neptoon.quality_control

saqc_methods_and_params

Classes:

• QAMethod
• QATarget
• ParameterSpec
• MethodParameters
• AboveN0Parameters
• BelowFactorofN0Parameters
• RangeCheckParameters
• UniLOFParameters
• SpikeZScoreParameters
• SpikeOffsetParameters
• WhatParamsDoINeed
• ParameterRegistry
• QAConfigRegistry

Functions:

• saqc_method
• variant
• show_required_params
• show_optional_params
• show_link_to_site
• show_all_params
• get_parameter_class
• get_target
• get_method

QAMethod

Bases: Enum

The methods that can be selected in neptoon. Methods are implemented using SaQC.

For methods that use the same underlying SaQC function but with different configurations (like ABOVE_N0 and BELOW_N0_FACTOR both using flagGeneric), we use a tuple to store both the SaQC method and a discriminator.

saqc_method property

saqc_method

Returns the underlying SaQC method name.

variant property

variant

Returns the variant discriminator if any.

QATarget

Bases: Enum

The target data for the quality assessment selection.

ParameterSpec dataclass

ParameterSpec(name, description, optional=False, units=None, default=None, saqc_name=None)

Specification for a single parameter.

Attributes:

Name	Type	Description
name	str	Parameter name
description	str	Parameter description
units	Optional[str]	Parameter units (if applicable)
default	Any	Default value (if optional)

MethodParameters

Base class for method parameter specifications. Subclasses define parameter requirements for each method.

BelowFactorofN0Parameters

Bases: MethodParameters

Parameter specifications for below N0 factor check method.

RangeCheckParameters

Bases: MethodParameters

Parameter specifications for range check method.

UniLOFParameters

Bases: MethodParameters

Parameter specifications for range check method.

WhatParamsDoINeed

WhatParamsDoINeed(method)

Helper class for discovering parameter requirements for QA methods.

Parameters:

Name	Type	Description	Default
method	SaQCMethodMap	The quality assessment method to investigate	required

Example

from neptoon.quality_control import WhatParamsDoINeed, QAMethod

WhatParamsDoINeed(QAMethod.RANGE_CHECK)

show_required_params

show_required_params()

Display essential parameters for the method.

show_optional_params

show_optional_params()

Display optional parameters for the method.

show_link_to_site

show_link_to_site()

Adds a link to the SaQC documentation

show_all_params

show_all_params()

Display the params for the method.

ParameterRegistry

Central registry for mapping quality assessment methods to their parameter types.

This class manages the relationships between methods and their parameter specifications, providing type safety and validation.

get_parameter_class classmethod

get_parameter_class(method)

Get the parameter class for a given method.

Parameters:

Name	Type	Description	Default
method	SaQCMethodMap	The quality assessment method	required

Returns:

Type	Description
Type[BaseParameters]	The corresponding parameter class

Raises:

Type	Description
KeyError	If the method is not registered

QAConfigRegistry

Registry system for mapping strings as found in the configuration file to specific QATarget and QAMethods.