Classes
class	ULeafOptics
	Opaque structure for LeafOptics C++ class. More...

Functions
	_check_error (result, func, args)
	Automatic error checking for all leaf optics functions.

ctypes.POINTER(ULeafOptics)	createLeafOptics (ctypes.POINTER(UContext) context)
	Create LeafOptics instance.

None	destroyLeafOptics (ctypes.POINTER(ULeafOptics) leafoptics)
	Destroy LeafOptics instance.

None	leafOpticsRun (ctypes.POINTER(ULeafOptics) leafoptics, List[int] uuids, List[float] properties, str label)
	Run LeafOptics model and assign spectra to primitives.

None	leafOpticsRunNoUUIDs (ctypes.POINTER(ULeafOptics) leafoptics, List[float] properties, str label)
	Run LeafOptics model without assigning to primitives.

Tuple[List[float], List[float], List[float]]	leafOpticsGetLeafSpectra (ctypes.POINTER(ULeafOptics) leafoptics, List[float] properties)
	Get leaf reflectance and transmittance spectra.

None	leafOpticsSetProperties (ctypes.POINTER(ULeafOptics) leafoptics, List[int] uuids, List[float] properties)
	Set leaf optical properties for primitives.

None	leafOpticsGetPropertiesFromSpectrum (ctypes.POINTER(ULeafOptics) leafoptics, List[int] uuids)
	Get PROSPECT parameters from reflectivity spectrum for primitives.

None	leafOpticsGetPropertiesFromSpectrumSingle (ctypes.POINTER(ULeafOptics) leafoptics, int uuid)
	Get PROSPECT parameters from reflectivity spectrum for a single primitive.

List[float]	leafOpticsGetPropertiesFromLibrary (ctypes.POINTER(ULeafOptics) leafoptics, str species)
	Get leaf optical properties from the built-in species library.

None	leafOpticsDisableMessages (ctypes.POINTER(ULeafOptics) leafoptics)
	Disable command-line output messages from LeafOptics.

None	leafOpticsEnableMessages (ctypes.POINTER(ULeafOptics) leafoptics)
	Enable command-line output messages from LeafOptics.

None	leafOpticsOptionalOutputPrimitiveData (ctypes.POINTER(ULeafOptics) leafoptics, str label)
	Selectively output primitive data for specific biochemical properties.

None	leafOpticsRunNitrogen (ctypes.POINTER(ULeafOptics) leafoptics, List[int] uuids, List[float] params, int num_bins)
	Run nitrogen-based automatic leaf optics for leaf primitives.

None	leafOpticsUpdateNitrogenBasedSpectra (ctypes.POINTER(ULeafOptics) leafoptics)
	Re-read leaf nitrogen for tracked primitives and reassign spectra where it changed.

bool	is_leafoptics_nitrogen_available ()
	Check if the LeafOptics nitrogen-mode functions are available in the current library.

bool	is_leafoptics_available ()
	Check if LeafOptics functions are available in the current library.

	mock_create (args, *kwargs)

	mock_method (args, *kwargs)

Function Documentation

◆ _check_error()

pyhelios.wrappers.ULeafOpticsWrapper._check_error	(	result,
		func,
		args )

protected

Automatic error checking for all leaf optics functions.

Definition at line 40 of file ULeafOpticsWrapper.py.

◆ createLeafOptics()

ctypes.POINTER(ULeafOptics) pyhelios.wrappers.ULeafOpticsWrapper.createLeafOptics ( ctypes.POINTER(UContext) context )

Create LeafOptics instance.

Parameters

context Pointer to the Helios Context

Returns: Pointer to the created LeafOptics instance

Exceptions

NotImplementedError	If LeafOptics functions not available
ValueError	If context is None

Definition at line 196 of file ULeafOpticsWrapper.py.

◆ destroyLeafOptics()

None pyhelios.wrappers.ULeafOpticsWrapper.destroyLeafOptics ( ctypes.POINTER(ULeafOptics) leafoptics )

Destroy LeafOptics instance.

Definition at line 211 of file ULeafOpticsWrapper.py.

◆ is_leafoptics_available()

bool pyhelios.wrappers.ULeafOpticsWrapper.is_leafoptics_available ( )

Check if LeafOptics functions are available in the current library.

Definition at line 509 of file ULeafOpticsWrapper.py.

◆ is_leafoptics_nitrogen_available()

bool pyhelios.wrappers.ULeafOpticsWrapper.is_leafoptics_nitrogen_available ( )

Check if the LeafOptics nitrogen-mode functions are available in the current library.

Definition at line 504 of file ULeafOpticsWrapper.py.

◆ leafOpticsDisableMessages()

None pyhelios.wrappers.ULeafOpticsWrapper.leafOpticsDisableMessages ( ctypes.POINTER(ULeafOptics) leafoptics )

Disable command-line output messages from LeafOptics.

Definition at line 418 of file ULeafOpticsWrapper.py.

◆ leafOpticsEnableMessages()

None pyhelios.wrappers.ULeafOpticsWrapper.leafOpticsEnableMessages ( ctypes.POINTER(ULeafOptics) leafoptics )

Enable command-line output messages from LeafOptics.

Definition at line 428 of file ULeafOpticsWrapper.py.

◆ leafOpticsGetLeafSpectra()

Tuple[List[float], List[float], List[float]] pyhelios.wrappers.ULeafOpticsWrapper.leafOpticsGetLeafSpectra	(	ctypes.POINTER(ULeafOptics)	leafoptics,
		List[float]	properties )

Get leaf reflectance and transmittance spectra.

Parameters

leafoptics	Pointer to LeafOptics instance
properties	List of 9 floats [numberlayers, brownpigments, chlorophyllcontent, carotenoidcontent, anthocyancontent, watermass, drymass, protein, carbonconstituents]

Returns

Tuple of (wavelengths, reflectivities, transmissivities) as lists of floats

wavelengths: 400-2500 nm at 1nm resolution (2101 points)
reflectivities: reflectance values at each wavelength
transmissivities: transmittance values at each wavelength

Definition at line 286 of file ULeafOpticsWrapper.py.

◆ leafOpticsGetPropertiesFromLibrary()

List[float] pyhelios.wrappers.ULeafOpticsWrapper.leafOpticsGetPropertiesFromLibrary	(	ctypes.POINTER(ULeafOptics)	leafoptics,
		str	species )

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

Parameters

leafoptics	Pointer to LeafOptics instance
species	Name of the species (case-insensitive). Available species: "default", "garden_lettuce", "alfalfa", "corn", "sunflower", "english_walnut", "rice", "soybean", "wine_grape", "tomato", "common_bean", "cowpea"

Returns: List of 9 floats [numberlayers, brownpigments, chlorophyllcontent, carotenoidcontent, anthocyancontent, watermass, drymass, protein, carbonconstituents]

Note: If species is not found, default properties are used and a warning is issued

Definition at line 400 of file ULeafOpticsWrapper.py.

◆ leafOpticsGetPropertiesFromSpectrum()

None pyhelios.wrappers.ULeafOpticsWrapper.leafOpticsGetPropertiesFromSpectrum	(	ctypes.POINTER(ULeafOptics)	leafoptics,
		List[int]	uuids )

Get PROSPECT parameters from reflectivity spectrum for primitives.

Parameters

leafoptics	Pointer to LeafOptics instance
uuids	List of primitive UUIDs to query

Note: Primitives without matching spectra are silently skipped

Definition at line 349 of file ULeafOpticsWrapper.py.

◆ leafOpticsGetPropertiesFromSpectrumSingle()

None pyhelios.wrappers.ULeafOpticsWrapper.leafOpticsGetPropertiesFromSpectrumSingle	(	ctypes.POINTER(ULeafOptics)	leafoptics,
		int	uuid )

Get PROSPECT parameters from reflectivity spectrum for a single primitive.

Parameters

leafoptics	Pointer to LeafOptics instance
uuid	Single primitive UUID to query

Note: If no matching spectrum is found, the primitive is silently skipped

Definition at line 372 of file ULeafOpticsWrapper.py.

◆ leafOpticsOptionalOutputPrimitiveData()

None pyhelios.wrappers.ULeafOpticsWrapper.leafOpticsOptionalOutputPrimitiveData	(	ctypes.POINTER(ULeafOptics)	leafoptics,
		str	label )

Selectively output primitive data for specific biochemical properties.

By default, all biochemical properties are written as primitive data. Use this method to select only needed properties for better performance.

Parameters

leafoptics	LeafOptics instance pointer
label	Property label - one of: "chlorophyll", "carotenoid", "anthocyanin", "brown", "water", "drymass", "protein", "cellulose"

Note: Added in helios-core v1.3.59

Definition at line 450 of file ULeafOpticsWrapper.py.

◆ leafOpticsRun()

None pyhelios.wrappers.ULeafOpticsWrapper.leafOpticsRun	(	ctypes.POINTER(ULeafOptics)	leafoptics,
		List[int]	uuids,
		List[float]	properties,
		str	label )

Run LeafOptics model and assign spectra to primitives.

Parameters

leafoptics	Pointer to LeafOptics instance
uuids	List of primitive UUIDs
properties	List of 9 floats [numberlayers, brownpigments, chlorophyllcontent, carotenoidcontent, anthocyancontent, watermass, drymass, protein, carbonconstituents]
label	Label for the spectra (appended to "leaf_reflectivity_" and "leaf_transmissivity_")

Definition at line 225 of file ULeafOpticsWrapper.py.

◆ leafOpticsRunNitrogen()

None pyhelios.wrappers.ULeafOpticsWrapper.leafOpticsRunNitrogen	(	ctypes.POINTER(ULeafOptics)	leafoptics,
		List[int]	uuids,
		List[float]	params,
		int	num_bins )

Run nitrogen-based automatic leaf optics for leaf primitives.

Parameters

leafoptics	Pointer to LeafOptics instance
uuids	List of leaf primitive UUIDs (must belong to objects with "leaf_nitrogen_gN_m2" data)
params	List of LEAF_OPTICS_NAUTO_FLOAT_COUNT floats [f_photosynthetic, N_to_Cab_coefficient, Car_to_Cab_ratio, numberlayers, anthocyancontent, brownpigments, watermass, drymass, protein, carbonconstituents, V2Z, fqe, reassignment_threshold, min_reassignment_change]
num_bins	Number of spectrum bins

Definition at line 472 of file ULeafOpticsWrapper.py.

◆ leafOpticsRunNoUUIDs()

None pyhelios.wrappers.ULeafOpticsWrapper.leafOpticsRunNoUUIDs	(	ctypes.POINTER(ULeafOptics)	leafoptics,
		List[float]	properties,
		str	label )

Run LeafOptics model without assigning to primitives.

Parameters

leafoptics	Pointer to LeafOptics instance
properties	List of 9 floats [numberlayers, brownpigments, chlorophyllcontent, carotenoidcontent, anthocyancontent, watermass, drymass, protein, carbonconstituents]
label	Label for the spectra

Definition at line 255 of file ULeafOpticsWrapper.py.

◆ leafOpticsSetProperties()

None pyhelios.wrappers.ULeafOpticsWrapper.leafOpticsSetProperties	(	ctypes.POINTER(ULeafOptics)	leafoptics,
		List[int]	uuids,
		List[float]	properties )

Set leaf optical properties for primitives.

Parameters

leafoptics	Pointer to LeafOptics instance
uuids	List of primitive UUIDs
properties	List of 9 floats [numberlayers, brownpigments, chlorophyllcontent, carotenoidcontent, anthocyancontent, watermass, drymass, protein, carbonconstituents]

Definition at line 322 of file ULeafOpticsWrapper.py.

◆ leafOpticsUpdateNitrogenBasedSpectra()

None pyhelios.wrappers.ULeafOpticsWrapper.leafOpticsUpdateNitrogenBasedSpectra ( ctypes.POINTER(ULeafOptics) leafoptics )

Re-read leaf nitrogen for tracked primitives and reassign spectra where it changed.

Definition at line 494 of file ULeafOpticsWrapper.py.

◆ mock_create()

pyhelios.wrappers.ULeafOpticsWrapper.mock_create	(	*	args,
		**	kwargs )

Definition at line 515 of file ULeafOpticsWrapper.py.

◆ mock_method()

pyhelios.wrappers.ULeafOpticsWrapper.mock_method	(	*	args,
		**	kwargs )

Definition at line 521 of file ULeafOpticsWrapper.py.

Variable Documentation

◆ _LEAFOPTICS_FUNCTIONS_AVAILABLE

bool pyhelios.wrappers.ULeafOpticsWrapper._LEAFOPTICS_FUNCTIONS_AVAILABLE

protected

Definition at line 136 of file ULeafOpticsWrapper.py.

◆ _LEAFOPTICS_NITROGEN_FUNCTIONS_AVAILABLE

bool pyhelios.wrappers.ULeafOpticsWrapper._LEAFOPTICS_NITROGEN_FUNCTIONS_AVAILABLE

protected

Definition at line 164 of file ULeafOpticsWrapper.py.

◆ _NITROGEN_NOT_AVAILABLE_MSG

tuple pyhelios.wrappers.ULeafOpticsWrapper._NITROGEN_NOT_AVAILABLE_MSG

protected

Definition at line 175 of file ULeafOpticsWrapper.py.

◆ argtypes

pyhelios.wrappers.ULeafOpticsWrapper.argtypes

Definition at line 47 of file ULeafOpticsWrapper.py.

◆ createLeafOptics

pyhelios.wrappers.ULeafOpticsWrapper.createLeafOptics = mock_create

Definition at line 528 of file ULeafOpticsWrapper.py.

◆ errcheck

pyhelios.wrappers.ULeafOpticsWrapper.errcheck

Definition at line 49 of file ULeafOpticsWrapper.py.

◆ LEAF_OPTICS_NAUTO_FLOAT_COUNT

int pyhelios.wrappers.ULeafOpticsWrapper.LEAF_OPTICS_NAUTO_FLOAT_COUNT = 14

Definition at line 34 of file ULeafOpticsWrapper.py.

◆ LEAF_OPTICS_PROPERTIES_COUNT

int pyhelios.wrappers.ULeafOpticsWrapper.LEAF_OPTICS_PROPERTIES_COUNT = 11

Definition at line 25 of file ULeafOpticsWrapper.py.

◆ LEAF_OPTICS_SPECTRAL_POINTS

int pyhelios.wrappers.ULeafOpticsWrapper.LEAF_OPTICS_SPECTRAL_POINTS = 2101

Definition at line 28 of file ULeafOpticsWrapper.py.

◆ leafOpticsGetLeafSpectra

pyhelios.wrappers.ULeafOpticsWrapper.leafOpticsGetLeafSpectra = mock_method

Definition at line 531 of file ULeafOpticsWrapper.py.

◆ leafOpticsGetPropertiesFromLibrary

pyhelios.wrappers.ULeafOpticsWrapper.leafOpticsGetPropertiesFromLibrary = mock_method

Definition at line 535 of file ULeafOpticsWrapper.py.

◆ leafOpticsGetPropertiesFromSpectrum

pyhelios.wrappers.ULeafOpticsWrapper.leafOpticsGetPropertiesFromSpectrum = mock_method

Definition at line 533 of file ULeafOpticsWrapper.py.

◆ leafOpticsGetPropertiesFromSpectrumSingle

pyhelios.wrappers.ULeafOpticsWrapper.leafOpticsGetPropertiesFromSpectrumSingle = mock_method

Definition at line 534 of file ULeafOpticsWrapper.py.

◆ leafOpticsRun

pyhelios.wrappers.ULeafOpticsWrapper.leafOpticsRun = mock_method

Definition at line 529 of file ULeafOpticsWrapper.py.

◆ leafOpticsRunNitrogen

pyhelios.wrappers.ULeafOpticsWrapper.leafOpticsRunNitrogen = mock_method

Definition at line 536 of file ULeafOpticsWrapper.py.

◆ leafOpticsRunNoUUIDs

pyhelios.wrappers.ULeafOpticsWrapper.leafOpticsRunNoUUIDs = mock_method

Definition at line 530 of file ULeafOpticsWrapper.py.

◆ leafOpticsSetProperties

pyhelios.wrappers.ULeafOpticsWrapper.leafOpticsSetProperties = mock_method

Definition at line 532 of file ULeafOpticsWrapper.py.

◆ leafOpticsUpdateNitrogenBasedSpectra

pyhelios.wrappers.ULeafOpticsWrapper.leafOpticsUpdateNitrogenBasedSpectra = mock_method

Definition at line 537 of file ULeafOpticsWrapper.py.

◆ restype

pyhelios.wrappers.ULeafOpticsWrapper.restype

Definition at line 48 of file ULeafOpticsWrapper.py.

Variables
int	LEAF_OPTICS_PROPERTIES_COUNT = 11

int	LEAF_OPTICS_SPECTRAL_POINTS = 2101

int	LEAF_OPTICS_NAUTO_FLOAT_COUNT = 14

	argtypes

	restype

	errcheck

bool	_LEAFOPTICS_FUNCTIONS_AVAILABLE

bool	_LEAFOPTICS_NITROGEN_FUNCTIONS_AVAILABLE

tuple	_NITROGEN_NOT_AVAILABLE_MSG

	createLeafOptics = mock_create

	leafOpticsRun = mock_method

	leafOpticsRunNoUUIDs = mock_method

	leafOpticsGetLeafSpectra = mock_method

	leafOpticsSetProperties = mock_method

	leafOpticsGetPropertiesFromSpectrum = mock_method

	leafOpticsGetPropertiesFromSpectrumSingle = mock_method

	leafOpticsGetPropertiesFromLibrary = mock_method

	leafOpticsRunNitrogen = mock_method

	leafOpticsUpdateNitrogenBasedSpectra = mock_method

Classes

Functions

Variables

Function Documentation

◆ _check_error()

◆ createLeafOptics()

◆ destroyLeafOptics()

◆ is_leafoptics_available()

◆ is_leafoptics_nitrogen_available()

◆ leafOpticsDisableMessages()

◆ leafOpticsEnableMessages()

◆ leafOpticsGetLeafSpectra()

◆ leafOpticsGetPropertiesFromLibrary()

◆ leafOpticsGetPropertiesFromSpectrum()

◆ leafOpticsGetPropertiesFromSpectrumSingle()

◆ leafOpticsOptionalOutputPrimitiveData()

◆ leafOpticsRun()

◆ leafOpticsRunNitrogen()

◆ leafOpticsRunNoUUIDs()

◆ leafOpticsSetProperties()

◆ leafOpticsUpdateNitrogenBasedSpectra()

◆ mock_create()

◆ mock_method()

Variable Documentation

◆ _LEAFOPTICS_FUNCTIONS_AVAILABLE

◆ _LEAFOPTICS_NITROGEN_FUNCTIONS_AVAILABLE

◆ _NITROGEN_NOT_AVAILABLE_MSG

◆ argtypes

◆ createLeafOptics

◆ errcheck

◆ LEAF_OPTICS_NAUTO_FLOAT_COUNT

◆ LEAF_OPTICS_PROPERTIES_COUNT

◆ LEAF_OPTICS_SPECTRAL_POINTS

◆ leafOpticsGetLeafSpectra

◆ leafOpticsGetPropertiesFromLibrary

◆ leafOpticsGetPropertiesFromSpectrum

◆ leafOpticsGetPropertiesFromSpectrumSingle

◆ leafOpticsRun

◆ leafOpticsRunNitrogen

◆ leafOpticsRunNoUUIDs

◆ leafOpticsSetProperties

◆ leafOpticsUpdateNitrogenBasedSpectra

◆ restype