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| import streamlit as st | |
| import pydicom | |
| import matplotlib.pyplot as plt | |
| import zipfile | |
| import os | |
| import subprocess | |
| from datetime import datetime | |
| import shutil | |
| # Flag to track if subprocess commands have been executed | |
| subprocess_executed = False | |
| # Streamlit app title | |
| st.title("DICOM Image Viewer") | |
| # Upload a ZIP file containing DICOM slices | |
| uploaded_zip_file = st.file_uploader("Upload a ZIP file containing DICOM slices", type=["zip"]) | |
| st.write("Upload a ZIP file containing DICOM slices to view the images.") | |
| def install_dependencies(): | |
| command = "chmod +x install.sh" | |
| try: | |
| subprocess.run(command, shell=True, check=True) | |
| print("Script 'install.sh' has been made executable.") | |
| except subprocess.CalledProcessError as e: | |
| print(f"Error while making the script executable: {e}") | |
| command = "./install.sh" | |
| try: | |
| subprocess.run(command, shell=True, check=True) | |
| print("Script 'install.sh' has started running.") | |
| install_script_executed = True | |
| except subprocess.CalledProcessError as e: | |
| print(f"Error while running the script: {e}") | |
| def run_inference(): | |
| command = "chmod +x inference.sh" | |
| try: | |
| subprocess.run(command, shell=True, check=True) | |
| print("Script 'inference.sh' has been made executable.") | |
| except subprocess.CalledProcessError as e: | |
| print(f"Error while making the script executable: {e}") | |
| command = "./inference.sh" | |
| try: | |
| subprocess.run(command, shell=True, check=True) | |
| print("Script 'inference.sh' has started running.") | |
| except subprocess.CalledProcessError as e: | |
| print(f"Error while running the script: {e}") | |
| # Function to read and display the DICOM image | |
| def convert_dicom_to_png(_dicom_data): | |
| # Convert DICOM to a PNG image | |
| plt.imshow(_dicom_data.pixel_array, cmap=plt.cm.bone) | |
| plt.axis("off") | |
| plt.title("DICOM Image") | |
| plt.tight_layout() | |
| img_buffer = BytesIO() | |
| plt.savefig(img_buffer, format="png") | |
| img_buffer.seek(0) | |
| return img_buffer | |
| if uploaded_zip_file is not None: | |
| try: | |
| install_dependencies() | |
| temp_dir = "/home/user/app/C2C/temp_dicom_dir" | |
| os.makedirs(temp_dir, exist_ok=True) | |
| full_path = os.path.abspath(temp_dir) | |
| st.write(f"Temporary directory path: {full_path}") | |
| with zipfile.ZipFile(uploaded_zip_file, "r") as zip_ref: | |
| zip_ref.extractall(temp_dir) | |
| # Get a list of DICOM files in the directory | |
| dicom_files = [os.path.join(temp_dir, f) for f in os.listdir(temp_dir) if f.endswith(".dcm")] | |
| dicom_files.sort() # Sort the files | |
| if len(dicom_files) == 0: | |
| st.error("No DICOM files found in the ZIP archive.") | |
| else: | |
| # Create a list of DICOM data | |
| dicom_data_list = [pydicom.dcmread(dicom_file) for dicom_file in dicom_files] | |
| # Convert DICOM slices to PNG frames | |
| png_frames = [convert_dicom_to_png(_dicom_data) for _dicom_data in dicom_data_list] | |
| # Create a list of image clips from PNG frames | |
| clips = [mp.ImageClip(png_frame, duration=1) for png_frame in png_frames] | |
| # Concatenate the image clips to create a video | |
| video_clip = mp.concatenate_videoclips(clips, method="compose") | |
| # Display the video in Streamlit | |
| st.video(video_clip, format="video/mp4") | |
| except Exception as e: | |
| st.error(f"Error: {str(e)}") | |
| if st.button("Analyze"): | |
| run_inference() | |
| # Assuming the 'outputs' directory is located at "/home/user/app/C2C/comp2comp/outputs" | |
| outputs_directory = "/home/user/app/C2C/outputs" | |
| # Get a list of subdirectories inside the 'outputs' directory | |
| subdirectories = [subdir for subdir in os.listdir(outputs_directory) | |
| if os.path.isdir(os.path.join(outputs_directory, subdir))] | |
| # Use the first (or only) subdirectory, or None if there are no subdirectories | |
| first_subdirectory = subdirectories[0] if subdirectories else None | |
| if first_subdirectory: | |
| # Construct the paths to the video and image files inside the first subdirectory | |
| video_path = os.path.join(outputs_directory, first_subdirectory, "temp_dicom_dir/images/summary/aaa.mp4") | |
| image_path = os.path.join(outputs_directory, first_subdirectory, "temp_dicom_dir/images/summary/diameter_graph.png") | |
| largest_slice = os.path.join(outputs_directory, first_subdirectory, "temp_dicom_dir/images/summary/out.png") | |
| if os.path.exists(largest_slice): | |
| st.title("Largest Slice") | |
| st.image(largest_slice, use_column_width=True) | |
| # Display the video generated by the inference script | |
| if os.path.exists(video_path): | |
| st.title("Video") | |
| st.video(video_path, format="video/mp4") | |
| # Display the image generated by the inference script | |
| if os.path.exists(image_path): | |
| st.title("Diameter Graph") | |
| st.image(image_path, use_column_width=True) | |
| else: | |
| st.warning("No subdirectories or folders found inside the 'outputs' directory.") |