prefab 0.4.7__py3-none-any.whl → 1.1.8__py3-none-any.whl

prefab/geometry.py

@@ -0,0 +1,394 @@
+"""Provides functions for manipulating ndarrays of device geometries."""
+
+from typing import Optional
+
+import cv2
+import numpy as np
+
+
+def normalize(device_array: np.ndarray) -> np.ndarray:
+    """
+    Normalize the input ndarray to have values between 0 and 1.
+
+    Parameters
+    ----------
+    device_array : np.ndarray
+        The input array to be normalized.
+
+    Returns
+    -------
+    np.ndarray
+        The normalized array with values scaled between 0 and 1.
+    """
+    return (device_array - np.min(device_array)) / (
+        np.max(device_array) - np.min(device_array)
+    )
+
+
+def binarize(
+    device_array: np.ndarray, eta: float = 0.5, beta: float = np.inf
+) -> np.ndarray:
+    """
+    Binarize the input ndarray based on a threshold and a scaling factor.
+
+    Parameters
+    ----------
+    device_array : np.ndarray
+        The input array to be binarized.
+    eta : float
+        The threshold value for binarization. Defaults to 0.5.
+    beta : float
+        The scaling factor for the binarization process. A higher value makes the
+        transition sharper. Defaults to np.inf, which results in a hard threshold.
+
+    Returns
+    -------
+    np.ndarray
+        The binarized array with elements scaled to 0 or 1.
+    """
+    return (np.tanh(beta * eta) + np.tanh(beta * (device_array - eta))) / (
+        np.tanh(beta * eta) + np.tanh(beta * (1 - eta))
+    )
+
+
+def binarize_hard(device_array: np.ndarray, eta: float = 0.5) -> np.ndarray:
+    """
+    Apply a hard threshold to binarize the input ndarray. The `binarize` function is
+    generally preferred for most use cases, but it can create numerical artifacts for
+    large beta values.
+
+    Parameters
+    ----------
+    device_array : np.ndarray
+        The input array to be binarized.
+    eta : float
+        The threshold value for binarization. Defaults to 0.5.
+
+    Returns
+    -------
+    np.ndarray
+        The binarized array with elements set to 0 or 1 based on the threshold.
+    """
+    return np.where(device_array < eta, 0.0, 1.0)
+
+
+def binarize_sem(sem_array: np.ndarray) -> np.ndarray:
+    """
+    Binarize a grayscale scanning electron microscope (SEM) image.
+
+    This function applies Otsu's method to automatically determine the optimal threshold
+    value for binarization of a grayscale SEM image.
+
+    Parameters
+    ----------
+    sem_array : np.ndarray
+        The input SEM image array to be binarized.
+
+    Returns
+    -------
+    np.ndarray
+        The binarized SEM image array with elements scaled to 0 or 1.
+    """
+    return cv2.threshold(
+        sem_array.astype("uint8"), 0, 1, cv2.THRESH_BINARY + cv2.THRESH_OTSU
+    )[1]
+
+
+def binarize_monte_carlo(
+    device_array: np.ndarray,
+    noise_magnitude: float,
+    blur_radius: float,
+) -> np.ndarray:
+    """
+    Binarize the input ndarray using a dynamic thresholding approach to simulate surface
+    roughness.
+
+    This function applies a dynamic thresholding technique where the threshold value is
+    determined by a base value perturbed by Gaussian-distributed random noise. The
+    threshold is then spatially varied across the array using Gaussian blurring,
+    simulating a potentially more realistic scenario where the threshold is not uniform
+    across the device.
+
+    Notes
+    -----
+    This is a temporary solution, where the defaults are chosen based on what looks
+    good. A better, data-driven approach is needed.
+
+    Parameters
+    ----------
+    device_array : np.ndarray
+        The input array to be binarized.
+    noise_magnitude : float
+        The standard deviation of the Gaussian distribution used to generate noise for
+        the threshold values. This controls the amount of randomness in the threshold.
+    blur_radius : float
+        The standard deviation for the Gaussian kernel used in blurring the threshold
+        map. This controls the spatial variation of the threshold across the array.
+
+    Returns
+    -------
+    np.ndarray
+        The binarized array with elements set to 0 or 1 based on the dynamically
+        generated threshold.
+    """
+    device_array = np.squeeze(device_array)
+    base_threshold = np.random.normal(loc=0.5, scale=0.1)
+    threshold_noise = np.random.normal(
+        loc=0, scale=noise_magnitude, size=device_array.shape
+    )
+    spatial_threshold = cv2.GaussianBlur(
+        threshold_noise, ksize=(0, 0), sigmaX=blur_radius
+    )
+    dynamic_threshold = base_threshold + spatial_threshold
+    binarized_array = np.where(device_array < dynamic_threshold, 0.0, 1.0)
+    binarized_array = np.expand_dims(binarized_array, axis=-1)
+    return binarized_array
+
+
+def ternarize(
+    device_array: np.ndarray, eta1: float = 1 / 3, eta2: float = 2 / 3
+) -> np.ndarray:
+    """
+    Ternarize the input ndarray based on two thresholds. This function is useful for
+    flattened devices with angled sidewalls (i.e., three segments).
+
+    Parameters
+    ----------
+    device_array : np.ndarray
+        The input array to be ternarized.
+    eta1 : float
+        The first threshold value for ternarization. Defaults to 1/3.
+    eta2 : float
+        The second threshold value for ternarization. Defaults to 2/3.
+
+    Returns
+    -------
+    np.ndarray
+        The ternarized array with elements set to 0, 0.5, or 1 based on the thresholds.
+    """
+    return np.where(device_array < eta1, 0.0, np.where(device_array >= eta2, 1.0, 0.5))
+
+
+def trim(
+    device_array: np.ndarray, buffer_thickness: Optional[dict[str, int]] = None
+) -> np.ndarray:
+    """
+    Trim the input ndarray by removing rows and columns that are completely zero.
+
+    Parameters
+    ----------
+    device_array : np.ndarray
+        The input array to be trimmed.
+    buffer_thickness : Optional[dict[str, int]]
+        A dictionary specifying the thickness of the buffer to leave around the non-zero
+        elements of the array. Should contain keys 'top', 'bottom', 'left', 'right'.
+        Defaults to None, which means no buffer is added.
+
+    Returns
+    -------
+    np.ndarray
+        The trimmed array, potentially with a buffer around the non-zero elements.
+    """
+    if buffer_thickness is None:
+        buffer_thickness = {"top": 0, "bottom": 0, "left": 0, "right": 0}
+
+    nonzero_rows, nonzero_cols = np.nonzero(np.squeeze(device_array))
+    row_min = max(nonzero_rows.min() - buffer_thickness.get("top", 0), 0)
+    row_max = min(
+        nonzero_rows.max() + buffer_thickness.get("bottom", 0) + 1,
+        device_array.shape[0],
+    )
+    col_min = max(nonzero_cols.min() - buffer_thickness.get("left", 0), 0)
+    col_max = min(
+        nonzero_cols.max() + buffer_thickness.get("right", 0) + 1,
+        device_array.shape[1],
+    )
+    return device_array[
+        row_min:row_max,
+        col_min:col_max,
+    ]
+
+
+def pad(device_array: np.ndarray, pad_width: int) -> np.ndarray:
+    """
+    Pad the input ndarray uniformly with a specified width on all sides.
+
+    Parameters
+    ----------
+    device_array : np.ndarray
+        The input array to be padded.
+    pad_width : int
+        The number of pixels to pad on each side.
+
+    Returns
+    -------
+    np.ndarray
+        The padded array.
+    """
+    return np.pad(
+        device_array,
+        pad_width=((pad_width, pad_width), (pad_width, pad_width), (0, 0)),
+        mode="constant",
+        constant_values=0,
+    )
+
+
+def blur(device_array: np.ndarray, sigma: float = 1.0) -> np.ndarray:
+    """
+    Apply Gaussian blur to the input ndarray and normalize the result.
+
+    Parameters
+    ----------
+    device_array : np.ndarray
+        The input array to be blurred.
+    sigma : float
+        The standard deviation for the Gaussian kernel. This controls the amount of
+        blurring. Defaults to 1.0.
+
+    Returns
+    -------
+    np.ndarray
+        The blurred and normalized array with values scaled between 0 and 1.
+    """
+    return np.expand_dims(
+        normalize(cv2.GaussianBlur(device_array, ksize=(0, 0), sigmaX=sigma)), axis=-1
+    )
+
+
+def rotate(device_array: np.ndarray, angle: float) -> np.ndarray:
+    """
+    Rotate the input ndarray by a given angle.
+
+    Parameters
+    ----------
+    device_array : np.ndarray
+        The input array to be rotated.
+    angle : float
+        The angle of rotation in degrees. Positive values mean counter-clockwise
+        rotation.
+
+    Returns
+    -------
+    np.ndarray
+        The rotated array.
+    """
+    center = (device_array.shape[1] / 2, device_array.shape[0] / 2)
+    rotation_matrix = cv2.getRotationMatrix2D(center=center, angle=angle, scale=1)
+    return np.expand_dims(
+        cv2.warpAffine(
+            device_array,
+            M=rotation_matrix,
+            dsize=(device_array.shape[1], device_array.shape[0]),
+        ),
+        axis=-1,
+    )
+
+
+def erode(device_array: np.ndarray, kernel_size: int) -> np.ndarray:
+    """
+    Erode the input ndarray using a specified kernel size and number of iterations.
+
+    Parameters
+    ----------
+    device_array : np.ndarray
+        The input array representing the device geometry to be eroded.
+    kernel_size : int
+        The size of the kernel used for erosion.
+
+    Returns
+    -------
+    np.ndarray
+        The eroded array.
+    """
+    kernel = np.ones((kernel_size, kernel_size), dtype=np.uint8)
+    return np.expand_dims(cv2.erode(device_array, kernel=kernel), axis=-1)
+
+
+def dilate(device_array: np.ndarray, kernel_size: int) -> np.ndarray:
+    """
+    Dilate the input ndarray using a specified kernel size.
+
+    Parameters
+    ----------
+    device_array : np.ndarray
+        The input array representing the device geometry to be dilated.
+    kernel_size : int
+        The size of the kernel used for dilation.
+
+    Returns
+    -------
+    np.ndarray
+        The dilated array.
+    """
+    kernel = np.ones((kernel_size, kernel_size), dtype=np.uint8)
+    return np.expand_dims(cv2.dilate(device_array, kernel=kernel), axis=-1)
+
+
+def flatten(device_array: np.ndarray) -> np.ndarray:
+    """
+    Flatten the input ndarray by summing the vertical layers and normalizing the result.
+
+    Parameters
+    ----------
+    device_array : np.ndarray
+        The input array to be flattened.
+
+    Returns
+    -------
+    np.ndarray
+        The flattened array with values scaled between 0 and 1.
+    """
+    return normalize(np.sum(device_array, axis=-1, keepdims=True))
+
+
+def enforce_feature_size(
+    device_array: np.ndarray, min_feature_size: int, strel: str = "disk"
+) -> np.ndarray:
+    """
+    Enforce a minimum feature size on the device geometry.
+
+    This function applies morphological operations to ensure that all features in the
+    device geometry are at least the specified minimum size. It uses either a disk
+    or square structuring element for the operations.
+
+    Notes
+    -----
+    This function does not guarantee that the minimum feature size is enforced in all
+    cases. A better process is needed.
+
+    Parameters
+    ----------
+    device_array : np.ndarray
+        The input array representing the device geometry.
+    min_feature_size : int
+        The minimum feature size to enforce, in nanometers.
+    strel : str
+        The type of structuring element to use. Can be either "disk" or "square".
+        Defaults to "disk".
+
+    Returns
+    -------
+    np.ndarray
+        The modified device array with enforced feature size.
+
+    Raises
+    ------
+    ValueError
+        If an invalid structuring element type is specified.
+    """
+    if strel == "disk":
+        kernel = cv2.getStructuringElement(
+            cv2.MORPH_ELLIPSE, (min_feature_size, min_feature_size)
+        )
+    elif strel == "square":
+        kernel = cv2.getStructuringElement(
+            cv2.MORPH_RECT, (min_feature_size, min_feature_size)
+        )
+    else:
+        raise ValueError(f"Invalid structuring element: {strel}")
+
+    device_array_2d = (device_array[:, :, 0] * 255).astype(np.uint8)
+    modified_geometry = cv2.morphologyEx(device_array_2d, cv2.MORPH_CLOSE, kernel)
+    modified_geometry = cv2.morphologyEx(modified_geometry, cv2.MORPH_OPEN, kernel)
+
+    return np.expand_dims(modified_geometry.astype(float) / 255, axis=-1)

prefab/models.py

@@ -0,0 +1,114 @@
+"""Models for the PreFab library."""
+
+import json
+from datetime import date
+
+from pydantic import BaseModel
+
+
+class Fab(BaseModel):
+    """
+    Represents a fabrication process in the PreFab model library.
+
+    Attributes
+    ----------
+    foundry : str
+        The name of the foundry where the fabrication process takes place.
+    process : str
+        The specific process used in the fabrication.
+    material : str
+        The material used in the fabrication process.
+    technology : str
+        The technology used in the fabrication process.
+    thickness : int
+        The thickness of the material used, measured in nanometers.
+    has_sidewall : bool
+        Indicates whether the fabrication has angled sidewalls.
+    """
+
+    foundry: str
+    process: str
+    material: str
+    technology: str
+    thickness: int
+    has_sidewall: bool
+
+
+class Model(BaseModel):
+    """
+    Represents a model of a fabrication process including versioning and dataset detail.
+
+    Attributes
+    ----------
+    fab : Fab
+        An instance of the Fab class representing the fabrication details.
+    version : str
+        The version identifier of the model.
+    version_date : date
+        The release date of this version of the model.
+    dataset : str
+        The identifier for the dataset used in this model.
+    dataset_date : date
+        The date when the dataset was last updated or released.
+    tag : str
+        An optional tag for additional categorization or notes.
+
+    Methods
+    -------
+    to_json()
+        Serializes the model instance to a JSON formatted string.
+    """
+
+    fab: Fab
+    version: str
+    version_date: date
+    dataset: str
+    dataset_date: date
+    tag: str
+
+    def to_json(self):
+        return json.dumps(self.dict(), default=str)
+
+
+ANT_NanoSOI = Fab(
+    foundry="ANT",
+    process="NanoSOI",
+    material="SOI",
+    technology="E-Beam",
+    thickness=220,
+    has_sidewall=False,
+)
+
+ANT_SiN = Fab(
+    foundry="ANT",
+    process="SiN",
+    material="SiN",
+    technology="E-Beam",
+    thickness=400,
+    has_sidewall=True,
+)
+
+ANT_NanoSOI_ANF1_d10 = Model(
+    fab=ANT_NanoSOI,
+    version="ANF1",
+    version_date=date(2024, 5, 6),
+    dataset="d10",
+    dataset_date=date(2024, 6, 8),
+    tag="",
+)
+
+ANT_SiN_ANF1_d1 = Model(
+    fab=ANT_SiN,
+    version="ANF1",
+    version_date=date(2024, 5, 6),
+    dataset="d1",
+    dataset_date=date(2024, 1, 31),
+    tag="",
+)
+
+models = dict(
+    ANT_NanoSOI=ANT_NanoSOI_ANF1_d10,
+    ANT_NanoSOI_ANF1_d10=ANT_NanoSOI_ANF1_d10,
+    ANT_SiN=ANT_SiN_ANF1_d1,
+    ANT_SiN_ANF1_d1=ANT_SiN_ANF1_d1,
+)