refactor: report runtimes (#176)

Co-authored-by: anna-grim <[email protected]>

src/deep_neurographs/intake.py

@@ -280,8 +280,7 @@ def build_neurograph(
     # Extract irreducibles
     n_components = len(swc_dicts)
     if progress_bar:
-        print("(1) Extract irreducible nodes and edges")
-        print("# connected components:", utils.reformat_number(n_components))
+        print("# swcs downloaded:", utils.reformat_number(n_components))
     irreducibles, n_nodes, n_edges = get_irreducibles(
         swc_dicts,
         bbox=img_bbox,
@@ -296,29 +295,17 @@ def build_neurograph(
 
     # Build neurograph
     if progress_bar:
-        print("\n(2) Combine irreducibles...")
+        print("\nGraph Overview...")
+        print("# connected components":, len(irreducibles))
         print("# nodes:", utils.reformat_number(n_nodes))
         print("# edges:", utils.reformat_number(n_edges))
 
     neurograph = NeuroGraph(
         img_path=img_path, node_spacing=node_spacing, swc_paths=swc_paths
     )
-    t0, t1 = utils.init_timers()
-    chunk_size = int(n_components * 0.02)
-    cnt, i = 1, 0
-    n_components = len(irreducibles)
     while len(irreducibles):
         irreducible_set = irreducibles.pop()
         neurograph.add_component(irreducible_set)
-        if i > cnt * chunk_size and progress_bar:
-            cnt, t1 = utils.report_progress(
-                i + 1, n_components, chunk_size, cnt, t0, t1
-            )
-        i += 1
-    if progress_bar:
-        t, unit = utils.time_writer(time() - t0)
-        print("\n" + f"add_irreducibles(): {round(t, 4)} {unit}")
-
     return neurograph
 
 
@@ -369,9 +356,6 @@ def get_irreducibles(
                 progress_cnt, t1 = utils.report_progress(
                     i + 1, n_components, chunk_size, progress_cnt, t0, t1
                 )
-    if progress_bar:
-        t, unit = utils.time_writer(time() - t0)
-        print("\n" + f"get_irreducibles(): {round(t, 4)} {unit}")
     return irreducibles, n_nodes, n_edges
 
 

src/deep_neurographs/swc_utils.py

@@ -179,7 +179,7 @@ def read_from_gcs_zip(zip_file, path):
         with zip_file.open(path) as text_file:
             return text_file.read().decode("utf-8").splitlines()
     except:
-        print(f"Failed to from {path}")
+        print(f"Failed to read {path}")
         return ""
 
 
@@ -222,7 +222,7 @@ def write_list(path, entry_list, color=None):
     ----------
     path : str
         Path that swc will be written to.
-    entry_list : list[list[int]]
+    entry_list : list[str]
         List of entries that will be written to an swc file.
     color : str, optional
         Color of nodes. The default is None.
@@ -370,11 +370,26 @@ def make_entry(graph, i, parent, node_to_idx):
 
 
 def set_radius(graph, i):
+    """
+    Sets the radius of node "i".
+
+    Parameters
+    ----------
+    graph : networkx.Graph
+        Graph containing node "i".
+    i : int
+        Node.
+
+    Returns
+    -------
+    float
+        Radius of node "i".
+    """
     try:
         radius = graph[i]["radius"]
         return radius
     except:
-        return 1
+        return 1.0
 
 
 def make_simple_entry(node, parent, xyz, radius=8):