Metadata-Version: 2.4 Name: Simple-Track Version: 2.3.0 Summary: Threshold-based object tracking algorithm for 2D data Author-email: Adam Gainford , Thorwald Stein License: 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. 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: >=3.10 Description-Content-Type: text/markdown License-File: LICENSE Requires-Dist: numpy>=2.2.0 Requires-Dist: pytest>=9.0 Requires-Dist: pytest-cov Requires-Dist: pytest-xdist Requires-Dist: pyyaml Requires-Dist: scipy>=1.15.0 Requires-Dist: scikit-image>=0.25.2 Provides-Extra: opencv Requires-Dist: opencv-python; extra == "opencv" Dynamic: license-file # Simple-Track

Feature field from Simple-Track Lifetime field from Simple-Track

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. Simple-Track compiles comprehensive information about feature merging, splitting, accretion, initiation and dissipation with an easy to use interface. # Installation Simple-Track can be installed using PyPi or conda-forge: ``` python3 -m pip install simple-track ``` ``` conda install conda-forge::simple-track ``` Coming soon to uv Alternatively, Simple-Track can be run on meteorological data in [CSET](https://metoffice.github.io/CSET/index.html#) using the `feature.track` operator. See CSET docs for more information. # User Guide This section describes the main methods of running Simple-Track. More details can be found [in the docs](docs/user_guide.md) ## 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. ## 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: ``` simpletrack my_config.yaml ``` * The `my_config.yaml` file contains the parameters for running Simple-Track. The required parameters are shown below: ```yaml INPUT: path: /path_to_folder_containing_data/*.data loader: /path_to_file_containing_function|function_name # See next section FEATURE: threshold: 1 # Threshold used for defining a feature ``` * 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 function 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 the `simpletrack` module. A 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/*.data", loader: "/path_to_file_containing_function|function_name" # See next section }, FEATURE: { threshold: 1, # Threshold used for defining a feature } } 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, the specified function 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 a separate function, 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 Each Simple-Track input must contain 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 three methods of providing these data pairs to Simple-Track: ### 1. Loading through config options * Simple-Track will load all data matching the structure given in `"INPUT": "path"` config section. This input supports wildcard matching (i.e., using `"./path_to_data/*.data"` would load all files with the `.data` suffix). * Each file contains one input to Simple-Track ([see here](docs/inputs.md#extra-loading-parameters) for more information) * 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 function that will perform these actions before passing the compatible data to the main processing workflow. * An example of a custom loader function is shown below: ```python 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 function is then specified in the `"INPUT": "loader"` config using the `./path_to_file.py|func_name` format. So in this case, the config option would be `./path_to_file.py|user_definable_load`. * Loading via the config 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). ### 2. Loading through the Command Line * The same `"INPUT"` config sections mentioned above can also be input [from the command line](#1-running-simple-track-from-the-command-line) ``` simpletrack my_config.yaml -i /path_to_folder/*.data -l ./path_to_file.py|func_name ``` * Each file contains one input to Simple-Track ([see here](docs/inputs.md#extra-loading-parameters) for more information) ### 3. 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. For example: ```python import datetime as dt import numpy as np from simpletrack import Tracker time1 = dt.datetime(year=2000, month=1, day=1, hour=10, minute=5) time2 = time1 + dt.timedelta(minutes=5) data1 = np.array(...) data2 = np.array(...) st_input = { time1: data1, time2: data2, } my_config = {...} Tracker(my_config).run(st_input) ``` * 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 `"INPUT":"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. * 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 * 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. See User Guide in docs for more details. # All Simple-Track Parameters A complete list of parameters and their default values are given below. For a more thorough explanation of each parameter, refer to the docs. ```yaml INPUT: path: ./path_to_input_data/*.data loader: /path_to_file_containing_function|function_name iterate_over_array: False # Whether to iterate a single array or multiple files iterating_dim: 0 # If iterate_over_array flag is enabled, this sets the dimension to 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 skip_tracking: false # Whether to skip tracking and just output feature properties output_raw_data: true # Whether to save a copy of the input data to the simple-track output folder. This is then used when re-loading data into a Timeline using the LoadOutput object. This ensures loaded Timelines are functionally identical to freshly generated timelines. If set to False, LoadOutput will only load data generated by Simple-Track. To make these timelines functionally identical to generated ones, the raw data will then need to be loaded separately into each Frame. 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: 0.3 # 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: 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: 0.3 # 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 ```