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import gradio as gr
import subprocess
import os
import shutil
import uuid
import zipfile
import nibabel as nib
import numpy as np
import matplotlib.pyplot as plt
def run_segmentation(uploaded_file, modality):
job_id = str(uuid.uuid4())
input_filename = f"input_{job_id}.nii.gz"
output_folder = f"segmentations_{job_id}"
with open(input_filename, "wb") as f:
f.write(uploaded_file.read())
command = ["TotalSegmentator", "-i", input_filename, "-o", output_folder]
if modality == "MR":
command.extend(["--task", "total_mr"])
try:
subprocess.run(command, check=True)
except subprocess.CalledProcessError as e:
return f"Error during segmentation: {e}", None
zip_filename = f"segmentations_{job_id}.zip"
with zipfile.ZipFile(zip_filename, "w", zipfile.ZIP_DEFLATED) as zipf:
for root, dirs, files in os.walk(output_folder):
for file in files:
file_path = os.path.join(root, file)
arcname = os.path.relpath(file_path, output_folder)
zipf.write(file_path, arcname)
seg_files = [os.path.join(output_folder, f) for f in os.listdir(output_folder) if f.endswith('.nii.gz')]
if seg_files:
seg_file = seg_files[0]
try:
seg_img = nib.load(seg_file)
seg_data = seg_img.get_fdata()
slice_idx = seg_data.shape[2] // 2
seg_slice = seg_data[:, :, slice_idx]
plt.figure(figsize=(6, 6))
plt.imshow(seg_slice.T, cmap="gray", origin="lower")
plt.axis('off')
image_filename = f"segmentation_preview_{job_id}.png"
plt.savefig(image_filename, bbox_inches='tight')
plt.close()
except Exception as e:
print(f"Error creating preview: {e}")
image_filename = None
else:
image_filename = None
os.remove(input_filename)
shutil.rmtree(output_folder)
return zip_filename, image_filename
with gr.Blocks() as demo:
gr.Markdown("# TotalSegmentator Gradio App")
gr.Markdown(
"Upload a CT or MR image (in NIfTI format) and run segmentation using TotalSegmentator. "
"For MR images, the task flag is set accordingly. A preview of one segmentation slice will be displayed."
)
with gr.Row():
uploaded_file = gr.File(label="Upload NIfTI Image (.nii.gz)")
modality = gr.Radio(choices=["CT", "MR"], label="Select Image Modality", value="CT")
with gr.Row():
zip_output = gr.File(label="Download Segmentation Output (zip)")
preview_output = gr.Image(label="Segmentation Preview")
run_btn = gr.Button("Run Segmentation")
run_btn.click(fn=run_segmentation, inputs=[uploaded_file, modality], outputs=[zip_output, preview_output])
demo.launch()
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