prefab 1.1.1__py3-none-any.whl → 1.1.3__py3-none-any.whl

prefab/__init__.py

@@ -5,9 +5,9 @@ Usage:
     import prefab as pf
 """
 
-__version__ = "1.1.1"
+__version__ = "1.1.3"
 
-from . import compare, geometry, read, shapes
+from . import compare, geometry, predict, read, shapes
 from .device import BufferSpec, Device
 from .models import models
 
@@ -15,6 +15,7 @@ __all__ = [
     "Device",
     "BufferSpec",
     "geometry",
+    "predict",
     "read",
     "shapes",
     "compare",

prefab/compare.py

@@ -1,5 +1,7 @@
 """Provides functions to measure the similarity between devices."""
 
+import warnings
+
 import numpy as np
 
 from .device import Device
@@ -42,6 +44,11 @@ def intersection_over_union(device_a: Device, device_b: Device) -> float:
     float
         The Intersection over Union between two devices.
     """
+    if not device_a.is_binary or not device_b.is_binary:
+        warnings.warn(
+            "One or both devices are not binarized.", UserWarning, stacklevel=2
+        )
+
     return np.sum(
         np.logical_and(device_a.device_array, device_b.device_array)
     ) / np.sum(np.logical_or(device_a.device_array, device_b.device_array))
@@ -65,6 +72,11 @@ def hamming_distance(device_a: Device, device_b: Device) -> int:
     int
         The Hamming distance between two devices.
     """
+    if not device_a.is_binary or not device_b.is_binary:
+        warnings.warn(
+            "One or both devices are not binarized.", UserWarning, stacklevel=2
+        )
+
     return np.sum(device_a.device_array != device_b.device_array)
 
 
@@ -86,6 +98,11 @@ def dice_coefficient(device_a: Device, device_b: Device) -> float:
     float
         The Dice coefficient between two devices.
     """
+    if not device_a.is_binary or not device_b.is_binary:
+        warnings.warn(
+            "One or both devices are not binarized.", UserWarning, stacklevel=2
+        )
+
     intersection = 2.0 * np.sum(
         np.logical_and(device_a.device_array, device_b.device_array)
     )

prefab/device.py

@@ -1,28 +1,21 @@
 """Provides the Device class for representing photonic devices."""
 
-import base64
-import io
-import json
-import os
 from typing import Optional
 
 import cv2
 import gdstk
 import matplotlib.pyplot as plt
 import numpy as np
-import requests
-import toml
 from matplotlib.axes import Axes
 from matplotlib.patches import Rectangle
 from PIL import Image
 from pydantic import BaseModel, Field, conint, root_validator, validator
 from scipy.ndimage import distance_transform_edt
 from skimage import measure
-from skimage.morphology import closing, disk, opening, square
-from tqdm import tqdm
 
 from . import compare, geometry
 from .models import Model
+from .predict import predict_array
 
 Image.MAX_IMAGE_PIXELS = None
 
@@ -193,6 +186,7 @@ class Device(BaseModel):
             raise ValueError("device_array must be a 2D array.")
         return values
 
+    @property
     def is_binary(self) -> bool:
         """
         Check if the device geometry is binary.
@@ -210,147 +204,6 @@ class Device(BaseModel):
             or np.array_equal(unique_values, [1])
         )
 
-    def _encode_array(self, array):
-        image = Image.fromarray(np.uint8(array * 255))
-        buffered = io.BytesIO()
-        image.save(buffered, format="PNG")
-        encoded_png = base64.b64encode(buffered.getvalue()).decode("utf-8")
-        return encoded_png
-
-    def _decode_array(self, encoded_png):
-        binary_data = base64.b64decode(encoded_png)
-        image = Image.open(io.BytesIO(binary_data))
-        return np.array(image) / 255
-
-    def _predict_array(
-        self,
-        model: Model,
-        model_type: str,
-        binarize: bool,
-        gpu: bool = False,
-    ) -> "Device":
-        try:
-            with open(os.path.expanduser("~/.prefab.toml")) as file:
-                content = file.readlines()
-                access_token = None
-                refresh_token = None
-                for line in content:
-                    if "access_token" in line:
-                        access_token = line.split("=")[1].strip().strip('"')
-                    if "refresh_token" in line:
-                        refresh_token = line.split("=")[1].strip().strip('"')
-                        break
-                if not access_token or not refresh_token:
-                    raise ValueError("Token not found in the configuration file.")
-        except FileNotFoundError:
-            raise FileNotFoundError(
-                "Could not validate user.\n"
-                "Please update prefab using: pip install --upgrade prefab.\n"
-                "Signup/login and generate a new token.\n"
-                "See https://www.prefabphotonics.com/docs/guides/quickstart."
-            ) from None
-
-        headers = {
-            "Authorization": f"Bearer {access_token}",
-            "X-Refresh-Token": refresh_token,
-        }
-
-        predict_data = {
-            "device_array": self._encode_array(self.device_array[:, :, 0]),
-            "model": model.to_json(),
-            "model_type": model_type,
-            "binary": binarize,
-        }
-        json_data = json.dumps(predict_data)
-
-        endpoint_url = (
-            "https://prefab-photonics--predict-gpu-v1.modal.run"
-            if gpu
-            else "https://prefab-photonics--predict-v1.modal.run"
-        )
-
-        try:
-            with requests.post(
-                endpoint_url, data=json_data, headers=headers, stream=True
-            ) as response:
-                response.raise_for_status()
-                event_type = None
-                model_descriptions = {
-                    "p": "Prediction",
-                    "c": "Correction",
-                    "s": "SEMulate",
-                }
-                progress_bar = tqdm(
-                    total=100,
-                    desc=f"{model_descriptions[model_type]}",
-                    unit="%",
-                    colour="green",
-                    bar_format="{l_bar}{bar:30}{r_bar}{bar:-10b}",
-                )
-
-                for line in response.iter_lines():
-                    if line:
-                        decoded_line = line.decode("utf-8").strip()
-                        if decoded_line.startswith("event:"):
-                            event_type = decoded_line.split(":")[1].strip()
-                        elif decoded_line.startswith("data:"):
-                            try:
-                                data_content = json.loads(
-                                    decoded_line.split("data: ")[1]
-                                )
-                                if event_type == "progress":
-                                    progress = round(100 * data_content["progress"])
-                                    progress_bar.update(progress - progress_bar.n)
-                                elif event_type == "result":
-                                    results = []
-                                    for key in sorted(data_content.keys()):
-                                        if key.startswith("result"):
-                                            decoded_image = self._decode_array(
-                                                data_content[key]
-                                            )
-                                            results.append(decoded_image)
-
-                                    if results:
-                                        prediction = np.stack(results, axis=-1)
-                                        if binarize:
-                                            prediction = geometry.binarize_hard(
-                                                prediction
-                                            )
-                                        progress_bar.close()
-                                        return prediction
-                                elif event_type == "end":
-                                    print("Stream ended.")
-                                    progress_bar.close()
-                                    break
-                                elif event_type == "auth":
-                                    if "new_refresh_token" in data_content["auth"]:
-                                        prefab_file_path = os.path.expanduser(
-                                            "~/.prefab.toml"
-                                        )
-                                        with open(
-                                            prefab_file_path, "w", encoding="utf-8"
-                                        ) as toml_file:
-                                            toml.dump(
-                                                {
-                                                    "access_token": data_content[
-                                                        "auth"
-                                                    ]["new_access_token"],
-                                                    "refresh_token": data_content[
-                                                        "auth"
-                                                    ]["new_refresh_token"],
-                                                },
-                                                toml_file,
-                                            )
-                                elif event_type == "error":
-                                    raise ValueError(f"{data_content['error']}")
-                            except json.JSONDecodeError:
-                                raise ValueError(
-                                    "Failed to decode JSON:",
-                                    decoded_line.split("data: ")[1],
-                                ) from None
-        except requests.RequestException as e:
-            raise RuntimeError(f"Request failed: {e}") from e
-
     def predict(
         self,
         model: Model,
@@ -393,7 +246,8 @@ class Device(BaseModel):
             If the prediction service returns an error or if the response from the
             service cannot be processed correctly.
         """
-        prediction_array = self._predict_array(
+        prediction_array = predict_array(
+            device_array=self.device_array,
             model=model,
             model_type="p",
             binarize=binarize,
@@ -445,7 +299,8 @@ class Device(BaseModel):
             If the correction service returns an error or if the response from the
             service cannot be processed correctly.
         """
-        correction_array = self._predict_array(
+        correction_array = predict_array(
+            device_array=self.device_array,
             model=model,
             model_type="c",
             binarize=binarize,
@@ -487,7 +342,8 @@ class Device(BaseModel):
             A new instance of the Device class with its geometry transformed to simulate
             an SEM image style.
         """
-        semulated_array = self._predict_array(
+        semulated_array = predict_array(
+            device_array=self.device_array,
             model=model,
             model_type="s",
             binarize=False,
@@ -550,6 +406,7 @@ class Device(BaseModel):
         cell_name: str = "prefab_device",
         gds_layer: tuple[int, int] = (1, 0),
         contour_approx_mode: int = 2,
+        origin: tuple[float, float] = (0.0, 0.0),
     ):
         """
         Exports the device geometry as a GDSII file.
@@ -572,11 +429,15 @@ class Device(BaseModel):
             The mode of contour approximation used during the conversion. Defaults to 2,
             which corresponds to `cv2.CHAIN_APPROX_SIMPLE`, a method that compresses
             horizontal, vertical, and diagonal segments and leaves only their endpoints.
+        origin : tuple[float, float], optional
+            The x and y coordinates of the origin for the GDSII export. Defaults to
+            (0.0, 0.0).
         """
         gdstk_cell = self.flatten()._device_to_gdstk(
             cell_name=cell_name,
             gds_layer=gds_layer,
             contour_approx_mode=contour_approx_mode,
+            origin=origin,
         )
         print(f"Saving GDS to '{gds_path}'...")
         gdstk_library = gdstk.Library()
@@ -588,6 +449,7 @@ class Device(BaseModel):
         cell_name: str = "prefab_device",
         gds_layer: tuple[int, int] = (1, 0),
         contour_approx_mode: int = 2,
+        origin: tuple[float, float] = (0.0, 0.0),
     ):
         """
         Converts the device geometry to a GDSTK cell object.
@@ -607,6 +469,9 @@ class Device(BaseModel):
             The mode of contour approximation used during the conversion. Defaults to 2,
             which corresponds to `cv2.CHAIN_APPROX_SIMPLE`, a method that compresses
             horizontal, vertical, and diagonal segments and leaves only their endpoints.
+        origin : tuple[float, float], optional
+            The x and y coordinates of the origin for the GDSTK cell. Defaults to
+            (0.0, 0.0).
 
         Returns
         -------
@@ -618,6 +483,7 @@ class Device(BaseModel):
             cell_name=cell_name,
             gds_layer=gds_layer,
             contour_approx_mode=contour_approx_mode,
+            origin=origin,
         )
         return gdstk_cell
 
@@ -626,6 +492,7 @@ class Device(BaseModel):
         cell_name: str,
         gds_layer: tuple[int, int],
         contour_approx_mode: int,
+        origin: tuple[float, float],
     ) -> gdstk.Cell:
         approx_mode_mapping = {
             1: cv2.CHAIN_APPROX_NONE,
@@ -662,8 +529,21 @@ class Device(BaseModel):
             polygons_to_process = hierarchy_polygons[level]
 
             if polygons_to_process:
+                center_x_nm = self.device_array.shape[1] / 2
+                center_y_nm = self.device_array.shape[0] / 2
+
+                center_x_um = center_x_nm / 1000
+                center_y_um = center_y_nm / 1000
+
+                adjusted_polygons = [
+                    [
+                        (x - center_x_um + origin[0], y - center_y_um + origin[1])
+                        for x, y in polygon
+                    ]
+                    for polygon in polygons_to_process
+                ]
                 processed_polygons = gdstk.boolean(
-                    polygons_to_process,
+                    adjusted_polygons,
                     processed_polygons,
                     operation,
                     layer=gds_layer[0],
@@ -1313,13 +1193,6 @@ class Device(BaseModel):
         """
         Trim the device geometry by removing empty space around it.
 
-        Parameters
-        ----------
-        buffer_thickness : dict, optional
-            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
         -------
         Device
@@ -1414,15 +1287,10 @@ class Device(BaseModel):
         Flatten the device geometry 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.
+        Device
+            A new instance of the Device with the flattened geometry.
         """
         flattened_device_array = geometry.flatten(device_array=self.device_array)
         return self.model_copy(update={"device_array": flattened_device_array})
@@ -1472,16 +1340,11 @@ class Device(BaseModel):
         ValueError
             If an invalid structuring element type is specified.
         """
-        if strel == "disk":
-            structuring_element = disk(radius=min_feature_size / 2)
-        elif strel == "square":
-            structuring_element = square(width=min_feature_size)
-        else:
-            raise ValueError(f"Invalid structuring element: {strel}")
-
-        modified_geometry = closing(self.device_array[:, :, 0], structuring_element)
-        modified_geometry = opening(modified_geometry, structuring_element)
-        modified_geometry = np.expand_dims(modified_geometry, axis=-1)
+        modified_geometry = geometry.enforce_feature_size(
+            device_array=self.device_array,
+            min_feature_size=min_feature_size,
+            strel=strel,
+        )
         return self.model_copy(update={"device_array": modified_geometry})
 
     def check_feature_size(self, min_feature_size: int, strel: str = "disk"):

prefab/geometry.py

@@ -2,6 +2,7 @@
 
 import cv2
 import numpy as np
+from skimage.morphology import closing, disk, opening, square
 
 
 def normalize(device_array: np.ndarray) -> np.ndarray:
@@ -248,7 +249,6 @@ def rotate(device_array: np.ndarray, angle: float) -> np.ndarray:
         ),
         axis=-1,
     )
-    return np.expand_dims(rotated_device_array, axis=-1)
 
 
 def erode(device_array: np.ndarray, kernel_size: int) -> np.ndarray:
@@ -306,3 +306,45 @@ def flatten(device_array: np.ndarray) -> 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.
+
+    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, optional
+        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":
+        structuring_element = disk(radius=min_feature_size / 2)
+    elif strel == "square":
+        structuring_element = square(width=min_feature_size)
+    else:
+        raise ValueError(f"Invalid structuring element: {strel}")
+
+    modified_geometry = closing(device_array[:, :, 0], structuring_element)
+    modified_geometry = opening(modified_geometry, structuring_element)
+    return np.expand_dims(modified_geometry, axis=-1)

prefab/models.py

@@ -10,7 +10,7 @@ class Fab(BaseModel):
     """
     Represents a fabrication process in the PreFab model library.
 
-    Parameters
+    Attributes
     ----------
     foundry : str
         The name of the foundry where the fabrication process takes place.