Getting Started with SIA-CE¶

This guide covers installation and initial system configuration for automated capillary electrophoresis with sequential injection.

Prerequisites¶

Required Hardware¶

Agilent CE7100 or compatible CE system controlled by ChemStation
SI Components: Syringe pump and valve selector with serial communication
Serial Ports: Available COM ports for SI device communication

Required Software¶

ChemStation: OpenLab CDS ChemStation (tested on version C.01.07 SR2)
Python: Version 3.7 or higher

Installation¶

Download and Install¶

Download the package from the project repository (download link)
Extract to desired location (e.g., C:\SIA-CE\)
Install dependencies by double-clicking install.bat

The install.bat file automatically runs:

python -m pip install -e .

This installs the package and all required dependencies: pyserial, tqdm, pandas, pywin32.

Verify Installation¶

import ChemstationAPI
import SIA_API
print("Installation successful")

Recommended Development Tools¶

Code Editor¶

Visual Studio Code - Free, powerful editor with excellent Python support

Built-in terminal and debugger
Python extension for syntax highlighting and IntelliSense
Integrated Git support for version control
Extensions for Jupyter notebook support

Interactive Development¶

Jupyter Notebook - Interactive development environment, ideal for analytical workflows

Cell-by-cell execution: Test individual operations without running full scripts
Real-time monitoring: Track syringe volume, system status, and analysis progress
Documentation: Combine code, markdown notes, and results in one document
Reproducibility: Save complete workflows with outputs for later reference

ChemStation Setup¶

Load Communication Macro¶

Start ChemStation and wait for complete loading
Get macro path - run this Python code to find the exact path:

import os
import ChemstationAPI
macro_path = os.path.join(os.path.dirname(ChemstationAPI.__file__), 
                          "core", "ChemPyConnect.mac")
print(f"Load this macro: {macro_path}")

Load macro in ChemStation - copy the path from above and execute:
```
macro "C:\your\path\to\ChemPyConnect.mac"; Python_Run
```

Expected output: Start Python communication

Hardware Setup¶

Identify COM Ports¶

Before configuring devices, discover which COM ports are available:

import serial.tools.list_ports

print("Available COM ports:")
for port in serial.tools.list_ports.comports():
    print(f"{port.device}: {port.description}")

Typical device descriptions:

Syringe pump: "USB Serial Port", "FTDI USB Serial Device"
Valve selector: "USB-SERIAL CH340", "Prolific USB-to-Serial"

Configure Devices¶

from SIA_API.devices import SyringeController, ValveSelector

# Replace COM ports with your actual ports from discovery above
syringe = SyringeController(port="COM3", syringe_size=1000)  # Your syringe port
valve = ValveSelector(port="COM4", num_positions=8)          # Your valve port

# Test basic functionality
syringe.initialize()
valve.position(1)
print("Hardware configured successfully")

System Verification¶

Complete System Test¶

Run this comprehensive validation to verify all components:

def validate_system():
    """Test all system components."""

    try:
        # Test ChemStation connection
        from ChemstationAPI import ChemstationAPI
        ce = ChemstationAPI()
        status = ce.system.status()
        print(f"✓ ChemStation connected: {status}")

        # Test SI devices  
        from SIA_API.devices import SyringeController, ValveSelector
        syringe = SyringeController(port="COM3", syringe_size=1000)  # Use your port
        valve = ValveSelector(port="COM4", num_positions=8)          # Use your port

        syringe.initialize()
        print("✓ Syringe initialized")

        valve.position(1)
        print("✓ Valve positioned")

        print("✓ System validation complete - ready to use!")
        return True

    except Exception as e:
        print(f"✗ Validation failed: {e}")
        return False

# Run validation
validate_system()

Quick Troubleshooting¶

ChemStation connection fails:

Verify ChemStation is running and responsive
Check macro loading: macro "path\ChemPyConnect.mac"; Python_Run
Look for "Start Python communication" message

SI device not found:

Check COM ports in Device Manager (Windows)
Verify device power and USB cable connections
Try different COM port numbers

Import errors:

Re-run install.bat to reinstall dependencies
Check Python version: python --version (requires 3.7+)
Restart Python environment after installation