Simple-Track 2.0.3__tar.gz → 2.0.5__tar.gz

{simple_track-2.0.3 → simple_track-2.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: Simple-Track
-Version: 2.0.3
+Version: 2.0.5
 Summary: Threshold-based object tracking algorithm for 2D data 
 Author-email: Adam Gainford <adam.gainford@reading.ac.uk>, Thorwald Stein <t.h.m.stein@reading.ac.uk>
 License-Expression: MPL-2.0
@@ -33,13 +33,15 @@ Features are tracked between consecutive frames of data by projecting feature fi
 
 # Installation
 
-Simple-Track can be installed using PyPi:
+Simple-Track can be installed using PyPi or conda-forge:
 
 ```
 python3 -m pip install simple-track
 ```
-
-Coming soon to conda-forge and uv
+```
+conda install conda-forge::simple-track
+```
+Coming soon to uv
 
 # User Guide
 
@@ -177,10 +179,10 @@ Fields (`.field` files):
 
 Features (`.csv` or `.txt` files):
 * ID: Unique feature identifier that persists between frames (i.e., a feature retains the same id across all frames that it is tracked).
-* Centroid: (y, x) tuple containing central location of feature.
-* Size: Number of pixels spanned by the feature.
+* centroid: (y, x) tuple containing central location of feature.
+* size: Number of pixels spanned by the feature.
 * dydx: (dy, dx) tuple containing motion vector that translated feature to its location in the current frame from the previous frame.
-* extreme: Maximum value contained within the feature in the input data.
+* max: Maximum value contained within the feature in the input data.
 * lifetime: Number of timesteps the feature has existed for.
 * accreted: List of IDs of features that were accreted by this feature, if applicable.
 * parent: ID of parent feature that this feature split from, if applicable

{simple_track-2.0.3 → simple_track-2.0.5}/README.md

@@ -11,13 +11,15 @@ Features are tracked between consecutive frames of data by projecting feature fi
 
 # Installation
 
-Simple-Track can be installed using PyPi:
+Simple-Track can be installed using PyPi or conda-forge:
 
 ```
 python3 -m pip install simple-track
 ```
-
-Coming soon to conda-forge and uv
+```
+conda install conda-forge::simple-track
+```
+Coming soon to uv
 
 # User Guide
 
@@ -155,10 +157,10 @@ Fields (`.field` files):
 
 Features (`.csv` or `.txt` files):
 * ID: Unique feature identifier that persists between frames (i.e., a feature retains the same id across all frames that it is tracked).
-* Centroid: (y, x) tuple containing central location of feature.
-* Size: Number of pixels spanned by the feature.
+* centroid: (y, x) tuple containing central location of feature.
+* size: Number of pixels spanned by the feature.
 * dydx: (dy, dx) tuple containing motion vector that translated feature to its location in the current frame from the previous frame.
-* extreme: Maximum value contained within the feature in the input data.
+* max: Maximum value contained within the feature in the input data.
 * lifetime: Number of timesteps the feature has existed for.
 * accreted: List of IDs of features that were accreted by this feature, if applicable.
 * parent: ID of parent feature that this feature split from, if applicable

{simple_track-2.0.3 → simple_track-2.0.5}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "Simple-Track"
-version = "2.0.3"
+version = "2.0.5"
 authors = [
   { name="Adam Gainford", email="adam.gainford@reading.ac.uk" },
   { name="Thorwald Stein", email="t.h.m.stein@reading.ac.uk"} 

{simple_track-2.0.3 → simple_track-2.0.5}/src/Simple_Track.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: Simple-Track
-Version: 2.0.3
+Version: 2.0.5
 Summary: Threshold-based object tracking algorithm for 2D data 
 Author-email: Adam Gainford <adam.gainford@reading.ac.uk>, Thorwald Stein <t.h.m.stein@reading.ac.uk>
 License-Expression: MPL-2.0
@@ -33,13 +33,15 @@ Features are tracked between consecutive frames of data by projecting feature fi
 
 # Installation
 
-Simple-Track can be installed using PyPi:
+Simple-Track can be installed using PyPi or conda-forge:
 
 ```
 python3 -m pip install simple-track
 ```
-
-Coming soon to conda-forge and uv
+```
+conda install conda-forge::simple-track
+```
+Coming soon to uv
 
 # User Guide
 
@@ -177,10 +179,10 @@ Fields (`.field` files):
 
 Features (`.csv` or `.txt` files):
 * ID: Unique feature identifier that persists between frames (i.e., a feature retains the same id across all frames that it is tracked).
-* Centroid: (y, x) tuple containing central location of feature.
-* Size: Number of pixels spanned by the feature.
+* centroid: (y, x) tuple containing central location of feature.
+* size: Number of pixels spanned by the feature.
 * dydx: (dy, dx) tuple containing motion vector that translated feature to its location in the current frame from the previous frame.
-* extreme: Maximum value contained within the feature in the input data.
+* max: Maximum value contained within the feature in the input data.
 * lifetime: Number of timesteps the feature has existed for.
 * accreted: List of IDs of features that were accreted by this feature, if applicable.
 * parent: ID of parent feature that this feature split from, if applicable

{simple_track-2.0.3 → simple_track-2.0.5}/src/run_simple_track.py

@@ -1,23 +1,20 @@
 import argparse
-import sys
 
 from simpletrack import Tracker
 
 
 def run_tracking():
-    if len(sys.argv) < 2:
-        raise Exception("Running SimpleTrack requires path to at least one config")
+    # TODO: make argparser default way of handling inputs, including configs and loaders
+    # Need to make sure that changes don't affect pyproject.toml entry points
+    # easiest just to pass the parser in to run_tracking.
+    parser = argparse.ArgumentParser(description="Run Simple-Track")
+    parser.add_argument("configs", help="Path to one or more yaml config files.")
+    args = parser.parse_args()
 
-    config_paths = sys.argv[1:]
-    for config_path in config_paths:
+    for config_path in args.configs:
         # With None passed into run method, uses input path in config
         Tracker(config_path).run()
 
 
 if __name__ == "__main__":
-    # TODO: make argparser default way of handling inputs, including configs and loaders
-    # Need to make sure that changes don't affect pyproject.toml entry points
-    # easiest just to pass the parser in to run_tracking.
-    msg = "Run Simple-Track. Requires path to at least one yaml config file"
-    parser = argparse.ArgumentParser(description=msg)
     run_tracking()

{simple_track-2.0.3 → simple_track-2.0.5}/src/simpletrack/feature.py

@@ -1,5 +1,4 @@
 import datetime as dt
-from typing import Union
 
 import numpy as np
 from numpy.typing import NDArray
@@ -10,7 +9,7 @@ from simpletrack.utils import check_arrays, check_valid_ids, native
 class Feature:
     """
     Object containing details about a specific feature, including its id, time,
-    centroid, extreme value, lifetime, and whether it has undergone any
+    centroid, maximum value, lifetime, and whether it has undergone any
     mergers of splits in the current timestep.
     """
 
@@ -31,7 +30,8 @@ class Feature:
         self._parent = None
         self._children = []
         self._dydx = ()
-        self._extreme = None
+        self._max = None
+        self._mean = None
 
     def __repr__(self) -> str:
         repr_str = f"Feature id: {self._id} (provisionally {self._provisional_id}), "
@@ -141,11 +141,18 @@ class Feature:
         return native(self._dydx)
 
     @property
-    def extreme(self) -> float:
+    def max(self) -> float:
         """
         Maximum value of the Feature in the raw input data
         """
-        return self._extreme
+        return self._max
+
+    @property
+    def mean(self) -> float:
+        """
+        Mean value of the Feature in the raw input data
+        """
+        return self._mean
 
     @coords.setter
     def coords(self, new_coords: NDArray[np.integer]) -> None:
@@ -185,9 +192,13 @@ class Feature:
         id_of_accreting_feature = check_valid_ids(id_of_accreting_feature)
         self._accreted_in_next_frame_by = id_of_accreting_feature
 
-    @extreme.setter
-    def extreme(self, extreme_val: float) -> None:
-        self._extreme = extreme_val
+    @max.setter
+    def max(self, max_val: float) -> None:
+        self._max = max_val
+
+    @mean.setter
+    def mean(self, mean_val: float) -> None:
+        self._mean = mean_val
 
     def calculate_centroid(self) -> tuple:
         """
@@ -261,7 +272,7 @@ class Feature:
 
     def summarise(
         self, output_type: str = "str", headers_only: bool = False
-    ) -> Union[str, dict, list]:
+    ) -> str | dict | list:
         """
         Return a summary of the Feature properties
 
@@ -280,7 +291,8 @@ class Feature:
             "size": self.get_size(),
             # native() does not convert dydx to python type for some reason
             "dydx": tuple([val.item() for val in self._dydx]),
-            "extreme": self._extreme,
+            "max": self._max,
+            "mean": self._mean,
             "lifetime": self._lifetime,
             "accreted": self._accreted,
             # This will not be output properly in the current workflow, since each

{simple_track-2.0.3 → simple_track-2.0.5}/src/simpletrack/flow_solver.py

@@ -1,7 +1,6 @@
 import itertools
 import warnings
 from collections.abc import Iterable
-from typing import Union
 
 import numpy as np
 import scipy.ndimage as ndimage
@@ -69,7 +68,7 @@ class FlowSolver:
         self.apply_tukey_filtering = apply_tukey_filtering
 
     def analyse_flow(
-        self, prev_field: Union[Frame, NDArray], current_field: Union[Frame, NDArray]
+        self, prev_field: Frame | NDArray, current_field: Frame | NDArray
     ) -> list[NDArray, NDArray]:
         """
         Analyses previous field and current field to identify flow field. Uses phase
@@ -330,7 +329,7 @@ class FlowSolver:
 
         subdomain_check = [
             dim % sd_shape / 2
-            for dim, sd_shape in zip(feature_field_shape, subdomain_shape)
+            for dim, sd_shape in zip(feature_field_shape, subdomain_shape, strict=True)
         ]
         return not any([remainder != 0 for remainder in subdomain_check])
 

{simple_track-2.0.3 → simple_track-2.0.5}/src/simpletrack/frame.py

@@ -1,5 +1,4 @@
 import datetime as dt
-from typing import Union
 
 import numpy as np
 import scipy.ndimage as ndimage
@@ -123,7 +122,7 @@ class Frame:
         else:
             return None
 
-    def get_flow(self) -> Union[NDArray, None]:
+    def get_flow(self) -> NDArray | None:
         """
         Get a list of the y-flow and x-flow fields derived by comparing features between
         this frame and a frame from a previous timestep. Flow fields are both numpy
@@ -212,7 +211,8 @@ class Frame:
             )
             # If raw field is not None, use this to find max value within Feature
             if self.raw_field is not None:
-                feature.extreme = max(self.raw_field[feature_mask])
+                feature.max = np.max(self.raw_field[feature_mask])
+                feature.mean = np.mean(self.raw_field[feature_mask])
             self._features[feature_id] = feature
 
     def assign_displacements(self, y_flow: NDArray, x_flow: NDArray) -> None:
@@ -388,6 +388,9 @@ class Timeline:
     def __init__(self):
         self.timeline = {}
 
+    def __len__(self) -> int:
+        return len(self.timeline)
+
     def add_to_timelime(self, frame: Frame) -> None:
         """
         Add the input frame to the timeline, using the frame.get_time() to

{simple_track-2.0.3 → simple_track-2.0.5}/src/simpletrack/frame_output.py

@@ -2,7 +2,6 @@ import csv
 import datetime
 from ast import literal_eval
 from pathlib import Path
-from typing import Union
 
 import numpy as np
 
@@ -152,7 +151,7 @@ class LoadOutput:
     (contanining Frames of field and Feature data) for further inspection and analysis.
     """
 
-    def __init__(self, st_data_path: Union[str | Path]):
+    def __init__(self, st_data_path: str | Path):
         self.path = Path(st_data_path)
         self.strftime = "%Y%m%d_%H%M"
         # Links field type names in outputs to attribute names in Frame

{simple_track-2.0.3 → simple_track-2.0.5}/src/simpletrack/frame_tracker.py

@@ -1,5 +1,3 @@
-from typing import Union
-
 import numpy as np
 from numpy.typing import NDArray
 
@@ -493,7 +491,7 @@ class FrameTracker:
         advected_feature_field: NDArray,
         current_feature_field: NDArray,
         current_feature_id: int,
-    ) -> list[Union[int, None], Union[NDArray, None]]:
+    ) -> list[int | None, NDArray | None]:
         """
         Use overlap histogram to find the closest matching feature id in the advected
         field for the current_feature_id in the current_field. Any other ids that are
@@ -865,7 +863,7 @@ def advect_field_using_motion_vectors(
         dx = np.mean(x_flow[feature_mask], dtype=int)
 
         # Now, advect the feature to the new position
-        for y_coord, x_coord in zip(*feature_mask):
+        for y_coord, x_coord in zip(*feature_mask, strict=True):
             advected_y_coord = y_coord + dy
             advected_x_coord = x_coord + dx
 

{simple_track-2.0.3 → simple_track-2.0.5}/src/simpletrack/load.py

@@ -1,5 +1,4 @@
 import datetime as dt
-from typing import Union
 
 from numpy.typing import NDArray
 
@@ -39,7 +38,7 @@ class BaseLoader:
     Loaders should be
     """
 
-    def __init__(self, input_data: Union[list[str] | dict]) -> None:
+    def __init__(self, input_data: list[str] | dict) -> None:
         self.domain_shape = None
         self.input_data = input_data
         # Set the iterating list

{simple_track-2.0.3 → simple_track-2.0.5}/src/simpletrack/track.py

@@ -3,7 +3,6 @@ Run the SimpleTrack algorithm to track objects through a sequence of images
 """
 
 from pathlib import Path
-from typing import Union
 
 from yaml import safe_load
 
@@ -19,7 +18,7 @@ class Tracker:
     Simple-Track manager controlling inputs, processing, outputs
     """
 
-    def __init__(self, config_input: Union[str | dict]) -> None:
+    def __init__(self, config_input: str | dict) -> None:
         """
         Initialize SimpleTrack with configuration file
 
@@ -59,7 +58,7 @@ class Tracker:
             self.frame_tracker = FrameTracker()
 
         if "OUTPUT" in self.config:
-            self.skip_tracking = self.config["TRACKING"].get("skip_tracking", False)
+            self.skip_tracking = self.config["OUTPUT"].get("skip_tracking", False)
             output_path = self.config["OUTPUT"].get("path", "./output")
             expt_name = self.config["OUTPUT"].get(
                 "experiment_name", "Simple-Track Experiment"
@@ -80,7 +79,7 @@ class Tracker:
                     config_path,
                 )
 
-    def run(self, input_data: Union[list[str] | dict] = None) -> Timeline:
+    def run(self, input_data: list[str] | dict = None) -> Timeline:
         """
         Runs SimpleTrack using the designated config options.
 

{simple_track-2.0.3 → simple_track-2.0.5}/tests/test_frame.py

@@ -103,7 +103,7 @@ def test_populate_features_valid_feature_field():
     assert test_frame.features == expected_dict
 
 
-def test_populate_features_sets_extreme_property():
+def test_populate_features_sets_max_property():
     test_time = dt.datetime.now()
     test_frame = Frame()
     test_frame.time = test_time
@@ -123,8 +123,33 @@ def test_populate_features_sets_extreme_property():
     test_frame.raw_field = test_raw_field
     test_frame.populate_features()
 
-    assert test_frame.get_feature(1).extreme == 10
-    assert test_frame.get_feature(2).extreme == 20
+    assert test_frame.get_feature(1).max == 10
+    assert test_frame.get_feature(2).max == 20
+
+
+def test_populate_features_sets_mean_property():
+    test_time = dt.datetime.now()
+    test_frame = Frame()
+    test_frame.time = test_time
+
+    test_feature_field = test_field.copy()
+    test_feature_field[2:6, 2:6] = 1
+    test_feature_field[6:9, 6:9] = 2
+
+    test_raw_field = test_field.copy()
+    test_raw_field[2:6, 2:6] = 10
+    test_raw_field[2:6, 4:6] = 50
+    test_raw_field[6:9, 6:9] = 20
+    # Set another higher maximum within the field to check mean
+    # only picks up the values within the feature mask
+    test_raw_field[0:2, 0:2] = 100
+
+    test_frame.feature_field = test_feature_field
+    test_frame.raw_field = test_raw_field
+    test_frame.populate_features()
+
+    assert test_frame.get_feature(1).mean == 30
+    assert test_frame.get_feature(2).mean == 20
 
 
 def test_populate_features_invalid_negative_features():