Read

Provides functions to create a Device from various data sources.

from_gds(gds_path, cell_name, gds_layer=(1, 0), bounds=None, **kwargs)

Create a Device from a GDS cell.

Parameters:

Name	Type	Description	Default
gds_path	str	The file path to the GDS file.	required
cell_name	str	The name of the cell within the GDS file to be converted into a Device object.	required
gds_layer	tuple[int, int]	A tuple specifying the layer and datatype to be used from the GDS file. Defaults to (1, 0).	(1, 0)
bounds	tuple[tuple[int, int], tuple[int, int]]	A tuple specifying the bounds for cropping the cell before conversion, formatted as ((min_x, min_y), (max_x, max_y)), in units of the GDS file. If None, the entire cell is used.	None
**kwargs		Additional keyword arguments to be passed to the Device constructor.	{}

Returns:

Type	Description
Device	A Device object representing the specified cell from the GDS file, after processing based on the specified layer.

Source code in prefab/read.py

def from_gds(
    gds_path: str,
    cell_name: str,
    gds_layer: tuple[int, int] = (1, 0),
    bounds: tuple[tuple[int, int], tuple[int, int]] = None,
    **kwargs,
):
    """
    Create a Device from a GDS cell.

    Parameters
    ----------
    gds_path : str
        The file path to the GDS file.
    cell_name : str
        The name of the cell within the GDS file to be converted into a Device object.
    gds_layer : tuple[int, int], optional
        A tuple specifying the layer and datatype to be used from the GDS file. Defaults
        to (1, 0).
    bounds : tuple[tuple[int, int], tuple[int, int]], optional
        A tuple specifying the bounds for cropping the cell before conversion, formatted
        as ((min_x, min_y), (max_x, max_y)), in units of the GDS file. If None, the
        entire cell is used.
    **kwargs
        Additional keyword arguments to be passed to the Device constructor.

    Returns
    -------
    Device
        A Device object representing the specified cell from the GDS file, after
        processing based on the specified layer.
    """
    gdstk_library = gdstk.read_gds(gds_path)
    gdstk_cell = gdstk_library[cell_name]
    device_array = _gdstk_to_device_array(
        gdstk_cell=gdstk_cell, gds_layer=gds_layer, bounds=bounds
    )
    return Device(device_array=device_array, **kwargs)

from_gdsfactory(component, **kwargs)

Create a Device from a gdsfactory component.

Parameters:

Name	Type	Description	Default
component	Component	The gdsfactory component to be converted into a Device object.	required
**kwargs		Additional keyword arguments to be passed to the Device constructor.	{}

Returns:

Type	Description
Device	A Device object representing the gdsfactory component.

Raises:

Type	Description
ImportError	If the gdsfactory package is not installed.

Source code in prefab/read.py

def from_gdsfactory(
    component: "gf.Component",  # noqa: F821
    **kwargs,
) -> Device:
    """
    Create a Device from a gdsfactory component.

    Parameters
    ----------
    component : gf.Component
        The gdsfactory component to be converted into a Device object.
    **kwargs
        Additional keyword arguments to be passed to the Device constructor.

    Returns
    -------
    Device
        A Device object representing the gdsfactory component.

    Raises
    ------
    ImportError
        If the gdsfactory package is not installed.
    """
    try:
        import gdsfactory as gf
    except ImportError:
        raise ImportError(
            "The gdsfactory package is required to use this function; "
            "try `pip install gdsfactory`."
        ) from None

    bounds = (
        (component.xmin * 1000, component.ymin * 1000),
        (component.xmax * 1000, component.ymax * 1000),
    )

    polygons = [
        polygon
        for polygons_list in component.get_polygons_points().values()
        for polygon in polygons_list
    ]

    contours = [
        np.array(
            [
                [
                    [
                        int(1000 * vertex[0] - bounds[0][0]),
                        int(1000 * vertex[1] - bounds[0][1]),
                    ]
                ]
                for vertex in polygon
            ]
        )
        for polygon in polygons
    ]

    device_array = np.zeros(
        (int(bounds[1][1] - bounds[0][1]), int(bounds[1][0] - bounds[0][0])),
        dtype=np.uint8,
    )
    cv2.fillPoly(img=device_array, pts=contours, color=(1, 1, 1))
    device_array = np.flipud(device_array)
    return Device(device_array=device_array, **kwargs)

from_gdstk(gdstk_cell, gds_layer=(1, 0), bounds=None, **kwargs)

Create a Device from a gdstk cell.

Parameters:

Name	Type	Description	Default
gdstk_cell	Cell	The gdstk.Cell object to be converted into a Device object.	required
gds_layer	tuple[int, int]	A tuple specifying the layer and datatype to be used from the cell. Defaults to (1, 0).	(1, 0)
bounds	tuple[tuple[int, int], tuple[int, int]]	A tuple specifying the bounds for cropping the cell before conversion, formatted as ((min_x, min_y), (max_x, max_y)), in units of the GDS file. If None, the entire cell is used.	None
**kwargs		Additional keyword arguments to be passed to the Device constructor.	{}

Returns:

Type	Description
Device	A Device object representing the gdstk.Cell, after processing based on the specified layer.

Source code in prefab/read.py

def from_gdstk(
    gdstk_cell: gdstk.Cell,
    gds_layer: tuple[int, int] = (1, 0),
    bounds: tuple[tuple[int, int], tuple[int, int]] = None,
    **kwargs,
):
    """
    Create a Device from a gdstk cell.

    Parameters
    ----------
    gdstk_cell : gdstk.Cell
        The gdstk.Cell object to be converted into a Device object.
    gds_layer : tuple[int, int], optional
        A tuple specifying the layer and datatype to be used from the cell. Defaults to
        (1, 0).
    bounds : tuple[tuple[int, int], tuple[int, int]], optional
        A tuple specifying the bounds for cropping the cell before conversion, formatted
        as ((min_x, min_y), (max_x, max_y)), in units of the GDS file. If None, the
        entire cell is used.
    **kwargs
        Additional keyword arguments to be passed to the Device constructor.

    Returns
    -------
    Device
        A Device object representing the gdstk.Cell, after processing based on the
        specified layer.
    """
    device_array = _gdstk_to_device_array(
        gdstk_cell=gdstk_cell, gds_layer=gds_layer, bounds=bounds
    )
    return Device(device_array=device_array, **kwargs)

from_img(img_path, img_width_nm=None, binarize=True, **kwargs)

Create a Device from an image file.

Parameters:

Name	Type	Description	Default
img_path	str	The path to the image file to be converted into a Device object.	required
img_width_nm	int	The width of the image in nanometers. If specified, the Device will be resized to this width while maintaining aspect ratio. If None, no resizing is performed.	None
binarize	bool	If True, the image will be binarized (converted to binary values) before conversion to a Device object. This is useful for processing grayscale images into binary masks. Defaults to True.	True
**kwargs		Additional keyword arguments to be passed to the Device constructor.	{}

Returns:

Type	Description
Device	A Device object representing the processed image, after optional resizing and binarization.

Source code in prefab/read.py

def from_img(
    img_path: str, img_width_nm: int = None, binarize: bool = True, **kwargs
) -> Device:
    """
    Create a Device from an image file.

    Parameters
    ----------
    img_path : str
        The path to the image file to be converted into a Device object.
    img_width_nm : int, optional
        The width of the image in nanometers. If specified, the Device will be resized
        to this width while maintaining aspect ratio. If None, no resizing is performed.
    binarize : bool, optional
        If True, the image will be binarized (converted to binary values) before
        conversion to a Device object. This is useful for processing grayscale images
        into binary masks. Defaults to True.
    **kwargs
        Additional keyword arguments to be passed to the Device constructor.

    Returns
    -------
    Device
        A Device object representing the processed image, after optional resizing and
        binarization.
    """
    device_array = cv2.imread(img_path, flags=cv2.IMREAD_GRAYSCALE) / 255
    if img_width_nm is not None:
        resolution = img_width_nm / device_array.shape[1]
        device_array = cv2.resize(
            device_array, dsize=(0, 0), fx=resolution, fy=resolution
        )
    if binarize:
        device_array = geometry.binarize_hard(device_array)
    return Device(device_array=device_array, **kwargs)

from_ndarray(ndarray, resolution=1.0, binarize=True, **kwargs)

Create a Device from an ndarray.

Parameters:

Name	Type	Description	Default
ndarray	ndarray	The input array representing the device layout.	required
resolution	float	The resolution of the ndarray in nanometers per pixel, defaulting to 1.0 nm per pixel. If specified, the input array will be resized based on this resolution to match the desired physical size.	1.0
binarize	bool	If True, the input array will be binarized (converted to binary values) before conversion to a Device object. This is useful for processing grayscale arrays into binary masks. Defaults to True.	True
**kwargs		Additional keyword arguments to be passed to the Device constructor.	{}

Returns:

Type	Description
Device	A Device object representing the input array, after optional resizing and binarization.

Source code in prefab/read.py

def from_ndarray(
    ndarray: np.ndarray, resolution: float = 1.0, binarize: bool = True, **kwargs
) -> Device:
    """
    Create a Device from an ndarray.

    Parameters
    ----------
    ndarray : np.ndarray
        The input array representing the device layout.
    resolution : float, optional
        The resolution of the ndarray in nanometers per pixel, defaulting to 1.0 nm per
        pixel. If specified, the input array will be resized based on this resolution to
        match the desired physical size.
    binarize : bool, optional
        If True, the input array will be binarized (converted to binary values) before
        conversion to a Device object. This is useful for processing grayscale arrays
        into binary masks. Defaults to True.
    **kwargs
        Additional keyword arguments to be passed to the Device constructor.

    Returns
    -------
    Device
        A Device object representing the input array, after optional resizing and
        binarization.
    """
    device_array = ndarray
    if resolution != 1.0:
        device_array = cv2.resize(
            device_array, dsize=(0, 0), fx=resolution, fy=resolution
        )
    if binarize:
        device_array = geometry.binarize_hard(device_array)
    return Device(device_array=device_array, **kwargs)

from_sem(sem_path, sem_resolution=None, sem_resolution_key=None, binarize=False, bounds=None, **kwargs)

Create a Device from a scanning electron microscope (SEM) image file.

Parameters:

Name	Type	Description	Default
sem_path	str	The file path to the SEM image.	required
sem_resolution	float	The resolution of the SEM image in nanometers per pixel. If not provided, it will be extracted from the image metadata using the sem_resolution_key.	None
sem_resolution_key	str	The key to look for in the SEM image metadata to extract the resolution. Required if sem_resolution is not provided.	None
binarize	bool	If True, the SEM image will be binarized (converted to binary values) before conversion to a Device object. This is needed for processing grayscale images into binary masks. Defaults to False.	False
bounds	tuple[tuple[int, int], tuple[int, int]]	A tuple specifying the bounds for cropping the image before conversion, formatted as ((min_x, min_y), (max_x, max_y)). If None, the entire image is used.	None
**kwargs		Additional keyword arguments to be passed to the Device constructor.	{}

Returns:

Type	Description
Device	A Device object representing the processed SEM image.

Raises:

Type	Description
ValueError	If neither sem_resolution nor sem_resolution_key is provided.

Source code in prefab/read.py

def from_sem(
    sem_path: str,
    sem_resolution: float = None,
    sem_resolution_key: str = None,
    binarize: bool = False,
    bounds: tuple[tuple[int, int], tuple[int, int]] = None,
    **kwargs,
) -> Device:
    """
    Create a Device from a scanning electron microscope (SEM) image file.

    Parameters
    ----------
    sem_path : str
        The file path to the SEM image.
    sem_resolution : float, optional
        The resolution of the SEM image in nanometers per pixel. If not provided, it
        will be extracted from the image metadata using the `sem_resolution_key`.
    sem_resolution_key : str, optional
        The key to look for in the SEM image metadata to extract the resolution.
        Required if `sem_resolution` is not provided.
    binarize : bool, optional
        If True, the SEM image will be binarized (converted to binary values) before
        conversion to a Device object. This is needed for processing grayscale images
        into binary masks. Defaults to False.
    bounds : tuple[tuple[int, int], tuple[int, int]], optional
        A tuple specifying the bounds for cropping the image before conversion,
        formatted as ((min_x, min_y), (max_x, max_y)). If None, the entire image is
        used.
    **kwargs
        Additional keyword arguments to be passed to the Device constructor.

    Returns
    -------
    Device
        A Device object representing the processed SEM image.

    Raises
    ------
    ValueError
        If neither `sem_resolution` nor `sem_resolution_key` is provided.
    """
    if sem_resolution is None and sem_resolution_key is not None:
        sem_resolution = get_sem_resolution(sem_path, sem_resolution_key)
    elif sem_resolution is None:
        raise ValueError("Either sem_resolution or resolution_key must be provided.")

    device_array = cv2.imread(sem_path, flags=cv2.IMREAD_GRAYSCALE)
    device_array = cv2.resize(
        device_array, dsize=(0, 0), fx=sem_resolution, fy=sem_resolution
    )
    if bounds is not None:
        device_array = device_array[
            device_array.shape[0] - bounds[1][1] : device_array.shape[0] - bounds[0][1],
            bounds[0][0] : bounds[1][0],
        ]
    if binarize:
        device_array = geometry.binarize_sem(device_array)
    return Device(device_array=device_array, **kwargs)

from_tidy3d(tidy3d_sim, eps_threshold, z, **kwargs)

Create a Device from a Tidy3D simulation.

Parameters:

Name	Type	Description	Default
tidy3d_sim	Simulation	The Tidy3D simulation object.	required
eps_threshold	float	The threshold value for the permittivity to binarize the device array.	required
z	float	The z-coordinate at which to extract the permittivity.	required
**kwargs		Additional keyword arguments to be passed to the Device constructor.	{}

Returns:

Type	Description
Device	A Device object representing the permittivity cross-section at the specified z-coordinate for the Tidy3D simulation.

Raises:

Type	Description
ValueError	If the z-coordinate is outside the bounds of the simulation size in the z-direction.
ImportError	If the tidy3d package is not installed.

Source code in prefab/read.py

def from_tidy3d(
    tidy3d_sim: "tidy3d.Simulation",  # noqa: F821
    eps_threshold: float,
    z: float,
    **kwargs,
) -> Device:
    """
    Create a Device from a Tidy3D simulation.

    Parameters
    ----------
    tidy3d_sim : tidy3d.Simulation
        The Tidy3D simulation object.
    eps_threshold : float
        The threshold value for the permittivity to binarize the device array.
    z : float
        The z-coordinate at which to extract the permittivity.
    **kwargs
        Additional keyword arguments to be passed to the Device constructor.

    Returns
    -------
    Device
        A Device object representing the permittivity cross-section at the specified
        z-coordinate for the Tidy3D simulation.

    Raises
    ------
    ValueError
        If the z-coordinate is outside the bounds of the simulation size in the
        z-direction.
    ImportError
        If the tidy3d package is not installed.
    """
    try:
        from tidy3d import Coords, Grid
    except ImportError:
        raise ImportError(
            "The tidy3d package is required to use this function; "
            "try `pip install tidy3d`."
        ) from None

    if not (
        tidy3d_sim.center[2] - tidy3d_sim.size[2] / 2
        <= z
        <= tidy3d_sim.center[2] + tidy3d_sim.size[2] / 2
    ):
        raise ValueError(
            f"z={z} is outside the bounds of the simulation size in the z-direction."
        )

    x = np.arange(
        tidy3d_sim.center[0] - tidy3d_sim.size[0] / 2,
        tidy3d_sim.center[0] + tidy3d_sim.size[0] / 2,
        0.001,
    )
    y = np.arange(
        tidy3d_sim.center[1] - tidy3d_sim.size[1] / 2,
        tidy3d_sim.center[1] + tidy3d_sim.size[1] / 2,
        0.001,
    )
    z = np.array([z])

    grid = Grid(boundaries=Coords(x=x, y=y, z=z))
    eps = np.real(tidy3d_sim.epsilon_on_grid(grid=grid, coord_key="boundaries").values)
    device_array = geometry.binarize_hard(device_array=eps, eta=eps_threshold)[:, :, 0]
    device_array = np.fliplr(np.rot90(device_array, k=-1))
    return Device(device_array=device_array, **kwargs)

get_sem_resolution(sem_path, sem_resolution_key)

Extracts the resolution of a scanning electron microscope (SEM) image from its metadata.

Parameters:

Name	Type	Description	Default
sem_path	str	The file path to the SEM image.	required
sem_resolution_key	str	The key to look for in the SEM image metadata to extract the resolution.	required

Returns:

Type	Description
float	The resolution of the SEM image in nanometers per pixel.

Raises:

Type	Description
ValueError	If the resolution key is not found in the SEM image metadata.

Source code in prefab/read.py

def get_sem_resolution(sem_path: str, sem_resolution_key: str) -> float:
    """
    Extracts the resolution of a scanning electron microscope (SEM) image from its
    metadata.

    Parameters
    ----------
    sem_path : str
        The file path to the SEM image.
    sem_resolution_key : str
        The key to look for in the SEM image metadata to extract the resolution.

    Returns
    -------
    float
        The resolution of the SEM image in nanometers per pixel.

    Raises
    ------
    ValueError
        If the resolution key is not found in the SEM image metadata.
    """
    with open(sem_path, "rb") as file:
        resolution_key_bytes = sem_resolution_key.encode("utf-8")
        for line in file:
            if resolution_key_bytes in line:
                line_str = line.decode("utf-8")
                match = re.search(r"-?\d+(\.\d+)?", line_str)
                if match:
                    value = float(match.group())
                    if value > 100:
                        value /= 1000
                    return value
    raise ValueError(f"Resolution key '{sem_resolution_key}' not found in {sem_path}.")