SIA Configuration¶
System configuration and parameter management.
dataclass
¶
SIConfig(waste_port: int = 1, air_port: int = 2, di_port: int = 3, transfer_port: int = 4, meoh_port: int = 5, naoh_port: int = 6, buffer_port: int = 7, sample_port: int = 8, wash_vial: int = 48, dry_vial: int = 49, waste_vial: int = 50, cleaning_solution_vial: int = 47, default_bubble_volume: int = 15, default_transfer_line_volume: int = 600, default_holding_coil_volume: int = 1000, default_needle_flush: int = 50, default_cleaning_solution_volume: int = 350, default_air_flush: int = 30, default_homogenization_volume: int = 320, speed_air: int = 5000, speed_fast: int = 3500, speed_normal: int = 2000, speed_slow: int = 1500, speed_cleaning: int = 2500, speed_homogenization_aspirate: int = 2000, speed_homogenization_dispense: int = 2000, homogenization_liquid_cycles: int = 2, homogenization_air_cycles: int = 3, homogenization_clean_after: bool = False, wait_vial_load: float = 2.0, wait_vial_unload: float = 1.0, wait_after_aspirate: float = 1.0, wait_after_dispense: float = 0.5, wait_homogenization_settle: float = 5.0, wait_cleaning_reaction: float = 3.0, verbose: bool = True)
Complete configuration for SI (Sequential Injection) system.
This dataclass contains all adjustable parameters organized into logical groups. All parameters have sensible defaults that work for most applications, but can be customized as needed.
The configuration covers: - Port assignments for different reagents and functions - Standard vial positions for system components - Volume parameters for various operations - Speed settings for different types of flows - Timing parameters for system operations - Homogenization settings - Display and logging preferences
Attributes are grouped logically and documented individually below.
Attributes¶
class-attribute
instance-attribute
¶
Port connected to waste line (typically port 1)
class-attribute
instance-attribute
¶
Port for air aspiration (typically port 2)
class-attribute
instance-attribute
¶
Port connected to deionized water reservoir (typically port 3)
class-attribute
instance-attribute
¶
Port connected to transfer line leading to sample needle (typically port 4)
class-attribute
instance-attribute
¶
Port connected to methanol reservoir for cleaning (typically port 5)
class-attribute
instance-attribute
¶
Port connected to sodium hydroxide solution for cleaning (typically port 6)
class-attribute
instance-attribute
¶
Port connected to buffer solution reservoir (typically port 7)
class-attribute
instance-attribute
¶
Port connected to sample input line (typically port 8)
class-attribute
instance-attribute
¶
Carousel position for needle wash vial (contains wash solution)
class-attribute
instance-attribute
¶
Carousel position for dry/empty vial (for air aspiration if needed)
class-attribute
instance-attribute
¶
Carousel position for waste collection vial
class-attribute
instance-attribute
¶
Carousel position for cleaning solution vial (e.g., NaOH solution)
class-attribute
instance-attribute
¶
Default volume for separating air bubbles between different solutions (µL)
class-attribute
instance-attribute
¶
Volume of the transfer line from valve to sample needle (µL)
class-attribute
instance-attribute
¶
Volume of the holding coil in the flow injection system (µL)
class-attribute
instance-attribute
¶
Default volume for flushing the sample needle to prevent contamination (µL)
class-attribute
instance-attribute
¶
Default volume of cleaning solution (e.g., NaOH) for system cleaning (µL)
class-attribute
instance-attribute
¶
Default volume of air for flushing operations (µL)
class-attribute
instance-attribute
¶
Default volume to aspirate/dispense during sample homogenization (µL)
class-attribute
instance-attribute
¶
High speed for air aspiration and fast transfers (µL/min)
class-attribute
instance-attribute
¶
Fast flow rate for routine liquid transfers (µL/min)
class-attribute
instance-attribute
¶
Normal flow rate for standard operations (µL/min)
class-attribute
instance-attribute
¶
Slow flow rate for precise operations or viscous liquids (µL/min)
class-attribute
instance-attribute
¶
Flow rate for cleaning operations (µL/min)
class-attribute
instance-attribute
¶
Flow rate for aspirating during sample homogenization (µL/min)
class-attribute
instance-attribute
¶
Flow rate for dispensing during sample homogenization (µL/min)
class-attribute
instance-attribute
¶
Number of aspiration/dispense cycles for liquid-based homogenization
class-attribute
instance-attribute
¶
Number of aspiration/dispense cycles for air bubble-based homogenization
class-attribute
instance-attribute
¶
Whether to automatically clean the transfer line after homogenization
class-attribute
instance-attribute
¶
Wait time after loading a vial to replenishment position (seconds)
class-attribute
instance-attribute
¶
Wait time after unloading a vial from replenishment position (seconds)
class-attribute
instance-attribute
¶
Wait time after liquid aspiration for system stabilization (seconds)
class-attribute
instance-attribute
¶
Wait time after liquid dispensing for system stabilization (seconds)
class-attribute
instance-attribute
¶
Wait time for sample settling during homogenization operations (seconds)
class-attribute
instance-attribute
¶
Wait time for cleaning solution to react before flushing (seconds)
class-attribute
instance-attribute
¶
Global verbose setting - controls whether status messages are displayed
Configuration Functions¶
Configuration management for SI (Sequential Injection) system.
This module provides centralized configuration for all adjustable parameters used in SI workflows. The SIConfig dataclass contains all system parameters organized into logical groups for easy maintenance and customization.
Example
from config import SIConfig, DEFAULT_CONFIG
Use default configuration¶
config = DEFAULT_CONFIG
Create custom configuration¶
custom_config = SIAConfig( ... speed_normal=1800, ... verbose=False, ... homogenization_liquid_cycles=3 ... )
Modify existing configuration¶
config.speed_fast = 4000 config.default_bubble_volume = 20
Functions¶
Validate a SIConfig instance and return any issues found.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
config
|
The SIConfig instance to validate |
required |
Returns:
| Type | Description |
|---|---|
list
|
List of validation error messages (empty if no issues) |
Example
config = SIConfig(speed_normal=-100) # Invalid negative speed errors = validate_config(config) if errors: ... print("Configuration issues:", errors)
Create a SIConfig instance from a dictionary.
Useful for loading configuration from JSON files or other sources. Unknown keys in the dictionary are ignored.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
config_dict
|
dict
|
Dictionary with configuration parameters |
required |
Returns:
| Type | Description |
|---|---|
SIConfig
|
New SIConfig instance with specified parameters |
Example
config_data = { ... 'speed_normal': 1800, ... 'verbose': False, ... 'default_bubble_volume': 20 ... } config = create_config_from_dict(config_data)
Convert a SIConfig instance to a dictionary.
Useful for saving configuration to JSON files or other formats.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
config
|
SIConfig
|
The SIConfig instance to convert |
required |
Returns:
| Type | Description |
|---|---|
dict
|
Dictionary representation of the configuration |
Example
config = SIConfig(speed_normal=1800) config_dict = config_to_dict(config) import json json.dump(config_dict, open('config.json', 'w'), indent=2)
Create a configuration optimized for high-throughput operations.
This preset uses faster flow rates and shorter wait times to maximize sample processing speed, at the cost of some precision.
Returns:
| Type | Description |
|---|---|
SIConfig
|
SIConfig instance optimized for speed |
Create a configuration optimized for high-precision operations.
This preset uses slower flow rates and longer wait times to maximize precision and reproducibility, at the cost of throughput.
Returns:
| Type | Description |
|---|---|
SIConfig
|
SIConfig instance optimized for precision |
Create a configuration with enhanced cleaning procedures.
This preset includes more thorough cleaning steps and larger cleaning volumes, suitable for applications requiring minimal cross-contamination.
Returns:
| Type | Description |
|---|---|
SIConfig
|
SIConfig instance with enhanced cleaning |