def test_segm_connect(self):
logging.debug(self.seg2d)
vertices, edges = seg_spx.make_graph_segm_connect_grid2d_conn4(self.seg2d)
logging.debug('vertices: {} -> edges: {}'.format(vertices, edges))
logging.debug(self.seg3d)
vertices, edges = seg_spx.make_graph_segm_connect_grid3d_conn6(self.seg3d)
logging.debug('vertices: {} -> edges: {}'.format(vertices, edges))
def get_vertexes_edges(segments):
""" wrapper - get list of vertexes edges for 2D / 3D images
:param ndarray segments:
:return:
"""
if segments.ndim == 3:
vertices, edges = make_graph_segm_connect_grid3d_conn6(segments)
elif segments.ndim == 2:
vertices, edges = make_graph_segm_connect_grid2d_conn4(segments)
else:
return None, None
return vertices, edges
def test_general(self):
slic = segment_slic_img2d(self.img, sp_size=15, relative_compact=0.2)
logging.debug(np.max(slic))
vertices, edges = make_graph_segm_connect_grid2d_conn4(slic)
logging.debug('vertices: %r', vertices)
logging.debug(len(edges))
logging.debug('edges: %r', edges)
fig, axarr = plt.subplots(ncols=2)
axarr[0].imshow(self.img)
axarr[1].imshow(slic, cmap=plt.cm.jet)
fig.savefig(os.path.join(PATH_OUTPUT, 'temp_superpixels.png'))
if logging.getLogger().getEffectiveLevel() == logging.DEBUG:
plt.show()
plt.close(fig)
def filter_boundary_points(segm, slic):
slic_centers = np.array(superpixel_centers(slic)).astype(int)
labels = segm[slic_centers[:, 0], slic_centers[:, 1]]
vertices, edges = make_graph_segm_connect_grid2d_conn4(slic)
nb_labels = labels.max() + 1
neighbour_labels = np.zeros((len(vertices), nb_labels))
for e1, e2 in edges:
# print e1, labels[e2], e2, labels[e1]
neighbour_labels[e1, labels[e2]] += 1
neighbour_labels[e2, labels[e1]] += 1
sums = np.tile(np.sum(neighbour_labels, axis=1), (nb_labels, 1)).T
neighbour_labels = neighbour_labels / sums
# border point nex to foreground
filter_bg = np.logical_and(labels == 0, neighbour_labels[:, 0] < 1)
# fulicul cells next to background
filter_fc = np.logical_and(labels == 1, neighbour_labels[:, 0] > 0)
points = slic_centers[np.logical_or(filter_bg, filter_fc)]
return points
