Add standalone predict.py module for ndarrays

prefab/__init__.py

@@ -7,14 +7,15 @@
 
 __version__ = "1.1.2"
 
-from . import compare, geometry, read, shapes
+from . import compare, geometry, predict, read, shapes
 from .device import BufferSpec, Device
 from .models import models
 
 __all__ = [
     "Device",
     "BufferSpec",
     "geometry",
+    "predict",
     "read",
     "shapes",
     "compare",

prefab/predict.py

@@ -0,0 +1,260 @@
+import base64
+import io
+import json
+import os
+
+import numpy as np
+import requests
+import toml
+from PIL import Image
+from tqdm import tqdm
+
+from .geometry import binarize_hard
+from .models import Model
+
+BASE_URL = "https://prefab-photonics--predict"
+
+
+def predict_array(
+    device_array: np.ndarray,
+    model: Model,
+    model_type: str,
+    binarize: bool,
+    gpu: bool = False,
+) -> np.ndarray:
+    """
+    Predicts the output array for a given device array using a specified model.
+
+    This function sends the device array to a prediction service, which uses a machine
+    learning model to predict the outcome of the nanofabrication process. The prediction
+    can be performed on a GPU if specified.
+
+    Parameters
+    ----------
+    device_array : np.ndarray
+        The input device array to be predicted.
+    model : Model
+        The model to use for prediction.
+    model_type : str
+        The type of model to use (e.g., 'p', 'c', 's').
+    binarize : bool
+        Whether to binarize the output.
+    gpu : bool, optional
+        Whether to use GPU for prediction. Defaults to False.
+
+    Returns
+    -------
+    np.ndarray
+        The predicted output array.
+
+    Raises
+    ------
+    RuntimeError
+        If the request to the prediction service fails.
+    """
+    headers = _prepare_headers()
+    predict_data = _prepare_predict_data(device_array, model, model_type, binarize)
+    endpoint_url = f"{BASE_URL}-gpu-v1.modal.run" if gpu else f"{BASE_URL}-v1.modal.run"
+
+    try:
+        with requests.post(
+            endpoint_url,
+            data=json.dumps(predict_data),
+            headers=headers,
+            stream=True,
+        ) as response:
+            response.raise_for_status()
+            return _process_response(response, model_type, binarize)
+    except requests.RequestException as e:
+        raise RuntimeError(f"Request failed: {e}") from e
+
+
+def predict_array_with_grad(
+    device_array: np.ndarray, model: Model, model_type: str
+) -> tuple[np.ndarray, np.ndarray]:
+    """
+    Predicts the output array and its gradient for a given device array using a
+    specified model.
+
+    This function sends the device array to a prediction service, which uses a machine
+    learning model to predict both the outcome and the gradient of the nanofabrication
+    process.
+
+    Parameters
+    ----------
+    device_array : np.ndarray
+        The input device array to be predicted.
+    model : Model
+        The model to use for prediction.
+    model_type : str
+        The type of model to use (e.g., 'p', 'c', 's').
+
+    Returns
+    -------
+    tuple[np.ndarray, np.ndarray]
+        A tuple containing the predicted output array and its gradient.
+
+    Raises
+    ------
+    RuntimeError
+        If the request to the prediction service fails.
+    """
+    headers = _prepare_headers()
+    predict_data = _prepare_predict_data(device_array, model, model_type, False)
+    endpoint_url = f"{BASE_URL}-with-grad-v1.modal.run"
+
+    response = requests.post(
+        endpoint_url, data=json.dumps(predict_data), headers=headers
+    )
+    prediction_array = _decode_array(response.json()["prediction_array"])
+    gradient_array = _decode_array(response.json()["gradient_array"])
+    gradient_min = response.json()["gradient_min"]
+    gradient_max = response.json()["gradient_max"]
+    gradient_range = gradient_max - gradient_min
+    gradient_array = gradient_array * gradient_range + gradient_min
+
+    return (prediction_array, gradient_array)
+
+
+def _encode_array(array):
+    """Encode a numpy array as a PNG image and return the base64 encoded string."""
+    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(encoded_png):
+    """Decode a base64 encoded PNG image and return a numpy array."""
+    binary_data = base64.b64decode(encoded_png)
+    image = Image.open(io.BytesIO(binary_data))
+    return np.array(image) / 255
+
+
+def _read_tokens():
+    """Read access and refresh tokens from the configuration file."""
+    token_file_path = os.path.expanduser("~/.prefab.toml")
+    try:
+        with open(token_file_path) as file:
+            tokens = toml.load(file)
+            access_token = tokens.get("access_token")
+            refresh_token = tokens.get("refresh_token")
+            if not access_token or not refresh_token:
+                raise ValueError("Tokens not found in the configuration file.")
+            return access_token, refresh_token
+    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
+
+
+def _prepare_headers():
+    """Prepare HTTP headers for the request."""
+    access_token, refresh_token = _read_tokens()
+    return {
+        "Authorization": f"Bearer {access_token}",
+        "X-Refresh-Token": refresh_token,
+    }
+
+
+def _prepare_predict_data(device_array, model, model_type, binarize):
+    """Prepare the data payload for the prediction request."""
+    return {
+        "device_array": _encode_array(np.squeeze(device_array)),
+        "model": model.to_json(),
+        "model_type": model_type,
+        "binary": binarize,
+    }
+
+
+def _process_response(response, model_type, binarize):
+    """Process the streaming response from the prediction request."""
+    event_type = None
+    model_descriptions = {
+        "p": "Prediction",
+        "c": "Correction",
+        "s": "SEMulate",
+    }
+    progress_bar = tqdm(
+        total=100,
+        desc=model_descriptions.get(model_type, "Processing"),
+        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)[1].strip()
+            elif decoded_line.startswith("data:"):
+                data_content = _parse_data_line(decoded_line)
+                result = _handle_event(event_type, data_content, progress_bar, binarize)
+                if result is not None:
+                    progress_bar.close()
+                    return result
+    progress_bar.close()
+
+
+def _parse_data_line(decoded_line):
+    """Parse a data line from the response stream."""
+    data_line = decoded_line.split(":", 1)[1].strip()
+    try:
+        return json.loads(data_line)
+    except json.JSONDecodeError:
+        raise ValueError(f"Failed to decode JSON: {data_line}") from None
+
+
+def _handle_event(event_type, data_content, progress_bar, binarize):
+    """Handle different types of events received from the server."""
+    if event_type == "progress":
+        _update_progress(progress_bar, data_content)
+    elif event_type == "result":
+        return _process_result(data_content, binarize)
+    elif event_type == "end":
+        print("Stream ended.")
+    elif event_type == "auth":
+        _update_tokens(data_content.get("auth", {}))
+    elif event_type == "error":
+        raise ValueError(f"{data_content['error']}")
+
+
+def _update_progress(progress_bar, data_content):
+    """Update the progress bar based on the progress event."""
+    progress = round(100 * data_content.get("progress", 0))
+    progress_bar.update(progress - progress_bar.n)
+
+
+def _process_result(data_content, binarize):
+    """Process the result event and return the prediction."""
+    results = [
+        _decode_array(data_content[key])
+        for key in sorted(data_content.keys())
+        if key.startswith("result")
+    ]
+    if results:
+        prediction = np.stack(results, axis=-1)
+        if binarize:
+            prediction = binarize_hard(prediction)
+        return prediction
+
+
+def _update_tokens(auth_data):
+    """Update tokens if new tokens are provided in the auth event."""
+    new_access_token = auth_data.get("new_access_token")
+    new_refresh_token = auth_data.get("new_refresh_token")
+    if new_access_token and new_refresh_token:
+        prefab_file_path = os.path.expanduser("~/.prefab.toml")
+        with open(prefab_file_path, "w", encoding="utf-8") as toml_file:
+            toml.dump(
+                {
+                    "access_token": new_access_token,
+                    "refresh_token": new_refresh_token,
+                },
+                toml_file,
+            )