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