import streamlit as st from idc_index import index from pathlib import Path import pydicom import pandas as pd from tempfile import TemporaryDirectory import os from pathlib import Path import pydicom.datadict as dd import shutil import papermill as pm import subprocess from PIL import Image st.write(os.listdir()) # Main Streamlit app code st.title("DICOM Classification Demo") st.write("Select IDC data to download, extract images and metadata, and perform inference using three pre-trained models") # Fetch IDC index client = index.IDCClient() index_df = client.index # Option to choose IDC data st.subheader("Choose IDC Data to Process") collection_ids = index_df["collection_id"].unique() selected_collection_id = st.selectbox("Select Collection ID", collection_ids) # Filter dataframe based on selected collection_id df_filtered_by_collection = index_df[index_df["collection_id"] == selected_collection_id] patients = df_filtered_by_collection["PatientID"].unique() selected_patient_id = st.selectbox("Select Patient ID", patients) # Filter dataframe based on selected patient_id df_filtered_by_patient = df_filtered_by_collection[df_filtered_by_collection["PatientID"] == selected_patient_id] modalities = df_filtered_by_patient["Modality"].unique() selected_modality = st.selectbox("Select Modality", modalities) # Filter dataframe based on selected modality df_filtered_by_modality = df_filtered_by_patient[df_filtered_by_patient["Modality"] == selected_modality] studies = df_filtered_by_modality["StudyInstanceUID"].unique() selected_study = st.selectbox("Select Study", studies) # Filter dataframe based on selected study df_filtered_by_study = df_filtered_by_modality[df_filtered_by_modality["StudyInstanceUID"] == selected_study] series = df_filtered_by_study["SeriesInstanceUID"].unique() selected_series = st.selectbox("Select Series", series) print('selected_series: ' + str(selected_series)) # Button to run the notebook - which loads the pretrained models and runs inference if st.button("Run inference"): # Code to run when the button is pressed st.write("Button pressed! Running inference") if not os.path.exists("DICOMScanClassification_user_demo.ipynb"): subprocess.run(["wget", "https://raw.githubusercontent.com/deepakri201/DICOMScanClassification_pw41/main/DICOMScanClassification_user_demo.ipynb"]) if not os.path.exists("scaling_factors.csv"): subprocess.run(["wget", "https://github.com/deepakri201/DICOMScanClassification/releases/download/v1.0.0/scaling_factors.csv"]) if not os.path.exists("metadata_only_model.zip"): subprocess.run(["wget", "https://github.com/deepakri201/DICOMScanClassification/releases/download/v1.0.0/metadata_only_model.zip"]) subprocess.run(["unzip", "metadata_only_model.zip"]) if not os.path.exists("images_and_metadata_model.zip"): subprocess.run(["wget", "https://github.com/deepakri201/DICOMScanClassification/releases/download/v1.0.0/images_and_metadata_model.zip"]) subprocess.run(["unzip", "images_and_metadata_model.zip"]) if not os.path.exists("images_only_model.zip"): subprocess.run(["wget", "https://github.com/deepakri201/DICOMScanClassification/releases/download/v1.0.0/images_only_model.zip"]) subprocess.run(["unzip", "images_only_model.zip"]) subprocess.run(["papermill", "-p", "SeriesInstanceUID", selected_series, "DICOMScanClassification_user_demo.ipynb", "output.ipynb"]) st.write(subprocess.run(["ls","-R"])) with open('output.ipynb', "rb") as f: st.download_button( label="Download the output notebook file", data=f, file_name="output.ipynb", mime="application/json" ) # show classification results df st.write(pd.read_csv('classification_results.csv')) # show image image_path = 'image_for_classification.png' image = Image.open(image_path).convert('L') st.image(image, caption='input image for classification', use_column_width=True)