fix: merge imports

Author: zhenyuen

.circleci/config.yml

@@ -38,7 +38,7 @@ jobs:
           command: |
             . venv/bin/activate
             mkdir test-reports
-            pytest --junitxml=test-reports/junit.xml --cov --cov-report=xml:test-reports/coverage.xml stonesoup
+            pytest --junitxml=test-reports/junit.xml --cov --cov-report=xml:test-reports/coverage.xml --slow stonesoup
       - store_test_results:
           path: test-reports/junit.xml
       - store_artifacts:

docs/demos/OpenSky_Demo.py

@@ -20,7 +20,8 @@
 # %%
 # Reading the CSV File
 # ---------------------
-# To read in our groundtruth data from a CSV file, we can use Stone Soup’s
+# To read in our groundtruth data from a
+# :download:`CSV file <../../demos/OpenSky_Plane_States.csv>`, we can use Stone Soup’s
 # :class:`~.CSVGroundTruthReader`. To convert our longitude and latitude data to Universal
 # Transverse Mercator (UTM) projection, we will use :class:`~.LongLatToUTMConverter`.
 
@@ -329,7 +330,7 @@
             'properties':{
                 'icon': 'marker',
                 'iconstyle':{
-                    'iconUrl': '../_static/sphinx_gallery/Radar_dish.png',
+                    'iconUrl': 'https://stonesoup.rtfd.io/en/latest/_static/sphinx_gallery/Radar_dish.png',
                     'iconSize': [24, 24],
                     'fillOpacity': 1,
                     'popupAnchor': [1, -17]},
@@ -492,7 +493,7 @@
             'properties':{
                 'icon': 'marker',
                 'iconstyle':{
-                    'iconUrl': f'../_static/sphinx_gallery/Plane_Headings/Plane_{angle}.png',
+                    'iconUrl': f'https://stonesoup.rtfd.io/en/latest/_static/sphinx_gallery/Plane_Headings/Plane_{angle}.png',
                     'iconSize': [24, 24],
                     'fillOpacity': 1,
                     'popupAnchor': [1, -17],

docs/examples/dataassociation/mht_example.py

@@ -0,0 +1,256 @@
+#!/usr/bin/env python
+# coding: utf-8
+
+"""
+========================================================
+General Multi Hypotheses tracking implementation example
+========================================================
+"""
+
+# %%
+# The multi hypotheses tracking (MHT) algorithm is considered one of the best tracking algorithms,
+# consisting of creating a tree of potential tracks for
+# each target candidate (in a multi-target scenario) and pruning such hypotheses
+# in the data association phase. It is particularly efficient in maintaining trajectories of
+# multiple objects and handling uncertainties and ambiguities of tracks (e.g. presence of
+# clutter).
+#
+# MHT, by definition, has several algorithms that fall under this definition, which
+# include Global Nearest Neighbour (GNN,
+# :doc:`tutorial <../../auto_tutorials/06_DataAssociation-MultiTargetTutorial>`),
+# Joint Probabilistic Data association (JPDA,
+# :doc:`tutorial <../../auto_tutorials/08_JPDATutorial>`),
+# Multi-frame assignment (MFA [#]_, :doc:`example <MFA_example>`),
+# Multi Bernoulli filter and Probabilistic multi hypotheses tracking (PMHT).
+# Some of these algorithms are already implemented the Stone Soup.
+#
+# In this example we employ the multi-frame assignment data associator and
+# hypothesiser using their Stone Soup implementation.
+#
+# This example follows this structure:
+#
+#   1. Create ground truth and detections;
+#   2. Instantiate the tracking components and tracker;
+#   3. Run the tracker and visualise the results.
+#
+
+# %%
+# General imports
+# ^^^^^^^^^^^^^^^
+import numpy as np
+from datetime import datetime, timedelta
+from itertools import tee
+
+# %%
+# Stone Soup imports
+# ^^^^^^^^^^^^^^^^^^
+from stonesoup.types.array import StateVector, CovarianceMatrix
+from stonesoup.types.state import GaussianState
+from stonesoup.models.transition.linear import CombinedLinearGaussianTransitionModel, \
+    ConstantVelocity
+from stonesoup.models.measurement.nonlinear import CartesianToBearingRange
+from stonesoup.simulator.simple import MultiTargetGroundTruthSimulator, SimpleDetectionSimulator
+
+# Simulation parameters
+np.random.seed(1908)  # fix a random seed
+start_time = datetime.now().replace(microsecond=0)
+simulation_steps = 50
+timestep_size = timedelta(seconds=2)
+prob_detection = 0.99
+initial_state_mean = StateVector([[10], [0], [10], [0]])
+initial_covariance = CovarianceMatrix(np.diag([30, 1, 40, 1]))
+
+# clutter will be generated uniformly in this area around the targets
+clutter_area = np.array([[-1, 1], [-1, 1]])*150
+clutter_rate = 9
+surveillance_area = ((clutter_area[0, 1] - clutter_area[0, 0]) *
+                     (clutter_area[1, 1] - clutter_area[1, 0]))
+clutter_spatial_density = clutter_rate/surveillance_area
+
+# %%
+# 1. Create ground truth and detections;
+# --------------------------------------
+# We have prepared all the general parameters for the simulation,
+# including the clutter spatial density. In this example we set
+# the birth rate and the death probability as zero, using only the knowledge of the
+# prior states to generate the tracks so the number of targets is fixed (3 in this case).
+#
+# We can instantiate the transition model of the targets and the measurement model.
+# In this example we employ a :class:`~.CartesianToBearingRange` non-linear measurement model.
+# Then, we pass all these details to a :class:`~.MultiTargetGroundTruthSimulator`
+# and use a :class:`~.SimpleDetectionSimulator`
+# to obtain the target ground truth, detections and clutter.
+#
+
+# Create an initial state
+initial_state = GaussianState(state_vector=initial_state_mean,
+                              covar=initial_covariance,
+                              timestamp=start_time)
+
+# Instantiate the transition model
+transition_model = CombinedLinearGaussianTransitionModel([ConstantVelocity(0.005),
+                                                          ConstantVelocity(0.005)])
+
+# Define the measurement model
+measurement_model = CartesianToBearingRange(ndim_state=4,
+                                            mapping=(0, 2),
+                                            noise_covar=np.diag([np.radians(1), 5]))
+
+# Instantiate the multi-target simulator
+ground_truth_simulator = MultiTargetGroundTruthSimulator(
+    transition_model=transition_model,
+    initial_state=initial_state,
+    timestep=timestep_size,
+    number_steps=simulation_steps,
+    birth_rate=0,  # no other targets more than the specified ones
+    death_probability=0,  # all targets will remain during the simulation
+    preexisting_states=[[10, 1, 10, 1], [-10, -1, -10, -1], [-10, -1, 10, 1]])
+
+# Create a detector
+detection_sim = SimpleDetectionSimulator(
+    groundtruth=ground_truth_simulator,
+    measurement_model=measurement_model,
+    detection_probability=prob_detection,
+    meas_range=clutter_area,
+    clutter_rate=clutter_rate)
+
+# Instantiate a set for detections/clutter and ground truths
+detections = set()
+ground_truth = set()
+timestamps = []
+
+# Duplicate the detection simulator
+plot, tracking = tee(detection_sim, 2)
+
+# Iterate in the detection simulator to generate the measurements
+for time, dets in plot:
+    detections |= dets
+    ground_truth |= ground_truth_simulator.groundtruth_paths
+    timestamps.append(time)
+
+# Visualise the detections and tracks
+from stonesoup.plotter import AnimatedPlotterly
+
+plotter = AnimatedPlotterly(timestamps)
+plotter.plot_ground_truths(ground_truth, [0, 2])
+plotter.plot_measurements(detections, [0, 2])
+plotter.fig
+
+# %%
+# 2. Instantiate the tracking components and tracker;
+# ---------------------------------------------------
+# We need to prepare the tracker and its components. In this example we consider an
+# Unscented Kalman filter since we are dealing with non-linear measurements.
+# We consider a :class:`~.UnscentedKalmanPredictor` and :class:`~.UnscentedKalmanUpdater`.
+#
+# As said previously, we consider a multi-frame assignment data associator
+# which wraps a :class:`~.PDAHypothesiser` probability hypothesiser into a
+# :class:`~.MFAHypothesiser` to work with the :class:`~.MFADataAssociator`.
+#
+# To instantiate the tracks we could use :class:`~.GaussianMixtureInitiator` which
+# uses a Gaussian Initiator (such as :class:`~.MultiMeasurementInitiator`) to
+# create GaussianMixture prior states, however, its current implementation
+# is intended for a GM-PHD filter making it troublesome to adapt for our needs.
+# Therefore, we consider :class:`~.TaggedWeightedGaussianState` to create the track priors,
+# which can be handled by MFA components, using the pre-existing states fed to the
+# multi-groundtruth simulator.
+# Such prior states are, then, wrapped in :class:`~.GaussianMixture` states.
+#
+# As it is now, there is not a tracker wrapper (as for the
+# :class:`~.MultiTargetMixtureTracker`) that can be applied directly when dealing with MFA,
+# so we need to specify the tracking loop explicitly.
+
+# load tracker the components
+from stonesoup.predictor.kalman import UnscentedKalmanPredictor
+from stonesoup.updater.kalman import UnscentedKalmanUpdater
+
+predictor = UnscentedKalmanPredictor(transition_model)
+updater = UnscentedKalmanUpdater(measurement_model)
+
+# Data associator and hypothesiser
+from stonesoup.dataassociator.mfa import MFADataAssociator
+from stonesoup.hypothesiser.mfa import MFAHypothesiser
+from stonesoup.hypothesiser.probability import PDAHypothesiser
+
+hypothesiser = PDAHypothesiser(predictor,
+                               updater,
+                               clutter_spatial_density,
+                               prob_gate=0.9999,
+                               prob_detect=prob_detection)
+
+hypothesiser = MFAHypothesiser(hypothesiser)
+data_associator = MFADataAssociator(hypothesiser,
+                                    slide_window=3)
+
+# Prepare the priors
+from stonesoup.types.state import TaggedWeightedGaussianState
+from stonesoup.types.track import Track
+from stonesoup.types.mixture import GaussianMixture
+from stonesoup.types.numeric import Probability
+from stonesoup.types.update import GaussianMixtureUpdate
+
+prior1 = GaussianMixture([TaggedWeightedGaussianState(
+    StateVector([10, 1, 10, 1]),
+    np.diag([10, 1, 10, 1]),
+    timestamp=initial_state.timestamp,
+    weight=Probability(1),
+    tag=[])])
+
+prior2 = GaussianMixture([TaggedWeightedGaussianState(
+    StateVector([-10, -1, -10, -1]),
+    np.diag([10, 1, 10, 1]),
+    timestamp=initial_state.timestamp,
+    weight=Probability(1),
+    tag=[])])
+
+prior3 = GaussianMixture([TaggedWeightedGaussianState(
+    StateVector([-10, -1, 10, 1]),
+    np.diag([10, 1, 10, 1]),
+    timestamp=initial_state.timestamp,
+    weight=Probability(1),
+    tag=[])])
+
+# instantiate the tracks
+tracks = {Track([prior1]),
+          Track([prior2]),
+          Track([prior3])}
+
+# %%
+# 3. Run the tracker and visualise the results;
+# ---------------------------------------------
+# We are ready to loop over the detections in the
+# simulation and obtain the final tracks.
+
+
+for time, detection in tracking:
+    association = data_associator.associate(tracks, detection, time)
+
+    for track, hypotheses in association.items():
+        components = []
+        for hypothesis in hypotheses:
+            if not hypothesis:
+                components.append(hypothesis.prediction)
+            else:
+                update = updater.update(hypothesis)
+                components.append(update)
+        track.append(GaussianMixtureUpdate(components=components,
+                                           hypothesis=hypotheses))
+
+    tracks.add(track)
+
+plotter.plot_tracks(tracks, [0, 2], track_label="Tracks", line=dict(color="Green"))
+plotter.fig
+
+# %%
+# Conclusion
+# ----------
+# In this example we have presented how to set up a multi-hypotheses tracking
+# (MHT) simulation, by employing the existing components present in Stone Soup
+# and perform the tracking in a heavy cluttered multi-target scenario.
+
+# %%
+# References
+# ----------
+# .. [#] Xia, Y., Granström, K., Svensson, L., García-Fernández, Á.F., and Williams, J.L.,
+#        2019. Multiscan Implementation of the Trajectory Poisson Multi-Bernoulli Mixture Filter.
+#        J. Adv. Information Fusion, 14(2), pp. 213–235.

docs/examples/eot/README.rst

@@ -0,0 +1,2 @@
+Extended Object Tracking
+------------------------