.

test_connection() → bool: Test the connection between the application and physical device.

turn_on_light(attribute=0, on=True)

Turn on/off photobioreactor LED panel.

Parameters

attribute – Given attribute
on – True turns on, False turns off

Returns

True if was successful, False otherwise.

GAS

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

Bases: app.workspace.devices.PSI.java.abstract.java_device.JavaDevice

The MS GAS is a compact benchtop gas analyzer with mass spectrometry detection designed for complex analysis of gases and volatiles including isotopes, solvents and volatile organics. Modular inlet, highly sensitive mass spectrometer and primarily unique freezing system allows continuous weeks-long operation.

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,

get_co2_air()

Measures CO2 in air.

Returns: measured CO2 in air

get_flow(repeats=5)

Actual flow being channeled from GAS to PBR.

Parameters: repeats – the number of measurements to be averaged
Returns: 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.

Returns: byte representation of vents settings.

measure_all(): Measures all basic measurable 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=0)

Changes settings of individual vents of GAS device. Can be set by one byte (converted to int), where first 6 bits represent vents.

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.java.classes.GMS.GMS(*args, **kwargs)

Bases: app.workspace.devices.PSI.java.abstract.java_device.JavaDevice

Gas Mixing System GMS 150 can produce precise mixtures of up to 4 different gases. The ﬂows of the individual input gases are measured by thermal mass ﬂow meters and adjusted by integrated mass ﬂow controllers.

Commands:

“1”: self.get_info,
“9”: self.measure_all,
“10”: self.get_valve_info,
“11”: self.get_valve_flow,
“12”: self.set_valve_flow,
“13”: self.get_device_type,
“14”: self.get_device_id,
“15”: self.get_serial_nr,
“16”: self.get_fw_ver

get_device_id(): Get device ID.

get_device_type(): Get type of device.

get_fw_ver()

get_info(): Get general information about the device.

get_serial_nr()

get_valve_flow(valve=0)

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=0)

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.

measure_all()

Measures all basic measurable values.

Returns: dictionary of all measured values

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.