用于多波束声纳数据处理的Matlab工具箱.zip

 # *CoFFee* Matlab toolbox for multibeam sonar data processing. ## Description *CoFFee* is a free and open-source MATLAB toolbox (libary of functions) for reading multibeam sonar raw data files, visualizing their contents, and applying various processsing algorithms. It serves as the engine for several apps/GUIs designed for specific applications. **IMPORTANT NOTE: This is a pre-release (v2), that is, still clunky. Use at your peril!** ## Getting Started ### Dependencies * [MATLAB](https://au.mathworks.com/products/get-matlab.html). We are currently using R2020b, but it may work on other versions. * Some MATLAB toolboxes (not all functions require them): * Signal Processing Toolbox * Mapping Toolbox * Statistics and Machine Learning Toolbox * Parallel Computing Toolbox ### Installing and using * Clone or download the repository. * Add the toolbox's folder and subfolders to the Matlab's path by adding the following lines at the top of your scripts: ``` coffeeFolder = 'C:\my\path\to\CoFFee'; addpath(genpath(coffeeFolder)); ``` ## Help There is no documentation yet. Contact the authors. ## Authors * Alexandre Schimel ([The Geological Survey of Norway](https://www.ngu.no), alexandre.schimel@ngu.no) * Yoann Ladroit (NIWA) * Amy Nay (CSIRO) ## Version History [See the releases page](https://github.com/alexschimel/CoFFee/releases) ## License Distributed under the MIT License. See `LICENSE` file for details. ## See Also All apps based on *CoFFee*: * [*Grounds*](https://github.com/alexschimel/Grounds): Elevation Change Analysis * [*Espresso*](https://github.com/alexschimel/Espresso): Multibeam water-column data visualization and processing (private) * [*Iskaffe*](https://github.com/alexschimel/Iskaffe): Multibeam backscatter quality control * [*Kopp*](https://github.com/alexschimel/Kopp): Tracking Multibeam raw data parameter changes ## References Articles using *CoFFee*, or apps based on *CoFFee*: * Lucieer, V., Flukes, E., Keane, J. P., Ling, S. D., Nau, A. W., & Shelamoff, V. (2023). Mapping warming reefs — An application of multibeam acoustic water column analysis to define threatened abalone habitat. Frontiers in Remote Sensing, 4(April), 1–15. https://doi.org/10.3389/frsen.2023.1149900 * Turco, F., Ladroit, Y., Watson, S. J., Seabrook, S., Law, C. S., Crutchley, G. J., Mountjoy, J., Pecher, I. A., Hillman, J. I. T., Woelz, S., & Gorman, A. R. (2022). Estimates of Methane Release From Gas Seeps at the Southern Hikurangi Margin, New Zealand. Frontiers in Earth Science, 10(March), 1–20. https://doi.org/10.3389/feart.2022.834047 * Nau, A. W., Scoulding, B., Kloser, R. J., Ladroit, Y., & Lucieer, V. (2022). Extended Detection of Shallow Water Gas Seeps From Multibeam Echosounder Water Column Data. Frontiers in Remote Sensing, 3(July), 1–18. https://doi.org/10.3389/frsen.2022.839417 * Porskamp, P., Schimel, A. C. G., Young, M., Rattray, A., Ladroit, Y., & Ierodiaconou, D. (2022). Integrating multibeam echosounder water‐column data into benthic habitat mapping. Limnology and Oceanography, 1–13. https://doi.org/10.1002/lno.12160 * Schimel, A. C. G., Brown, C. J., & Ierodiaconou, D. (2020). Automated Filtering of Multibeam Water-Column Data to Detect Relative Abundance of Giant Kelp (Macrocystis pyrifera). Remote Sensing, 12(9), 1371. https://doi.org/10.3390/rs12091371 * Mountjoy, J. J., Howarth, J. D., Orpin, A. R., Barnes, P. M., Bowden, D. A., Rowden, A. A., Schimel, A. C. G., Holden, C., Horgan, H. J., Nodder, S. D., Patton, J. R., Lamarche, G., Gerstenberger, M., Micallef, A., Pallentin, A., & Kane, T. (2018). Earthquakes drive large-scale submarine canyon development and sediment supply to deep-ocean basins. Science Advances, 4(3). https://doi.org/10.1126/sciadv.aar3748 * Nau, A. W., Lucieer, V. L., & Alexandre Schimel, C. G. (2018). Modeling the along-track sidelobe interference artifact in multibeam sonar water-column data. OCEANS 2018 MTS/IEEE Charleston, 1–5. https://doi.org/10.1109/OCEANS.2018.8604866 * Schimel, A. C. G., Ierodiaconou, D., Hulands, L., & Kennedy, D. M. (2015). Accounting for uncertainty in volumes of seabed change measured with repeat multibeam sonar surveys. Continental Shelf Research, 111, 52–68. https://doi.org/10.1016/j.csr.2015.10.019 * Schimel, A. C. G., Healy, T. R., McComb, P., & Immenga, D. (2010). Comparison of a self-processed EM3000 multibeam echosounder dataset with a QTC view habitat mapping and a sidescan sonar imagery, Tamaki Strait, New Zealand. Journal of Coastal Research, 26(4). https://doi.org/10.2112/08-1132.1 ## For developers Please maintain the *CoFFee* coding philosophy, which is that any core functionality (raw file reading, conversion, data processing, etc.) is coded as *CoFFee* functions, so that only user-interaction functionalities (display, user interface, callbacks, etc.) are coded in apps. This allows reusing core functionalities across apps. Therefore, the development of an app requires the joint development of *CoFFee*, and since there are multiple apps built on *CoFFee*, careful version-controlling and dependency-management is necessary to avoid breaking compatibility. We use [Semantic Versioning](https://semver.org/) to attribute version numbers: * The version of *CoFFee* is hard-coded in function `CFF_coffee_version.m`. * The version of an app is (usually) a static property of the app (`Version`), alongside the *CoFFee* version it was built on (`CoffeeVersion`). A careful sequence to develop an app is the following: 1. Checkout the latest commits on the main branches of both *CoFFee* and the app you wish to develop. 2. Check if that latest version of the app uses the latest version of *CoFFee* (in the code, or warning at start-up). 3. If the app is running on an older version of *CoFFee*, fix that first: * Start with updating the app to use that latest version of *CoFFee*. * Before committing those changes, increase the app's version number and update which *CoFFee* version it runs on. * After committing, remember to add the new tag on git. 4. Develop the app as you wish. Remember that all processing goes ideally in *CoFFee* and all display and user interface on the app. 5. When done, increase the app's version number (app property `Version`) 6. If *CoFFee* was modified, increase *CoFFee*'s version number (`CFF_coffee_version.m`), and update in the app which *CoFFee* version it was built on (app property `CoffeeVersion`). 7. Verify that everything works: * In MATLAB, run `restoredefaultpath` to ensure you get a clean path. * Delete the user folder to start from a clean slate. * Start the app, check on the start messages that all versions are correct * Test all features of the app. 8. Push the app up on git. Add a version tag. 9. If *CoFFee* was modified, push it up on git. Add a version tag. 10. If you wish to compile/release this new version of the app: * Compile: * Double-click on the app's `*.prj` file to start the Application Compiler with existing settings. * Reset dependencies: * Remove the app's "main file" (the `*.mlapp` file if using the app designer) to remove all the files required. This might take a few seconds. * Remove any remaining files and folders in the list of files required. * Add the "main file" again and wait for the application compiler to find all required files. This might take a few seconds. * Add any other files and folders in the list of files required. * Update the version number: * In the setup file name ("Packaging Options" panel, "Runtime downloaded from web" field) * In the "application information" panel * In the "Default installation folder" field. * Details: * All paths in "Settings" should be in the "Espresso\bin" folder. * Click on "Save". * Click on "Package". * Test that the com