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/tests/utils/test_connected_components.py

+import numpy as np
+import pytest
+
+from qim3d.utils.connected_components import get_3d_connected_components
+
+
+@pytest.fixture(scope="module")
+def setup_data():
+    components = np.array([[0,0,1,1,0,0],
+                           [0,0,0,1,0,0],
+                           [1,1,0,0,1,0],
+                           [0,0,0,1,0,0]])
+    num_components = 4
+    connected_components = get_3d_connected_components(components)
+    return connected_components, components, num_components
+
+def test_connected_components_property(setup_data):
+    connected_components, _, _ = setup_data
+    components = np.array([[0,0,1,1,0,0],
+                            [0,0,0,1,0,0],
+                            [2,2,0,0,3,0],
+                            [0,0,0,4,0,0]])
+    assert np.array_equal(connected_components.connected_components, components)
+
+def test_num_connected_components_property(setup_data):
+    connected_components, _, num_components = setup_data
+    assert connected_components.num_connected_components == num_components
+
+def test_get_connected_component_with_index(setup_data):
+    connected_components, _, _ = setup_data
+    expected_component = np.array([[0,0,1,1,0,0],
+                                    [0,0,0,1,0,0],
+                                    [0,0,0,0,0,0],
+                                    [0,0,0,0,0,0]], dtype=bool)
+    print(connected_components.get_connected_component(index=1))
+    print(expected_component)
+    assert np.array_equal(connected_components.get_connected_component(index=1), expected_component)
+
+def test_get_connected_component_without_index(setup_data):
+    connected_components, _, _ = setup_data
+    component = connected_components.get_connected_component()
+    assert np.any(component)
+
+def test_get_connected_component_with_invalid_index(setup_data):
+    connected_components, _, num_components = setup_data
+    with pytest.raises(AssertionError):
+        connected_components.get_connected_component(index=0)
+    with pytest.raises(AssertionError):
+        connected_components.get_connected_component(index=num_components + 1)
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