Refactoring structures/..

brainatlas_api/core.py

@@ -1,8 +1,6 @@
 import numpy as np
 from pathlib import Path
 
-from treelib import Tree
-
 from brainatlas_api.utils import open_json, read_tiff, make_hemispheres_stack
 from brainatlas_api.structures.structure_tree import StructureTree
 from brainatlas_api.obj_utils import read_obj
@@ -190,67 +188,6 @@ def get_structure_descendants(self, regions):
  def get_structure_parent(self, acronyms):
  pass
 
- def print_structures(self):
- """ 
- Prints the name of every structure in the structure tree to the console.
- """
- acronyms, names = self.structures_acronyms, self.structures_names
- sort_idx = np.argsort(acronyms)
- acronyms, names = (
- np.array(acronyms)[sort_idx],
- np.array(names)[sort_idx],
- )
- [print("({}) - {}".format(a, n)) for a, n in zip(acronyms, names)]
-
- def print_structures_tree(self, to_file=False, save_filepath=None):
- """
- Prints a 'tree' graph with the hierarchical organisation of all structures
-
- :param to_file: bool, default False. If True the tree structure is saved to 
- a file (at save_filepath) instead of printd to REPL
- :param save_filepath: str, if to_file = True, pass the path to a .txt file 
- where the tree structure will be saved.
- """
-
- def add_descendants_to_tree(atlas, tree, structure_id, parent_id):
- """
- Recursively goes through all the the descendants of a region and adds them to the tree
- """
- tree.create_node(
- tag=atlas.id_to_acronym_map[structure_id],
- identifier=structure_id,
- parent=parent_id,
- )
- descendants = atlas.structures.child_ids([structure_id])[0]
-
- if len(descendants):
- for child in descendants:
- add_descendants_to_tree(atlas, tree, child, structure_id)
-
- # Create a Tree structure and initialise with root
- root = self.acronym_to_id_map["root"]
- tree = Tree()
- tree.create_node(tag="root", identifier=root)
-
- # Recursively iterate through hierarchy#
- for child in self.structures.child_ids([root])[0]:
- add_descendants_to_tree(self, tree, child, root)
-
- if not to_file:
- tree.show()
- else:
- if save_filepath is None:
- raise ValueError(
- "If setting to_file as True, you need to pass the path to \
- a .txt file where the tree will be saved"
- )
- elif not save_filepath.endswith(".txt"):
- raise ValueError(
- f"save_filepath should point to a .txt file, not: {save_filepath}"
- )
-
- tree.save2file(save_filepath)
-
  # # functions to create oriented planes that can be used to slice actors etc
  # def get_plane_at_point(self, pos, norm, sx, sy,
  # color='lightgray', alpha=.25,

brainatlas_api/structures/simple_tree.py

@@ -38,8 +38,6 @@
 from collections import defaultdict
 from six import iteritems
 
-from allensdk.deprecated import deprecated
-
 
 class SimpleTree(object):
  def __init__(self, nodes, node_id_cb, parent_id_cb):
@@ -180,10 +178,6 @@ def node_ids(self):
 
  return list(self._nodes)
 
- @deprecated("Use SimpleTree.parent_ids instead.")
- def parent_id(self, node_ids):
- return self.parent_ids(node_ids)
-
  def parent_ids(self, node_ids):
  """Obtain the ids of one or more nodes' parents
 
@@ -198,8 +192,10 @@ def parent_ids(self, node_ids):
  Items are ids of input nodes' parents in order.
 
  """
-
- return [self._parent_ids[nid] for nid in node_ids]
+ if isinstance(node_ids, list):
+ return [self._parent_ids[nid] for nid in node_ids]
+ else:
+ return self._parent_ids[node_ids]
 
  def child_ids(self, node_ids):
  """Obtain the ids of one or more nodes' children
@@ -215,8 +211,10 @@ def child_ids(self, node_ids):
  Items are lists of input nodes' children's ids.
 
  """
-
- return [self._child_ids[nid] for nid in node_ids]
+ if isinstance(node_ids, list):
+ return [self._child_ids[nid] for nid in node_ids]
+ else:
+ return self._child_ids[node_ids]
 
  def ancestor_ids(self, node_ids):
  """Obtain the ids of one or more nodes' ancestors
@@ -291,10 +289,6 @@ def descendant_ids(self, node_ids):
  out.append(current)
  return out
 
- @deprecated("Use SimpleTree.nodes instead")
- def node(self, node_ids=None):
- return self.nodes(node_ids)
-
  def nodes(self, node_ids=None):
  """Get one or more nodes' full dictionaries from their ids.
 
@@ -312,14 +306,13 @@ def nodes(self, node_ids=None):
  if node_ids is None:
  node_ids = self.node_ids()
 
- return [
- self._nodes[nid] if nid in self._nodes else None
- for nid in node_ids
- ]
-
- @deprecated("Use SimpleTree.parents instead")
- def parent(self, node_ids):
- return self.parents(node_ids)
+ if isinstance(node_ids, list):
+ return [
+ self._nodes[nid] if nid in self._nodes else None
+ for nid in node_ids
+ ]
+ else:
+ return self._nodes[node_ids] if node_ids in self._nodes else None
 
  def parents(self, node_ids):
  """Get one or mode nodes' parent nodes
@@ -335,8 +328,10 @@ def parents(self, node_ids):
  Items are parents of nodes corresponding to argued ids.
 
  """
-
- return self.nodes([self._parent_ids[nid] for nid in node_ids])
+ if isinstance(node_ids, list):
+ return self.nodes([self._parent_ids[nid] for nid in node_ids])
+ else:
+ return self.nodes(self._parent_ids[node_ids])
 
  def children(self, node_ids):
  """Get one or mode nodes' child nodes

brainatlas_api/structures/structure_tree.py

@@ -41,6 +41,7 @@
 
 import numpy as np
 import pandas as pd
+from treelib import Tree
 
 from .simple_tree import SimpleTree
 
@@ -97,8 +98,10 @@ def get_structures_by_id(self, structure_ids):
  Each item describes a structure.
 
  """
-
- return self.nodes(structure_ids)
+ if isinstance(structure_ids, list):
+ return self.nodes(structure_ids)
+ else:
+ return self.nodes([structure_ids])[0]
 
  def get_structures_by_name(self, names):
  """Obtain a list of brain structures from their names,
@@ -114,8 +117,10 @@ def get_structures_by_name(self, names):
  Each item describes a structure.
 
  """
-
- return self.nodes_by_property("name", names)
+ if isinstance(names, list):
+ return self.nodes_by_property("name", names)
+ else:
+ return self.nodes_by_property("name", [names])[0]
 
  def get_structures_by_acronym(self, acronyms):
  """Obtain a list of brain structures from their acronyms
@@ -131,8 +136,10 @@ def get_structures_by_acronym(self, acronyms):
  Each item describes a structure.
 
  """
-
- return self.nodes_by_property("acronym", acronyms)
+ if isinstance(acronyms, list):
+ return self.nodes_by_property("acronym", acronyms)
+ else:
+ return self.nodes_by_property("acronym", [acronyms])[0]
 
  def get_colormap(self):
  """Get a dictionary mapping structure ids to colors across all nodes.
@@ -389,3 +396,93 @@ def path_to_list(path):
  return list(path)
 
  return [int(stid) for stid in path.split("/") if stid != ""]
+
+ def print_structures(self, to_file=False, save_filepath=None):
+ """ 
+ Prints the name of every structure in the structure tree to the console.
+ :param to_file: bool, default False. If True the tree structure is saved to 
+ a file (at save_filepath) instead of printd to REPL
+ :param save_filepath: str, if to_file = True, pass the path to a .txt file 
+ where the tree structure will be saved.
+ """
+ names = [n["name"] for n in self.nodes()]
+ acronyms = [n["acronym"] for n in self.nodes()]
+
+ sort_idx = np.argsort(acronyms)
+ acronyms, names = (
+ np.array(acronyms)[sort_idx],
+ np.array(names)[sort_idx],
+ )
+
+ if not to_file:
+ [print("({}) - {}".format(a, n)) for a, n in zip(acronyms, names)]
+ else:
+ if save_filepath is None:
+ raise ValueError(
+ "If setting to_file as True, you need to pass the path to \
+ a .txt file where the tree will be saved"
+ )
+ elif not save_filepath.endswith(".txt"):
+ raise ValueError(
+ f"save_filepath should point to a .txt file, not: {save_filepath}"
+ )
+
+ with open(save_filepath, "w") as out:
+ for a, n in zip(acronyms, names):
+ out.write("({}) - {}\n".format(a, n))
+
+ def print_structures_tree(self, to_file=False, save_filepath=None):
+ """
+ Prints a 'tree' graph with the hierarchical organisation of all structures
+
+ :param to_file: bool, default False. If True the tree structure is saved to 
+ a file (at save_filepath) instead of printd to REPL
+ :param save_filepath: str, if to_file = True, pass the path to a .txt file 
+ where the tree structure will be saved.
+ """
+
+ def add_descendants_to_tree(
+ self, id_to_acronym_map, tree, structure_id, parent_id
+ ):
+ """
+ Recursively goes through all the the descendants of a region and adds them to the tree
+ """
+ tree.create_node(
+ tag=id_to_acronym_map[structure_id],
+ identifier=structure_id,
+ parent=parent_id,
+ )
+ descendants = self.child_ids([structure_id])[0]
+
+ if len(descendants):
+ for child in descendants:
+ add_descendants_to_tree(
+ self, id_to_acronym_map, tree, child, structure_id
+ )
+
+ # Create a Tree structure and initialise with root
+ acronym_to_id_map = self.get_id_acronym_map()
+ id_to_acronym_map = {v: k for k, v in acronym_to_id_map.items()}
+
+ root = acronym_to_id_map["root"]
+ tree = Tree()
+ tree.create_node(tag="root", identifier=root)
+
+ # Recursively iterate through hierarchy#
+ for child in self.child_ids([root])[0]:
+ add_descendants_to_tree(self, id_to_acronym_map, tree, child, root)
+
+ if not to_file:
+ tree.show()
+ else:
+ if save_filepath is None:
+ raise ValueError(
+ "If setting to_file as True, you need to pass the path to \
+ a .txt file where the tree will be saved"
+ )
+ elif not save_filepath.endswith(".txt"):
+ raise ValueError(
+ f"save_filepath should point to a .txt file, not: {save_filepath}"
+ )
+
+ tree.save2file(save_filepath)

setup.py

@@ -1,6 +1,6 @@
 from setuptools import setup, find_namespace_packages
 
-requirements = ["allensdk", "tqdm", "numpy", "tifffile"]
+requirements = ["tqdm", "numpy", "tifffile", "treelib"]
 
 
 setup(