Simple-Track 2.0.0__tar.gz

simple_track-2.0.0/LICENSE

@@ -0,0 +1,373 @@
+Mozilla Public License Version 2.0
+==================================
+
+1. Definitions
+--------------
+
+1.1. "Contributor"
+    means each individual or legal entity that creates, contributes to
+    the creation of, or owns Covered Software.
+
+1.2. "Contributor Version"
+    means the combination of the Contributions of others (if any) used
+    by a Contributor and that particular Contributor's Contribution.
+
+1.3. "Contribution"
+    means Covered Software of a particular Contributor.
+
+1.4. "Covered Software"
+    means Source Code Form to which the initial Contributor has attached
+    the notice in Exhibit A, the Executable Form of such Source Code
+    Form, and Modifications of such Source Code Form, in each case
+    including portions thereof.
+
+1.5. "Incompatible With Secondary Licenses"
+    means
+
+    (a) that the initial Contributor has attached the notice described
+        in Exhibit B to the Covered Software; or
+
+    (b) that the Covered Software was made available under the terms of
+        version 1.1 or earlier of the License, but not also under the
+        terms of a Secondary License.
+
+1.6. "Executable Form"
+    means any form of the work other than Source Code Form.
+
+1.7. "Larger Work"
+    means a work that combines Covered Software with other material, in
+    a separate file or files, that is not Covered Software.
+
+1.8. "License"
+    means this document.
+
+1.9. "Licensable"
+    means having the right to grant, to the maximum extent possible,
+    whether at the time of the initial grant or subsequently, any and
+    all of the rights conveyed by this License.
+
+1.10. "Modifications"
+    means any of the following:
+
+    (a) any file in Source Code Form that results from an addition to,
+        deletion from, or modification of the contents of Covered
+        Software; or
+
+    (b) any new file in Source Code Form that contains any Covered
+        Software.
+
+1.11. "Patent Claims" of a Contributor
+    means any patent claim(s), including without limitation, method,
+    process, and apparatus claims, in any patent Licensable by such
+    Contributor that would be infringed, but for the grant of the
+    License, by the making, using, selling, offering for sale, having
+    made, import, or transfer of either its Contributions or its
+    Contributor Version.
+
+1.12. "Secondary License"
+    means either the GNU General Public License, Version 2.0, the GNU
+    Lesser General Public License, Version 2.1, the GNU Affero General
+    Public License, Version 3.0, or any later versions of those
+    licenses.
+
+1.13. "Source Code Form"
+    means the form of the work preferred for making modifications.
+
+1.14. "You" (or "Your")
+    means an individual or a legal entity exercising rights under this
+    License. For legal entities, "You" includes any entity that
+    controls, is controlled by, or is under common control with You. For
+    purposes of this definition, "control" means (a) the power, direct
+    or indirect, to cause the direction or management of such entity,
+    whether by contract or otherwise, or (b) ownership of more than
+    fifty percent (50%) of the outstanding shares or beneficial
+    ownership of such entity.
+
+2. License Grants and Conditions
+--------------------------------
+
+2.1. Grants
+
+Each Contributor hereby grants You a world-wide, royalty-free,
+non-exclusive license:
+
+(a) under intellectual property rights (other than patent or trademark)
+    Licensable by such Contributor to use, reproduce, make available,
+    modify, display, perform, distribute, and otherwise exploit its
+    Contributions, either on an unmodified basis, with Modifications, or
+    as part of a Larger Work; and
+
+(b) under Patent Claims of such Contributor to make, use, sell, offer
+    for sale, have made, import, and otherwise transfer either its
+    Contributions or its Contributor Version.
+
+2.2. Effective Date
+
+The licenses granted in Section 2.1 with respect to any Contribution
+become effective for each Contribution on the date the Contributor first
+distributes such Contribution.
+
+2.3. Limitations on Grant Scope
+
+The licenses granted in this Section 2 are the only rights granted under
+this License. No additional rights or licenses will be implied from the
+distribution or licensing of Covered Software under this License.
+Notwithstanding Section 2.1(b) above, no patent license is granted by a
+Contributor:
+
+(a) for any code that a Contributor has removed from Covered Software;
+    or
+
+(b) for infringements caused by: (i) Your and any other third party's
+    modifications of Covered Software, or (ii) the combination of its
+    Contributions with other software (except as part of its Contributor
+    Version); or
+
+(c) under Patent Claims infringed by Covered Software in the absence of
+    its Contributions.
+
+This License does not grant any rights in the trademarks, service marks,
+or logos of any Contributor (except as may be necessary to comply with
+the notice requirements in Section 3.4).
+
+2.4. Subsequent Licenses
+
+No Contributor makes additional grants as a result of Your choice to
+distribute the Covered Software under a subsequent version of this
+License (see Section 10.2) or under the terms of a Secondary License (if
+permitted under the terms of Section 3.3).
+
+2.5. Representation
+
+Each Contributor represents that the Contributor believes its
+Contributions are its original creation(s) or it has sufficient rights
+to grant the rights to its Contributions conveyed by this License.
+
+2.6. Fair Use
+
+This License is not intended to limit any rights You have under
+applicable copyright doctrines of fair use, fair dealing, or other
+equivalents.
+
+2.7. Conditions
+
+Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted
+in Section 2.1.
+
+3. Responsibilities
+-------------------
+
+3.1. Distribution of Source Form
+
+All distribution of Covered Software in Source Code Form, including any
+Modifications that You create or to which You contribute, must be under
+the terms of this License. You must inform recipients that the Source
+Code Form of the Covered Software is governed by the terms of this
+License, and how they can obtain a copy of this License. You may not
+attempt to alter or restrict the recipients' rights in the Source Code
+Form.
+
+3.2. Distribution of Executable Form
+
+If You distribute Covered Software in Executable Form then:
+
+(a) such Covered Software must also be made available in Source Code
+    Form, as described in Section 3.1, and You must inform recipients of
+    the Executable Form how they can obtain a copy of such Source Code
+    Form by reasonable means in a timely manner, at a charge no more
+    than the cost of distribution to the recipient; and
+
+(b) You may distribute such Executable Form under the terms of this
+    License, or sublicense it under different terms, provided that the
+    license for the Executable Form does not attempt to limit or alter
+    the recipients' rights in the Source Code Form under this License.
+
+3.3. Distribution of a Larger Work
+
+You may create and distribute a Larger Work under terms of Your choice,
+provided that You also comply with the requirements of this License for
+the Covered Software. If the Larger Work is a combination of Covered
+Software with a work governed by one or more Secondary Licenses, and the
+Covered Software is not Incompatible With Secondary Licenses, this
+License permits You to additionally distribute such Covered Software
+under the terms of such Secondary License(s), so that the recipient of
+the Larger Work may, at their option, further distribute the Covered
+Software under the terms of either this License or such Secondary
+License(s).
+
+3.4. Notices
+
+You may not remove or alter the substance of any license notices
+(including copyright notices, patent notices, disclaimers of warranty,
+or limitations of liability) contained within the Source Code Form of
+the Covered Software, except that You may alter any license notices to
+the extent required to remedy known factual inaccuracies.
+
+3.5. Application of Additional Terms
+
+You may choose to offer, and to charge a fee for, warranty, support,
+indemnity or liability obligations to one or more recipients of Covered
+Software. However, You may do so only on Your own behalf, and not on
+behalf of any Contributor. You must make it absolutely clear that any
+such warranty, support, indemnity, or liability obligation is offered by
+You alone, and You hereby agree to indemnify every Contributor for any
+liability incurred by such Contributor as a result of warranty, support,
+indemnity or liability terms You offer. You may include additional
+disclaimers of warranty and limitations of liability specific to any
+jurisdiction.
+
+4. Inability to Comply Due to Statute or Regulation
+---------------------------------------------------
+
+If it is impossible for You to comply with any of the terms of this
+License with respect to some or all of the Covered Software due to
+statute, judicial order, or regulation then You must: (a) comply with
+the terms of this License to the maximum extent possible; and (b)
+describe the limitations and the code they affect. Such description must
+be placed in a text file included with all distributions of the Covered
+Software under this License. Except to the extent prohibited by statute
+or regulation, such description must be sufficiently detailed for a
+recipient of ordinary skill to be able to understand it.
+
+5. Termination
+--------------
+
+5.1. The rights granted under this License will terminate automatically
+if You fail to comply with any of its terms. However, if You become
+compliant, then the rights granted under this License from a particular
+Contributor are reinstated (a) provisionally, unless and until such
+Contributor explicitly and finally terminates Your grants, and (b) on an
+ongoing basis, if such Contributor fails to notify You of the
+non-compliance by some reasonable means prior to 60 days after You have
+come back into compliance. Moreover, Your grants from a particular
+Contributor are reinstated on an ongoing basis if such Contributor
+notifies You of the non-compliance by some reasonable means, this is the
+first time You have received notice of non-compliance with this License
+from such Contributor, and You become compliant prior to 30 days after
+Your receipt of the notice.
+
+5.2. If You initiate litigation against any entity by asserting a patent
+infringement claim (excluding declaratory judgment actions,
+counter-claims, and cross-claims) alleging that a Contributor Version
+directly or indirectly infringes any patent, then the rights granted to
+You by any and all Contributors for the Covered Software under Section
+2.1 of this License shall terminate.
+
+5.3. In the event of termination under Sections 5.1 or 5.2 above, all
+end user license agreements (excluding distributors and resellers) which
+have been validly granted by You or Your distributors under this License
+prior to termination shall survive termination.
+
+************************************************************************
+*                                                                      *
+*  6. Disclaimer of Warranty                                           *
+*  -------------------------                                           *
+*                                                                      *
+*  Covered Software is provided under this License on an "as is"       *
+*  basis, without warranty of any kind, either expressed, implied, or  *
+*  statutory, including, without limitation, warranties that the       *
+*  Covered Software is free of defects, merchantable, fit for a        *
+*  particular purpose or non-infringing. The entire risk as to the     *
+*  quality and performance of the Covered Software is with You.        *
+*  Should any Covered Software prove defective in any respect, You     *
+*  (not any Contributor) assume the cost of any necessary servicing,   *
+*  repair, or correction. This disclaimer of warranty constitutes an   *
+*  essential part of this License. No use of any Covered Software is   *
+*  authorized under this License except under this disclaimer.         *
+*                                                                      *
+************************************************************************
+
+************************************************************************
+*                                                                      *
+*  7. Limitation of Liability                                          *
+*  --------------------------                                          *
+*                                                                      *
+*  Under no circumstances and under no legal theory, whether tort      *
+*  (including negligence), contract, or otherwise, shall any           *
+*  Contributor, or anyone who distributes Covered Software as          *
+*  permitted above, be liable to You for any direct, indirect,         *
+*  special, incidental, or consequential damages of any character      *
+*  including, without limitation, damages for lost profits, loss of    *
+*  goodwill, work stoppage, computer failure or malfunction, or any    *
+*  and all other commercial damages or losses, even if such party      *
+*  shall have been informed of the possibility of such damages. This   *
+*  limitation of liability shall not apply to liability for death or   *
+*  personal injury resulting from such party's negligence to the       *
+*  extent applicable law prohibits such limitation. Some               *
+*  jurisdictions do not allow the exclusion or limitation of           *
+*  incidental or consequential damages, so this exclusion and          *
+*  limitation may not apply to You.                                    *
+*                                                                      *
+************************************************************************
+
+8. Litigation
+-------------
+
+Any litigation relating to this License may be brought only in the
+courts of a jurisdiction where the defendant maintains its principal
+place of business and such litigation shall be governed by laws of that
+jurisdiction, without reference to its conflict-of-law provisions.
+Nothing in this Section shall prevent a party's ability to bring
+cross-claims or counter-claims.
+
+9. Miscellaneous
+----------------
+
+This License represents the complete agreement concerning the subject
+matter hereof. If any provision of this License is held to be
+unenforceable, such provision shall be reformed only to the extent
+necessary to make it enforceable. Any law or regulation which provides
+that the language of a contract shall be construed against the drafter
+shall not be used to construe this License against a Contributor.
+
+10. Versions of the License
+---------------------------
+
+10.1. New Versions
+
+Mozilla Foundation is the license steward. Except as provided in Section
+10.3, no one other than the license steward has the right to modify or
+publish new versions of this License. Each version will be given a
+distinguishing version number.
+
+10.2. Effect of New Versions
+
+You may distribute the Covered Software under the terms of the version
+of the License under which You originally received the Covered Software,
+or under the terms of any subsequent version published by the license
+steward.
+
+10.3. Modified Versions
+
+If you create software not governed by this License, and you want to
+create a new license for such software, you may create and use a
+modified version of this License if you rename the license and remove
+any references to the name of the license steward (except to note that
+such modified license differs from this License).
+
+10.4. Distributing Source Code Form that is Incompatible With Secondary
+Licenses
+
+If You choose to distribute Source Code Form that is Incompatible With
+Secondary Licenses under the terms of this version of the License, the
+notice described in Exhibit B of this License must be attached.
+
+Exhibit A - Source Code Form License Notice
+-------------------------------------------
+
+  This Source Code Form is subject to the terms of the Mozilla Public
+  License, v. 2.0. If a copy of the MPL was not distributed with this
+  file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
+If it is not possible or desirable to put the notice in a particular
+file, then You may include the notice in a location (such as a LICENSE
+file in a relevant directory) where a recipient would be likely to look
+for such a notice.
+
+You may add additional accurate notices of copyright ownership.
+
+Exhibit B - "Incompatible With Secondary Licenses" Notice
+---------------------------------------------------------
+
+  This Source Code Form is "Incompatible With Secondary Licenses", as
+  defined by the Mozilla Public License, v. 2.0.

simple_track-2.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: Simple-Track
+Version: 2.0.0
+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
+Project-URL: Homepage, https://github.com/ParaChute-UK/simple-track/
+Project-URL: Issues, https://github.com/ParaChute-UK/simple-track/issues
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=2.3.4
+Requires-Dist: pytest>=9.0
+Requires-Dist: pytest-cov
+Requires-Dist: pytest-xdist
+Requires-Dist: pyyaml
+Requires-Dist: scipy>=1.16.3
+Requires-Dist: scikit-image>=0.25.2
+Dynamic: license-file
+
+# Simple-Track
+
+<p align="center">
+<img src="docs/anim_feature.gif" alt="Feature field from Simple-Track" width="400"/>
+<img src="docs/anim_lifetime.gif" alt="Lifetime field from Simple-Track" width="400"/>
+</p>
+
+Simple-Track is a data-agnostic, threshold-based feature tracking algorithm for 2D data. 
+
+Features are tracked between consecutive frames of data by projecting feature fields onto common timeframes and matching between them based on the degree of overlap. Matched features retain the same identification between all tracked fields, while new features are assigned a unique label. Comprehensive information about feature merging, splitting, accretion, initiation and dissipation is compiled using Simple-Track. 
+
+# Installation
+
+Coming soon to PyPi and conda-forge
+
+# User Guide
+
+## Input Requirements
+While Simple-Track is designed to accept a wide range of input data, certain requirements must be met for the tool to function as intended:
+
+* The input data must be gridded and contain a consistent spatial domain and resolution between frames.
+
+* The features of interest must be defined by a threshold value, and these features must translate as a result of a spatially consistent background flow.
+
+* The time between frames should be sufficiently short such that features can be reasonably expected to persist between frames. This is not a strict requirement since the tool includes an artificial advection step that projects data onto a common time, but it is likely that longer time steps will lead to more errors in feature matching and therefore less accurate tracking statistics. 
+
+* It is currently a requirement that the timestep between frames is fixed, although future updates may relax this requirement. 
+
+## Running Simple-Track
+
+Simple-Track can be run in two ways:
+
+### 1. Running Simple-Track from the Command Line
+* Simple-Track can be run from the command line with a config file as an additional argument:
+
+	```
+	run_simple_track my_config.yaml 
+	```
+
+* The `my_config.yaml` file contains the parameters for running Simple-Track. The necessary parameters for running Simple-Track from the command line are shown below:
+
+	```yaml
+	INPUT:
+		path: /path_to_folder_containing_data
+		loader: LoaderName # See next section
+	FEATURE:
+		threshold: 1 # Threshold used for defining a feature
+		under_threshold: false # Whether features are defined above or below the threshold
+	```
+	
+* Other parameters, such as `experiment_name`, `output_path` and `save_data`, along with more technical options, can also be set in this config file. See [All Simple-Track Parameters](#all-simple-track-parameters) for a full list.
+
+* A valid `Loader` object is required for pre-processing input data before tracking. See [Loading Data](#loading-data) for more information.
+
+* Any number of config files can be provided as additional arguments, Simple-Track will iterate over each one in turn.
+
+### 2. Importing Simple-Track to a python file
+* Simple-Track can be run by importing the `Tracker` class from `track.py` or directly from the `simpletrack` module. The config can be input either using a path to a yaml file, or by passing a dict when instantiating the object:
+
+	```python
+	from simpletrack import Tracker
+
+	my_config = {
+		INPUT: {
+			path: "/path_to_folder_containing_data",
+			loader: "LoaderName" # See next section
+		},
+		FEATURE: {
+			threshold: 1, # Threshold used for defining a feature
+			under_threshold: False # Whether features are defined above or below the threshold
+		}
+	}
+
+	timeline = Tracker(my_config).run()
+
+	# Alternatively, if these parameters are saved in a config file, the path to this config can also be set as input
+	timeline = Tracker("./my_config.yaml").run()
+	```
+* Other parameters, such as `experiment_name`, `output_path` and `save_data`, along with more technical options, can also be set in this config. See [All Simple-Track Parameters](#all-simple-track-parameters) for a full list.
+
+* If `loader` is included as a config input, a valid `Loader` object is used for pre-processing input data before tracking. Alternatively, valid pre-processed data may be passed to the `Tracker.run()` method, bypassing the use of the `Loader` class, and eliminating the need for the `INPUT` config section. See [Loading Data](#loading-data) for more information.
+
+* `Tracker.run()` returns a `Timeline` object which is used to store all tracking and feature data. This can be inspected and analysed beyond the [outputs](#outputs) that are saved as part of standard operation.
+
+## Loading Data
+
+For Simple-Track to operate effectively, each input must consist of two sets of data:
+
+1. A `datetime` object specifying the time that the data is valid for
+2. A `numpy.array` object containing the data to track
+
+There are two methods of providing these data pairs to Simple-Track:
+
+### 1. Using a Loader object
+* Since Simple-Track is a data-agnostic tool, there may be any number of bespoke tools for loading and pre-processing data before it is suitable for tracking. This functionality can be contained in a custom `Loader` class that will perform these actions before passing the compatible data (and time) to the main processing methods.
+
+* A custom `Loader` object should be defined in the `load.py` file and should inherit from the `BaseLoader` object, which 
+will perform additional checks to ensure the loaded data is in the correct format. An example of a loader class is shown in the code snippet below:
+
+	```python
+	class ChilboltonLoader(BaseLoader):
+		def __init__(self):
+			super().__init__()
+
+		def user_definable_load(self, filename):
+			import iris # Import any required libraries here
+
+			# Get 2D data from input file as a numpy array
+			cube = iris.load_cube(filename, "precipitation_flux")
+			data = cube.data
+
+			# Additional data pre-processing can be performed here too!
+
+			# Get time from input file, in datetime format
+			tcoord = cube.coord("time")
+			time = tcoord.units.num2pydate(tcoord.points)[0]
+
+			# Method must return a tuple of 
+			# (datetime.datetime, numpy.NDArray, ), where the 
+			# first element is the time the data is valid for
+			# and second element is the 2D array of data to be tracked
+			return time, data
+	```
+
+* This loader class must then be added to the `available_loaders` dict in the `get_loader` function of `load.py`, where the key for this loader is used to specify the loader in the config file. This structure allows users to easily define their own loading procedures for their specific datasets, while still being able to use the core functionality of Simple-Track without modification.
+
+* A Loader object can be used whether Simple-Track is being run [from the command line](#1-running-simple-track-from-the-command-line) or [from a python file](#2-importing-simple-track-to-a-python-file). 
+
+* The list of filenames which will be iteratively loaded using a custom `Loader` object can be obtained and input in multiple ways:
+	* If running Simple-Track [from the command line](#1-running-simple-track-from-the-command-line), the code will find all files in the config `[INPUT][path]` directory matching a given extension defined in `Tracker.get_filenames_from_input_path()`
+	* If running Simple-Track [from a python file](#2-importing-simple-track-to-a-python-file), a list of filenames can be passed to `Tracker.run()`. Alternatively, if no filenames are passed to this method, the code will find all files in the config `[INPUT][path]` directory matching a given extension defined in `Tracker.get_filenames_from_input_path()`
+
+### 2. Passing a dict directly to Tracker.run()
+* If SimpleTrack is being run [from a python file](#2-importing-simple-track-to-a-python-file) and a suitable set of data has already been loaded, this data can be passed directly to `Tracker.run()` as a `dict`, with the `datetime` object as the key and a `numpy.array` object as the value
+
+* Any number of time:data pairs can be passed to `Tracker.run()` and the code will iterate over the ordered dict.
+
+* Passing data into `Tracker.run()` via this method will bypass any `Loader` or `[INPUT][path]` inputs specified in the corresponding config file. 
+
+
+# Outputs
+
+For each frame of data, Simple-Track compiles a set of fields and tracked feature properties. Each 2D field is of the same shape as the input fields, and contains an overview of feature properties across the space. 
+
+Fields (`.field` files):
+* Feature field: 2D array of positive integers showing unique feature id present at each location (zero indicating no feature present)
+* Lifetime field: 2D array of positive integers showing lifetime of the feature present at each location (zero indicating no feature present)
+* x-flow, y-flow: 2D array of floats containing the x- and y-components of the motion vectors at each location that translate features from the previous frame to the current frame
+
+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.
+* 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.
+* 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
+* children: List of IDs of features that split from this feature, if applicable
+
+It it also possible to perform further analysis of tracking statistics using the data structures and tools of Simple-Track. This can be done using the `Timeline` object returned by `Tracker.run()`, which contains `Frame` and `Feature` data and built-in methods for easily accessing relevant data. 
+
+Alternatively, the data that is output by Simple-Track can be read back in to a `Timeline` object using the `LoadOutput` class in `frame_output.py`. This object only requires a path to the stored Simple-Track data. The `LoadOutput.load_to_timeline()` method will return a `Timeline` object containing all of the loaded data in the same data structures that Simple-Track stores its data. (Note: this does not currently load the raw input data back into the system, and therefore some methods such as `Frame.identify_features()` will not work. This data can be added manually to the `Frame.raw_field` attribute). 
+
+# All Simple-Track Parameters
+A complete list of parameters and their default values are given below:
+
+```yaml
+INPUT:
+  path: ./path_to_input_data
+  loader: MyLoader # Custom loader class name
+  file_type: .nc # File extension to search for when compiling files to load and iterate over
+
+OUTPUT:
+  path: ./output
+  experiment_name: Simple-Track Experiment # Name of experiment to add to output files 
+  save_data: true # Whether to save data to output
+
+FEATURE:
+  threshold: 1 # Threshold used for defining a feature
+  under_threshold: false # Whether features are defined above or below the threshold
+  min_size: 4 # Minimum size of feature to be tracked (in pixels)
+
+FLOW_SOLVER:
+  overlap_threshold: 0.6 # Minimum fraction of overlap between features for use in flow_solver
+  subdomain_size: 100 # Size in pixels of individual squares to run fft for (dy, dx) displacement. Must divide (y,x) lengths of the array. Defaults to domain size / 5
+  min_fractional_coverage: 0.01  # Minimum fractional cover of objects required for fft to obtain (dy, dx) displacement
+  subdomain_tolerance: 3.0  # Maximum difference in displacement values between adjacent squares (to remove spurious values)
+  apply_tukey_filtering: True # Apply a 2D Tukey window to each subdomain before phase cross-correlation
+
+TRACKING:
+  skip_tracking: false # Whether to skip tracking and just output feature properties
+  overlap_nbhood: 5 # Radius of halo in pixels for orphan storms - big halo assumes storms may spawn "children" at a distance multiple pixels away
+  overlap_threshold: 0.6 # Minimum fraction of overlap 
+  retain_lifetime_on_split: True # If a child Feature splits from its parent feature, this determines whether the child Feature should carry over the lifetime from the parent or whether its lifetime should be set to 1
+```