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import os
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import streamlit as st
from transformers import CLIPProcessor
from medclip.modeling_hybrid_clip import FlaxHybridCLIP
@st.cache(allow_output_mutation=True)
def load_model():
model, _ = FlaxHybridCLIP.from_pretrained("flax-community/medclip-roco", _do_init=False)
processor = CLIPProcessor.from_pretrained("openai/clip-vit-base-patch32")
return model, processor
@st.cache(allow_output_mutation=True)
def load_image_embeddings():
embeddings_df = pd.read_hdf('feature_store/image_embeddings_large.hdf', key='emb')
image_embeds = np.stack(embeddings_df['image_embedding'])
image_files = np.asarray(embeddings_df['files'].tolist())
return image_files, image_embeds
k = 5
img_dir = './images'
st.sidebar.header("MedCLIP")
st.sidebar.image("./assets/logo.png", width=100)
st.sidebar.empty()
st.sidebar.markdown("""Search for medical images with natural language powered by a CLIP model [[Model Card]](https://huggingface.co/flax-community/medclip-roco) finetuned on the
[Radiology Objects in COntext (ROCO) dataset](https://github.com/razorx89/roco-dataset).""")
st.sidebar.markdown("Example queries:")
# * `ultrasound scans`🔍
# * `pathology`🔍
# * `pancreatic carcinoma`🔍
# * `PET scan`🔍""")
ex1_button = st.sidebar.button("🔍 pathology")
ex2_button = st.sidebar.button("🔍 ultrasound scans")
ex3_button = st.sidebar.button("🔍 pancreatic carcinoma")
ex4_button = st.sidebar.button("🔍 PET scan")
k_slider = st.sidebar.slider("Number of images", min_value=1, max_value=10, value=5)
st.sidebar.markdown("Kaushalya Madhawa, 2021")
st.title("MedCLIP 🩺")
# st.image("./assets/logo.png", width=100)
# st.markdown("""Search for medical images with natural language powered by a CLIP model [[Model Card]](https://huggingface.co/flax-community/medclip-roco) finetuned on the
# [Radiology Objects in COntext (ROCO) dataset](https://github.com/razorx89/roco-dataset).""")
# st.markdown("""Example queries:
# * `ultrasound scans`🔍
# * `pathology`🔍
# * `pancreatic carcinoma`🔍
# * `PET scan`🔍""")
text_value = ''
if ex1_button:
text_value = 'pathology'
elif ex2_button:
text_value = 'ultrasound scans'
elif ex3_button:
text_value = 'pancreatic carcinoma'
elif ex4_button:
text_value = 'PET scan'
image_list, image_embeddings = load_image_embeddings()
model, processor = load_model()
query = st.text_input("Enter your query here:", value=text_value)
dot_prod = None
if len(query)==0:
query = text_value
if st.button("Search") or k_slider:
if len(query)==0:
st.write("Please enter a valid search query")
else:
with st.spinner(f"Searching ROCO test set for {query}..."):
k = k_slider
inputs = processor(text=[query], images=None, return_tensors="jax", padding=True)
query_embedding = model.get_text_features(**inputs)
query_embedding = np.asarray(query_embedding)
query_embedding = query_embedding / np.linalg.norm(query_embedding, axis=-1, keepdims=True)
dot_prod = np.sum(np.multiply(query_embedding, image_embeddings), axis=1)
topk_images = dot_prod.argsort()[-k:]
matching_images = image_list[topk_images]
top_scores = 1. - dot_prod[topk_images]
#show images
for img_path, score in zip(matching_images, top_scores):
img = plt.imread(os.path.join(img_dir, img_path))
st.image(img, width=300)
st.write(f"{img_path} ({score:.2f})", help="score")
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