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| import os | |
| import token | |
| import matplotlib.pyplot as plt | |
| import numpy as np | |
| import pandas as pd | |
| import streamlit as st | |
| from transformers import CLIPProcessor, AutoTokenizer | |
| from medclip.modeling_hybrid_clip import FlaxHybridCLIP | |
| def load_model(): | |
| model = FlaxHybridCLIP.from_pretrained("flax-community/medclip-roco", _do_init=True) | |
| tokenizer = AutoTokenizer.from_pretrained('allenai/scibert_scivocab_uncased') | |
| return model, tokenizer | |
| 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, tokenizer = 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 = tokenizer(text=[query], return_tensors="jax", padding=True) | |
| # st.write(f"Query inputs: {inputs}") | |
| 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})") | |