app.py

import gradio as gr
import nibabel as nib
import numpy as np
import matplotlib.pyplot as plt
import matplotlib
matplotlib.use('Agg')

def visualize_nifti(file, volume_idx=0, slice_idx=0):
    if file is None:
        return None, "No file uploaded."
    
    try:
        # Load the NIfTI file
        img = nib.load(file.name)
        data = img.get_fdata()
        shape = data.shape
        
        # Determine if 3D or 4D
        if len(shape) == 3:
            # 3D data
            max_slice = shape[2] - 1
            slice_idx = min(slice_idx, max_slice)
            
            # Extract the axial slice
            slice_data = data[:, :, slice_idx]
            
            # Create the plot
            fig, ax = plt.subplots(figsize=(8, 8))
            ax.imshow(slice_data.T, cmap='gray', origin='lower')
            ax.axis('off')
            plt.title(f'Axial Slice: {slice_idx}/{max_slice}')
            plt.tight_layout()
            
            return fig, f'3D Volume - Displaying Slice {slice_idx}/{max_slice}'
            
        elif len(shape) == 4:
            # 4D data
            max_volume = shape[3] - 1
            max_slice = shape[2] - 1
            volume_idx = min(volume_idx, max_volume)
            slice_idx = min(slice_idx, max_slice)
            
            # Extract the axial slice from the specified volume
            slice_data = data[:, :, slice_idx, volume_idx]
            
            # Create the plot
            fig, ax = plt.subplots(figsize=(8, 8))
            ax.imshow(slice_data.T, cmap='gray', origin='lower')
            ax.axis('off')
            plt.title(f'Volume: {volume_idx}/{max_volume}, Slice: {slice_idx}/{max_slice}')
            plt.tight_layout()
            
            return fig, f'4D Volume - Displaying Volume {volume_idx}/{max_volume}, Slice {slice_idx}/{max_slice}'
        else:
            return None, f"Unsupported dimensions: {len(shape)}D"
            
    except Exception as e:
        return None, f"Error loading file: {str(e)}"

# Create Gradio interface with Blocks for dynamic controls
with gr.Blocks() as demo:
    gr.Markdown("# NIfTI File Visualizer")
    gr.Markdown("Upload a NIfTI (.nii or .nii.gz) file to visualize axial slices.")
    
    with gr.Row():
        file_input = gr.File(label="Upload NIfTI file (.nii or .nii.gz)")
    
    with gr.Row():
        volume_slider = gr.Slider(minimum=0, maximum=100, step=1, value=0, label="Volume/Frame (for 4D)")
        slice_slider = gr.Slider(minimum=0, maximum=100, step=1, value=0, label="Axial Slice (Z-plane)")
    
    with gr.Row():
        visualize_btn = gr.Button("Visualize")
    
    with gr.Row():
        output_plot = gr.Plot(label="Slice Visualization")
    
    with gr.Row():
        output_text = gr.Textbox(label="Info", lines=2)
    
    visualize_btn.click(
        fn=visualize_nifti,
        inputs=[file_input, volume_slider, slice_slider],
        outputs=[output_plot, output_text]
    )

if __name__ == "__main__":
    demo.launch()