Autonomous Liquid–Liquid Extraction Platform Scripts

Script groups and purposes

Group	Script	Purpose
Standard automatic pair	data_input.py	Editable configuration for experiment samples, pump inputs, cuvette positions, cleaning, hardware connections, and spectrometer mode.
Standard automatic pair	automatic_run.py	Runs the configured pump, valve, conditioning, filling, stage, cleaning, and spectrometer operations. It saves the measured spectrum without automatic peak analysis.
Automatic peak-analysis pair	data_input_with_peak_analysis.py	Editable configuration for the automatic experiment and optional spectrometer use.
Automatic peak-analysis pair	automatic_run_with_peak_analysis.py	Runs the configured fluid-handling workflow, measures every filled cuvette, performs three absorbance scans, checks clipping and spectral quality, and reports peak absorbance.
Standalone interactive workflow	interactive_experiment_workflow.py	A prompt-driven, single-file version of the integrated cleaning, experiment, stage, and spectrometer workflow. It does not use a separate data-input file. Useful for manual testing and troubleshooting.
Standalone spectrometer analysis	spec_analysis_ver3.py	Operates only the stage and spectrometer for manually filled cuvettes. It performs automatic absorbance peak and clipping analysis without operating pumps, valves, filling, cleaning, or producing graphs.

The two files in each automatic pair must be kept in the same folder.

Spectrometer modes

Script group	Absorbance	Reflectivity	Transmittance
Standard automatic pair	Yes	Yes	Yes
Automatic peak-analysis pair	Yes	No	No
interactive_experiment_workflow.py	Yes	Yes	Yes
spec_analysis_ver3.py	Yes	No	No

Automatic clipping and peak analysis require absorbance data. The standard automatic pair records the selected spectrum but does not calculate the final peak absorbance.

Hardware configuration

Hardware or connection	Configuration
Syringe pumps	Four pumps, addressed as Pumps 1–4
Pump and external-valve serial connection	COM3, 9600 baud
Pump initialisation ports	Input port 2 and output port 11
Pump output to external valve	Pump port 8
Fresh-water source	Pump port 2
External switch valve	Address 0x01, nine ports
Cuvette routes	External-valve ports 1–8 correspond to Cuvettes 1–8
Waste route	External-valve port 9
Moving stage	COM5, 115200 baud, address 1, eight channels
Stage motion	Acceleration 50; speed 200; first channel offset 15,872 pulses; remaining channel offsets 12,800 pulses each
Spectrometer	Channel 1 through FLA5000DLL.dll on Windows
Spectral range	350–950 nm at 1 nm intervals
Calibration position	Cuvette 8

Cuvette drainage connections

Cuvette	Drain pump	Pump drain port
1	4	12
2	4	10
3	3	12
4	3	10
5	2	12
6	2	10
7	1	12
8	1	10

Limitations

• Pump syringe capacity: 5 mL.
• Cuvette capacity: 4 mL.
• Spectrometer measurement volume: 3–4 mL.
• Tubing longer than approximately 75–80 cm caused insufficient suction.
• A CLIPPED result reports the highest non-clipped fallback, not the true peak. (Diluted samples tend to be caught more accurately on the spectrometer)
• Keep the light on while determining the spectrometer integration time.