neptoon.workflow

process_with_config¶

Classes:

ProcessWithConfig
QualityAssessmentFromConfig
CorrectionSelectorFromConfig

Functions:

run_full_process
create_checks
return_a_check
select_corrections

ProcessWithConfig ¶

ProcessWithConfig(path_to_sensor_config=None, path_to_process_config=None, configuration_object=None)

Processes CRNS data according to configuration files.

This class implements the complete CRNS data processing pipeline using configurations for both sensor parameters and processing steps. It handles all stages from raw data import to final data output and visualization.

Users can provide configurations either as file paths or as a pre-configured ConfigurationManager object.

Example:

Using string paths to configuration files¶

sensor_config_path = "/path/to/configuration_files/A101_station.yaml" processing_config_path = "/path/to/configuration_files/v1_processing_method.yaml"

Initialize the processor with paths to config files¶

config_processor = ProcessWithConfig( ... path_to_sensor_config=sensor_config_path, ... path_to_process_config=processing_config_path ... )

Run the full processing pipeline¶

config_processor.run_full_process()

Alternatively, with a pre-configured ConfigurationManager:¶

config_manager = ConfigurationManager() config_manager.load_configuration(file_path=sensor_config_path) config_manager.load_configuration(file_path=processing_config_path)

Initialize using the configuration manager¶

config_processor = ProcessWithConfig(configuration_manager=config_manager) config_processor.run_full_process()

run_full_process ¶

run_full_process()

Executes the complete CRNS data processing pipeline.

This method performs the following steps in sequence:

Creates a data hub using the sensor configuration
Attaches NMDB reference data
Prepares static values and performs initial quality assessment
Applies appropriate corrections to neutron counts
Performs calibration if requested
Applies additional quality assessment and smoothing
Calculates soil moisture estimates with uncertainty bounds
Creates visualizations
Saves processed data and updated configurations

Raises:

Type	Description
`ValueError`	When no N0 calibration parameter is available and calibration is not enabled

QualityAssessmentFromConfig ¶

QualityAssessmentFromConfig(partial_config, sensor_config, name_of_target=None)

Builds quality assessment checks from configuration data.

This class translates quality assessment configuration parameters into executable QualityCheck objects that can be applied to CRNS data. It supports various check types and automatically handles parameter inheritance from sensor information (e.g., N0 values).

Parameters:

Name	Type	Description	Default
`partial_config`	`BaseConfig`	Configuration section containing quality assessment parameters	required
`sensor_config`	`BaseConfig`	Sensor configuration containing reference parameters	required
`name_of_target`	`(Literal['raw_neutrons', 'corrected_neutrons'],)`		`None`
`optional`		Specific target to process; if None, processes all targets in config	required

Attributes

Parameters:

Name	Type	Description	Default
`partial_config`	`ConfigurationObject`	A selection from the ConfigurationObject which stores QA selections	required
`sensor_config`	`ConfigurationObject`	The config object describing station variables	required
`name_of_target`	`str`	The name of the target for QA. If None it will loop through any provided in partial config.	`None`

Notes

The name_of_section should match the final part of the supplied partial_config. For example:

partial_config = ( config.process_config.neutron_quality_assessment.flag_raw_neutrons )

Therefore:

name_of_section = 'flag_raw_neutrons'

create_checks ¶

create_checks()

Creates quality check objects based on the provided configuration.

This method processes the configuration and converts it into a list of QualityCheck objects ready to be applied to data.

Returns:

Type	Description
`List[QualityCheck]`	List of configured quality check objects

return_a_check ¶

return_a_check(name_of_target, target_dict)

Process checks for a specific target.

CorrectionSelectorFromConfig ¶

CorrectionSelectorFromConfig(data_hub, process_config, sensor_config)

Selects and configures neutron count corrections based on configuration.

This class translates correction configuration parameters into the appropriate correction objects to be applied to neutron count data. It supports various correction types including pressure, humidity, incoming intensity, and above-ground biomass.

Parameters:

Name	Type	Description	Default
`data_hub`	`CRNSDataHub`	The data hub instance to which corrections will be applied	required
`process_config`	`BaseConfig`	Process configuration containing correction specifications	required
`sensor_config`	`BaseConfig`	Sensor configuration containing site-specific parameters	required

Attributes

Parameters:

Name	Type	Description	Default
`data_hub`	`CRNSDataHub`	A CRNSDataHub hub instance	required
`process_config`		The process YAML as an object.	required
`sensor_config`		The station information YAML as an object	required

select_corrections ¶

select_corrections()

Applies all configured corrections to the data hub.

This method processes all correction specifications in the process configuration and applies them to the data hub in the appropriate sequence.

Returns:

Type	Description
`CRNSDataHub`	The data hub with all corrections selected and ready to be applied