pythonimageslice

Simple Python question: How to Image3D of Mathematica can be done in Python?

In Mathematica,

id = Image3DSlices["ImageData"]

(Sorry the "ImageData" is the Yellow Image of the First Example in the following URl, but I couldn't attach here. https://reference.wolfram.com/language/ref/Image3DSlices.html.en ) Then just

Image3D[id]

gives us the 3D image data from sliced images. The 3D image can be rotated freely by drag. But how can I do "Image3D" of sliced images with python?

If someone knows how to do, please help me!!

Solution

  • You can use PyVista:

    

def load_slices(folder_path):
    """
    Load slices from a folder and stack them into a 3D numpy array.
    """
    slices = []
    for file_name in sorted(os.listdir(folder_path)):
        if file_name.endswith(('.png', '.jpg', '.jpeg', '.bmp', '.tif')):
            image = Image.open(os.path.join(folder_path, file_name))
            slices.append(np.array(image))
    # Stack into a 3D array
    volume = np.stack(slices, axis=0)
    return volume

def visualize_3d(volume):
    """
    Visualize the 3D volume using PyVista.
    """
    # Convert the volume to a pyvista UniformGrid
    grid = pv.UniformGrid()
    grid.dimensions = volume.shape
    grid.point_data["values"] = volume.flatten(order="F")
    # Visualize the volume
    plotter = pv.Plotter()
    plotter.add_volume(grid, opacity="sigmoid", cmap="viridis")
    plotter.show()

# Specify the folder containing image slices
folder_path = "path_to_folder"

# Load and visualize
volume_data = load_slices(folder_path)
visualize_3d(volume_data)