calebweinreb
commented
8 months ago Hello,
Could you let us know what kpms version you are using? Also, if possible, could you send the results.h5 file, config, and ideally the input data? (calebsw@gmail.com)
When trying to get my trajectory plots in Jupyter Notebook, the following error occurs and I can not get my trajectories plotted. is there anything I can do to alleviate this issue?
results = kpms.load_results(project_dir, model_name) kpms.generate_trajectory_plots(coordinates, results, project_dir, model_name, **config())ypeError Traceback (most recent call last) Cell In[14], line 2 1 results = kpms.load_results(project_dir, model_name) ----> 2 kpms.generate_trajectory_plots(coordinates, results, project_dir, model_name, **config())
File ~/miniconda3/envs/keypoint_moseq/lib/python3.9/site-packages/keypoint_moseq/viz.py:1767, in generate_trajectory_plots(coordinates, results, project_dir, model_name, output_dir, pre, post, min_frequency, min_duration, skeleton, bodyparts, use_bodyparts, keypoint_colormap, plot_options, get_limits_pctl, padding, lims, save_individually, save_gifs, save_mp4s, fps, projection_planes, interactive, density_sample, sampling_options, kwargs) 1763 desc = "Generating trajectory plots" 1764 for title, X in tqdm.tqdm( 1765 zip(titles, Xs_2D), desc=desc, total=len(titles), ncols=72 1766 ): -> 1767 fig, ax, rasters = plot_trajectories( 1768 [title], 1769 X[None], 1770 lims, 1771 edges=edges, 1772 return_rasters=(save_gifs or save_mp4s), 1773 plot_options, 1774 ) 1776 plt.savefig(os.path.join(output_dir, f"{title}{suffix}.pdf")) 1777 plt.close(fig=fig)
File ~/miniconda3/envs/keypoint_moseq/lib/python3.9/site-packages/keypoint_moseq/viz.py:1473, in plot_trajectories(titles, Xs, lims, edges, n_cols, invert, keypoint_colormap, keypoint_colors, node_size, line_width, alpha, num_timesteps, plot_width, overlap, return_rasters) 1469 n_cols = min(n_cols, len(Xs)) 1470 n_rows = np.ceil(len(Xs) / n_cols) 1471 offsets = np.stack( 1472 np.meshgrid( -> 1473 np.arange(n_cols) np.diff(lims[:, 0]) (1 - overlap[0]), 1474 np.arange(n_rows) np.diff(lims[:, 1]) (overlap[1] - 1), 1475 ), 1476 axis=-1, 1477 ).reshape(-1, 2)[: len(Xs)] 1479 Xs = interpolate_along_axis( 1480 np.linspace(0, Xs[0].shape[0], num_timesteps), 1481 np.arange(Xs[0].shape[0]), 1482 np.array(Xs), 1483 axis=1, 1484 ) 1486 Xs = Xs + offsets[:, None, None]
TypeError: 'NoneType' object is not subscriptable