app.py

import cv2
import torch
import numpy as np
import torch.nn.functional as F
from torch import nn
from transformers import AutoImageProcessor, Swinv2ForImageClassification, SegformerForSemanticSegmentation
import streamlit as st
from PIL import Image
import io
import zipfile
import pandas as pd
from datetime import datetime
import os
import tempfile
import base64

# --- GlaucomaModel Class ---
class GlaucomaModel(object):
    def __init__(self, 
                 cls_model_path="pamixsun/swinv2_tiny_for_glaucoma_classification", 
                 seg_model_path='pamixsun/segformer_for_optic_disc_cup_segmentation',
                 device=torch.device('cpu')):
        self.device = device
        # Classification model for glaucoma
        self.cls_extractor = AutoImageProcessor.from_pretrained(cls_model_path)
        self.cls_model = Swinv2ForImageClassification.from_pretrained(cls_model_path).to(device).eval()
        # Segmentation model for optic disc and cup
        self.seg_extractor = AutoImageProcessor.from_pretrained(seg_model_path)
        self.seg_model = SegformerForSemanticSegmentation.from_pretrained(seg_model_path).to(device).eval()
        # Mapping for class labels
        self.cls_id2label = self.cls_model.config.id2label

    def glaucoma_pred(self, image):
        inputs = self.cls_extractor(images=image.copy(), return_tensors="pt")
        with torch.no_grad():
            inputs.to(self.device)
            outputs = self.cls_model(**inputs).logits
            probs = F.softmax(outputs, dim=-1)
            disease_idx = probs.cpu()[0, :].numpy().argmax()
            confidence = probs.cpu()[0, disease_idx].item() * 100
        return disease_idx, confidence

    def optic_disc_cup_pred(self, image):
        inputs = self.seg_extractor(images=image.copy(), return_tensors="pt")
        with torch.no_grad():
            inputs.to(self.device)
            outputs = self.seg_model(**inputs)
        logits = outputs.logits.cpu()
        upsampled_logits = nn.functional.interpolate(
            logits, size=image.shape[:2], mode="bilinear", align_corners=False
        )
        seg_probs = F.softmax(upsampled_logits, dim=1)
        pred_disc_cup = upsampled_logits.argmax(dim=1)[0]
        
        # Calculate segmentation confidence based on probability distribution
        # For each pixel classified as cup/disc, check how confident the model is
        cup_mask = pred_disc_cup == 2
        disc_mask = pred_disc_cup == 1
        
        # Get confidence only for pixels predicted as cup/disc
        cup_confidence = seg_probs[0, 2, cup_mask].mean().item() * 100 if cup_mask.any() else 0
        disc_confidence = seg_probs[0, 1, disc_mask].mean().item() * 100 if disc_mask.any() else 0
        
        return pred_disc_cup.numpy().astype(np.uint8), cup_confidence, disc_confidence

    def process(self, image):
        disease_idx, cls_confidence = self.glaucoma_pred(image)
        disc_cup, cup_confidence, disc_confidence = self.optic_disc_cup_pred(image)

        try:
            vcdr = simple_vcdr(disc_cup)
        except:
            vcdr = np.nan

        mask = (disc_cup > 0).astype(np.uint8)
        x, y, w, h = cv2.boundingRect(mask)
        padding = max(50, int(0.2 * max(w, h)))
        x = max(x - padding, 0)
        y = max(y - padding, 0)
        w = min(w + 2 * padding, image.shape[1] - x)
        h = min(h + 2 * padding, image.shape[0] - y)

        cropped_image = image[y:y+h, x:x+w] if w >= 50 and h >= 50 else image.copy()
        _, disc_cup_image = add_mask(image, disc_cup, [1, 2], [[0, 255, 0], [255, 0, 0]], 0.2)

        return disease_idx, disc_cup_image, vcdr, cls_confidence, cup_confidence, disc_confidence, cropped_image

# --- Utility Functions ---
def simple_vcdr(mask):
    disc_area = np.sum(mask == 1)
    cup_area = np.sum(mask == 2)
    if disc_area == 0:
        return np.nan
    vcdr = cup_area / disc_area
    return vcdr

def add_mask(image, mask, classes, colors, alpha=0.5):
    overlay = image.copy()
    for class_id, color in zip(classes, colors):
        overlay[mask == class_id] = color
    output = cv2.addWeighted(overlay, alpha, image, 1 - alpha, 0)
    return output, overlay

def get_confidence_level(confidence):
    if confidence >= 90:
        return "Very High"
    elif confidence >= 75:
        return "High"
    elif confidence >= 60:
        return "Moderate"
    elif confidence >= 45:
        return "Low"
    else:
        return "Very Low"

def process_batch(model, images_data, progress_bar=None):
    results = []
    for idx, (file_name, image) in enumerate(images_data):
        try:
            disease_idx, disc_cup_image, vcdr, cls_conf, cup_conf, disc_conf, cropped_image = model.process(image)
            results.append({
                'file_name': file_name,
                'diagnosis': model.cls_id2label[disease_idx],
                'confidence': cls_conf,
                'vcdr': vcdr,
                'cup_conf': cup_conf,
                'disc_conf': disc_conf,
                'processed_image': disc_cup_image,
                'cropped_image': cropped_image
            })
            if progress_bar:
                progress_bar.progress((idx + 1) / len(images_data))
        except Exception as e:
            st.error(f"Error processing {file_name}: {str(e)}")
    return results

def save_results(results, original_images):
    # Create temporary directory for results
    with tempfile.TemporaryDirectory() as temp_dir:
        # Save report as CSV
        df = pd.DataFrame([{
            'File': r['file_name'],
            'Diagnosis': r['diagnosis'],
            'Confidence (%)': f"{r['confidence']:.1f}",
            'VCDR': f"{r['vcdr']:.3f}",
            'Cup Confidence (%)': f"{r['cup_conf']:.1f}",
            'Disc Confidence (%)': f"{r['disc_conf']:.1f}"
        } for r in results])
        
        report_path = os.path.join(temp_dir, 'report.csv')
        df.to_csv(report_path, index=False)
        
        # Save processed images
        for result, orig_img in zip(results, original_images):
            img_name = result['file_name']
            base_name = os.path.splitext(img_name)[0]
            
            # Save original
            orig_path = os.path.join(temp_dir, f"{base_name}_original.jpg")
            Image.fromarray(orig_img).save(orig_path)
            
            # Save segmentation
            seg_path = os.path.join(temp_dir, f"{base_name}_segmentation.jpg")
            Image.fromarray(result['processed_image']).save(seg_path)
            
            # Save ROI
            roi_path = os.path.join(temp_dir, f"{base_name}_roi.jpg")
            Image.fromarray(result['cropped_image']).save(roi_path)
        
        # Create ZIP file
        zip_path = os.path.join(temp_dir, 'results.zip')
        with zipfile.ZipFile(zip_path, 'w') as zipf:
            for root, _, files in os.walk(temp_dir):
                for file in files:
                    if file != 'results.zip':
                        file_path = os.path.join(root, file)
                        arcname = os.path.basename(file_path)
                        zipf.write(file_path, arcname)
        
        with open(zip_path, 'rb') as f:
            return f.read()

# --- Streamlit Interface ---
def main():
    st.set_page_config(layout="wide", page_title="Glaucoma Screening Tool")
    
    print("App started") # Debug print
    
    st.markdown("""
        <h1 style='text-align: center;'>Glaucoma Screening from Retinal Fundus Images</h1>
        <p style='text-align: center; color: gray;'>Upload retinal images for automated glaucoma detection and optic disc/cup segmentation</p>
        """, unsafe_allow_html=True)
    
    # Simple sidebar without columns
    st.sidebar.markdown("### 📤 Upload Images")
    uploaded_files = st.sidebar.file_uploader(
        "Upload Retinal Images", 
        type=['png', 'jpeg', 'jpg'], 
        accept_multiple_files=True,
        help="Support multiple images in PNG, JPEG formats"
    )
    
    print(f"Files uploaded: {uploaded_files}") # Debug print
    
    st.sidebar.markdown("### Settings")
    max_batch = st.sidebar.number_input("Max Batch Size", 
        min_value=1, 
        max_value=100, 
        value=20)
    
    if uploaded_files:
        print("Processing uploaded files") # Debug print
        
        if len(uploaded_files) > max_batch:
            st.warning(f"Please upload maximum {max_batch} images at once.")
            return

        st.markdown(f"Total images: {len(uploaded_files)}")
        st.markdown(f"Using: {'GPU' if torch.cuda.is_available() else 'CPU'}")
        
        try:
            # Initialize model
            print("Initializing model") # Debug print
            model = GlaucomaModel(device=torch.device("cuda:0" if torch.cuda.is_available() else "cpu"))
            
            # Process images
            images_data = []
            original_images = []
            print("Starting image processing") # Debug print
            
            for file in uploaded_files:
                try:
                    print(f"Processing file: {file.name}") # Debug print
                    image = Image.open(file).convert('RGB')
                    image_np = np.array(image)
                    images_data.append((file.name, image_np))
                    original_images.append(image_np)
                except Exception as e:
                    print(f"Error processing file {file.name}: {str(e)}") # Debug print
                    st.error(f"Error loading {file.name}: {str(e)}")
                    continue
            
            if not images_data:
                st.error("No valid images to process!")
                return
                
            progress = st.progress(0)
            st.write(f"Processing {len(images_data)} images...")
            
            # Process all images
            print("Starting batch processing") # Debug print
            results = process_batch(model, images_data, progress)
            print(f"Batch processing complete. Results: {len(results)}") # Debug print
            
            if results:
                print("Showing results") # Debug print
                # Show results one by one
                for result in results:
                    st.markdown(f"### Results for {result['file_name']}")
                    st.markdown(f"**Diagnosis:** {result['diagnosis']}")
                    st.markdown(f"**Confidence:** {result['confidence']:.1f}%")
                    st.markdown(f"**VCDR:** {result['vcdr']:.3f}")
                    
                    # Display images
                    st.image(result['processed_image'], caption="Segmentation")
                    st.image(result['cropped_image'], caption="ROI")
                    st.markdown("---")
                
                # Generate downloads
                print("Generating ZIP file") # Debug print
                zip_data = save_results(results, original_images)
                
                st.markdown("### Download Results")
                # Replace download_button with direct download link
                filename = f"glaucoma_screening_{datetime.now().strftime('%Y%m%d_%H%M%S')}.zip"
                st.markdown(
                    f'<a href="data:application/zip;base64,{base64.b64encode(zip_data).decode()}" download="{filename}">Download All Results (ZIP)</a>', 
                    unsafe_allow_html=True
                )
                
                # Simple summary
                st.markdown("### Summary")
                glaucoma_count = sum(1 for r in results if r['diagnosis'] == 'Glaucoma')
                normal_count = len(results) - glaucoma_count
                st.markdown(f"**Total Processed:** {len(results)}")
                st.markdown(f"**Glaucoma Detected:** {glaucoma_count}")
                st.markdown(f"**Normal:** {normal_count}")
                st.markdown(f"**Average Confidence:** {sum(r['confidence'] for r in results) / len(results):.1f}%")
        
        except Exception as e:
            print(f"Error in main processing: {str(e)}") # Debug print
            st.error(f"An error occurred: {str(e)}")

if __name__ == "__main__":
    print("Starting main") # Debug print
    main()