Add example python scripts

examples/local.py

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+#!/usr/bin/env python
+
+__doc__ = """
+Simple example script showing how to use the Sybil library locally to predict risk scores for a set of DICOM files.
+"""
+
+import sybil
+from sybil import visualize_attentions
+
+from utils import get_demo_data
+
+
+def main():
+    # Load a trained model
+    model = sybil.Sybil("sybil_ensemble")
+
+    dicom_files = get_demo_data()
+
+    # Get risk scores
+    serie = sybil.Serie(dicom_files)
+    print(f"Processing {len(dicom_files)} DICOM files")
+    prediction = model.predict([serie], return_attentions=True)
+    scores = prediction.scores
+
+    print(f"Risk scores: {scores}")
+
+    # Visualize attention maps
+    output_dir = "sybil_attention_output"
+
+    print(f"Writing attention images to {output_dir}")
+    series_with_attention = visualize_attentions(
+        serie,
+        attentions=prediction.attentions,
+        save_directory=output_dir,
+        gain=3,
+    )
+
+    print(f"Finished writing attention images to {output_dir}")
+
+if __name__ == "__main__":
+    main()

examples/remote_ark_sybil.py

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+#!/usr/bin/env python
+
+__doc__ = """
+This example shows how to use a client to access a 
+remote Sybil server (running Ark) to predict risk scores for a set of DICOM files.
+
+The server must be started separately.
+
+https://github.com/reginabarzilaygroup/Sybil/wiki
+https://github.com/reginabarzilaygroup/ark/wiki
+"""
+import json
+import os
+
+import numpy as np
+import requests
+
+import sybil.utils.visualization
+
+from utils import get_demo_data
+
+if __name__ == "__main__":
+
+    dicom_files = get_demo_data()
+    serie = sybil.Serie(dicom_files)
+
+    # Set the URL of the remote Sybil server
+    ark_hostname = "localhost"
+    ark_port = 5000
+
+    # Set the URL of the remote Sybil server
+    ark_host = f"http://{ark_hostname}:{ark_port}"
+
+    data_dict = {"return_attentions": True}
+    payload = {"data": json.dumps(data_dict)}
+
+    # Check if the server is running and reachable
+    resp = requests.get(f"{ark_host}/info")
+    if resp.status_code != 200:
+        raise ValueError(f"Failed to connect to ARK server. Status code: {resp.status_code}")
+
+    info_data = resp.json()["data"]
+    assert info_data["modelName"].lower() == "sybil", "The ARK server is not running Sybil"
+    print(f"ARK server info: {info_data}")
+
+    # Submit prediction to ARK server.
+    files = [('dicom', open(file_path, 'rb')) for file_path in dicom_files]
+    r = requests.post(f"{ark_host}/dicom/files", files=files, data=payload)
+    _ = [f[1].close() for f in files]
+    if r.status_code != 200:
+        raise ValueError(f"Error occurred processing DICOM files. Status code: {r.status_code}.\n{r.text}")
+
+    r_json = r.json()
+    predictions = r_json["data"]["predictions"]
+
+    scores = predictions[0]
+    print(f"Risk scores: {scores}")
+
+    attentions = predictions[1]
+    attentions = np.array(attentions)
+    print(f"Attention shape: {attentions.shape}")
+
+    # Visualize attention maps
+    save_directory = "remote_ark_sybil_attention_output"
+
+    print(f"Writing attention images to {save_directory}")
+
+    images = serie.get_raw_images()
+    overlayed_images = sybil.utils.visualization.build_overlayed_images(images, attentions, gain=3)
+
+    if save_directory is not None:
+        serie_idx = 0
+        save_path = os.path.join(save_directory, f"serie_{serie_idx}")
+        sybil.utils.visualization.save_images(overlayed_images, save_path, f"serie_{serie_idx}")
+
+    print(f"Finished writing attention images to {save_directory}")
+

examples/utils.py

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+import os
+from urllib.request import urlopen
+
+
+def download_file(url, filepath):
+    response = urlopen(url)
+
+    target_dir = os.path.dirname(filepath)
+    if target_dir and not os.path.exists(target_dir):
+        os.makedirs(target_dir)
+
+    # Check if the request was successful
+    if response.status == 200:
+        with open(filepath, 'wb') as f:
+            f.write(response.read())
+    else:
+        print(f"Failed to download file. Status code: {response.status_code}")
+
+    return filepath
+
+def get_demo_data():
+    demo_data_url = "https://www.dropbox.com/scl/fi/covbvo6f547kak4em3cjd/sybil_example.zip?rlkey=7a13nhlc9uwga9x7pmtk1cf1c&st=dqi0cf9k&dl=1"
+
+    zip_file_name = "sybil_example.zip"
+    cache_dir = os.path.expanduser("~/.sybil")
+    zip_file_path = os.path.join(cache_dir, zip_file_name)
+    os.makedirs(cache_dir, exist_ok=True)
+    if not os.path.exists(zip_file_path):
+        print(f"Downloading demo data to {zip_file_path}")
+        download_file(demo_data_url, zip_file_path)
+
+    demo_data_dir = os.path.join(cache_dir, "sybil_example")
+    image_data_dir = os.path.join(demo_data_dir, "sybil_demo_data")
+    if not os.path.exists(demo_data_dir):
+        print(f"Extracting demo data to {demo_data_dir}")
+        import zipfile
+        with zipfile.ZipFile(zip_file_path, 'r') as zip_ref:
+            zip_ref.extractall(demo_data_dir)
+
+    dicom_files = os.listdir(image_data_dir)
+    dicom_files = [os.path.join(image_data_dir, x) for x in dicom_files]
+    return dicom_files