Merge pull request #13 from AllenNeuralDynamics/10-helper-function-to…

…-directly-access-leaf-nodes

feat: add direct access to leaf nodes from atlas.leaf_nodes

brainglobe_atlasapi/core.py

@@ -15,7 +15,7 @@
  STRUCTURES_FILENAME,
 )
 from brainglobe_atlasapi.structure_class import StructuresDict
-from brainglobe_atlasapi.utils import read_json, read_tiff
+from brainglobe_atlasapi.utils import read_json, read_tiff, get_leaves_from_tree
 
 LEFT_HEMI_VAL = 1
 RIGHT_HEMI_VAL = 2
@@ -47,6 +47,10 @@ def __init__(self, path):
 
  self.structures = StructuresDict(structures_list)
 
+ # Parse the structure list to find leaf nodes
+ self.leaf_nodes = get_leaves_from_tree(self.structures_list)
+
+
  # Instantiate SpaceConvention object describing the current atlas:
  self.space = AnatomicalSpace(
  origin=self.orientation,

brainglobe_atlasapi/utils.py

@@ -317,3 +317,40 @@ def read_tiff(path):
 
  """
  return tifffile.imread(str(path))
+
+
+def get_leaves_from_tree(structures_list):
+ """Parse a structure tree (in list format) to find leaf nodes
+
+ We'll do this by going through the list once to create a dictionary mapping ID->node
+ A second time to map nodes to their parents (as children)
+ And a third time to pull all the nodes with no children
+
+ Parameters
+ ----------
+ structures_list : list
+ List of structures from BrainGlobeAtlas.structures_list
+ """
+
+ id_map = {}
+
+ # Get a map of id -> structure
+ for structure in structures_list:
+ structure['children'] = []
+ id_map[structure['id']] = structure
+
+ # Map each node to it's parent.children list
+ for structure in structures_list:
+ if len(structure['structure_id_path']) > 1:
+ parent_id = structure['structure_id_path'][-2]
+
+ if not parent_id == structure['id']:
+ id_map[parent_id]['children'].append(structure['id'])
+
+ # Get leaf nodes
+ leaf_nodes = []
+ for id in id_map.keys():
+ if not id_map[id]['children']:
+ leaf_nodes.append(id)
+
+ return leaf_nodes

tests/atlasapi/test_core_atlas.py

@@ -6,6 +6,7 @@
 import pytest
 import tifffile
 
+import brainglobe_atlasapi.core as core
 from brainglobe_atlasapi.core import AdditionalRefDict
 
 
@@ -92,7 +93,7 @@ def test_data_from_coords(atlas, coords):
  )
  == "root"
  )
- assert atlas.hemisphere_from_coords(coords) == atlas.right_hemisphere_value
+ assert atlas.hemisphere_from_coords(coords) == core.RIGHT_HEMI_VAL
  assert atlas.hemisphere_from_coords(coords, as_string=True) == "right"
  assert (
  atlas.hemisphere_from_coords(
@@ -177,8 +178,18 @@ def test_descendants(atlas):
 
 
 def test_mask(atlas):
- mask = atlas.get_structure_mask('VISp')
- mask_left = atlas.get_structure_mask('VISp', hemisphere=-1)
+ mask = atlas.get_structure_mask('root')
+ mask_left = atlas.get_structure_mask('root', hemisphere=-1)
 
- assert np.sum(mask > 0) == 7113
- assert np.sum((mask > 0) & (mask_left > 0)) == 3548
+ assert np.sum(mask > 0) == 3589
+ assert np.sum((mask > 0) & (mask_left > 0)) == 1709
+
+
+def test_leaf(atlas):
+ leaf_nodes = atlas.leaf_nodes
+
+ known_leaves = [567]
+
+ print(leaf_nodes)
+ print(known_leaves)
+ assert all(item in leaf_nodes for item in known_leaves)

tests/atlasapi/test_utils.py

@@ -81,3 +81,14 @@ def test_get_download_size_HTTPError():
 
  with pytest.raises(HTTPError):
  utils.get_download_size(test_url)
+
+
+def test_get_leaves():
+ structures_list = [
+ {'acronym': 'root', 'id': 997, 'name': 'root', 'structure_id_path': [997], 'rgb_triplet': [255, 255, 255], 'children': [8, 1009, 73]},
+ {'acronym': 'grey', 'id': 8, 'name': 'Basic cell groups and regions', 'structure_id_path': [997, 8], 'rgb_triplet': [191, 218, 227], 'children': [567, 343, 512]}
+ ]
+
+ leaf_nodes = utils.get_leaves_from_tree(structures_list)
+
+ assert leaf_nodes == [8]