IFMedTech/NIfTI

1import gradio as gr2import nibabel as nib3import numpy as np4import matplotlib.pyplot as plt5import matplotlib6matplotlib.use('Agg')7 8def visualize_nifti(file, volume_idx=0, slice_idx=0):9    if file is None:10        return None11    12    try:13        # Load the NIfTI file14        img = nib.load(file.name)15        data = img.get_fdata()16        shape = data.shape17        18        # Determine if 3D or 4D19        if len(shape) == 3:20            # 3D data21            max_slice = shape[2] - 122            slice_idx = min(slice_idx, max_slice)23            24            # Extract the axial slice25            slice_data = data[:, :, slice_idx]26            27            # Create the plot28            fig, ax = plt.subplots(figsize=(8, 8))29            ax.imshow(slice_data.T, cmap='gray', origin='lower')30            ax.axis('off')31            plt.title(f'Axial Slice: {slice_idx}/{max_slice}')32            plt.tight_layout()33            34            return fig35            36        elif len(shape) == 4:37            # 4D data38            max_volume = shape[3] - 139            max_slice = shape[2] - 140            volume_idx = min(volume_idx, max_volume)41            slice_idx = min(slice_idx, max_slice)42            43            # Extract the axial slice from the specified volume44            slice_data = data[:, :, slice_idx, volume_idx]45            46            # Create the plot47            fig, ax = plt.subplots(figsize=(8, 8))48            ax.imshow(slice_data.T, cmap='gray', origin='lower')49            ax.axis('off')50            plt.title(f'Volume: {volume_idx}/{max_volume}, Slice: {slice_idx}/{max_slice}')51            plt.tight_layout()52            53            return fig54        else:55            return None56            57    except Exception as e:58        return None59 60# Create Gradio interface with Blocks for dynamic controls61with gr.Blocks() as demo:62    gr.Markdown("# NIfTI File Visualizer")63    gr.Markdown("Upload a NIfTI (.nii or .nii.gz) file to visualize axial slices.")64    65    with gr.Row():66        file_input = gr.File(label="Upload NIfTI file (.nii or .nii.gz)")67    68    with gr.Row():69        volume_slider = gr.Slider(minimum=0, maximum=100, step=1, value=0, label="Volume/Frame (for 4D)")70        slice_slider = gr.Slider(minimum=0, maximum=100, step=1, value=0, label="Axial Slice (Z-plane)")71    72    with gr.Row():73        visualize_btn = gr.Button("Visualize")74    75    with gr.Row():76        output_plot = gr.Plot(label="Slice Visualization")77    78    visualize_btn.click(79        fn=visualize_nifti,80        inputs=[file_input, volume_slider, slice_slider],81        outputs=[output_plot]82    )83 84if __name__ == "__main__":85    demo.launch()