Merge pull request #104 from tlambert03/future

style: cleanup string type annotations

src/traccuracy/_run_metrics.py

@@ -1,19 +1,16 @@
-from typing import TYPE_CHECKING
+from __future__ import annotations
 
 from traccuracy._tracking_graph import TrackingGraph
 from traccuracy.matchers._base import Matcher
 from traccuracy.metrics._base import Metric
 
-if TYPE_CHECKING:
-    from typing import Dict, List
-
 
 def run_metrics(
-    gt_data: "TrackingGraph",
-    pred_data: "TrackingGraph",
-    matcher: "Matcher",
-    metrics: "List[Metric]",
-) -> "List[Dict]":
+    gt_data: TrackingGraph,
+    pred_data: TrackingGraph,
+    matcher: Matcher,
+    metrics: list[Metric],
+) -> list[dict]:
     """Compute given metrics on data using the given matcher.
 
     The returned result dictionary will contain all metrics computed by

src/traccuracy/cli.py

@@ -13,10 +13,10 @@
 
 
 def load_all_ctc(
-    gt_dir: "str",
-    pred_dir: "str",
-    gt_track_path: "Optional[str]" = None,
-    pred_track_path: "Optional[str]" = None,
+    gt_dir: str,
+    pred_dir: str,
+    gt_track_path: Optional[str] = None,
+    pred_track_path: Optional[str] = None,
 ):
     gt_data = load_ctc_data(gt_dir, gt_track_path)
     pred_data = load_ctc_data(pred_dir, pred_track_path)
@@ -25,18 +25,18 @@ def load_all_ctc(
 
 @app.command()
 def run_ctc(
-    gt_dir: "str" = typer.Argument(..., help="Path to GT tiffs", show_default=False),
-    pred_dir: "str" = typer.Argument(
+    gt_dir: str = typer.Argument(..., help="Path to GT tiffs", show_default=False),
+    pred_dir: str = typer.Argument(
         ..., help="Path to prediction/RES tiffs", show_default=False
     ),
-    gt_track_path: "Optional[str]" = typer.Option(
+    gt_track_path: Optional[str] = typer.Option(
         None, help="Path to ctc gt track file", show_default=False
     ),
-    pred_track_path: "Optional[str]" = typer.Option(
+    pred_track_path: Optional[str] = typer.Option(
         None, help="Path to predicted track file", show_default=False
     ),
-    loader: "str" = typer.Option("ctc", help="Loader to bring data into memory"),
-    out_path: "str" = typer.Option("ctc_log.json", help="Path to save results"),
+    loader: str = typer.Option("ctc", help="Loader to bring data into memory"),
+    out_path: str = typer.Option("ctc_log.json", help="Path to save results"),
 ):
     """
     Run TRA and DET metric on gt and pred data using CTC matching.
@@ -66,34 +66,34 @@ def run_ctc(
 
 @app.command()
 def run_aogm(
-    gt_dir: "str" = typer.Argument(..., help="Path to GT tiffs", show_default=False),
-    pred_dir: "str" = typer.Argument(
+    gt_dir: str = typer.Argument(..., help="Path to GT tiffs", show_default=False),
+    pred_dir: str = typer.Argument(
         ..., help="Path to prediction/RES tiffs", show_default=False
     ),
-    gt_track_path: "Optional[str]" = typer.Option(
+    gt_track_path: Optional[str] = typer.Option(
         None, help="Path to ctc gt track file", show_default=False
     ),
-    pred_track_path: "Optional[str]" = typer.Option(
+    pred_track_path: Optional[str] = typer.Option(
         None, help="Path to predicted track file", show_default=False
     ),
-    loader: "str" = typer.Option("ctc", help="Loader to bring data into memory"),
-    out_path: "str" = typer.Option("aogm_log.json", help="Path to save results"),
-    vertex_ns_weight: "float" = typer.Option(
+    loader: str = typer.Option("ctc", help="Loader to bring data into memory"),
+    out_path: str = typer.Option("aogm_log.json", help="Path to save results"),
+    vertex_ns_weight: float = typer.Option(
         1, help="Weight to assign to nonsplit vertex errors"
     ),
-    vertex_fp_weight: "float" = typer.Option(
+    vertex_fp_weight: float = typer.Option(
         1, help="Weight to assign to false positive vertex errors"
     ),
-    vertex_fn_weight: "float" = typer.Option(
+    vertex_fn_weight: float = typer.Option(
         1, help="Weight to assign to false negative vertex errors"
     ),
-    edge_fp_weight: "float" = typer.Option(
+    edge_fp_weight: float = typer.Option(
         1, help="Weight to assign to false positive edge errors"
     ),
-    edge_fn_weight: "float" = typer.Option(
+    edge_fn_weight: float = typer.Option(
         1, help="Weight to assign to false negative edge errors"
     ),
-    edge_ws_weight: "float" = typer.Option(
+    edge_ws_weight: float = typer.Option(
         1, help="Weight to assign to edges with incorrect semantics"
     ),
 ):
@@ -139,24 +139,24 @@ def run_aogm(
 
 @app.command()
 def run_divisions_on_iou(
-    gt_dir: "str" = typer.Argument(..., help="Path to GT tiffs", show_default=False),
-    pred_dir: "str" = typer.Argument(
+    gt_dir: str = typer.Argument(..., help="Path to GT tiffs", show_default=False),
+    pred_dir: str = typer.Argument(
         ..., help="Path to prediction/RES tiffs", show_default=False
     ),
-    gt_track_path: "Optional[str]" = typer.Option(
+    gt_track_path: Optional[str] = typer.Option(
         None, help="Path to ctc gt track file", show_default=False
     ),
-    pred_track_path: "Optional[str]" = typer.Option(
+    pred_track_path: Optional[str] = typer.Option(
         None, help="Path to predicted track file", show_default=False
     ),
-    loader: "str" = typer.Option("ctc", help="Loader to bring data into memory"),
-    out_path: "str" = typer.Option("div_log_iou.json", help="Path to save results"),
-    match_threshold: "float" = typer.Option(
+    loader: str = typer.Option("ctc", help="Loader to bring data into memory"),
+    out_path: str = typer.Option("div_log_iou.json", help="Path to save results"),
+    match_threshold: float = typer.Option(
         1,
         help="Threshold above which the intersection over union of a gt and predicted"
         " detection match. Default of 1 requires exact matching.",
     ),
-    frame_buffer: "int" = typer.Option(
+    frame_buffer: int = typer.Option(
         0,
         help="Number of frames to use for division tolerance."
         " Numbers greater than 0 will produce metrics for 0...n inclusive.",
@@ -199,19 +199,19 @@ def run_divisions_on_iou(
 
 @app.command()
 def run_divisions_on_ctc(
-    gt_dir: "str" = typer.Argument(..., help="Path to GT tiffs", show_default=False),
-    pred_dir: "str" = typer.Argument(
+    gt_dir: str = typer.Argument(..., help="Path to GT tiffs", show_default=False),
+    pred_dir: str = typer.Argument(
         ..., help="Path to prediction/RES tiffs", show_default=False
     ),
-    gt_track_path: "Optional[str]" = typer.Option(
+    gt_track_path: Optional[str] = typer.Option(
         None, help="Path to ctc gt track file", show_default=False
     ),
-    pred_track_path: "Optional[str]" = typer.Option(
+    pred_track_path: Optional[str] = typer.Option(
         None, help="Path to predicted track file", show_default=False
     ),
-    loader: "str" = typer.Option("ctc", help="Loader to bring data into memory"),
-    out_path: "str" = typer.Option("div_log_ctc.json", help="Path to save results"),
-    frame_buffer: "int" = typer.Option(
+    loader: str = typer.Option("ctc", help="Loader to bring data into memory"),
+    out_path: str = typer.Option("div_log_ctc.json", help="Path to save results"),
+    frame_buffer: int = typer.Option(
         0,
         help="Number of frames to use for division tolerance."
         " Numbers greater than 0 will produce metrics for 0...n inclusive.",

src/traccuracy/matchers/_ctc.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from typing import TYPE_CHECKING
 
 import networkx as nx
@@ -24,7 +26,7 @@ class CTCMatcher(Matcher):
     for complete details.
     """
 
-    def _compute_mapping(self, gt_graph: "TrackingGraph", pred_graph: "TrackingGraph"):
+    def _compute_mapping(self, gt_graph: TrackingGraph, pred_graph: TrackingGraph):
         """Run ctc matching
 
         Args:
@@ -95,7 +97,7 @@ def _compute_mapping(self, gt_graph: "TrackingGraph", pred_graph: "TrackingGraph
         return Matched(gt_graph, pred_graph, mapping)
 
 
-def detection_test(gt_blob: "np.ndarray", comp_blob: "np.ndarray") -> int:
+def detection_test(gt_blob: np.ndarray, comp_blob: np.ndarray) -> int:
     """Check if computed marker overlaps majority of the reference marker.
 
     Given a reference marker and computer marker in original coordinates,

src/traccuracy/matchers/_iou.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import numpy as np
 from tqdm import tqdm
 
@@ -110,7 +112,7 @@ class IOUMatcher(Matcher):
     def __init__(self, iou_threshold=0.6):
         self.iou_threshold = iou_threshold
 
-    def _compute_mapping(self, gt_graph: "TrackingGraph", pred_graph: "TrackingGraph"):
+    def _compute_mapping(self, gt_graph: TrackingGraph, pred_graph: TrackingGraph):
         """Computes IOU mapping for a set of grpahs
 
         Args:

src/traccuracy/metrics/_ctc.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from typing import TYPE_CHECKING
 
 from traccuracy._tracking_graph import EdgeAttr, NodeAttr
@@ -32,7 +34,7 @@ def __init__(
             "ws": edge_ws_weight,
         }
 
-    def compute(self, data: "Matched"):
+    def compute(self, data: Matched):
         evaluate_ctc_events(data)
 
         vertex_error_counts = {
@@ -84,7 +86,7 @@ def __init__(self):
             edge_ws_weight=edge_weight_ws,
         )
 
-    def compute(self, data: "Matched"):
+    def compute(self, data: Matched):
         # AOGM-0 is the cost of creating the gt graph from scratch
         gt_graph = data.gt_graph.graph
         n_nodes = gt_graph.number_of_nodes()

src/traccuracy/track_errors/_ctc.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import logging
 from collections import defaultdict
 from typing import TYPE_CHECKING
@@ -12,7 +14,7 @@
 logger = logging.getLogger(__name__)
 
 
-def evaluate_ctc_events(matched_data: "Matched"):
+def evaluate_ctc_events(matched_data: Matched):
     """Annotates ground truth and predicted graph with node and edge error types
 
     Annotations are made in place
@@ -21,7 +23,7 @@ def evaluate_ctc_events(matched_data: "Matched"):
     get_edge_errors(matched_data)
 
 
-def get_vertex_errors(matched_data: "Matched"):
+def get_vertex_errors(matched_data: Matched):
     """Count vertex errors and assign class to each comp/gt node.
 
     Parameters
@@ -70,7 +72,7 @@ def get_vertex_errors(matched_data: "Matched"):
     gt_graph.node_errors = True
 
 
-def get_edge_errors(matched_data: "Matched"):
+def get_edge_errors(matched_data: Matched):
     comp_graph = matched_data.pred_graph
     gt_graph = matched_data.gt_graph
     node_mapping = matched_data.mapping

src/traccuracy/track_errors/divisions.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import copy
 import itertools
 import logging
@@ -13,7 +15,7 @@
 logger = logging.getLogger(__name__)
 
 
-def _classify_divisions(matched_data: "Matched"):
+def _classify_divisions(matched_data: Matched):
     """Identify each division as a true positive, false positive or false negative
 
     This function only works on node mappers that are one-to-one
@@ -139,7 +141,7 @@ def _get_succ_by_t(g, node, delta_frames):
     return node
 
 
-def _correct_shifted_divisions(matched_data: "Matched", n_frames=1):
+def _correct_shifted_divisions(matched_data: Matched, n_frames=1):
     """Allows for divisions to occur within a frame buffer and still be correct
 
     This implementation asserts that the parent lineages and daughter lineages must match.
@@ -236,7 +238,7 @@ def _correct_shifted_divisions(matched_data: "Matched", n_frames=1):
     return new_matched
 
 
-def _evaluate_division_events(matched_data: "Matched", frame_buffer=(0)):
+def _evaluate_division_events(matched_data: Matched, frame_buffer=(0)):
     """Classify division errors and correct shifted divisions according to frame_buffer
 
     Note: A copy of matched_data will be created for each frame_buffer other than 0.