Error when loading in numpy array to automated_separation.generic_tree() #5
Description
Hi @mattbv, @philwilkes. I've been getting this error when loading a NumPy array into automated_separation.generic_tree(). The array is the correct dimension. This error isn't present when using tlseparation with Python 2.7. Thanks for any assistance.
`---------------------------------------------------------------------------
AssertionError Traceback (most recent call last)
in
----> 1 wood_final, leaf_final = tlseparation.scripts.automated_separation.generic_tree(arr, knn_list=[40, 50, 80, 100, 120], voxel_size=0.04, retrace_steps=40)
/opt/conda/lib/python3.7/site-packages/tlseparation/scripts/automated_separation.py in generic_tree(arr, knn_list, voxel_size, retrace_steps)
662 # root of the tree.
663 path_mask = voxel_path_detection(arr, voxel_size, retrace_steps, 100,
--> 664 voxel_size * 1.77, False)
665 # Filtering path_mask points by feature threshold. In this case,
666 # feature 4 has a very distinctive pattern for wood and leaf. Usually
/opt/conda/lib/python3.7/site-packages/tlseparation/classification/path_detection.py in voxel_path_detection(point_cloud, voxel_size, k_retrace, knn, nbrs_threshold, verbose)
173 detect_main_pathways with %s number of steps retraced' % k_retrace)
174 path_mask_voxel = detect_main_pathways(vox_coords, k_retrace, knn,
--> 175 nbrs_threshold, verbose=verbose)
176 # Re-indexing point_cloud indices from voxels coordinates detected as
177 # part of the path.
/opt/conda/lib/python3.7/site-packages/tlseparation/classification/path_detection.py in detect_main_pathways(point_cloud, k_retrace, knn, nbrs_threshold, verbose, max_iter)
228 # dimensions.
229 assert point_cloud.ndim == 2, "point_cloud must be an array with 2
--> 230 dimensions, n_points x 3 (x, y, z)."
231 assert point_cloud.shape[1] == 3, "point_cloud must be a 3D point cloud.
232 Make sure it has the shape n_points x 3 (x, y, z)."
AssertionError: point_cloud must be an array with 2 dimensions, n_points x 3 (x, y, z).`
