Update documentation

examples/labels/plot_path_maps.py

@@ -73,6 +73,9 @@
 ps = [a.get_particle() for a in IMP.atom.get_leaves(hier)]
 path_map.set_particles(ps)
 path_map.sample_obstacles(extra_radius=0.0)
+# The origin is located on an atom and hence blocked. Thus, there cannot be
+# a path to the origin. Hence, unblock sphere around the origin.
+path_map.fill_sphere(path_origin, radius=3.0, value=0.0, inverse=False)
 path_map.update_tiles()
 
 # %%
@@ -92,7 +95,7 @@
 path_map.find_path_dijkstra(start_idx, -1)  # if the end_idx
 # %%
 # Now, we can backtrace the shortest path from every tile (voxel) to the
-# start index. A path is a squence of tile/voxel ids.
+# start index. A path is a sequence of tile/voxel ids.
 t = path_map.get_tiles()
 end_idx_1 = 829
 path_1 = t[end_idx_1].backtrack_to_path()
@@ -102,6 +105,7 @@
 path_2 = t[end_idx_2].backtrack_to_path()
 print(path_2)
 
+
 # %%
 # Not to all tiles a path can be found. A tile without a path to the
 # starting tile has a path-length of 1.

examples/labels/plot_search.py

@@ -44,9 +44,13 @@
 # The PathMapHeader defines the grid spacing and the size of the grid used
 # in the path search. The grid will have an edge that has twice the maximum
 # path length.
-max_path_length = 20.0
-grid_spacing = 1.0
-path_map_header = IMP.bff.PathMapHeader(max_path_length, grid_spacing)
+path_map_header_parameter = {
+    "max_path_length": 20.0,
+    "grid_spacing": 1.0,
+    "neighbor_radius": 2,
+    "obstacle_threshold": 1e-5
+}
+path_map_header = IMP.bff.PathMapHeader(**path_map_header_parameter)
 path_map_header.set_path_origin(path_origin)
 
 # %%

examples/release_highlights/plot_release_highlights_0_12_0.py

@@ -60,13 +60,17 @@
 ps = [a.get_particle() for a in IMP.atom.get_leaves(hier)]
 path_map.set_particles(ps)
 path_map.sample_obstacles(extra_radius=0.0)
+# The origin is located on an atom and hence blocked. Thus, there cannot be
+# a path to the origin. Hence, unblock sphere around the origin.
+path_map.fill_sphere(path_origin, radius=3.0, value=0.0, inverse=False)
 path_map.update_tiles()
 start_idx = path_map.get_voxel_by_location(path_origin)
 path_map.find_path_dijkstra(start_idx, -1)  # if the end_idx
 
 t = path_map.get_tiles()
 end_idx_1 = 829
 path_1 = t[end_idx_1].backtrack_to_path()
+print(path_1)
 
 end_idx_2 = 229
 path_2 = t[end_idx_2].backtrack_to_path()