# app.py import torch import numpy as np from PIL import Image import io import gradio as gr from torchvision import models, transforms from transformers import AutoTokenizer, AutoModelForSeq2SeqLM from huggingface_hub import hf_hub_download from model import CombinedModel, ImageToTextProjector import pydicom import os import gc from fastapi import FastAPI, File, UploadFile, HTTPException from fastapi.middleware.cors import CORSMiddleware from typing import List import base64 from fastapi.responses import JSONResponse device = torch.device("cuda" if torch.cuda.is_available() else "cpu") HF_TOKEN = os.getenv("HF_TOKEN") os.environ["HF_HOME"] = "/tmp/huggingface_cache" # Model loading tokenizer = AutoTokenizer.from_pretrained("baliddeki/phronesis-ml", token=HF_TOKEN) video_model = models.video.r3d_18(weights="KINETICS400_V1") video_model.fc = torch.nn.Linear(video_model.fc.in_features, 512) report_generator = AutoModelForSeq2SeqLM.from_pretrained("GanjinZero/biobart-v2-base") projector = ImageToTextProjector(512, report_generator.config.d_model) num_classes = 4 class_names = ["acute", "normal", "chronic", "lacunar"] combined_model = CombinedModel(video_model, report_generator, num_classes, projector, tokenizer) model_file = hf_hub_download("baliddeki/phronesis-ml", "pytorch_model.bin", token=HF_TOKEN) state_dict = torch.load(model_file, map_location=device) combined_model.load_state_dict(state_dict) combined_model.to(device) combined_model.eval() image_transform = transforms.Compose([ transforms.Resize((112, 112)), transforms.ToTensor(), transforms.Normalize(mean=[0.43216, 0.394666, 0.37645], std=[0.22803, 0.22145, 0.216989]), ]) def dicom_to_image(file_bytes): """Convert DICOM file bytes to PIL Image""" dicom_file = pydicom.dcmread(io.BytesIO(file_bytes)) pixel_array = dicom_file.pixel_array.astype(np.float32) pixel_array = ((pixel_array - pixel_array.min()) / pixel_array.ptp()) * 255.0 pixel_array = pixel_array.astype(np.uint8) return Image.fromarray(pixel_array).convert("RGB") def process_images(file_data_list): """Core image processing logic used by both Gradio and FastAPI""" if not file_data_list: return "No images uploaded.", "" processed_imgs = [] for file_data in file_data_list: filename = file_data.get('filename', '').lower() file_content = file_data.get('content') try: if filename.endswith((".dcm", ".ima")): img = dicom_to_image(file_content) else: img = Image.open(io.BytesIO(file_content)).convert("RGB") processed_imgs.append(img) except Exception as e: print(f"Error processing file {filename}: {e}") continue if not processed_imgs: return "No valid images processed.", "" # Sample frames for video model n_frames = 16 if len(processed_imgs) >= n_frames: images_sampled = [ processed_imgs[i] for i in np.linspace(0, len(processed_imgs)-1, n_frames, dtype=int) ] else: images_sampled = processed_imgs + [processed_imgs[-1]] * (n_frames - len(processed_imgs)) # Transform images to tensors tensor_imgs = [image_transform(img) for img in images_sampled] input_tensor = torch.stack(tensor_imgs).permute(1, 0, 2, 3).unsqueeze(0).to(device) # Model inference with torch.no_grad(): class_logits, report, _ = combined_model(input_tensor) class_pred = torch.argmax(class_logits, dim=1).item() class_name = class_names[class_pred] # Cleanup gc.collect() if torch.cuda.is_available(): torch.cuda.empty_cache() return class_name, report[0] if report else "No report generated." def predict_gradio(files): """Gradio interface wrapper""" if not files: return "No images uploaded.", "" file_data_list = [] for file_obj in files: try: file_content = file_obj.read() if hasattr(file_obj, 'read') else open(file_obj.name, 'rb').read() file_data_list.append({ 'filename': file_obj.name if hasattr(file_obj, 'name') else str(file_obj), 'content': file_content }) except Exception as e: print(f"Error reading file: {e}") continue return process_images(file_data_list) # Create FastAPI app app = FastAPI( title="Phronesis ML API", description="Medical Image Analysis API with Gradio Interface", version="1.0.0" ) # Add CORS middleware app.add_middleware( CORSMiddleware, allow_origins=["*"], allow_credentials=True, allow_methods=["*"], allow_headers=["*"], ) @app.get("/") async def root(): """Root endpoint""" return { "message": "Phronesis ML API", "status": "running", "endpoints": { "predict": "/predict", "health": "/health", "gradio": "/gradio" } } @app.get("/health") async def health_check(): """Health check endpoint""" return { "status": "healthy", "model_loaded": True, "device": str(device) } @app.post("/predict") async def predict_api(files: List[UploadFile] = File(...)): """ API endpoint for medical image prediction Args: files: List of uploaded image files (DICOM, JPG, PNG, etc.) Returns: JSON response with predicted class and generated report """ try: if not files: raise HTTPException(status_code=400, detail="No files uploaded") # Process uploaded files file_data_list = [] for file in files: try: content = await file.read() file_data_list.append({ 'filename': file.filename or 'unknown', 'content': content }) except Exception as e: print(f"Error reading uploaded file {file.filename}: {e}") continue if not file_data_list: raise HTTPException(status_code=400, detail="No valid files processed") # Get predictions predicted_class, generated_report = process_images(file_data_list) # Return results return JSONResponse(content={ "status": "success", "data": { "predicted_class": predicted_class, "generated_report": generated_report, "processed_files": len(file_data_list) } }) except HTTPException: raise except Exception as e: print(f"Prediction error: {e}") raise HTTPException(status_code=500, detail=f"Prediction failed: {str(e)}") @app.exception_handler(Exception) async def global_exception_handler(request, exc): """Global exception handler""" return JSONResponse( status_code=500, content={ "status": "error", "message": "Internal server error", "detail": str(exc) } ) # Create Gradio interface demo = gr.Interface( fn=predict_gradio, inputs=gr.File( file_count="multiple", file_types=[".dcm", ".ima", ".jpg", ".jpeg", ".png", ".bmp"], label="Upload Medical Images" ), outputs=[ gr.Textbox(label="Predicted Class"), gr.Textbox(label="Generated Report", lines=5) ], title="🩺 Phronesis Medical Report Generator", description=""" Upload CT scan images to generate a medical report and classification. **Supported formats:** DICOM (.dcm, .ima), JPEG, PNG, BMP **API Endpoint:** `/predict` (POST) """, examples=[], allow_flagging="never" ) # Mount Gradio app to FastAPI app = gr.mount_gradio_app(app, demo, path="/gradio") # Launch configuration if __name__ == "__main__": import uvicorn # For local development # uvicorn.run(app, host="0.0.0.0", port=7860) # For Hugging Face Spaces demo.launch( server_name="0.0.0.0", server_port=7860, share=True, show_error=True )