Overview

The process configuration file tells neptoon about the sensor being processed. The sections in this file are: config, neutron_quality_assessment, correction_steps, and data_smoothing. Below is an example file which you can use a starting point for your own sensor.

Cosmos Standard

There are ongoing discussion in the community to set a standard for CRNS which users can use as a jumping off point. The standard is considered to be using established methods that have been tested in the field and produce good results. There are arguably better technique (and ones we've yet to discover) - we endeavour to keep up to date with the scienfitic knowledge.

The below processing yaml will be up to date with the current standard.

config: process

# Neutron QA
neutron_quality_assessment:
  raw_neutrons:
    spike_offset:
      threshold_relative: [0.2, -0.2] # + or - 20%
      window: 12h
  corrected_neutrons:
    greater_than_N0:
      percent_maximum: 1.075 # Köhli 2021
    below_N0_factor:
      percent_minimum: 0.3

# Correction methods
correction_steps:
  air_humidity:
    method: rosolem_2013
    coefficient: 0.0054
    humidity_ref: 0
  air_pressure:
    method: tirado_bueno_2021
  incoming_radiation:
    method: hawdon_2014
    reference_neutron_monitor:
      station: JUNG
      resolution: 60 # minutes
      nmdb_table: revori # recommend revori
  above_ground_biomass:
    method: none
    biomass_units:
  soil_moisture_estimation:
    method: desilets_etal_2010 # or koehli_etal_2021
    koehli_etal_2021_parameterset: Mar21_mcnp_drf

# Data Smoothing
data_smoothing:
  smooth_corrected_neutrons: True
  smooth_soil_moisture: False
  settings:
    algorithm: rolling_mean
    window: 12h
    min_proportion_good_data: 0.7

temporal_aggregation:
  aggregate_data: false
  output_resolution: 1h
  align_timestamps: true
  alignment_method: time
  aggregate_method: bagg
  aggregate_func: mean
  aggregate_maxna_fraction: 0.3

Configuration Quick Reference Guide

Neutron Quality Assessment

Raw Neutron Quality Control Parameters

Here we conduct spike detection to account for problems in the raw count rate. There are a few algorithms to choose from, however we currently recommend using spike_offset with the defaults set to what you cna see in the above yaml file. This follows the current literature by identifying spikes as anything >20% of previous value.

Parameter	Required	Type	Example	Description
spike_offset.threshold_relative	Yes	list	[0.2, -0.2]	Maximum percent (as decimal) that an observation can jump, before being designated a spike. Add two values in list format (with square brackets []), one with a postive sign and one with a negative sign. Advised to stick to uniform.
spike_offset.window	Yes	integer	12h	The window to use to identify whether a spike as returned back to base line after a plateau of spikes

Corrected Neutron Quality Control Parameters

These are some quality checks we do on corrected neutrons based on the literature.

It's recommended to not touch this section unless your experimenting.

Parameter	Required	Type	Example	Description
greater_than_N0.percent_maximum	Yes	float	1.075	Maximum allowed neutron count as percentage of N0 (Köhli 2021)
below_N0_factor.percent_minimum	Yes	float	0.3	Minimum allowed neutron count as percentage of N0

Correction Steps

The following section is for applying corrections to the neutron count rate to account for additional influences, besides soil moisture, that influence the count rate.

If you wish to turn off a particular correction - set the method to "none".

Air Humidity Correction

Air humidity corrections can be left as the example values shown below when being applied as these are based on the literature.

Köhli et al., 2021 method for neutron conversion

• If you are using the koehli_etal_2021 method for neutron to soil moisture conversion - set the method to "none". The humidity correction is integrated to this method already. (If you forget neptoon will disapply this correction during neutron conversion, but it's best to not apply it in the first place)

Parameter	Required	Type	Example	Description
method	No	string	"rosolem_2013" or "none"	Method used for humidity correction
omega	No	float	0.0054	Correction coefficient for humidity
humidity_ref	No	float	0	Reference humidity value for correction

Air Pressure Correction

Air pressure correction - very important to leave on as CRNS are very sensitive to atmospheric pressure changes.

Parameter	Required	Type	Example	Description
method	Yes	string	"desilets_zreda_2003" or "desilets_2021" or "tirado_bueno_2021" or "none"	Method used for pressure correction
dunai_inclination	No	float	-	Inclination parameter for dunai method

Incoming Intensity Correction

Parameter	Required	Type	Example	Description
method	Yes	string	"hawdon_2014" or "zreda_2012" or "mcjannet_desilets_2023" or "none"	Method used for incoming intensity correction
reference_neutron_monitor.station	Yes	string	"AATB" or "INVK" or "JUNG" or "KERG" or "KIEL" or "MXCO" or "NEWK" or "OULU" or "PSNM" or "SOPO" or "TERA" or "THUL"	Reference neutron monitor station
reference_neutron_monitor.resolution	Yes	integer	60	Time resolution in minutes
reference_neutron_monitor.nmdb_table	Yes	string	"revori" or "ori"	NMDB table name (revori recommended)

Above Ground Biomass Correction

Parameter	Required	Type	Example	Description
method	No	string	"baatz_2015" or "morris_2024" or "none"	Method used for biomass correction
biomass_units	No	string	-	Units for biomass measurements

Soil Moisture Estimation

Here we state how we will convert neutrons to soil mositure. If you choose koehli_etal_2021 then koehli_method_form is required.

Parameter	Required	Type	Example	Description
method	Yes	string	"desilets_etal_2010" or "koehli_etal_2021" or "none"	Method for converting neutrons to soil mositure
koehli_etal_2021_parameterset	No	string	"Jan23_uranos" or "Jan23_mcnpfull" or "Mar12_atmprof" or "Mar21_mcnp_drf" or "Mar21_mcnp_ewin" or "Mar21_uranos_drf" or "Mar21_uranos_ewin" or "Mar22_mcnp_drf_Jan" or "Mar22_mcnp_ewin_gd" or "Mar22_uranos_drf_gd" or "Mar22_uranos_ewin_chi2" or "Mar22_uranos_drf_h200m" or "Aug08_mcnp_drf" or "Aug08_mcnp_ewin" or "Aug12_uranos_drf" or "Aug12_uranos_ewin" or "Aug13_uranos_atmprof" or "Aug13_uranos_atmprof2"	Thats a lot of options... just stick with "Mar21_mcnp_drf" if you want simple. This sets the parameters when using the koehlie et al., 2021 method

Data Smoothing

In this section we state whether to do smoothing on the neutron data, and how to do it. The boolean statement is required. If this is set to true then the further options need to be set too, otherwise they can be left blank.

Parameter	Required	Type	Example	Description
smooth_corrected_neutrons	Yes	boolean	true	Enable smoothing for corrected neutron counts
smooth_soil_moisture	Yes	boolean	false	Enable smoothing for soil moisture data
settings.algorithm	No	string	"rolling_mean"	Smoothing algorithm selection
settings.window	No	string	12h or 12hours or 1day or 1d or 30min or 30m	Window size for smoothing operation, provided as a string which neptoon will automatically parse into a timedelta window
settings.min_proportion_good_data	No	float	0.7	The minimum proportion of available data for the smoothing window to succeed. If less than this is available in the window the observation is nan

Additional Information

• The smoothing algorithm supports only rolling_mean until a future update.

Temporal Aggregation

In this section we state whether to do smoothing on the neutron data, and how to do it.

The boolean statements are required. If they are set to true then the further options need to be set too, otherwise they can be left blank.

Alignment is used if you want to have your data output on rounded time points, but don't wish to change the resolution of your data (e.g., data at 15:04 realigned to be at 15:00).

Aggregation does what it says, converts your data to a new resolution via aggregation. The output_resolution should be larger than original timestep resolution of your data (no downscaling).

More info on this found here

Parameter	Required	Type	Example	Description
aggregate_data	Yes	boolean	true or false	Whether to aggregate data
output_resolution	No	string	1h or None	Desired time step of output data. Should be pandas style FreqStr (e.g., 1h, 1m)
aggregate_method	No	string	bagg	Method for data aggregation
aggregate_func	No	string	mean	Function used for aggregation
aggregate_maxna_fraction	No	float	0.3	Maximum allowed fraction of NA values in the aggregation period
align_timestamps	Yes	boolean	true or false	Whether to align timestamps
alignment_method	No	string	time	Method for timestamp alignment