upds

Author: anna-grim

src/segmentation_skeleton_metrics/skeleton_metric.py

@@ -64,26 +64,23 @@ def __init__(
 
         Parameters
         ----------
-        gt_pointer : dict/str/list[str]
+        gt_pointer : Any
             Pointer to ground truth swcs, see "swc_util.Reader" for further
-            documentation. Note these swc files are assumed to be stored in
+            documentation. Note these SWC files are assumed to be stored in
             image coordinates.
-        pred_labels : numpy.ndarray or tensorstore.TensorStore
+        pred_labels : ArrayLike
             Predicted segmentation mask.
-        anisotropy : list[float], optional
-            Image to real-world coordinates scaling factors applied to swc
-            stored at "fragments_pointer". The default is [1.0, 1.0, 1.0].
+        anisotropy : Tuple[float], optional
+            Image to physical coordinate scaling factors applied to SWC files
+            stored at "fragments_pointer". The default is (1.0, 1.0, 1.0).
         connections_path : str, optional
             Path to a txt file containing pairs of segment ids of segments
             that were merged into a single segment. The default is None.
-        fragments_pointer : dict/str/list[str], optional
-            Pointer to fragments (i.e. swcs) corresponding to "pred_labels",
-            see "swc_util.Reader" for further documentation. Note these swc
-            files may be stored in either world or image coordinates. If the
-            swcs are stored in world coordinates, then provide the world to
-            image coordinates anisotropy factor. Note the filename of each swc
-            is assumed to "segment_id.swc" where segment_id cooresponds to the
-            segment id from "pred_labels". The default is None.
+        fragments_pointer : Any, optional
+            Pointer to SWC files corresponding to "pred_labels", see
+            "swc_util.Reader" for further documentation. Note that these SWC
+            file may be stored in physical coordiantes, but the anisotropy
+            scaling factors must be provided. The default is None.
         output_dir : str, optional
             Path to directory that mistake sites are written to. The default
             is None.
@@ -168,7 +165,7 @@ def init_graphs(self, paths):
         None
 
         """
-        # Read graphs
+        # Build graphs
         self.graphs = swc_util.Reader().load(paths)
         self.fragment_graphs = None
 
@@ -204,11 +201,9 @@ def set_node_labels(self, key):
                 threads.append(executor.submit(self.get_label, i, voxel))
 
             # Store label
-            pbar = tqdm(total=len(threads), desc="threads finished")
             for thread in as_completed(threads):
                 i, label = thread.result()
                 self.graphs[key].nodes[i].update({"label": label})
-                pbar.update(1)
 
     def get_label(self, i, voxel):
         """

src/segmentation_skeleton_metrics/utils/swc_util.py

@@ -155,7 +155,7 @@ def load_from_local_paths(self, swc_paths):
 
             # Store results
             graph_dict = dict()
-            pbar = tqdm(total=len(filenames), desc="Label Graph")
+            pbar = tqdm(total=len(threads), desc="Load SWCs")
             for thread in as_completed(threads):
                 graph_dict.update(thread.result())
                 pbar.update(1)
@@ -200,7 +200,7 @@ def load_from_local_zips(self, zip_dir):
                 pbar.update(1)
         return graph_dict
 
-    def load_from_local_zip(self, zip_path, verbose=True):
+    def load_from_local_zip(self, zip_path):
         """
         Reads SWC files from zip on the local machine.
 
@@ -376,9 +376,12 @@ def get_graph(self, content):
         graph = nx.Graph()
         offset = [0, 0, 0]
         for line in content:
+            # Check for offset
             if line.startswith("# OFFSET"):
                 parts = line.split()
                 offset = self.read_voxel(parts[2:5])
+
+            # Check for entry
             if not line.startswith("#"):
                 parts = line.split()
                 child = int(parts[0])
@@ -398,65 +401,6 @@ def get_graph(self, content):
 
 
 # --- Write ---
-def save(path, xyz_1, xyz_2, color=None):
-    """
-    Writes an swc file.
-
-    Parameters
-    ----------
-    path : str
-        Path on local machine that swc file will be written to.
-    xyz_1 : ...
-        ...
-    xyz_2 : ...
-        ...
-    color : str, optional
-        Color of nodes. The default is None.
-
-    Returns
-    -------
-    None.
-
-    """
-    with open(path, "w") as f:
-        # Preamble
-        if color is not None:
-            f.write("# COLOR " + color)
-        else:
-            f.write("# id, type, z, y, x, r, pid")
-        f.write("\n")
-
-        # Entries
-        f.write(make_entry(1, -1, xyz_1))
-        f.write("\n")
-        f.write(make_entry(2, 1, xyz_2))
-
-
-def make_entry(node, parent, xyz):
-    """
-    Makes an entry to be written in an SWC file.
-
-    Parameters
-    ----------
-    graph : networkx.Graph
-        Graph that "node_id" and "parent_id" belong to.
-    node : int
-        Node ID that entry corresponds to.
-    parent_id : int
-         Parent ID of the given node.
-    voxel : ...
-        Voxel coordinate of the given node.
-
-    Returns
-    -------
-    entry : str
-        Entry to be written in an swc file.
-
-    """
-    x, y, z = tuple(util.to_physical(voxel, (0.748, 0.748, 1.0)))
-    return f"{node} 2 {x} {y} {z} 3 {parent}"
-
-
 def to_zipped_swc(zip_writer, graph, color=None):
     """
     Writes a graph to an swc file that is to be stored in a zip.