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fix with endpoints
Browse files
app.py
CHANGED
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@@ -14,9 +14,11 @@ import gc
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device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
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#
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HF_TOKEN = os.getenv("HF_TOKEN")
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tokenizer = AutoTokenizer.from_pretrained("baliddeki/phronesis-ml", token=HF_TOKEN)
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video_model = models.video.r3d_18(weights="KINETICS400_V1")
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video_model.fc = torch.nn.Linear(video_model.fc.in_features, 512)
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@@ -26,27 +28,20 @@ projector = ImageToTextProjector(512, report_generator.config.d_model)
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num_classes = 4
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class_names = ["acute", "normal", "chronic", "lacunar"]
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combined_model = CombinedModel(
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)
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model_file = hf_hub_download(
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"baliddeki/phronesis-ml", "pytorch_model.bin", token=HF_TOKEN
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)
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state_dict = torch.load(model_file, map_location=device)
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combined_model.load_state_dict(state_dict)
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combined_model.eval()
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# Image transforms
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image_transform = transforms.Compose(
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mean=[0.43216, 0.394666, 0.37645], std=[0.22803, 0.22145, 0.216989]
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),
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]
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)
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def dicom_to_image(file_bytes):
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dicom_file = pydicom.dcmread(io.BytesIO(file_bytes))
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@@ -55,23 +50,21 @@ def dicom_to_image(file_bytes):
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pixel_array = pixel_array.astype(np.uint8)
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return Image.fromarray(pixel_array).convert("RGB")
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def predict(images):
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if not images:
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return "No image uploaded.", ""
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# Convert images
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processed_imgs = []
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for img in images:
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filename = img.name.lower()
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if filename.endswith((".dcm", ".ima")):
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processed_imgs.append(dicom_img)
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else:
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pil_img = Image.open(img).convert("RGB")
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processed_imgs.append(pil_img)
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# Sample or pad
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n_frames = 16
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if len(processed_imgs) >= n_frames:
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images_sampled = [
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@@ -79,9 +72,7 @@ def predict(images):
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for i in np.linspace(0, len(processed_imgs) - 1, n_frames, dtype=int)
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]
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else:
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images_sampled = processed_imgs + [processed_imgs[-1]] * (
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n_frames - len(processed_imgs)
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)
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tensor_imgs = [image_transform(i) for i in images_sampled]
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input_tensor = torch.stack(tensor_imgs).permute(1, 0, 2, 3).unsqueeze(0).to(device)
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@@ -97,8 +88,7 @@ def predict(images):
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return class_name, report[0] if report else "No report generated."
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# Gradio interface
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demo = gr.Interface(
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fn=predict,
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inputs=gr.File(
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@@ -106,9 +96,13 @@ demo = gr.Interface(
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file_count="multiple",
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label="Upload CT Scan Images",
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),
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outputs=[
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title="Phronesis Medical Report Generator",
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description="Upload CT scan DICOM or image files. Returns diagnosis classification and generated report.",
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)
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demo.launch()
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device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
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# Environment setup
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HF_TOKEN = os.getenv("HF_TOKEN")
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os.environ["HF_HOME"] = "/tmp/huggingface_cache"
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# Model initialization
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tokenizer = AutoTokenizer.from_pretrained("baliddeki/phronesis-ml", token=HF_TOKEN)
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video_model = models.video.r3d_18(weights="KINETICS400_V1")
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video_model.fc = torch.nn.Linear(video_model.fc.in_features, 512)
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num_classes = 4
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class_names = ["acute", "normal", "chronic", "lacunar"]
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combined_model = CombinedModel(video_model, report_generator, num_classes, projector, tokenizer)
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model_file = hf_hub_download("baliddeki/phronesis-ml", "pytorch_model.bin", token=HF_TOKEN)
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state_dict = torch.load(model_file, map_location=device)
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combined_model.load_state_dict(state_dict)
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combined_model.to(device)
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combined_model.eval()
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# Image transforms
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image_transform = transforms.Compose([
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transforms.Resize((112, 112)),
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transforms.ToTensor(),
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transforms.Normalize(mean=[0.43216, 0.394666, 0.37645], std=[0.22803, 0.22145, 0.216989]),
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])
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def dicom_to_image(file_bytes):
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dicom_file = pydicom.dcmread(io.BytesIO(file_bytes))
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pixel_array = pixel_array.astype(np.uint8)
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return Image.fromarray(pixel_array).convert("RGB")
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def predict(images):
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if not images:
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return "No image uploaded.", ""
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processed_imgs = []
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for img in images:
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filename = img.name.lower()
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if filename.endswith((".dcm", ".ima")):
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file_bytes = img.read()
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dicom_img = dicom_to_image(file_bytes)
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processed_imgs.append(dicom_img)
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else:
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pil_img = Image.open(img).convert("RGB")
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processed_imgs.append(pil_img)
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n_frames = 16
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if len(processed_imgs) >= n_frames:
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images_sampled = [
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for i in np.linspace(0, len(processed_imgs) - 1, n_frames, dtype=int)
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]
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else:
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images_sampled = processed_imgs + [processed_imgs[-1]] * (n_frames - len(processed_imgs))
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tensor_imgs = [image_transform(i) for i in images_sampled]
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input_tensor = torch.stack(tensor_imgs).permute(1, 0, 2, 3).unsqueeze(0).to(device)
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return class_name, report[0] if report else "No report generated."
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# Define Gradio Interface explicitly
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demo = gr.Interface(
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fn=predict,
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inputs=gr.File(
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file_count="multiple",
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label="Upload CT Scan Images",
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),
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outputs=[
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gr.Textbox(label="Predicted Class"),
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gr.Textbox(label="Generated Report")
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],
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title="Phronesis Medical Report Generator",
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description="Upload CT scan DICOM or image files. Returns diagnosis classification and generated report.",
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)
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# Launch with explicit api_name for REST API compatibility
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demo.launch()
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