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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 matplotlib.pyplot as plt
import streamlit as st
from PIL import Image
import io
import zipfile
import os
# --- 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]
cup_confidence = seg_probs[0, 2, :, :].mean().item() * 100
disc_confidence = seg_probs[0, 1, :, :].mean().item() * 100
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
# --- Streamlit Interface ---
def main():
st.set_page_config(layout="wide")
st.title("Batch Glaucoma Screening from Retinal Fundus Images")
# Explanation for the confidence threshold
st.sidebar.write("**Confidence Threshold** (optional): Set a threshold to filter images based on the model's confidence in glaucoma classification.")
confidence_threshold = st.sidebar.slider("Confidence Threshold (%)", 0, 100, 70)
uploaded_files = st.sidebar.file_uploader("Upload Images", type=['png', 'jpeg', 'jpg'], accept_multiple_files=True)
confident_images = []
download_confident_images = []
if uploaded_files:
for uploaded_file in uploaded_files:
image = Image.open(uploaded_file).convert('RGB')
image_np = np.array(image).astype(np.uint8)
with st.spinner(f'Processing {uploaded_file.name}...'):
model = GlaucomaModel(device=torch.device("cuda:0" if torch.cuda.is_available() else "cpu"))
disease_idx, disc_cup_image, vcdr, cls_conf, cup_conf, disc_conf, cropped_image = model.process(image_np)
# Confidence-based grouping
is_confident = cls_conf >= confidence_threshold
if is_confident:
confident_images.append(uploaded_file.name)
download_confident_images.append((cropped_image, uploaded_file.name))
# Display Results
st.subheader(f"Results for {uploaded_file.name}")
cols = st.beta_columns(4) # Use st.beta_columns for compatibility with older Streamlit
cols[0].image(image_np, caption="Input Image", use_column_width=True)
cols[1].image(disc_cup_image, caption="Disc/Cup Segmentation", use_column_width=True)
cols[2].image(image_np, caption="Class Activation Map", use_column_width=True)
cols[3].image(cropped_image, caption="Cropped Image", use_column_width=True)
# Display confidence and metrics
st.write(f"**Vertical cup-to-disc ratio:** {vcdr:.04f}")
st.write(f"**Category:** {model.cls_id2label[disease_idx]} ({cls_conf:.02f}% confidence)")
st.write(f"**Optic Cup Segmentation Confidence:** {cup_conf:.02f}%")
st.write(f"**Optic Disc Segmentation Confidence:** {disc_conf:.02f}%")
st.write(f"**Confidence Group:** {'Confident' if is_confident else 'Not Confident'}")
# Download Link for Confident Images
if download_confident_images:
with zipfile.ZipFile("confident_cropped_images.zip", "w") as zf:
for cropped_image, name in download_confident_images:
img_buffer = io.BytesIO()
Image.fromarray(cropped_image).save(img_buffer, format="PNG")
zf.writestr(f"{name}_cropped.png", img_buffer.getvalue())
# Provide a markdown link to the ZIP file
st.sidebar.markdown(
f"[Download Confident Cropped Images](./confident_cropped_images.zip)",
unsafe_allow_html=True
)
else:
st.sidebar.info("Upload images to begin analysis.")
if __name__ == '__main__':
main() |