Public Member Functions
	LeafOptics (helios::Context *a_context)
	Constructor.

void	run (const std::vector< uint > &UUIDs, const LeafOpticsProperties &leafproperties, const std::string &label)
	Run the LeafOptics model to generate reflectivity and transmissivity spectra, create associated global data, and assign to specified primitives.

void	run (const LeafOpticsProperties &leafproperties, const std::string &label)
	Run the LeafOptics model to generate reflectivity and transmissivity spectra and create associated global data.

void	PROSPECT (float numberlayers, float Chlorophyllcontent, float carotenoidcontent, float anthocyancontent, float brownpigments, float watermass, float drymass, float protein, float carbonconstituents, std::vector< float > &reflectivities_fit, std::vector< float > &transmissivities_fit)
	LeafOptics model kernel.

void	getLeafSpectra (const LeafOpticsProperties &leafproperties, std::vector< helios::vec2 > &reflectivities_fit, std::vector< helios::vec2 > &transmissivities_fit)
	Get the leaf spectra.

void	setProperties (const std::vector< uint > &UUIDs, const LeafOpticsProperties &leafproperties)
	Set leaf optical properties for a set of primitives.

void	getPropertiesFromSpectrum (const std::vector< uint > &UUIDs)
	Get PROSPECT parameters from reflectivity spectrum for a set of primitives.

void	getPropertiesFromSpectrum (uint UUID)
	Get PROSPECT parameters from reflectivity spectrum for a single primitive.

void	getPropertiesFromLibrary (const std::string &species, LeafOpticsProperties &leafproperties)
	Get leaf optical properties from the built-in species library.

void	disableMessages ()
	Disable command-line output messages from this plug-in.

void	enableMessages ()
	Enable command-line output messages from this plug-in.

void	optionalOutputPrimitiveData (const char *label)
	Add optional primitive data output.

void	run (const std::vector< uint > &UUIDs, const LeafOpticsProperties_Nauto &params)
	Run nitrogen-based leaf optics for the specified primitives.

void	updateNitrogenBasedSpectra ()
	Update nitrogen-based spectra for currently tracked primitives.

Static Public Member Functions
static int	selfTest (int argc=0, char **argv=nullptr)
	Self-test.

Detailed Description

Definition at line 123 of file LeafOptics.h.

Constructor & Destructor Documentation

◆ LeafOptics()

LeafOptics::LeafOptics ( helios::Context * a_context )

Constructor.

Definition at line 20 of file LeafOptics.cpp.

Member Function Documentation

◆ disableMessages()

void LeafOptics::disableMessages ( )

Disable command-line output messages from this plug-in.

Definition at line 766 of file LeafOptics.cpp.

◆ enableMessages()

void LeafOptics::enableMessages ( )

Enable command-line output messages from this plug-in.

Definition at line 770 of file LeafOptics.cpp.

◆ getLeafSpectra()

void LeafOptics::getLeafSpectra	(	const LeafOpticsProperties &	leafproperties,
		std::vector< helios::vec2 > &	reflectivities_fit,
		std::vector< helios::vec2 > &	transmissivities_fit
	)

Get the leaf spectra.

Parameters

[in]	leafproperties	LeafOptics properties.
[out]	reflectivities_fit	reflectivities of the leaf. Any existing contents are overwritten.
[out]	transmissivities_fit	transmissivities of the leaf. Any existing contents are overwritten.

Note: Throws a runtime error if numberlayers is less than 1 or if any constituent content is negative.

Definition at line 512 of file LeafOptics.cpp.

◆ getPropertiesFromLibrary()

void LeafOptics::getPropertiesFromLibrary	(	const std::string &	species,
		LeafOpticsProperties &	leafproperties
	)

Get leaf optical properties from the built-in species library.

Parameters

[in]	species	Name of the species to retrieve properties for (e.g., "default"). Species names are case-insensitive.
[out]	leafproperties	LeafOpticsProperties struct to be populated with the species-specific properties. If the species is not found in the library, default properties are used and a warning is issued.

Definition at line 744 of file LeafOptics.cpp.

◆ getPropertiesFromSpectrum() [1/2]

void LeafOptics::getPropertiesFromSpectrum ( const std::vector< uint > & UUIDs )

Get PROSPECT parameters from reflectivity spectrum for a set of primitives.

Parameters

[in] UUIDs UUIDs for primitives to query. For each primitive, this method retrieves the "reflectivity_spectrum" primitive data and checks if it matches a spectrum generated by this LeafOptics instance. If a match is found, the corresponding PROSPECT model parameters are assigned as primitive data using the same labels as setProperties() ("chlorophyll", "carotenoid", "anthocyanin", "brown", "water", "drymass", "protein", "cellulose"). Primitives without matching spectra are silently skipped.

Definition at line 687 of file LeafOptics.cpp.

◆ getPropertiesFromSpectrum() [2/2]

void LeafOptics::getPropertiesFromSpectrum ( uint UUID )

Get PROSPECT parameters from reflectivity spectrum for a single primitive.

Parameters

[in] UUID UUID for primitive to query. This method retrieves the "reflectivity_spectrum" primitive data and checks if it matches a spectrum generated by this LeafOptics instance. If a match is found, the corresponding PROSPECT model parameters are assigned as primitive data using the same labels as setProperties() ("chlorophyll", "carotenoid", "anthocyanin", "brown", "water", "drymass", "protein", "cellulose"). If no matching spectrum is found, the primitive is silently skipped.

Definition at line 740 of file LeafOptics.cpp.

◆ optionalOutputPrimitiveData()

void LeafOptics::optionalOutputPrimitiveData ( const char * label )

Add optional primitive data output.

Parameters

[in] label Label of the primitive data to output. Available labels: "chlorophyll", "carotenoid", "anthocyanin", "brown", "water", "drymass", "protein", "cellulose".

Definition at line 774 of file LeafOptics.cpp.

◆ PROSPECT()

void LeafOptics::PROSPECT	(	float	numberlayers,
		float	Chlorophyllcontent,
		float	carotenoidcontent,
		float	anthocyancontent,
		float	brownpigments,
		float	watermass,
		float	drymass,
		float	protein,
		float	carbonconstituents,
		std::vector< float > &	reflectivities_fit,
		std::vector< float > &	transmissivities_fit
	)

LeafOptics model kernel.

Parameters

[in]	numberlayers	number of layers in the leaf
[in]	Chlorophyllcontent	chlorophyll content in the leaf
[in]	carotenoidcontent	carotenoid content in the leaf
[in]	anthocyancontent	anthocyan content in the leaf
[in]	brownpigments	brown pigment content in the leaf
[in]	watermass	water mass in the leaf
[in]	drymass	dry mass in the leaf
[in]	protein	protein content in the leaf
[in]	carbonconstituents	carbon constituents in the leaf
[out]	reflectivities_fit	reflectivities of the leaf at each of the 2101 wavelengths. Any existing contents are overwritten.
[out]	transmissivities_fit	transmissivities of the leaf at each of the 2101 wavelengths. Any existing contents are overwritten.

Definition at line 389 of file LeafOptics.cpp.

◆ run() [1/3]

void LeafOptics::run	(	const LeafOpticsProperties &	leafproperties,
		const std::string &	label
	)

Run the LeafOptics model to generate reflectivity and transmissivity spectra and create associated global data.

Parameters

[in]	leafproperties	LeafOptics properties.
[in]	label	label of spectra that will be created. This label will be appended to "leaf_reflectivity_" and "leaf_transmissivity_" (e.g., "leaf_reflectivity_bean" if the label is "bean").

Definition at line 362 of file LeafOptics.cpp.

◆ run() [2/3]

void LeafOptics::run	(	const std::vector< uint > &	UUIDs,
		const LeafOpticsProperties &	leafproperties,
		const std::string &	label
	)

Run the LeafOptics model to generate reflectivity and transmissivity spectra, create associated global data, and assign to specified primitives.

Parameters

[in]	UUIDs	UUIDs for primitives that will be assigned the generated reflectivity and transmissivity spectra.
[in]	leafproperties	LeafOptics properties.
[in]	label	label of spectra that will be created. This label will be appended to "leaf_reflectivity_" and "leaf_transmissivity_" (e.g., "leaf_reflectivity_bean" if the label is "bean").

Definition at line 320 of file LeafOptics.cpp.

◆ run() [3/3]

void LeafOptics::run	(	const std::vector< uint > &	UUIDs,
		const LeafOpticsProperties_Nauto &	params
	)

Run nitrogen-based leaf optics for the specified primitives.

Computes leaf optical properties based on nitrogen content. Groups primitives by parent object, reads "leaf_nitrogen_gN_m2" from each object, and assigns spectra accordingly.

Behavior depends on call sequence:

First call: Creates adaptive spectrum bins based on nitrogen distribution, generates PROSPECT spectra for each bin, assigns primitives to bins.
Subsequent calls: New primitives assigned to nearest existing bin, removed primitives untracked, existing primitives checked for nitrogen changes and reassigned if threshold exceeded.

All primitives belonging to the same parent object receive the same spectrum.

Parameters

[in]	UUIDs	Primitive UUIDs of leaf surfaces
[in]	params	Nitrogen-auto parameters specifying conversion coefficients, fixed PROSPECT values, and binning configuration

Note: Requires "leaf_nitrogen_gN_m2" object data to be set on each leaf object (typically by PlantArchitecture::NitrogenModel)

Definition at line 998 of file LeafOptics.cpp.

◆ selfTest()

int LeafOptics::selfTest	(	int	argc = `0`,
		char **	argv = `nullptr`
	)

static

Self-test.

Returns: 0 if test was successful, 1 if test failed

Definition at line 1929 of file selfTest.cpp.

◆ setProperties()

void LeafOptics::setProperties	(	const std::vector< uint > &	UUIDs,
		const LeafOpticsProperties &	leafproperties
	)

Set leaf optical properties for a set of primitives.

Parameters

[in]	UUIDs	UUIDs for primitives for which optical properties should be set.
[in]	leafproperties	LeafOptics properties.

Definition at line 665 of file LeafOptics.cpp.

◆ updateNitrogenBasedSpectra()

void LeafOptics::updateNitrogenBasedSpectra ( )

Update nitrogen-based spectra for currently tracked primitives.

Efficient update method for when nitrogen values have changed but the primitive set is unchanged. Re-reads nitrogen from parent objects and reassigns primitives if the change exceeds configured thresholds.

This is equivalent to calling run() with the same UUIDs but faster since it skips primitive grouping and add/remove processing.

Note: Nitrogen mode must be active (run() called with LeafOpticsProperties_Nauto)

Definition at line 1161 of file LeafOptics.cpp.

The documentation for this class was generated from the following files:

plugins/leafoptics/include/LeafOptics.h
plugins/leafoptics/src/LeafOptics.cpp
plugins/leafoptics/tests/selfTest.cpp

	1.3.82

Public Member Functions

Static Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ LeafOptics()

Member Function Documentation

◆ disableMessages()

◆ enableMessages()

◆ getLeafSpectra()

◆ getPropertiesFromLibrary()

◆ getPropertiesFromSpectrum() [1/2]

◆ getPropertiesFromSpectrum() [2/2]

◆ optionalOutputPrimitiveData()

◆ PROSPECT()

◆ run() [1/3]

◆ run() [2/3]

◆ run() [3/3]

◆ selfTest()

◆ setProperties()

◆ updateNitrogenBasedSpectra()