Geoscience Australia's Semi-automated Morphological Mapping Tools (GA-SaMMT) for Seabed Characterisation

Brief description

The Geoscience Australia’s Semi-automated Morphological Mapping Tools (GA-SaMMT) were developed as ArcGIS Pro Python tools using Python 3+ to map ten bathymetric high and eight bathymetric low Morphology Features (defined in Dove et al., 2020; cf. Nanson et al., 2023). These tools comprise seven toolboxes: 1. The BathymetricHigh.pyt toolbox is used to map bathymetric high features, and includes three tools: (i) TPI Tool Bathymetric High; (ii) TPI LMI Tool Bathymetric High; (iii) and Openness Tool Bathymetric High. 2. The BathymetricLow.pyt toolbox is used to map bathymetric low features, and includes three tools: (i) TPI Tool Bathymetric Low; (ii) TPI CI Tool Bathymetric Low; and (iii) Openness Tool Bathymetric Low. 3. The AddAttributes.pyt toolbox is used to calculate attributes for bathymetric high and low features, and includes six tools: (i) Add Shape Attributes High Tool; (ii) Add Shape Attributes Low Tool; (iii) Add Topographic Attributes High Tool; (iv) Add Topographic Attributes Low Tool; (v) Add Profile Attributes High Tool; and (vi) Add Profile Attributes Low Tool. 4. The AddAttributesFast.pyt toolbox is also used to calculate attributes for bathymetric high and low features, and has the advantage (over the AddAttributes.pyt toolbox) of having multiprocessing capabilities. This version of the add attributes toolbox contains four tools: (i) Add Shape Attributes High Tool Fast; (ii) Add Shape Attributes Low Tool Fast; (iii) Add Profile Attributes High Tool Fast; and (iv) Add Profile Attributes Low Tool Fast. The two add topographic attributes tools do not require multiprocessing capabilities to improve their performance. 5. The ClassificationFeature.pyt toolbox is used to classify bathymetric high and low features into Morphological Feature categories defined in Dove et al. (2020), and includes two tools: (i) Classify Bathymetric High Features; and (ii) Classify Bathymetric Low Features. 6. The Accessory_Tools.pyt toolbox provides four accessory tools to help the mapping processes: (i) Merge Connected Features Tool; (ii) Connect Nearby Linear Features Tool; (iii) Connect Nearby Linear HF Features Tool; and (iv) Update Feature Boundary Tool. 7. The Surface.pyt toolbox is used to map three classes of Morphological surfaces (Dove et al., 2020), and includes two tools: (i) Morphological Surface Tool Bathymetry; and (ii) Morphological Surface Tool Slope. The system and data format requirements of these ArcGIS tools are described in the tutorials and user guide that accompany the tools, which also include sampled data and step-by-step examples of their application. Further details of these tools, including their description, graphic illustrations and usages, and python code examples, are also available in their metadata. These tools have been applied to many study areas with real world applications, including those published in Huang et al. (2023) which should be used as the key reference to the GA-SaMMT. Dove, D., Nanson, R., Bjarnadóttir, L., Guinan, J., Gafeira, J., Post, A., Dolan, M.; Stewart, H.; Arosio, R, Scott, G. (October, 2020). A two-part seabed geomorphology classification scheme (v.2); Part 1: morphology features glossary. Zenodo. http://doi.org/10.5281/zenodo.4075248 Nanson, R., Arosio, R., Gafeira, J., McNeil, M., Dove, D., Bjarnadóttir, L., Dolan, M., Guinan, J., Post, A., Webb, J., & Nichol, S. (2023). A two-part seabed geomorphology classification scheme; Part 2: Geomorphology classification framework and glossary (Version 1.0) (1.0). Zenodo. https://doi.org/10.5281/zenodo.7804019 Huang, Z., Nanson, R., McNeil, M., Wenderlich, M., Gafeira, J., Post, A, Nichol, S., 2023. Rule-based semi-automated tools for mapping seabed morphology from bathymetry data, Frontiers in Marine Science, 10, 1236788.

Lineage

Maintenance and Update Frequency: asNeeded

Statement: These ArcGIS tools Version 2 (GA-SaMMT v2.0) update version 1 (GA-SaMMT v1.2); both versions were developed by Geoscience Australia’s Marine Geomorphology Working Group to support the implementation of Part 1 (Dove et al., 2020) of an international two-part seabed geomorphology mapping scheme (Nanson et al., 2023). This new version has implemented the following bug fixes, improvements and new tools/features, and future updates can be accessed from https://github.com/GeoscienceAustralia/GA-SaMMT.

Bugs Fixing and Improvements

This current version fixed a number of bugs in the previous version. They are listed as follows:

1. Issue in calculating the skewness attribute in the AddAttributes.pyt. A new option “numeric_only = True” was added to deal with the requirement of the new Pandas version.
2. Issue in calculating the sideslope variable in the AddAttributes.pyt. Some codes were added to prevent the “divide by 0” issue. 3. Issue in calculating the bottomDepth variable in the AddAttributes.pyt. The incorrect code using the max() function was changed to using the min() function.
4. Schema.ini issue in the AddAttributes.pyt. The schema.ini file in the temporary folder may indicate incorrect data types for the generated .csv files. Some codes were implemented to delete the existing schema.ini each time before generating a .csv file.
5. Mix type issue in reading a .csv file as a Pandas dataframe in the AddAttributes.pyt. In the current version, the dtype parameter was explicitly defined and added to Pandas’ read_csv() function. This is to prevent the potential mix type warning.
6. Issue in generating the centre point of a multipart feature in the AddAttributes.pyt. Using the linear connection tools in the Accessory_Tools.pyt may result in multipart feature(s). In such case, the centre point generated using the arcpy’s FeatureToPoint function with the “CENTROID” option may not be located inside one of the feature polygons, which would cause problem in the subsequent profile generation. In the current version, some codes were implemented to identify such cases and then use the “INSIDE” option to forcefully generate centre point inside one of the polygons.
7. Issue in calculating the widthThicknessRatio attribute in the AddAttributes.pyt. In the rare case of “thickness = 0”, the widthThicknessRatio calculation would throw a “divide by 0” warning. In the current version, some codes were implemented to resolve this issue.

This current version also implemented the following improvements:

1. It provided user an option (the Calculate additional attributes checkbox) not to generate seven complex shape attributes for the bathymetric low features in the Add Shape Attributes Low Tool. With this option unchecked, the tool would require less time to complete.
2. It implemented codes to compact relevant geodatabase regularly. This would reduce the size of the geodatabase and also potentially improve the tool performance.
3. It added some codes for the Add Profile Attributes High Tool and the Add Profile Attributes Low Tool to prevent them from generating a large number of points along a profile of a very large feature. This would also improve the tool performance.

New Add Attributes Fast Tools

In the current version, a new toolbox AddAttributesFast.pyt was added. The new toolbox contains the following four tools:
1. Add Shape Attributes High Tool Fast: This tool generates shape attributes for each bathymetric high feature using multiprocessing capability.
2. Add Shape Attributes Low Tool Fast: This tool generates shape attributes for each bathymetric low feature using multiprocessing capability.
3. Add Profile Attributes High Tool Fast: This tool generates profile attributes for each bathymetric high feature using multiprocessing capability.
4. Add Profile Attributes Low Tool Fast: This tool generates profile attributes for each bathymetric low feature using multiprocessing capability.

Because of the utilisation of the multiprocessing capability, these tools are able to yield a much faster performance than their equivalents in the AddAttributes.pyt. As a result, these tools have largely alleviated the bottlenecked performance issue in calculating shape and profile attributes.

New Multiprocessing Python Scripts

In addition to the above four new tools in the AddAttributesFast.pyt that can be directly run within the ArcGIS Pro, two new Python scripts are included in the current version:

1. Multiprocessing_BH_run.py: This script uses multiprocessing capability to batch process the three add attributes high tools in the AddAttributes.pyt.
2. Multiprocessing_BL_run.py: This script uses multiprocessing capability to batch process the three add attributes low tools in the AddAttributes.pyt.

Again, because of the utilisation of the multiprocessing capability, these Python scripts are able to yield a similarly fast performance as the tools in the AddAttributesFast.pyt. The only difference is that these two scripts are to be run outside the ArcGIS Pro in a batch processing mode. These scripts can also be modified and customised by advanced Python users for even more complex batch processing tasks.

New Accessory Tools

There were significant changes in the Accessory_Tools.pyt in the current version:

1. The Connect Nearby Linear Features Tool has been significantly changed. The tool is now able to connect not only linear bathymetric low features (e.g., canyons) but also linear bathymetric high features (e.g., ridges).
2. A new Connect Nearby Linear HF Features Tool has been added. The tool can be used to connect nearby linear bathymetric low features through their feet and heads.
3. A new Update Feature Boundary Tool has been added. The tool can be used to update the boundaries of one mapping output using the boundaries of another mapping output.

Notes

Purpose
These seabed morphology mapping tools aim to provide user-friendly semi-automatic method to map seabed morphology features from bathymetry data.