SASKTRAN2

https://sasktran2.readthedocs.io
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SASKTRAN2 is an atmospheric radiative transfer model developed at the University of Saskatchewan. It...
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### Import SASKTRAN2

Source: https://sasktran2.readthedocs.io/en/latest/_sources/quickstart

Imports the SASKTRAN2 library, aliasing it as 'sk' for convenience. This is the initial step for any SASKTRAN2 operation.

```python
import sasktran2 as sk
```

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

### Initialize sasktran2 Engine

Source: https://sasktran2.readthedocs.io/en/latest/_sources/quickstart

Initializes the sasktran2 Engine object with configuration and geometry. This step calculates and caches all geometry information.

```python
engine = sk.Engine(config, model_geometry, viewing_geo)
```

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

### Basic SASKTRAN2 Configuration

Source: https://sasktran2.readthedocs.io/en/latest/users_guide/performance

This snippet demonstrates the basic setup for using the SASKTRAN2 library by importing the package and initializing a configuration object. It serves as a starting point for performance-related tasks.

```python
import sasktran2 as sk

config = sk.Config()
```

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

### Test SASKTRAN2 with Pixi

Source: https://sasktran2.readthedocs.io/en/latest/_sources/developer/compiling

Runs the provided tests to verify the SASKTRAN2 development environment setup. This ensures the installation and compilation were successful.

```shell
pixi run test
```

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

### Print and Plot sasktran2 Output

Source: https://sasktran2.readthedocs.io/en/latest/_sources/quickstart

Demonstrates how to print the calculated output, which is usually an xarray.Dataset, and how to plot specific fields like 'radiance'.

```python
print(output)
```

```python
output['radiance'].isel(los=0).plot()
```

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

### Configure SASKTRAN2 Calculation

Source: https://sasktran2.readthedocs.io/en/latest/_sources/quickstart

Initializes and configures the SASKTRAN2 calculation settings. This includes setting up scattering sources and adjusting accuracy parameters like the number of streams.

```python
config = sk.Config()
config.multiple_scatter_source = sk.MultipleScatterSource.DiscreteOrdinates
config.num_streams = 2
```

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

### Install and Run Pre-commit Hooks

Source: https://sasktran2.readthedocs.io/en/latest/developer/contributing

Instructions for installing the pre-commit tool and running its hooks manually to format and check code. This ensures code quality and consistency across the project.

```shell
pip install pre-commit
```

```shell
pre-commit run -a
```

```shell
pre-commit install
```

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

### Install Dependencies with Pixi

Source: https://sasktran2.readthedocs.io/en/latest/_sources/developer/compiling

Installs the necessary dependencies for SASKTRAN2 development using the pixi package manager. This command sets up the required environment on any platform.

```shell
pixi install
```

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

### Install SASKTRAN2 via pip

Source: https://sasktran2.readthedocs.io/en/latest/installation

Installs the SASKTRAN2 library using the pip package manager. This is the recommended installation method.

```shell
pip install sasktran2

```

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

### SASKTRAN2 Examples - Using Constituents

Source: https://sasktran2.readthedocs.io/en/latest/examples/examples

Example demonstrating the inclusion of basic aerosols in SASKTRAN2.

```APIDOC
aerosol/basic.html:
  Description: Demonstrates basic aerosol inclusion in SASKTRAN2.
```

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

### Activate Environment and Install Package

Source: https://sasktran2.readthedocs.io/en/latest/_sources/developer/codespaces

Activates the development environment using micromamba and installs the SASKTRAN2 package in editable mode. This command needs to be re-run after C++ code changes.

```shell
micromamba activate sasktran2-dev-env
pip install -e .
```

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

### SASKTRAN2 Examples - Calculating Derivatives

Source: https://sasktran2.readthedocs.io/en/latest/examples/examples

Example demonstrating the calculation of derivatives, specifically Air Mass Factors.

```APIDOC
wf/amf.html:
  Description: Example for calculating Air Mass Factors (AMF) in SASKTRAN2.
```

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

### SASKTRAN2: Setup and Atmosphere Configuration

Source: https://sasktran2.readthedocs.io/en/latest/weighting_functions

Demonstrates the initialization of SASKTRAN2 components including geometry, viewing, atmosphere, and engine. It shows how to define atmospheric constituents and load standard atmospheric models.

```Python
import sasktran2 as sk
import numpy as np

config = sk.Config()

model_geometry = sk.Geometry1D(cos_sza=0.6,
                                solar_azimuth=0,
                                earth_radius_m=6372000,
                                altitude_grid_m=np.arange(0, 65001, 1000),
                                interpolation_method=sk.InterpolationMethod.LinearInterpolation,
                                geometry_type=sk.GeometryType.Spherical)

viewing_geo = sk.ViewingGeometry()

for alt in [10000, 20000, 30000, 40000]:
    ray = sk.TangentAltitudeSolar(tangent_altitude_m=alt,
                                    relative_azimuth=0,
                                    observer_altitude_m=200000,
                                    cos_sza=0.6)
    viewing_geo.add_ray(ray)

wavel = np.arange(280.0, 800.0, 0.1)

atmosphere = sk.Atmosphere(model_geometry, config, wavelengths_nm=wavel)

sk.climatology.us76.add_us76_standard_atmosphere(atmosphere)

atmosphere['rayleigh'] = sk.constituent.Rayleigh()

atmosphere['ozone'] = sk.climatology.mipas.constituent("O3", sk.optical.O3DBM())

atmosphere['no2'] = sk.climatology.mipas.constituent("NO2", sk.optical.NO2Vandaele())

engine = sk.Engine(config, model_geometry, viewing_geo)
```

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

### Build and View Documentation

Source: https://sasktran2.readthedocs.io/en/latest/_sources/developer/codespaces

Builds the SASKTRAN2 documentation using Sphinx and the Makefile, then opens the generated HTML index file in a preview. Requires the 'Live Preview' VS Code extension.

```shell
cd docs/sphinx
make html
```

```shell
Explorer -> docs/sphinx/build -> index.html -> Right Click -> Show Preview
Navigate to docs/sphinx/build in the preview window.
```

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

### Calculate Radiance with sasktran2 Engine

Source: https://sasktran2.readthedocs.io/en/latest/_sources/quickstart

Performs the radiative transfer calculation by passing an Atmosphere object to the engine's calculate_radiance method. The output is typically an xarray.Dataset.

```python
output = engine.calculate_radiance(atmosphere)
```

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

### Setting up SASKTRAN-2 Calculations

Source: https://sasktran2.readthedocs.io/en/latest/required_components

Guides on configuring SASKTRAN-2 simulations, including model geometry, viewing directions, atmospheric sources, and atmospheric state parameters.

```APIDOC
Calculation Setup Guide:

1. Model Geometry Configuration:
   - Description: Define global model grids (e.g., altitude) and the overall geometry type (spherical, plane-parallel).
   - Related Components: components/model_geometry.html

2. Viewing Geometry Specification:
   - Description: Set up viewing directions for radiance output.
   - Related Components: components/viewing_geometry.html

3. Atmospheric Sources Selection:
   - Description: Determine which source terms to include in the calculation (e.g., multiple scattering, thermal sources).
   - Related Components: components/sources.html

4. Atmospheric State Definition:
   - Description: Configure atmospheric constituents, such as Rayleigh scattering and ozone absorption.
   - Related Components: components/atmosphere.html
```

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

### Build and View Documentation

Source: https://sasktran2.readthedocs.io/en/latest/developer/codespaces

Commands to build the Sphinx HTML documentation and instructions on how to preview it within VS Code using the Live Preview extension.

```shell
cd docs/sphinx
make html
```

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

### Define Viewing Geometry

Source: https://sasktran2.readthedocs.io/en/latest/_sources/quickstart

Creates a ViewingGeometry object to specify the radiance output conditions. This involves adding individual viewing rays, such as tangent altitude rays for limb viewing.

```python
viewing_geo = sk.ViewingGeometry()

for alt in [10000, 20000, 30000, 40000]:
    ray = sk.TangentAltitudeSolar(tangent_altitude_m=alt,
                                    relative_azimuth=0,
                                    observer_altitude_m=200000,
                                    cos_sza=0.6)
    viewing_geo.add_ray(ray)
```

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

### SASKTRAN2 Configuration Initialization

Source: https://sasktran2.readthedocs.io/en/latest/components/sources

Demonstrates how to import the sasktran2 library and initialize the configuration object, which is central to setting up various model parameters including source terms.

```python
import sasktran2 as sk

config = sk.Config()
```

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

### Add Standard Atmosphere Climatology

Source: https://sasktran2.readthedocs.io/en/latest/_sources/quickstart

Applies a standard atmosphere model, such as the US Standard Atmosphere (US76), to the Atmosphere object. This populates pressure and temperature profiles, which are often required for calculating constituent properties.

```python
sk.climatology.us76.add_us76_standard_atmosphere(atmosphere)
```

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

### Define Atmospheric State

Source: https://sasktran2.readthedocs.io/en/latest/_sources/quickstart

Constructs the Atmosphere object, which defines the atmospheric state for the calculation. This includes specifying wavelengths and adding atmospheric constituents like Rayleigh scattering and absorption due to ozone and nitrogen dioxide.

```python
import numpy as np

wavel = np.arange(280.0, 800.0, 0.1)
atmosphere = sk.Atmosphere(model_geometry, config, wavelengths_nm=wavel)

atmosphere['rayleigh'] = sk.constituent.Rayleigh()
atmosphere['ozone'] = sk.climatology.mipas.constituent("O3", sk.optical.O3DBM())
atmosphere['no2'] = sk.climatology.mipas.constituent("NO2", sk.optical.NO2Vandaele())
```

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

### Define 1D Model Geometry

Source: https://sasktran2.readthedocs.io/en/latest/_sources/quickstart

Sets up the model geometry for the radiative transfer calculation, specifying parameters like solar zenith angle, solar azimuth, Earth radius, altitude grid, and interpolation method for a spherical geometry.

```python
import numpy as np

model_geometry = sk.Geometry1D(cos_sza=0.6,
                                solar_azimuth=0,
                                earth_radius_m=6372000,
                                altitude_grid_m=np.arange(0, 65001, 1000),
                                interpolation_method=sk.InterpolationMethod.LinearInterpolation,
                                geometry_type=sk.GeometryType.Spherical)
```

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

### Sasktran2 API Reference - Config

Source: https://sasktran2.readthedocs.io/en/latest/examples/examples

References the configuration module for Sasktran2, likely containing classes and functions for setting up simulation parameters.

```APIDOC
sasktran2.Config:
  Description: Module for configuration settings in Sasktran2.
  Methods/Classes:
    - Likely includes classes or functions to manage simulation parameters, atmospheric profiles, sensor configurations, etc.
```

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

### Install SASKTRAN2 via conda

Source: https://sasktran2.readthedocs.io/en/latest/installation

Installs the SASKTRAN2 library using the conda package manager from the conda-forge channel.

```shell
conda install conda-forge::sasktran2

```

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

### Pixi Development Commands

Source: https://sasktran2.readthedocs.io/en/latest/developer/compiling

Commands for setting up, building, and testing the SASKTRAN2 project using the pixi package manager. These commands facilitate environment creation, project compilation, and verification through tests.

```shell
pixi install
```

```shell
pixi run build
```

```shell
pixi run test
```

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

### Sasktran2 Core API Reference

Source: https://sasktran2.readthedocs.io/en/latest/_modules/sasktran2/constituent/brdf/kokhanovsky

Documentation for core Sasktran2 components including configuration, engine, geometry, and atmosphere handling.

```APIDOC
sasktran2.Config:
  Description: Configuration management for Sasktran2 simulations.

sasktran2.Engine:
  Description: The main simulation engine for running radiative transfer calculations.

sasktran2.Geometry1D:
  Description: Represents one-dimensional model geometry, typically atmospheric layers.

sasktran2.Atmosphere:
  Description: Defines the atmospheric state, including composition and vertical profiles.
```

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

### WGS84 Example Usage

Source: https://sasktran2.readthedocs.io/en/latest/_modules/sasktran2/geodetic

Example demonstrating the initialization and usage of the WGS84 geodetic object, including setting the frame from a tangent point and printing its location.

```python
import sasktran2 as sk

geodetic = sk.WGS84()
geodetic.from_tangent_point([ 3.676013154788849600e+005, 1.009976313640051500e+006,
                                            -6.871601202127538600e+006], [ 2.884568631765662100e-001,
                                            7.925287180643269000e-001,  5.372996083468238900e-001])
print(geodetic)
```

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

### Clone SASKTRAN2 Repository

Source: https://sasktran2.readthedocs.io/en/latest/developer/contributing

Instructions for cloning the SASKTRAN2 repository from GitHub to your local machine. This is the initial step required before making any contributions to the project.

```shell
git clone git@github.com:YOURUSERNAME/sasktran2.git
```

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

### sasktran2 Configuration API

Source: https://sasktran2.readthedocs.io/en/latest/components/source_terms/singlescatter

API reference for the sasktran2 configuration module, detailing how to set up and manage simulation parameters.

```APIDOC
sasktran2.Config:
  Description: Manages simulation configuration settings.
  Methods:
    __init__(...):
      Initializes the configuration object.
    load_config(filepath: str):
      Loads configuration from a file.
    set_parameter(key: str, value: any):
      Sets a specific configuration parameter.
    get_parameter(key: str) -> any:
      Retrieves a configuration parameter.
```

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

### Sasktran2 Core Modules

Source: https://sasktran2.readthedocs.io/en/latest/installation

Overview of key modules within the Sasktran2 library, including configuration, engine, geometry, atmosphere, constituents, optical properties, and viewing geometry.

```APIDOC
sasktran2.Config:
  Description: Handles the configuration settings for Sasktran2 calculations.
  Methods:
    - __init__(self, ...): Initializes the configuration object.

sasktran2.Engine:
  Description: The main engine for running radiative transfer simulations.
  Methods:
    - __init__(self, ...): Initializes the simulation engine.
    - run_simulation(self, ...): Executes the radiative transfer calculation.

sasktran2.Geometry1D:
  Description: Represents one-dimensional geometry for atmospheric profiles.
  Methods:
    - __init__(self, ...): Initializes the 1D geometry.

sasktran2.Atmosphere:
  Description: Defines the atmospheric state, including layers and constituents.
  Methods:
    - __init__(self, ...): Initializes the atmosphere object.

sasktran2.constituent.Rayleigh:
  Description: Represents Rayleigh scattering properties.
  Methods:
    - __init__(self, ...): Initializes Rayleigh scattering.

sasktran2.constituent.VMRAltitudeAbsorber:
  Description: Defines an absorber with volume mixing ratio dependent on altitude.
  Methods:
    - __init__(self, ...): Initializes the VMR absorber.

sasktran2.constituent.NumberDensityScatterer:
  Description: Represents a scatterer defined by number density.
  Methods:
    - __init__(self, ...): Initializes the number density scatterer.

sasktran2.constituent.ExtinctionScatterer:
  Description: Represents a scatterer defined by extinction properties.
  Methods:
    - __init__(self, ...): Initializes the extinction scatterer.

sasktran2.constituent.CollisionInducedAbsorber:
  Description: Defines collision-induced absorption properties.
  Methods:
    - __init__(self, ...): Initializes collision-induced absorption.

sasktran2.constituent.LambertianSurface:
  Description: Represents a Lambertian reflecting surface.
  Methods:
    - __init__(self, ...): Initializes the Lambertian surface.

sasktran2.constituent.SnowKokhanovsky:
  Description: Implements snow optical properties using the Kokhanovsky model.
  Methods:
    - __init__(self, ...): Initializes snow properties.

sasktran2.constituent.MODIS:
  Description: Integrates MODIS aerosol properties.
  Methods:
    - __init__(self, ...): Initializes MODIS aerosol properties.

sasktran2.constituent.SolarIrradiance:
  Description: Represents solar irradiance models.
  Methods:
    - __init__(self, ...): Initializes solar irradiance.

sasktran2.constituent.ThermalEmission:
  Description: Defines thermal emission models.
  Methods:
    - __init__(self, ...): Initializes thermal emission.

sasktran2.constituent.SurfaceThermalEmission:
  Description: Represents thermal emission from the surface.
  Methods:
    - __init__(self, ...): Initializes surface thermal emission.

sasktran2.constituent.AirMassFactor:
  Description: Calculates air mass factors.
  Methods:
    - __init__(self, ...): Initializes air mass factor calculation.

sasktran2.optical.O3DBM:
  Description: Optical depth model for Ozone (DBM).
  Methods:
    - __init__(self, ...): Initializes O3DBM.

sasktran2.optical.NO2Vandaele:
  Description: Optical properties for NO2 based on Vandaele data.
  Methods:
    - __init__(self, ...): Initializes NO2 Vandaele properties.

sasktran2.optical.HITRANUV:
  Description: HITRAN-based absorption cross-sections in the UV range.
  Methods:
    - __init__(self, ...): Initializes HITRAN UV absorption.

sasktran2.optical.HITRANAbsorber:
  Description: General HITRAN absorber class.
  Methods:
    - __init__(self, ...): Initializes HITRAN absorber.

sasktran2.optical.HITRANTabulated:
  Description: Tabulated HITRAN absorption data.
  Methods:
    - __init__(self, ...): Initializes tabulated HITRAN data.

sasktran2.optical.HITRANCollision:
  Description: HITRAN data for collision-induced absorption.
  Methods:
    - __init__(self, ...): Initializes HITRAN collision-induced absorption.

sasktran2.optical.database.OpticalDatabase:
  Description: Base class for optical property databases.
  Methods:
    - __init__(self, ...): Initializes the optical database.

sasktran2.optical.database.OpticalDatabaseGenericAbsorber:
  Description: Generic absorber for optical databases.
  Methods:
    - __init__(self, ...): Initializes generic absorber.

sasktran2.optical.database.OpticalDatabaseGenericScatterer:
  Description: Generic scatterer for optical databases.
  Methods:
    - __init__(self, ...): Initializes generic scatterer.

sasktran2.optical.Mie:
  Description: Mie scattering calculations.
  Methods:
    - __init__(self, ...): Initializes Mie scattering.

sasktran2.optical.rayleigh:
  Description: Rayleigh scattering calculations.
  Methods:
    - __init__(self, ...): Initializes Rayleigh scattering.

sasktran2.ViewingGeometry:
  Description: Defines viewing geometry parameters.
  Methods:
    - __init__(self, ...): Initializes viewing geometry.

sasktran2.TangentAltitudeSolar:
  Description: Represents tangent altitude geometry relative to the sun.
  Methods:
    - __init__(self, ...): Initializes tangent altitude solar geometry.

```

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

### Activate Environment and Install Package

Source: https://sasktran2.readthedocs.io/en/latest/developer/codespaces

Activates the development environment using micromamba and installs the project in editable mode. This command is necessary after any changes to the C++ code within the model.

```shell
micromamba activate sasktran2-dev-env
pip install -e .
```

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

### Sasktran2 API Reference Overview

Source: https://sasktran2.readthedocs.io/en/latest/quickstart

Provides an overview of the Sasktran2 API, categorizing key components like configuration, engine, geometry, atmosphere, constituents, optical properties, and viewing geometry. This serves as a high-level guide to the library's structure.

```APIDOC
Sasktran2 API Reference:

This section details the programmatic interface for the Sasktran2 radiative transfer model.

Key Modules and Components:

1.  **Config**: Handles the configuration settings for Sasktran2 calculations.
    - `sasktran2.Config`: Main configuration class.

2.  **Engine**: The core engine responsible for running radiative transfer simulations.
    - `sasktran2.Engine`: The primary simulation engine.

3.  **Model Geometry**: Defines the geometric setup for the atmospheric model.
    - `sasktran2.Geometry1D`: Represents a one-dimensional atmospheric geometry.

4.  **Atmosphere**: Describes the atmospheric state and its properties.
    - `sasktran2.Atmosphere`: Class for defining atmospheric profiles.

5.  **Constituents**: Represents various atmospheric components and their properties.
    - `sasktran2.constituent.Rayleigh`: Rayleigh scattering properties.
    - `sasktran2.constituent.VMRAltitudeAbsorber`: Absorber with volume mixing ratio dependent on altitude.
    - `sasktran2.constituent.NumberDensityScatterer`: Scatterer defined by number density.
    - `sasktran2.constituent.ExtinctionScatterer`: Scatterer defined by extinction properties.
    - `sasktran2.constituent.CollisionInducedAbsorber`: Absorber due to collision-induced absorption.
    - `sasktran2.constituent.LambertianSurface`: Represents a Lambertian reflecting surface.
    - `sasktran2.constituent.SnowKokhanovsky`: Snow optical properties using the Kokhanovsky model.
    - `sasktran2.constituent.MODIS`: Properties derived from MODIS data.
    - `sasktran2.constituent.SolarIrradiance`: Defines solar irradiance.
    - `sasktran2.constituent.ThermalEmission`: Defines thermal emission properties.
    - `sasktran2.constituent.SurfaceThermalEmission`: Defines surface thermal emission.
    - `sasktran2.constituent.AirMassFactor`: Calculates air mass factors.

6.  **Optical Properties**: Defines optical properties like absorption and scattering.
    - `sasktran2.optical.O3DBM`: Ozone absorption cross-sections from DB M.
    - `sasktran2.optical.NO2Vandaele`: Nitrogen dioxide cross-sections from Vandaele.
    - `sasktran2.optical.HITRANUV`: HITRAN data for UV absorbers.
    - `sasktran2.optical.HITRANAbsorber`: General HITRAN absorber class.
    - `sasktran2.optical.HITRANTabulated`: Tabulated HITRAN data.
    - `sasktran2.optical.HITRANCollision`: Collision-induced absorption from HITRAN.
    - `sasktran2.optical.database.OpticalDatabase`: Base class for optical property databases.
    - `sasktran2.optical.database.OpticalDatabaseGenericAbsorber`: Generic absorber database.
    - `sasktran2.optical.database.OpticalDatabaseGenericScatterer`: Generic scatterer database.
    - `sasktran2.optical.Mie`: Mie scattering calculations.
    - `sasktran2.optical.rayleigh`: Rayleigh scattering calculations.

7.  **Viewing Geometry**: Defines the geometry from which the scene is viewed.
    - `sasktran2.ViewingGeometry`: General viewing geometry class.
    - `sasktran2.TangentAltitudeSolar`: Specific viewing geometry related to tangent altitude and solar position.
```

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

### Install pre-commit Hook Manager

Source: https://sasktran2.readthedocs.io/en/latest/_sources/developer/contributing

Installs the pre-commit framework, a Python package that helps manage and run pre-commit hooks for code formatting and linting. This is a prerequisite for setting up automatic code checks.

```shell
pip install pre-commit
```

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

### WGS84 Altitude Intercepts Example

Source: https://sasktran2.readthedocs.io/en/latest/_modules/sasktran2/geodetic

Example demonstrating the calculation of altitude intercepts using the WGS84 geodetic object. It shows how to find intersection points of a line of sight with a specified altitude.

```python
import sasktran2 as sk
import numpy as np

geodetic = sk.WGS84()
look = geodetic.from_tangent_altitude(15322, [3.676013154788849600e+005, 1.009976313640051500e+006, 
                                                    -6.871601202127538600e+006], [0, 0, 1])
obs = geodetic.location
intercept1, intercept2 = geodetic.altitude_intercepts(16000, obs, look)
print(np.array_str(intercept1, precision=3))
print(np.array_str(intercept2, precision=3))
```

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

### Setup SASKTRAN2 Calculation Environment

Source: https://sasktran2.readthedocs.io/en/latest/examples/wf/amf

Initializes the SASKTRAN2 configuration, defines the atmospheric geometry, viewing conditions, wavelengths, and atmospheric constituents (Rayleigh, Ozone, NO2). It also sets up the radiative transfer engine.

```Python
import sasktran2 as sk
import numpy as np
import matplotlib.pyplot as plt

config = sk.Config()
config.multiple_scatter_source = sk.MultipleScatterSource.DiscreteOrdinates

model_geometry = sk.Geometry1D(
    cos_sza=0.6,
    solar_azimuth=0,
    earth_radius_m=6372000,
    altitude_grid_m=np.arange(0, 65001, 1000),
    interpolation_method=sk.InterpolationMethod.LinearInterpolation,
    geometry_type=sk.GeometryType.Spherical
)

viewing_geo = sk.ViewingGeometry()

viewing_geo.add_ray(
    sk.GroundViewingSolar(
        cos_sza=0.6,
        relative_azimuth=0,
        cos_viewing_zenith=0.8,
        observer_altitude_m=200000,
    )
)

wavel = np.array([290, 310, 330, 350, 400, 600])
atmosphere = sk.Atmosphere(model_geometry, config, wavelengths_nm=wavel)

atmosphere.surface.albedo[:] = 0.3

sk.climatology.us76.add_us76_standard_atmosphere(atmosphere)

atmosphere["rayleigh"] = sk.constituent.Rayleigh()
atmosphere['ozone'] = sk.climatology.mipas.constituent("O3", sk.optical.O3DBM())
atmosphere['no2'] = sk.climatology.mipas.constituent("NO2", sk.optical.NO2Vandaele())

engine = sk.Engine(config, model_geometry, viewing_geo)

```

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

### Install pre-commit Hooks

Source: https://sasktran2.readthedocs.io/en/latest/_sources/developer/contributing

Sets up the Git pre-commit hooks to automatically run formatting and checks on every commit. This is highly recommended to ensure code quality and consistency.

```shell
pre-commit install
```

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

### SolarGeometryHandlerAstropy API

Source: https://sasktran2.readthedocs.io/en/latest/api/generated/sasktran2.solar.SolarGeometryHandlerAstropy

Provides methods to calculate solar angles using the astropy package. Requires astropy to be installed.

```APIDOC
class sasktran2.solar.SolarGeometryHandlerAstropy(SolarGeometryHandlerBase):
    """Solar handler where the astropy package is used to calculate the solar angles.
    Must have astropy installed in the Python environment in order to use this solar handler.

    Interface class for the solar handler. A solar handler is used to calculate the
    solar angles for a give time and location.
    """

    def __init__():
        """Interface class for the solar handler. A solar handler is used to calculate the
        solar angles for a give time and location.
        """
        pass

    def target_solar_angles(latitude: float, longitude: float, altitude: float, time: pandas.Timestamp) -> tuple[float, float]:
        """Calculates the solar zenith and solar azimuth angles for a given location and time.

        Parameters:
            latitude (float): Latitude in degrees north.
            longitude (float): Longitude in degrees east.
            altitude (float): Altitude in meters.
            time (pd.Timestamp): Time of interest.

        Returns:
            tuple[float, float]: A tuple containing the solar zenith and solar azimuth angles in degrees.
                                 Solar azimuth is relative to true north, defined clockwise from north.
                                 The azimuthal direction points towards the sun.
        """
        pass
```

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

### sasktran2 Configuration API

Source: https://sasktran2.readthedocs.io/en/latest/index

Documentation for the sasktran2 configuration module, detailing how to set up and manage simulation parameters.

```APIDOC
sasktran2.Config:
  Description: Manages simulation configuration settings.
  Methods:
    __init__(...):
      Initializes the configuration object.
    load_config(filepath: str):
      Loads configuration from a specified file.
    get_setting(key: str):
      Retrieves a specific configuration setting.
    set_setting(key: str, value: any):
      Sets a specific configuration setting.
```

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

### Get Atmosphere Surface (Python)

Source: https://sasktran2.readthedocs.io/en/latest/_modules/sasktran2/atmosphere

Retrieves the surface object associated with the atmosphere. This is a read-only property.

```python
    @property
    def surface(self) -> sk.SurfaceStokes_1 | sk.SurfaceStokes_3:
        """
        The surface object

        Returns
        -------
        sk.Surface
        """
        return self._atmosphere.surface
```

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

### Sasktran2 Core API Reference

Source: https://sasktran2.readthedocs.io/en/latest/_modules/sasktran2/constituent/brdf/modis

Documentation for core Sasktran2 components including configuration, engine, geometry, and atmosphere handling.

```APIDOC
sasktran2.Config:
  Description: Configuration management for Sasktran2 simulations.

sasktran2.Engine:
  Description: The main simulation engine for running radiative transfer calculations.

sasktran2.Geometry1D:
  Description: Represents one-dimensional model geometry, typically atmospheric layers.

sasktran2.Atmosphere:
  Description: Defines the atmospheric state, including composition and vertical profiles.
```

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

### Get Number of Wavelengths (Python)

Source: https://sasktran2.readthedocs.io/en/latest/_modules/sasktran2/atmosphere

Retrieves the number of wavelengths the atmosphere is specified at. This is a read-only property.

```python
    @property
    def num_wavel(self) -> int:
        """
        The number of wavelengths the atmosphere is specified at

        Returns
        -------
        int
        """
        return self._nwavel
```

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

### Get Pressure Derivative Flag (Python)

Source: https://sasktran2.readthedocs.io/en/latest/_modules/sasktran2/atmosphere

Checks if the derivative with respect to pressure is being calculated. This is a read-only property.

```python
    @property
    def calculate_pressure_derivative(self) -> bool:
        """
        True if we are calculating the derivative with respect to pressure

        Returns
        -------
        bool
        """
        return self._pressure_derivative
```
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