PyHelios

https://plantsimulationlab.github.io/PyHelios/
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PyHelios provides Python bindings for the Helios 3D plant simulation library, enabling biophysical...
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### Interactive selection (guided setup)

Source: https://plantsimulationlab.github.io/PyHelios/PluginBuildSystem.html

Starts an interactive guided setup for plugin selection.

```bash
build_scripts/build_helios --interactive
```

--------------------------------

### Quick start with PlantArchitecture

Source: https://plantsimulationlab.github.io/PyHelios/PlantArchitectureDoc.html

Quick start example that creates a PyHelios context and PlantArchitecture plugin, then retrieves and prints the available plant models.

```python
from pyhelios import Context, PlantArchitecture
from pyhelios.types import *
# Create context and plugin
with Context() as context:
    with PlantArchitecture(context) as plantarch:
        # Get available plant models
        models = plantarch.getAvailablePlantModels()
        print(f"Available models: {models}")
```

--------------------------------

### Quick Start Example

Source: https://plantsimulationlab.github.io/PyHelios/BoundaryLayerConductanceDoc.html

A basic example demonstrating how to initialize the PyHelios context and add a leaf patch using the BoundaryLayerConductanceModel.

```python
from pyhelios import Context, BoundaryLayerConductanceModel
from pyhelios.types import vec3, vec2
with Context() as context:
# Create leaf geometry
leaf_uuid = context.addPatch(center=vec3(0, 0, 1), size=vec2(0.1, 0.1))
```

--------------------------------

### Quick Start: Using Visualizer with Context

Source: https://plantsimulationlab.github.io/PyHelios/VisualizerDoc.html

Initializes a PyHelios Context and Visualizer. Requires OpenGL 3.3+ and X11/xorg on Mac/Linux. The example shows the import statements and the start of a with block.

```python
from pyhelios import Context, Visualizer
from pyhelios.types import vec3, vec2, RGBcolor
with Context() as context:
```

--------------------------------

### Setup prerequisites on CentOS/RHEL

Source: https://plantsimulationlab.github.io/PyHelios/CrossPlatform.html

Commands to install development tools and dependencies on RHEL-based systems.

```bash
sudo yum groupinstall "Development Tools"
sudo yum install cmake python3-devel
```

--------------------------------

### LeafOptics Quick Start

Source: https://plantsimulationlab.github.io/PyHelios/LeafOpticsDoc.html

Quick start example for the LeafOptics plugin. It imports the required classes and creates a leaf patch geometry using the context's addPatch method.

```python
from pyhelios import Context, LeafOptics
from pyhelios.types import vec3, vec2
with Context() as context:
# Create leaf geometry
uuid = context.addPatch(center=vec3(0, 0, 1), size=vec2(0.1, 0.1))
```

--------------------------------

### Minimal SIF Wiring Example

Source: https://plantsimulationlab.github.io/PyHelios/LeafOpticsDoc.html

Demonstrates the basic setup for configuring leaf properties and running the LeafOptics simulation for SIF.

```python
from pyhelios import Context, LeafOptics
from pyhelios.LeafOptics import LeafOpticsProperties
from pyhelios.types import vec3, vec2
with Context() as context:
leaf_uuids = [context.addPatch(center=vec3(0, 0, 1), size=vec2(0.1, 0.1))]
with LeafOptics(context) as leafoptics:
props = LeafOpticsProperties()
props.chlorophyllcontent = 40.0 # Cab, ug/cm^2
props.carotenoidcontent = 10.0 # Cca, ug/cm^2
props.numberlayers = 1.5
props.watermass = 0.009 # cm
props.drymass = 0.012 # g/cm^2
props.V2Z = 0.0 # dark-adapted; SIF-only
props.fqe = 1.0 # no calibration scalar; SIF-only
leafoptics.run(leaf_uuids, props, "myleaf")
```

--------------------------------

### Initialize SolarPosition Context

Source: https://plantsimulationlab.github.io/PyHelios/SolarPositionDoc.html

A quick start example showing how to import necessary modules, initialize a context, and set the date and time.

```python
from pyhelios import Context, SolarPosition
from pyhelios.types import *
with Context() as context:
# Set date and time
context.setDate(2015, 5, 1) # May 1, 2015
context.setTime(12, 30) # 12:30
```

--------------------------------

### Run Plant Architecture File I/O Example

Source: https://plantsimulationlab.github.io/PyHelios/PlantArchitectureDoc.html

Command to execute the comprehensive file I/O example script provided in the documentation examples directory.

```bash
python docs/examples/plantarch_file_io_sample.py
```

--------------------------------

### Example usage of run()

Source: https://plantsimulationlab.github.io/PyHelios/classpyhelios_1_1EnergyBalance_1_1EnergyBalanceModel.html

Examples demonstrating steady-state and dynamic simulation calls for the EnergyBalanceModel.

```python
>>> # Steady state for all primitives >>> energy_balance.run()
```

```python
>>> # Dynamic simulation with 60-second timestep >>> energy_balance.run(dt=60.0)
```

```python
>>> # Steady state for specific patches >>> energy_balance.run(uuids=[patch1_uuid, patch2_uuid])
```

```python
>>> # Dynamic simulation for specific patches >>> energy_balance.run(uuids=[patch1_uuid, patch2_uuid], dt=30.0)
```

--------------------------------

### Build a Weber-Penn Tree

Source: https://plantsimulationlab.github.io/PyHelios/WeberPennTreeDoc.html

A quick start example demonstrating how to initialize a PyHelios context and build a lemon tree at the origin.

```python
from pyhelios import Context, WeberPennTree, WPTType
from pyhelios.types import vec3
with Context() as context:
with WeberPennTree(context) as wpt:
# Build a lemon tree
tree_id = wpt.buildTree(WPTType.LEMON, origin=vec3(0, 0, 0))
```

--------------------------------

### Initialize PhotosynthesisModel Context

Source: https://plantsimulationlab.github.io/PyHelios/PhotosynthesisDoc.html

A quick start example demonstrating how to initialize the PyHelios context and create a simple patch.

```python
from pyhelios import Context, PhotosynthesisModel
from pyhelios.types import vec3, vec2
with Context() as context:
# Create a simple patch
patch_uuid = context.addPatch(center=vec3(0, 0, 0), size=vec2(0.1, 0.1))
```

--------------------------------

### Install CUDA Toolkit on Ubuntu 22.04

Source: https://plantsimulationlab.github.io/PyHelios/CUDASetup.html

Commands to download the keyring, install the toolkit, update the PATH, and verify the installation on Ubuntu.

```bash
wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/x86_64/cuda-keyring_1.1-1_all.deb
sudo dpkg -i cuda-keyring_1.1-1_all.deb
sudo apt-get update
sudo apt-get install cuda-toolkit-12-3
export PATH=/usr/local/cuda-12.3/bin:$PATH
export LD_LIBRARY_PATH=/usr/local/cuda-12.3/lib64:$LD_LIBRARY_PATH
source ~/.bashrc
nvidia-smi
nvcc --version
```

--------------------------------

### Install CUDA on Ubuntu

Source: https://plantsimulationlab.github.io/PyHelios/CrossPlatform.html

Steps to configure the NVIDIA repository and install CUDA drivers.

```bash
wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-ubuntu2004.pin
sudo mv cuda-ubuntu2004.pin /etc/apt/preferences.d/cuda-repository-pin-600
sudo apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/7fa2af80.pub
sudo add-apt-repository "deb https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/ /"
sudo apt-get update
sudo apt-get install cuda
```

--------------------------------

### Install PyHelios on General Systems

Source: https://plantsimulationlab.github.io/PyHelios/index.html

Standard installation sequence for cloning the repository, building native libraries, and installing Python dependencies.

```bash
git clone --recursive https://github.com/PlantSimulationLab/PyHelios.git
cd PyHelios/
# Build native libraries (optional - pre-built binaries included)
./build_scripts/build_helios
# Install PyHelios dependencies
pip install -e .
```

--------------------------------

### PhotosynthesisModel Usage Example

Source: https://plantsimulationlab.github.io/PyHelios/PhotosynthesisDoc.html

Example showing how to set required primitive data, create a PhotosynthesisModel, run it, and retrieve the net photosynthesis result.

```APIDOC
## PhotosynthesisModel Usage Example

### Description
Demonstrates setting required primitive data, creating a PhotosynthesisModel, running the model, and retrieving the net photosynthesis output.

### Usage
```python
# Set required primitive data
context.setPrimitiveDataFloat(patch_uuid, "radiation_flux_PAR", 500.0) # W/m²
context.setPrimitiveDataFloat(patch_uuid, "temperature", 298.15) # K
context.setPrimitiveDataFloat(patch_uuid, "air_CO2", 400.0) # µmol/mol
context.setPrimitiveDataFloat(patch_uuid, "moisture_conductance", 0.3) # mol/m²-s
context.setPrimitiveDataFloat(patch_uuid, "boundarylayer_conductance", 1.0) # mol/m²-s

# Create photosynthesis model
with PhotosynthesisModel(context) as photo:
    # Use species from library
    photo.setFarquharCoefficientsFromLibrary("Almond")
    # Run model
    photo.run()

# Get results
A = context.getPrimitiveData(patch_uuid, "net_photosynthesis")
print(f"Net photosynthesis: {A[0]:.2f} µmol CO₂/m²-s")
```

### Input Primitive Data
- **radiation_flux_PAR** (float) - Required - Radiative flux in PAR band (W/m2). Automatically converted to photon flux density.
- **temperature** (float) - Required - Primitive surface temperature (Kelvin).
- **air_CO2** (float) - Required - CO2 concentration of air outside of primitive boundary-layer (μmol CO2/mol air).
- **moisture_conductance** (float) - Required - Conductance to moisture between sub-stomatal cells and leaf surface (mol air/m2-s).
- **boundarylayer_conductance** (float) - Required - Conductance to heat between leaf surface and outside of the boundary-layer (mol air/m2-s).
- **twosided_flag** (uint) - Optional - Flag indicating number of primitive faces with heat transfer (0 for one-sided, 1 for two-sided).
- **stomatal_sidedness** (float) - Optional - Ratio of stomatal density on upper leaf surface to total stomatal density.

### Output Primitive Data
- **net_photosynthesis** (float) - Default output - Net rate of carbon transfer per unit one-sided area (μmol CO2/m2-sec).
- **Ci** (float) - Optional - Intercellular CO2 concentration (μmol CO2/mol).
- **Gamma_CO2** (float) - Optional - Photosynthetic CO2 compensation point (μmol CO2/mol).
- **limitation_state** (int) - Optional - Photosynthesis limitation state.
- **Cm** (float) - Optional - Mesophyll cytosolic CO2 partial pressure (μbar). C4 model only.
- **Vp** (float) - Optional - PEP carboxylation rate (μmol CO2/m2-sec). C4 model only.
```

--------------------------------

### Visualizer printWindow usage examples

Source: https://plantsimulationlab.github.io/PyHelios/Visualizer_8py_source.html

Examples showing how to save the current visualization window to a file, with automatic or explicit format detection.

```python
>>> visualizer.printWindow("output.jpg") # Auto-detects JPEG
>>> visualizer.printWindow("output.png") # Auto-detects PNG
>>> visualizer.printWindow("output.img", image_format="png") # Explicit PNG
```

--------------------------------

### Install PyHelios on macOS

Source: https://plantsimulationlab.github.io/PyHelios/index.html

Installation workflow for macOS, including C++ dependency setup and native library building.

```bash
git clone --recursive https://github.com/PlantSimulationLab/PyHelios.git
cd PyHelios/
# Install c++ dependencies and build native libraries
source helios-core/utilities/dependencies.sh
./build_scripts/build_helios
# Install PyHelios dependencies
pip install -e .
```

--------------------------------

### Install dependencies and build native libraries

Source: https://plantsimulationlab.github.io/PyHelios/CrossPlatform.html

Standard commands to prepare the environment and build native components.

```bash
source helios-core/utilities/dependencies.sh
build_scripts/build_helios
pip install -e .
```

--------------------------------

### Build a plant instance from library

Source: https://plantsimulationlab.github.io/PyHelios/classpyhelios_1_1PlantArchitecture_1_1PlantArchitecture.html

Demonstrates building a plant instance with default and custom parameters.

```python
>>> plant_id = plantarch.buildPlantInstanceFromLibrary(base_position=vec3(2.0, 3.0, 0.0), age=45.0) >>> # With custom parameters >>> plant_id = plantarch.buildPlantInstanceFromLibrary( ... base_position=vec3(0, 0, 0), ... age=30.0, ... build_parameters={'trunk_height': 2.0} ... )
```

--------------------------------

### LiDARCloud.syntheticScan() discrete-return and full-waveform examples

Source: https://plantsimulationlab.github.io/PyHelios/LiDARCloud_8py_source.html

Two usage examples for LiDARCloud.syntheticScan(): a discrete-return scan (rays_per_pulse=None) and a full-waveform scan (rays_per_pulse=100). The discrete-return example shows the required setup with Context and LiDARCloud, including addScan() parameters. The full-waveform example requires pulse_distance_threshold and raises ValueError if it is missing.

```python
>>> from pyhelios import Context, LiDARCloud
>>> from pyhelios.types import vec3
>>> with Context() as context:
...     # Add geometry
...     context.addPatch(center=vec3(0, 0, 0.5), size=vec2(1, 1))
...
...     with LiDARCloud() as lidar:
...         # Define scan parameters
...         scan_id = lidar.addScan(
...             origin=vec3(0, 0, 2),
...             Ntheta=100, theta_range=(0, 1.57),
...             Nphi=100, phi_range=(0, 6.28),
...             exit_diameter=0, beam_divergence=0
...         )
...
...         # Perform discrete-return scan
...         lidar.syntheticScan(context)
```

```python
>>> lidar.syntheticScan(
...     context,
...     rays_per_pulse=100,
...     pulse_distance_threshold=0.02,
...     record_misses=True
... )
```

--------------------------------

### Initialize Visualizer

Source: https://plantsimulationlab.github.io/PyHelios/VisualizerDoc.html

Basic setup for importing the Visualizer and required types.

```python
from pyhelios import Visualizer
from pyhelios.types import vec3, SphericalCoord
with Visualizer(width=1200, height=800) as vis:
```

--------------------------------

### Get Sun Direction Vector

Source: https://plantsimulationlab.github.io/PyHelios/SolarPosition_8py_source.html

Example of retrieving the sun's direction as a vector.

```python
>>> direction = solar.getSunDirectionVector()
>>> print(f"Sun direction vector: ({direction.x:.3f}, {direction.y:.3f}, {direction.z:.3f})")
```

--------------------------------

### Enable Headless Mode

Source: https://plantsimulationlab.github.io/PyHelios/VisualizerDoc.html

Example showing how to initialize the Visualizer in headless mode by setting the headless parameter to True in the constructor.

```python
from pyhelios import Context, Visualizer
from pyhelios.types import vec3
with Context() as context:

```

--------------------------------

### Get Geometry Vertices Example

Source: https://plantsimulationlab.github.io/PyHelios/Visualizer_8py_source.html

Demonstrates how to retrieve and iterate over the vertices of a geometry primitive.

```python
>>> vertices = visualizer.getGeometryVertices(geometry_id)
>>> for vertex in vertices:
... print(f"Vertex: ({vertex.x}, {vertex.y}, {vertex.z})")
```

--------------------------------

### Get Diffuse Flux

Source: https://plantsimulationlab.github.io/PyHelios/RadiationModel_8py_source.html

Example of retrieving the diffuse flux for a specific band using getDiffuseFlux.

```python
>>> flux = radiation.getDiffuseFlux("SW")
```

--------------------------------

### Build from source on Ubuntu/Debian

Source: https://plantsimulationlab.github.io/PyHelios/CrossPlatform.html

Steps to install prerequisites and build the project from source on Debian-based systems.

```bash
# Install prerequisites
sudo apt-get update
sudo apt-get install build-essential cmake python3-dev
git clone --recursive https://github.com/PlantSimulationLab/PyHelios.git
cd PyHelios/
```

--------------------------------

### Get Shoot Hierarchy Map Example

Source: https://plantsimulationlab.github.io/PyHelios/PlantArchitecture_8py_source.html

Demonstrates how to retrieve a mapping of shoot IDs to their direct children IDs.

```python
>>> hierarchy = plantarch.getShootHierarchyMap(plant_id)
>>> print(f"{len(hierarchy)} shoots carry branches")
```

--------------------------------

### loadPlantModelFromLibrary usage example

Source: https://plantsimulationlab.github.io/PyHelios/classpyhelios_1_1PlantArchitecture_1_1PlantArchitecture.html

Demonstrates loading different plant models from the built-in library.

```python
>>> plantarch.loadPlantModelFromLibrary("bean") >>> plantarch.loadPlantModelFromLibrary("almond")
```

--------------------------------

### Get Sun Direction Spherical

Source: https://plantsimulationlab.github.io/PyHelios/SolarPosition_8py_source.html

Example of retrieving the sun's direction as spherical coordinates with radius, elevation, and azimuth.

```python
>>> spherical = solar.getSunDirectionSpherical()
>>> print(f"Spherical: r={spherical.radius}, elev={spherical.elevation:.3f}, az={spherical.azimuth:.3f}")
```

--------------------------------

### Import PyHelios context and types

Source: https://plantsimulationlab.github.io/PyHelios/API.html

Initial setup for using the PyHelios library.

```python
from pyhelios import Context
from pyhelios.types import vec3, vec2
```

--------------------------------

### Example usage of enableSolidObstacleAvoidance

Source: https://plantsimulationlab.github.io/PyHelios/classpyhelios_1_1PlantArchitecture_1_1PlantArchitecture.html

Demonstrates both a simple configuration of solid obstacles and a more specific setup involving reduced avoidance distance and fruit adjustment.

```python
>>> # Simple solid obstacle avoidance >>> wall_uuids = [1, 2, 3, 4] # UUIDs of wall primitives >>> plantarch.enableSolidObstacleAvoidance(wall_uuids) >>> >>> # Close avoidance with fruit adjustment >>> plantarch.enableSolidObstacleAvoidance( ... obstacle_UUIDs=wall_uuids, ... avoidance_distance=0.1, ... enable_fruit_adjustment=True ... )
```

--------------------------------

### PhotosynthesisModel usage example

Source: https://plantsimulationlab.github.io/PyHelios/PhotosynthesisModel_8py_source.html

Demonstrates how to initialize the PhotosynthesisModel within a context, configure it with empirical model coefficients, and execute the simulation.

```python
>>> from pyhelios import Context, PhotosynthesisModel
>>> from pyhelios.types import EmpiricalModelCoefficients
>>> context = Context()
>>> with PhotosynthesisModel(context) as photosynthesis:
... # Configure empirical model
... coeffs = EmpiricalModelCoefficients(
... Tref=298.0, # Reference temperature (K)
... Ci_ref=290.0, # Reference CO2 concentration (μmol/mol)
... Asat=20.0, # Light-saturated photosynthesis rate (μmol/m²/s)
... theta=65.0 # Light response curvature (µmol/m²·s PPFD)
... )
... photosynthesis.setEmpiricalModelCoefficients(coeffs)
... photosynthesis.run()
```

--------------------------------

### Get camera orientation with getCameraOrientation

Source: https://plantsimulationlab.github.io/PyHelios/classpyhelios_1_1RadiationModel_1_1RadiationModel.html

Retrieves the camera orientation as a SphericalCoord [radius, elevation, azimuth] for the given camera label. The example prints the returned orientation.

```python
>>> orientation = radiation.getCameraOrientation("cam1")
>>> print(f"Camera orientation: {orientation}")
```

--------------------------------

### Add Disks with Various Configurations

Source: https://plantsimulationlab.github.io/PyHelios/Context_8py_source.html

Examples demonstrating how to create a simple red disk, a semi-transparent blue elliptical disk, and a disk with specific polar and radial subdivisions.

```python
>>> context = Context()
>>> # Create a red disk at (0, 0, 1) with radius 0.5
>>> disk_uuids = context.addDisk(
... center=vec3(0, 0, 1),
... size=vec2(0.5, 0.5),
... ndivs=30,
... color=RGBcolor(1, 0, 0)
... )
>>> print(f"Created disk with {len(disk_uuids)} triangles")
>>>
>>> # Create a semi-transparent blue elliptical disk
>>> disk_uuids = context.addDisk(
... center=vec3(0, 0, 2),
... size=vec2(1.0, 0.5),
... ndivs=40,
... rotation=SphericalCoord(1, 0.5, 0),
... color=RGBAcolor(0, 0, 1, 0.5)
... )
>>>
>>> # Create disk with polar/radial subdivisions for finer control
>>> disk_uuids = context.addDisk(
... center=vec3(0, 0, 3),
... size=vec2(1, 1),
... ndivs=int2(10, 20), # 10 radial, 20 azimuthal divisions
... color=RGBcolor(0, 1, 0)
... )
```

--------------------------------

### Configure and run photosynthesis simulation

Source: https://plantsimulationlab.github.io/PyHelios/classpyhelios_1_1PhotosynthesisModel_1_1PhotosynthesisModel.html

Demonstrates initializing a photosynthesis model within a context manager, configuring empirical model coefficients, and executing the simulation.

```python
>>> from pyhelios import Context, PhotosynthesisModel >>> from pyhelios.types import EmpiricalModelCoefficients >>> context = Context() >>> with PhotosynthesisModel(context) as photosynthesis: ... # Configure empirical model ... coeffs = EmpiricalModelCoefficients( ... Tref=298.0, # Reference temperature (K) ... Ci_ref=290.0, # Reference CO2 concentration (μmol/mol) ... Asat=20.0, # Light-saturated photosynthesis rate (μmol/m²/s) ... theta=65.0 # Light response curvature (µmol/m²·s PPFD) ... ) ... photosynthesis.setEmpiricalModelCoefficients(coeffs) ... photosynthesis.run()
```

--------------------------------

### Get Plant Leaf Areas Example

Source: https://plantsimulationlab.github.io/PyHelios/PlantArchitecture_8py_source.html

Demonstrates how to retrieve the built one-sided surface area of every leaf on a plant. Requires helios-core v1.3.85 or newer.

```python
>>> areas = plantarch.getPlantLeafAreas(plant_id)
>>> print(f"{len(areas)} leaves, mean {sum(areas)/len(areas):.4f} m^2")
```

--------------------------------

### Add utility objects with Visualizer

Source: https://plantsimulationlab.github.io/PyHelios/VisualizerDoc.html

Shows the setup for adding utility objects like coordinate axes and grid wireframes. The example opens a Visualizer and is followed by calls to addCoordinateAxes(), addCoordinateAxesCustom(), or addGridWireFrame().

```python
from pyhelios import Visualizer
from pyhelios.types import vec3

with Visualizer(width=1200, height=800) as vis:
```

--------------------------------

### Build a plant instance from the library

Source: https://plantsimulationlab.github.io/PyHelios/PlantArchitecture_8py_source.html

Shows how to create a plant instance at a specific position and age, with optional custom build parameters for supported models.

```python
>>> plant_id = plantarch.buildPlantInstanceFromLibrary(base_position=vec3(2.0, 3.0, 0.0), age=45.0)
>>> # With custom parameters
>>> plant_id = plantarch.buildPlantInstanceFromLibrary(
... base_position=vec3(0, 0, 0),
... age=30.0,
... build_parameters={'trunk_height': 2.0}
... )
```

--------------------------------

### Set coefficients for different species using UUIDs

Source: https://plantsimulationlab.github.io/PyHelios/StomatalConductanceDoc.html

Shows the import statements and context setup for a UUID-based coefficient setting example. The code is incomplete in the source, showing only the beginning of a context block.

```python
from pyhelios import Context, StomatalConductanceModel, WeberPennTree, WPTType
from pyhelios.types import vec3, vec2
with Context() as context:
```

--------------------------------

### Create an empty plant instance

Source: https://plantsimulationlab.github.io/PyHelios/PlantArchitecture_8py_source.html

Demonstrates how to initialize a new plant at a specific location and add a base stem shoot to it.

```python
>>> # Create empty plant at origin
>>> plant_id = plantarch.addPlantInstance(vec3(0, 0, 0), 0.0)
>>>
>>> # Now add shoots to build custom plant structure
>>> shoot_id = plantarch.addBaseStemShoot(
... plant_id, 1, AxisRotation(0, 0, 0), 0.01, 0.1, 1.0, 1.0, 0.8, "mainstem"
... )
```

--------------------------------

### LiDARCloud usage example

Source: https://plantsimulationlab.github.io/PyHelios/LiDARCloud_8py_source.html

Demonstrates initializing a LiDARCloud, adding a scan, adding hit points, and exporting the resulting point cloud.

```python
>>> from pyhelios import LiDARCloud
>>> from pyhelios.types import vec3
>>>
>>> with LiDARCloud() as lidar:
... # Add a scan
... scan_id = lidar.addScan(
... origin=vec3(0, 0, 1),
... Ntheta=100, theta_range=(0, 1.57),
... Nphi=100, phi_range=(-3.14, 3.14),
... exit_diameter=0.01, beam_divergence=0.001
... )
...
... # Add hit points
... lidar.addHitPoint(scan_id, vec3(1, 0, 0), vec3(1, 0, 0))
...
... # Export point cloud
... lidar.exportPointCloud("output.xyz")
```

--------------------------------

### Example: Define a custom shoot type

Source: https://plantsimulationlab.github.io/PyHelios/PlantArchitecture_8py_source.html

Shows how to load a plant model, get shoot parameters, modify them, and define a new shoot type. Uses RandomParameterFloat to set constant and uniform parameters.

```python
>>> from pyhelios.plant_architecture_params import ShootParameters, RandomParameterFloat
>>> plantarch.loadPlantModelFromLibrary("bean")
>>> sp = plantarch.getCurrentShootParameters("trifoliate", return_typed=True)
>>> sp.max_nodes = RandomParameterFloat.constant(20)
>>> sp.phytomer_parameters.leaf.pitch = RandomParameterFloat.uniform(40, 50)
>>> plantarch.defineShootType("TallStem", sp)
```

--------------------------------

### PyHelios plugin CLI usage

Source: https://plantsimulationlab.github.io/PyHelios/____main_____8py_source.html

Command-line usage examples for the PyHelios plugin management CLI. These commands check plugin status, discover optimal configurations, get plugin information, and validate plugin lists.

```bash
python -m pyhelios.plugins status
python -m pyhelios.plugins discover 
python -m pyhelios.plugins info <plugin_name>
python -m pyhelios.plugins validate <plugin_list>
```

--------------------------------

### __init__(self, Context context)

Source: https://plantsimulationlab.github.io/PyHelios/classpyhelios_1_1RadiationModel_1_1RadiationModel.html

Initializes a RadiationModel instance with graceful plugin handling.

```APIDOC
## __init__(self, Context context)

### Description
Initializes RadiationModel with graceful plugin handling.

### Parameters
- **context** (Context) - Required - The context object for the radiation model.

### Returns
None
```

--------------------------------

### Install CUDA via Direct Runfile

Source: https://plantsimulationlab.github.io/PyHelios/CUDASetup.html

Alternative installation method using the NVIDIA runfile installer for more control.

```bash
wget https://developer.download.nvidia.com/compute/cuda/12.3.0/local_installers/cuda_12.3.0_545.23.06_linux.run
sudo sh cuda_12.3.0_545.23.06_linux.run
```

--------------------------------

### Calculate boundary-layer conductance

Source: https://plantsimulationlab.github.io/PyHelios/BoundaryLayerConductanceDoc.html

Example demonstrating how to set environmental conditions, configure the boundary-layer model, and retrieve the calculated conductance.

```python
# Set environmental conditions (optional - defaults used if not set)
context.setPrimitiveDataFloat(leaf_uuid, "wind_speed", 2.0) # m/s
context.setPrimitiveDataFloat(leaf_uuid, "air_temperature", 298.0) # K
# Use boundary-layer conductance model
with BoundaryLayerConductanceModel(context) as blc:
# Set model for all primitives (default is Pohlhausen)
blc.setBoundaryLayerModel("InclinedPlate")
# Run calculation
blc.run()
# Get results
gH = context.getPrimitiveData(leaf_uuid, "boundarylayer_conductance")
print(f"Boundary-layer conductance: {gH[0]:.3f} mol air/m²-s")
```

--------------------------------

### Initialize Context and Add Timeseries Data

Source: https://plantsimulationlab.github.io/PyHelios/API.html

Demonstrates creating a Context object and populating it with temperature data points using Date and Time objects.

```python
context = Context()
# Add data to timeseries
# Date constructor: Date(year, month, day)
date = Date(2000, 1, 2) # 2 Jan. 2000
time = Time(13, 0, 0) # 13:00:00
context.addTimeseriesData("temperature", 301.23, date, time) # index #0
time = Time(13, 15, 0) # 13:15:00
context.addTimeseriesData("temperature", 301.92, date, time) # index #1
time = Time(13, 30, 0) # 13:30:00
context.addTimeseriesData("temperature", 302.56, date, time) # index #2
time = Time(13, 45, 0) # 13:45:00
context.addTimeseriesData("temperature", 303.05, date, time) # index #3
```

--------------------------------

### Install CUDA Toolkit on CentOS/RHEL

Source: https://plantsimulationlab.github.io/PyHelios/CUDASetup.html

Commands to install the CUDA repository, the toolkit, update the environment variables, and verify the installation on RHEL 8.

```bash
sudo yum install https://developer.download.nvidia.com/compute/cuda/repos/rhel8/x86_64/cuda-keyring-1.1-1-1.noarch.rpm
sudo yum install cuda-toolkit-12-3
export PATH=/usr/local/cuda-12.3/bin:$PATH
export LD_LIBRARY_PATH=/usr/local/cuda-12.3/lib64:$LD_LIBRARY_PATH
source ~/.bashrc
nvidia-smi
nvcc --version
```

--------------------------------

### Retrieve PROSPECT parameters using getPropertiesFromSpectrum()

Source: https://plantsimulationlab.github.io/PyHelios/LeafOpticsDoc.html

This example demonstrates initializing LeafOptics, generating spectra for different leaf types, assigning them to primitives, and finally retrieving the parameters using getPropertiesFromSpectrum().

```python
from pyhelios import Context, LeafOptics
from pyhelios.LeafOptics import LeafOpticsProperties
from pyhelios.types import vec3, vec2
with Context() as context:
with LeafOptics(context) as leafoptics:
# Generate spectra for different leaf types
healthy_leaf = LeafOpticsProperties()
healthy_leaf.chlorophyllcontent = 45.0
healthy_leaf.carotenoidcontent = 12.0
stressed_leaf = LeafOpticsProperties()
stressed_leaf.chlorophyllcontent = 20.0
stressed_leaf.brownpigments = 0.3
# Create primitives
healthy_IDs = [context.addPatch(center=vec3(0, 0, 1), size=vec2(0.1, 0.1))]
stressed_IDs = [context.addPatch(center=vec3(0, 0, 2), size=vec2(0.1, 0.1))]
# Run model for each leaf type
leafoptics.run(healthy_IDs, healthy_leaf, "healthy")
leafoptics.run(stressed_IDs, stressed_leaf, "stressed")
# Later, retrieve parameters from primitives based on their assigned spectra
all_leaves = healthy_IDs + stressed_IDs
leafoptics.getPropertiesFromSpectrum(all_leaves)
```

--------------------------------

### Example usage of setBBLCoefficients()

Source: https://plantsimulationlab.github.io/PyHelios/StomatalConductance_8py_source.html

Example usage of setBBLCoefficients() with a BBLCoefficients instance.

```python
>>> bbl_coeffs = BBLCoefficients(gs0=0.0743, a1=4.265, D0=14570.0)
>>> stomatal.setBBLCoefficients(bbl_coeffs)
```

--------------------------------

### Example usage of setBWBCoefficients()

Source: https://plantsimulationlab.github.io/PyHelios/StomatalConductance_8py_source.html

Example usage of setBWBCoefficients() with a BWBCoefficients instance.

```python
>>> bwb_coeffs = BWBCoefficients(gs0=0.0733, a1=9.422)
>>> stomatal.setBWBCoefficients(bwb_coeffs)
```

--------------------------------

### Initialize PhotosynthesisModel

Source: https://plantsimulationlab.github.io/PyHelios/PhotosynthesisDoc.html

Demonstrates the default initialization of the PhotosynthesisModel within a context.

```python
from pyhelios import Context, PhotosynthesisModel
with Context() as context:
with PhotosynthesisModel(context) as photo:
```

--------------------------------

### __init__(self, Context context)

Source: https://plantsimulationlab.github.io/PyHelios/classpyhelios_1_1LeafOptics_1_1LeafOptics.html

Initializes a new LeafOptics instance with the provided Context, handling plugin availability gracefully.

```APIDOC
## __init__(self, Context context)

### Description
Initializes the LeafOptics object with graceful plugin handling.

### Parameters
- **context** (Context) - Required - The Context object used for initialization.

### Returns
None
```
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