High-level interface for stomatal conductance modeling and gas exchange calculations. More...

Detailed Description

High-level interface for stomatal conductance modeling and gas exchange calculations.

This class provides a user-friendly wrapper around the native Helios stomatal conductance plugin with automatic plugin availability checking and graceful error handling.

The stomatal conductance model implements five different stomatal response models:

BWB: Ball, Woodrow, Berry (1987) - original model
BBL: Ball, Berry, Leuning (1990, 1995) - includes VPD response
MOPT: Medlyn et al. (2011) - optimality-based model
BMF: Buckley, Mott, Farquhar - simplified mechanistic model
BB: Bailey - hydraulic-based model

The plugin includes a species library with pre-calibrated coefficients for common plant species (Almond, Apple, Avocado, Grape, Lemon, Olive, Walnut, etc.).

Both steady-state and dynamic (time-stepping) calculations are supported, with configurable time constants for stomatal opening and closing dynamics.

System requirements:

Cross-platform support (Windows, Linux, macOS)
No GPU required
No special dependencies
Stomatal conductance plugin compiled into PyHelios

Examples

>>> with Context() as context:
...     # Add leaf geometry
...     leaf_uuid = context.addPatch(center=[0, 0, 1], size=[0.1, 0.1])
...
...     with StomatalConductanceModel(context) as stomatal:
...         # Set model coefficients using species library
...         stomatal.setBMFCoefficientsFromLibrary("Almond")
...
...         # Run steady-state calculation
...         stomatal.run()
...
...         # Or run dynamic simulation with timestep
...         stomatal.run(dt=60.0)  # 60 second timestep
...
...         # Set custom BMF coefficients for specific leaves
...         bmf_coeffs = BMFCoefficients(Em=258.25, i0=38.65, k=232916.82, b=609.67)
...         stomatal.setBMFCoefficients(bmf_coeffs, uuids=[leaf_uuid])

Definition at line 109 of file StomatalConductance.py.

Public Member Functions
	__init__ (self, Context context)
	Initialize StomatalConductanceModel with graceful plugin handling.

	__enter__ (self)
	Context manager entry.

	__exit__ (self, exc_type, exc_value, traceback)
	Context manager exit with proper cleanup.

	getNativePtr (self)
	Get the native pointer for advanced operations.

None	enableMessages (self)
	Enable console output messages from the stomatal conductance model.

None	disableMessages (self)
	Disable console output messages from the stomatal conductance model.

None	run (self, Optional[List[int]] uuids=None, Optional[float] dt=None)
	Run the stomatal conductance model.

None	setBWBCoefficients (self, BWBCoefficients coeffs, Optional[List[int]] uuids=None)
	Set Ball-Woodrow-Berry model coefficients.

None	setBBLCoefficients (self, BBLCoefficients coeffs, Optional[List[int]] uuids=None)
	Set Ball-Berry-Leuning model coefficients.

None	setMOPTCoefficients (self, MOPTCoefficients coeffs, Optional[List[int]] uuids=None)
	Set Medlyn et al.

None	setBMFCoefficients (self, BMFCoefficients coeffs, Optional[List[int]] uuids=None)
	Set Buckley-Mott-Farquhar model coefficients.

None	setBBCoefficients (self, BBCoefficients coeffs, Optional[List[int]] uuids=None)
	Set Bailey model coefficients.

None	setBMFCoefficientsFromLibrary (self, str species, Optional[List[int]] uuids=None)
	Set BMF model coefficients using the built-in species library.

None	setDynamicTimeConstants (self, float tau_open, float tau_close, Optional[List[int]] uuids=None)
	Set time constants for dynamic stomatal opening and closing.

None	optionalOutputPrimitiveData (self, str label)
	Add optional output primitive data to the Context.

None	printDefaultValueReport (self, Optional[List[int]] uuids=None)
	Print a report detailing usage of default input values.

bool	is_available (self)
	Check if StomatalConductanceModel is available in current build.

Public Attributes
	context = context

	stomatal_model = None

Constructor & Destructor Documentation

◆ init()

pyhelios.StomatalConductance.StomatalConductanceModel.__init__	(		self,
		Context	context )

Initialize StomatalConductanceModel with graceful plugin handling.

Parameters

context Helios Context instance

Exceptions

TypeError	If context is not a Context instance
StomatalConductanceModelError	If stomatal conductance plugin is not available

Definition at line 121 of file StomatalConductance.py.

Member Function Documentation

◆ enter()

pyhelios.StomatalConductance.StomatalConductanceModel.__enter__ ( self )

Context manager entry.

Definition at line 181 of file StomatalConductance.py.

◆ exit()

pyhelios.StomatalConductance.StomatalConductanceModel.__exit__	(	self,
		exc_type,
		exc_value,
		traceback )

Context manager exit with proper cleanup.

Definition at line 185 of file StomatalConductance.py.

◆ disableMessages()

None pyhelios.StomatalConductance.StomatalConductanceModel.disableMessages ( self )

Disable console output messages from the stomatal conductance model.

Exceptions

StomatalConductanceModelError If operation fails

Definition at line 217 of file StomatalConductance.py.

◆ enableMessages()

None pyhelios.StomatalConductance.StomatalConductanceModel.enableMessages ( self )

Enable console output messages from the stomatal conductance model.

Exceptions

StomatalConductanceModelError If operation fails

Definition at line 205 of file StomatalConductance.py.

◆ getNativePtr()

pyhelios.StomatalConductance.StomatalConductanceModel.getNativePtr ( self )

Get the native pointer for advanced operations.

Definition at line 196 of file StomatalConductance.py.

◆ is_available()

bool pyhelios.StomatalConductance.StomatalConductanceModel.is_available ( self )

Check if StomatalConductanceModel is available in current build.

Returns: True if plugin is available, False otherwise

Definition at line 595 of file StomatalConductance.py.

◆ optionalOutputPrimitiveData()

None pyhelios.StomatalConductance.StomatalConductanceModel.optionalOutputPrimitiveData	(		self,
		str	label )

Add optional output primitive data to the Context.

Parameters

label Name of primitive data to output (e.g., "Ci", "gs", "E")

Exceptions

ValueError	If label is invalid
StomatalConductanceModelError	If operation fails

Examples

>>> # Output stomatal conductance values
>>> stomatal.optionalOutputPrimitiveData("gs")
 
>>> # Output intercellular CO2 concentration
>>> stomatal.optionalOutputPrimitiveData("Ci")

Definition at line 553 of file StomatalConductance.py.

◆ printDefaultValueReport()

None pyhelios.StomatalConductance.StomatalConductanceModel.printDefaultValueReport	(		self,
		Optional[List[int]]	uuids = None )

Print a report detailing usage of default input values.

Parameters

uuids Optional list of primitive UUIDs. If None, reports on all primitives.

Exceptions

StomatalConductanceModelError If operation fails

Examples

>>> # Print report for all primitives
>>> stomatal.printDefaultValueReport()
 
>>> # Print report for specific leaves
>>> stomatal.printDefaultValueReport(uuids=[leaf1_uuid, leaf2_uuid])

Definition at line 580 of file StomatalConductance.py.

◆ run()

None pyhelios.StomatalConductance.StomatalConductanceModel.run	(		self,
		Optional[List[int]]	uuids = None,
		Optional[float]	dt = None )

Run the stomatal conductance model.

   This method supports multiple execution modes:
   - Steady state for all primitives: run()
   - Dynamic with timestep for all primitives: run(dt=60.0)
   - Steady state for specific primitives: run(uuids=[1, 2, 3])
   - Dynamic with timestep for specific primitives: run(uuids=[1, 2, 3], dt=60.0)

Parameters

uuids	Optional list of primitive UUIDs to process. If None, processes all primitives.
dt	Optional timestep in seconds for dynamic simulation. If None, runs steady-state.

Exceptions

ValueError	If parameters are invalid
StomatalConductanceModelError	If calculation fails

Examples

>>> # Steady state for all primitives
>>> stomatal.run()
 
>>> # Dynamic simulation with 60-second timestep
>>> stomatal.run(dt=60.0)
 
>>> # Steady state for specific leaves
>>> stomatal.run(uuids=[leaf1_uuid, leaf2_uuid])
 
>>> # Dynamic simulation for specific leaves
>>> stomatal.run(uuids=[leaf1_uuid, leaf2_uuid], dt=30.0)

Definition at line 255 of file StomatalConductance.py.

◆ setBBCoefficients()

None pyhelios.StomatalConductance.StomatalConductanceModel.setBBCoefficients	(		self,
		BBCoefficients	coeffs,
		Optional[List[int]]	uuids = None )

Set Bailey model coefficients.

Parameters

coeffs	BB model coefficients (pi_0, pi_m, theta, sigma, chi)
uuids	Optional list of primitive UUIDs. If None, applies to all primitives.

Exceptions

ValueError	If coefficients are invalid
StomatalConductanceModelError	If operation fails

Examples

>>> bb_coeffs = BBCoefficients(pi_0=1.0, pi_m=1.67, theta=211.22, sigma=0.4408, chi=2.076)

>>> stomatal.setBBCoefficients(bb_coeffs)

Definition at line 433 of file StomatalConductance.py.

◆ setBBLCoefficients()

None pyhelios.StomatalConductance.StomatalConductanceModel.setBBLCoefficients	(		self,
		BBLCoefficients	coeffs,
		Optional[List[int]]	uuids = None )

Set Ball-Berry-Leuning model coefficients.

Parameters

coeffs	BBL model coefficients (gs0, a1, D0)
uuids	Optional list of primitive UUIDs. If None, applies to all primitives.

Exceptions

ValueError	If coefficients are invalid
StomatalConductanceModelError	If operation fails

Examples

>>> bbl_coeffs = BBLCoefficients(gs0=0.0743, a1=4.265, D0=14570.0)

>>> stomatal.setBBLCoefficients(bbl_coeffs)

Definition at line 325 of file StomatalConductance.py.

◆ setBMFCoefficients()

None pyhelios.StomatalConductance.StomatalConductanceModel.setBMFCoefficients	(		self,
		BMFCoefficients	coeffs,
		Optional[List[int]]	uuids = None )

Set Buckley-Mott-Farquhar model coefficients.

Parameters

coeffs	BMF model coefficients (Em, i0, k, b)
uuids	Optional list of primitive UUIDs. If None, applies to all primitives.

Exceptions

ValueError	If coefficients are invalid
StomatalConductanceModelError	If operation fails

Examples

>>> bmf_coeffs = BMFCoefficients(Em=258.25, i0=38.65, k=232916.82, b=609.67)

>>> stomatal.setBMFCoefficients(bmf_coeffs)

Definition at line 395 of file StomatalConductance.py.

◆ setBMFCoefficientsFromLibrary()

None pyhelios.StomatalConductance.StomatalConductanceModel.setBMFCoefficientsFromLibrary	(		self,
		str	species,
		Optional[List[int]]	uuids = None )

Set BMF model coefficients using the built-in species library.

Parameters

species	Species name from the library (e.g., "Almond", "Apple", "Grape", "Walnut")
uuids	Optional list of primitive UUIDs. If None, applies to all primitives.

Exceptions

ValueError	If species name is invalid
StomatalConductanceModelError	If operation fails

Examples

>>> # Set coefficients for almond tree
>>> stomatal.setBMFCoefficientsFromLibrary("Almond")
 
>>> # Set coefficients for specific leaves only
>>> stomatal.setBMFCoefficientsFromLibrary("Grape", uuids=[leaf1_uuid, leaf2_uuid])

Definition at line 476 of file StomatalConductance.py.

◆ setBWBCoefficients()

None pyhelios.StomatalConductance.StomatalConductanceModel.setBWBCoefficients	(		self,
		BWBCoefficients	coeffs,
		Optional[List[int]]	uuids = None )

Set Ball-Woodrow-Berry model coefficients.

Parameters

coeffs	BWB model coefficients (gs0, a1)
uuids	Optional list of primitive UUIDs. If None, applies to all primitives.

Exceptions

ValueError	If coefficients are invalid
StomatalConductanceModelError	If operation fails

Examples

>>> bwb_coeffs = BWBCoefficients(gs0=0.0733, a1=9.422)

>>> stomatal.setBWBCoefficients(bwb_coeffs)

Definition at line 291 of file StomatalConductance.py.

◆ setDynamicTimeConstants()

None pyhelios.StomatalConductance.StomatalConductanceModel.setDynamicTimeConstants	(		self,
		float	tau_open,
		float	tau_close,
		Optional[List[int]]	uuids = None )

Set time constants for dynamic stomatal opening and closing.

Parameters

tau_open	Time constant (seconds) for stomatal opening
tau_close	Time constant (seconds) for stomatal closing
uuids	Optional list of primitive UUIDs. If None, applies to all primitives.

Exceptions

ValueError	If time constants are invalid
StomatalConductanceModelError	If operation fails

Examples

>>> # Set time constants for all leaves
>>> stomatal.setDynamicTimeConstants(tau_open=120.0, tau_close=240.0)
 
>>> # Set different time constants for specific leaves
>>> stomatal.setDynamicTimeConstants(tau_open=60.0, tau_close=180.0, uuids=[leaf1_uuid])

Definition at line 519 of file StomatalConductance.py.

◆ setMOPTCoefficients()

None pyhelios.StomatalConductance.StomatalConductanceModel.setMOPTCoefficients	(		self,
		MOPTCoefficients	coeffs,
		Optional[List[int]]	uuids = None )

Set Medlyn et al.

optimality model coefficients.

Parameters

coeffs	MOPT model coefficients (gs0, g1)
uuids	Optional list of primitive UUIDs. If None, applies to all primitives.

Exceptions

ValueError	If coefficients are invalid
StomatalConductanceModelError	If operation fails

Examples

>>> mopt_coeffs = MOPTCoefficients(gs0=0.0825, g1=2.637)

>>> stomatal.setMOPTCoefficients(mopt_coeffs)

Definition at line 361 of file StomatalConductance.py.

Member Data Documentation

◆ context

pyhelios.StomatalConductance.StomatalConductanceModel.context = context

Definition at line 128 of file StomatalConductance.py.

◆ stomatal_model

pyhelios.StomatalConductance.StomatalConductanceModel.stomatal_model = None

Definition at line 129 of file StomatalConductance.py.

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

pyhelios/StomatalConductance.py

Detailed Description

Public Member Functions

Public Attributes

Constructor & Destructor Documentation

◆ __init__()

Member Function Documentation

◆ __enter__()

◆ __exit__()

◆ disableMessages()

◆ enableMessages()

◆ getNativePtr()

◆ is_available()

◆ optionalOutputPrimitiveData()

◆ printDefaultValueReport()

◆ run()

◆ setBBCoefficients()

◆ setBBLCoefficients()

◆ setBMFCoefficients()

◆ setBMFCoefficientsFromLibrary()

◆ setBWBCoefficients()

◆ setDynamicTimeConstants()

◆ setMOPTCoefficients()

Member Data Documentation

◆ context

◆ stomatal_model

◆ init()

◆ enter()

◆ exit()