Refactor rename fragmentsgraph (#281)

* refactor: updated fragment filtering

* refactor: renamed neurograph to fragments graph

---------

Co-authored-by: anna-grim <anna.grim@alleninstitute.org>

src/deep_neurographs/fragment_filtering.py

@@ -8,83 +8,98 @@
 other from a FragmentsGraph.
 
 """
+
 from collections import defaultdict
 
+import networkx as nx
 import numpy as np
-from networkx import connected_components
 from tqdm import tqdm
 
 from deep_neurographs import geometry
-from deep_neurographs.utils import util
 
-COLOR = "1.0 0.0 0.0"
 QUERY_DIST = 15
 
 
 # --- Curvy Removal ---
-def remove_curvy(graph, max_length, ratio=0.5):
+def remove_curvy(fragments_graph, max_length, ratio=0.5):
+    """
+    Removes connected components with 2 nodes from "fragments_graph" that are
+    "curvy" fragments, based on a specified ratio of endpoint distance to edge
+    length and a maximum length threshold.
+
+    Parameters
+    ----------
+    fragments_graph : FragmentsGraph
+        Graph generated from fragments of a predicted segmentation.
+    max_length : float
+        The maximum allowable length (in microns) for an edge to be considered
+        for removal.
+    ratio : float, optional
+        Threshold ratio of endpoint distance to edge length. Components with a
+        ratio below this value are considered "curvy" and are removed. The
+        default is 0.5.
+
+    Returns
+    -------
+    int
+        Number of fragments removed from the graph.
+
+    """
     deleted_ids = set()
-    components = [c for c in connected_components(graph) if len(c) == 2]
-    for nodes in tqdm(components, desc="Filter Curvy Fragment"):
-        if len(nodes) == 2:
-            i, j = tuple(nodes)
-            length = graph.edges[i, j]["length"]
-            endpoint_dist = graph.dist(i, j)
-            if endpoint_dist / length < ratio and length < max_length:
-                deleted_ids.add(graph.edges[i, j]["swc_id"])
-                delete_fragment(graph, i, j)
+    components = get_line_components(fragments_graph)
+    for nodes in tqdm(components, desc="Filter Curvy Fragments"):
+        i, j = tuple(nodes)
+        length = fragments_graph.edges[i, j]["length"]
+        endpoint_dist = fragments_graph.dist(i, j)
+        if endpoint_dist / length < ratio and length < max_length:
+            deleted_ids.add(fragments_graph.edges[i, j]["swc_id"])
+            delete_fragment(fragments_graph, i, j)
     return len(deleted_ids)
 
 
 # --- Doubles Removal ---
-def remove_doubles(graph, max_length, node_spacing, output_dir=None):
+def remove_doubles(fragments_graph, max_length, node_spacing):
     """
-    Removes connected components from "neurgraph" that are likely to be a
-    double.
+    Removes connected components from "fragments_graph" that are likely to be
+    a double -- caused by ghosting in the image.
 
     Parameters
     ----------
-    graph : FragmentsGraph
+    fragments_graph : FragmentsGraph
         Graph to be searched for doubles.
     max_length : int
         Maximum size of connected components to be searched.
     node_spacing : int
-        Expected distance in microns between nodes in "graph".
-    output_dir : str or None, optional
-        Directory that doubles will be written to. The default is None.
+        Expected distance (in microns) between nodes in "fragments_graph".
 
     Returns
     -------
-    graph
-        Graph with doubles removed.
+    int
+        Number of fragments removed from graph.
 
     """
     # Initializations
-    components = [c for c in connected_components(graph) if len(c) == 2]
+    components = get_line_components(fragments_graph)
     deleted_ids = set()
-    kdtree = graph.get_kdtree()
-    if output_dir:
-        util.mkdir(output_dir, delete=True)
+    kdtree = fragments_graph.get_kdtree()
 
     # Main
-    desc = "Filter Doubled Fragment"
+    desc = "Filter Doubled Fragments"
     for idx in tqdm(np.argsort([len(c) for c in components]), desc=desc):
         i, j = tuple(components[idx])
-        swc_id = graph.nodes[i]["swc_id"]
+        swc_id = fragments_graph.nodes[i]["swc_id"]
         if swc_id not in deleted_ids:
-            if graph.edges[i, j]["length"] < max_length:
+            if fragments_graph.edges[i, j]["length"] < max_length:
                 # Check doubles criteria
-                n_points = len(graph.edges[i, j]["xyz"])
-                hits = compute_projections(graph, kdtree, (i, j))
+                n_points = len(fragments_graph.edges[i, j]["xyz"])
+                hits = compute_projections(fragments_graph, kdtree, (i, j))
                 if check_doubles_criteria(hits, n_points):
-                    if output_dir:
-                        graph.to_swc(output_dir, [i, j], color=COLOR)
-                    delete_fragment(graph, i, j)
+                    delete_fragment(fragments_graph, i, j)
                     deleted_ids.add(swc_id)
     return len(deleted_ids)
 
 
-def compute_projections(graph, kdtree, edge):
+def compute_projections(fragments_graph, kdtree, edge):
     """
     Given a fragment defined by "edge", this routine iterates of every xyz in
     the fragment and projects it onto the closest fragment. For each detected
@@ -93,11 +108,11 @@ def compute_projections(graph, kdtree, edge):
 
     Parameters
     ----------
-    graph : graph
+    fragments_graph : graph
         Graph that contains "edge".
     kdtree : KDTree
         KD-Tree that contains all xyz coordinates of every fragment in
-        "graph".
+        "fragments_graph".
     edge : tuple
         Pair of leaf nodes that define a fragment.
 
@@ -109,13 +124,13 @@ def compute_projections(graph, kdtree, edge):
 
     """
     hits = defaultdict(list)
-    query_id = graph.edges[edge]["swc_id"]
-    for i, xyz in enumerate(graph.edges[edge]["xyz"]):
+    query_id = fragments_graph.edges[edge]["swc_id"]
+    for i, xyz in enumerate(fragments_graph.edges[edge]["xyz"]):
         # Compute projections
         best_id = None
         best_dist = np.inf
         for hit_xyz in geometry.query_ball(kdtree, xyz, QUERY_DIST):
-            hit_id = graph.xyz_to_swc(hit_xyz)
+            hit_id = fragments_graph.xyz_to_swc(hit_xyz)
             if hit_id is not None and hit_id != query_id:
                 if geometry.dist(hit_xyz, xyz) < best_dist:
                     best_dist = geometry.dist(hit_xyz, xyz)
@@ -157,54 +172,54 @@ def check_doubles_criteria(hits, n_points):
     return False
 
 
-def delete_fragment(graph, i, j):
+def delete_fragment(fragments_graph, i, j):
     """
-    Deletes nodes "i" and "j" from "graph", where these nodes form a connected
-    component.
+    Deletes nodes "i" and "j" from "fragments_graph", where these nodes form a
+    connected component.
 
     Parameters
     ----------
-    graph : FragmentsGraph
-        Graph that contains nodes to be deleted.
+    fragments_graph : FragmentsGraph
+        Graph that contains nodes to be removed.
     i : int
         Node to be removed.
     j : int
         Node to be removed.
 
     Returns
     -------
-    graph
+    fragments_graph
         Graph with nodes removed.
 
     """
-    graph = remove_xyz_entries(graph, i, j)
-    graph.swc_ids.remove(graph.nodes[i]["swc_id"])
-    graph.remove_nodes_from([i, j])
+    fragments_graph = remove_xyz_entries(fragments_graph, i, j)
+    fragments_graph.swc_ids.remove(fragments_graph.nodes[i]["swc_id"])
+    fragments_graph.remove_nodes_from([i, j])
 
 
-def remove_xyz_entries(graph, i, j):
+def remove_xyz_entries(fragments_graph, i, j):
     """
-    Removes dictionary entries from "graph.xyz_to_edge" corresponding to
-    the edge {i, j}.
+    Removes dictionary entries from "fragments_graph.xyz_to_edge"
+    corresponding to the edge {i, j}.
 
     Parameters
     ----------
-    graph : graph
+    fragments_graph : graph
         Graph to be updated.
     i : int
-        Node in "graph".
+        Node in graph.
     j : int
-        Node in "graph".
+        Node in graph.
 
     Returns
     -------
     graph
         Updated graph.
 
     """
-    for xyz in graph.edges[i, j]["xyz"]:
-        del graph.xyz_to_edge[tuple(xyz)]
-    return graph
+    for xyz in fragments_graph.edges[i, j]["xyz"]:
+        del fragments_graph.xyz_to_edge[tuple(xyz)]
+    return fragments_graph
 
 
 def upd_hits(hits, key, value):
@@ -215,8 +230,8 @@ def upd_hits(hits, key, value):
     Parameters
     ----------
     hits : dict
-        Stores swd_ids of fragments that are within a certain distance a query
-        fragment along with the corresponding distances.
+        Stores swd_ids of fragments within a certain distance a query fragment
+        along with the corresponding distances.
     key : str
         swc id of some fragment.
     value : float
@@ -229,9 +244,30 @@ def upd_hits(hits, key, value):
         Updated version of hits.
 
     """
-    if key in hits.keys():
+    if key in hits:
         if value < hits[key]:
             hits[key] = value
     else:
         hits[key] = value
     return hits
+
+
+# --- utils ---
+def get_line_components(graph):
+    """
+    Identifies and returns all line components in the given graph. A line
+    component is defined as a connected component with exactly two nodes.
+
+    Parameters
+    ----------
+    graph : networkx.Graph
+        Input graph in which line components are to be identified.
+
+    Returns
+    -------
+    List[set]
+        List of sets, where each set contains two nodes representing a
+        connected component with exactly two nodes.
+
+    """
+    return [c for c in nx.connected_components(graph) if len(c) == 2]