def test_build_graph(): """Test the method to build a graph from the heatmap.""" # Load the data with only a single serie currdir = os.path.dirname(os.path.abspath(__file__)) path_data = os.path.join(currdir, 'data', 'dce') # Create an object to handle the data dce_mod = DCEModality() # Read the data dce_mod.read_data_from_path(path_data) # Load the GT data path_gt = [os.path.join(currdir, 'data', 'gt_folders', 'prostate')] label_gt = ['prostate'] gt_mod = GTModality() gt_mod.read_data_from_path(label_gt, path_gt) # Build a heatmap from the dce data # Reduce the number of bins to enforce low memory consumption nb_bins = [100] * dce_mod.n_serie_ heatmap, bins_heatmap = dce_mod.build_heatmap(gt_mod.extract_gt_data( label_gt[0]), nb_bins=nb_bins) # Build the graph by taking the inverse exponential of the heatmap graph = StandardTimeNormalization._build_graph(heatmap, .5) graph_dense = graph.toarray() data = np.load(os.path.join(currdir, 'data', 'graph.npy')) assert_array_equal(graph_dense, data)
def test_walk_through_graph_shortest_path(): """Test the routine to go through the graph using shortest path.""" # Load the data with only a single serie currdir = os.path.dirname(os.path.abspath(__file__)) path_data = os.path.join(currdir, 'data', 'dce') # Create an object to handle the data dce_mod = DCEModality() # Read the data dce_mod.read_data_from_path(path_data) # Load the GT data path_gt = [os.path.join(currdir, 'data', 'gt_folders', 'prostate')] label_gt = ['prostate'] gt_mod = GTModality() gt_mod.read_data_from_path(label_gt, path_gt) # Build a heatmap from the dce data # Reduce the number of bins to enforce low memory consumption nb_bins = [10] * dce_mod.n_serie_ heatmap, bins_heatmap = dce_mod.build_heatmap(gt_mod.extract_gt_data( label_gt[0]), nb_bins=nb_bins) # Build the graph by taking the inverse exponential of the heatmap heatmap_inv_exp = np.exp(img_as_float(1. - (heatmap / np.max(heatmap)))) graph = StandardTimeNormalization._build_graph(heatmap_inv_exp, .99) start_end_tuple = ((0, 6), (3, 6)) # Call the algorithm to walk through the graph path = StandardTimeNormalization._walk_through_graph(graph, heatmap_inv_exp, start_end_tuple, 'shortest-path') gt_path = np.array([[0, 6], [1, 6], [2, 6], [3, 6]]) assert_array_equal(path, gt_path)