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
# --- 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("Starting app...") # Debug print
st.markdown("""
Glaucoma Screening from Retinal Fundus Images
Upload retinal images for automated glaucoma detection and optic disc/cup segmentation
""", unsafe_allow_html=True)
print("Header rendered...") # Debug print
# Add session state for better state management
if 'processed_count' not in st.session_state:
st.session_state.processed_count = 0
# Add a more informative sidebar
with st.sidebar:
st.markdown("### 📤 Upload Images")
uploaded_files = st.file_uploader(
"Upload Retinal Images",
type=['png', 'jpeg', 'jpg'],
accept_multiple_files=True,
help="Support multiple images in PNG, JPEG formats"
)
st.markdown("### 📊 Processing Stats")
if 'processed_count' in st.session_state:
# Replace st.metric with regular markdown
st.markdown(f"**Images Processed:** {st.session_state.processed_count}")
st.markdown("---")
# Add batch size limit
max_batch = st.number_input("Max Batch Size",
min_value=1,
max_value=100,
value=20,
help="Maximum number of images to process in one batch")
if uploaded_files:
# Validate batch size
if len(uploaded_files) > max_batch:
st.warning(f"⚠️ Please upload maximum {max_batch} images at once. Current: {len(uploaded_files)}")
return
# Add loading animation
with st.spinner('🔄 Initializing model...'):
model = GlaucomaModel(device=torch.device("cuda:0" if torch.cuda.is_available() else "cpu"))
# Add summary metrics at the top
col1, col2 = st.columns(2)
with col1:
st.info(f"📁 Total images: {len(uploaded_files)}")
with col2:
st.info(f"⚙️ Using: {'GPU' if torch.cuda.is_available() else 'CPU'}")
# Prepare images data
images_data = []
original_images = []
for file in uploaded_files:
try:
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:
st.error(f"Error loading {file.name}: {str(e)}")
continue
progress_bar = st.progress(0)
st.write(f"Processing {len(images_data)} images...")
# Process all images
results = process_batch(model, images_data, progress_bar)
if results:
# Generate ZIP with results
zip_data = save_results(results, original_images)
# Add export options
st.markdown("### 📥 Export Options")
col1, col2 = st.columns(2)
with col1:
st.download_button(
label="📥 Download All Results (ZIP)",
data=zip_data, # Now zip_data is properly defined
file_name=f"glaucoma_screening_{datetime.now().strftime('%Y%m%d_%H%M%S')}.zip",
mime="application/zip"
)
with col2:
# Add CSV-only download
csv_data = pd.DataFrame([{
'File': r['file_name'],
'Diagnosis': r['diagnosis'],
'Confidence': r['confidence'],
'VCDR': r['vcdr']
} for r in results]).to_csv(index=False)
st.download_button(
label="📊 Download Report (CSV)",
data=csv_data,
file_name=f"glaucoma_report_{datetime.now().strftime('%Y%m%d_%H%M%S')}.csv",
mime="text/csv"
)
# Add this at the end of the file
if __name__ == "__main__":
print("Running main...") # Debug print
main()