Implemented 3D connected components as wrapper class for scipy.ndimage.label

Ticket: https://www.notion.so/qim-dtu/3D-connected-components-ca5c410fef49444eac7c6efd0b56ead4?pvs=4

I have made a simple plot functions that takes the ConnectedComponents object and extracts the connected_components volume.

However I don't know if it is necessary as the user could do this manually.

def plot_connected_components(connected_components: ConnectedComponents, **kwargs):
    """ Plots connected components from the ConnectedComponents class as 2d slices.

    Args:
        connected_components (ConnectedComponents): The connected components class from the qim3d.utils.connected_components module.
        **kwargs: Additional keyword arguments to pass to qim3d.viz.img.slice_viz.

    Returns:
        matplotlib.pyplot: the 3D plot of the connected components.
    """
    fig = slice_viz(connected_components.connected_components, **kwargs)
    return fig

qim3d/utils/3d_connected_components.py

+import numpy as np
+from scipy.ndimage import label
+
+
+class ConnectedComponents:
+    def __init__(self, connected_components, num_connected_components):
+        """
+        Initializes a ConnectedComponents object.
+
+        Args:
+            connected_components (np.ndarray): The connected components.
+            num_connected_components (int): The number of connected components.
+        """
+        self._connected_components = connected_components
+        self._num_connected_components = num_connected_components
+
+    @property
+    def connected_components(self):
+        """
+        Get the connected components.
+
+        Returns:
+            np.ndarray: The connected components.
+        """
+        return self._connected_components
+
+    @property
+    def num_connected_components(self):
+        """
+        Get the number of connected components.
+
+        Returns:
+            int: The number of connected components.
+        """
+        return self._num_connected_components
+
+    def get_connected_component(self, index=None):
+        """ 
+        Get the connected component with the given index, if index is None selects a random component.
+
+        Args:
+            index (int): The index of the connected component. If none selects a random component.
+
+        Returns:
+            np.ndarray: The connected component as a binary mask.
+        """
+        assert 1 <= index <= self._num_connected_components, "Index out of range."
+
+        if index:
+            return self._connected_components == index
+        else:
+            return self._connected_components == np.random.randint(1, self._num_connected_components + 1)
+
+
+def get_3d_connected_components(image, connectivity=1):
+    """Get the connected components of a 3D binary image.
+
+    Args:
+        image (np.ndarray): The 3D binary image.
+        connectivity (int, optional): The connectivity of the connected components. Defaults to 1.
+
+    Returns:
+        class: Returns class object of the connected components.
+    """
+    connected_components, num_connected_components = label(image, connectivity)
+    return ConnectedComponents(connected_components, num_connected_components)