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

Full 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; Nanson et al., 2026). These tools comprise seven toolboxes:

1. The BathymetricHigh.pyt toolbox is used to map bathymetric high features, and includes five tools: (i) TPI Tool Bathymetric High; (ii) TPI LMI Tool Bathymetric High; (iii) Openness Tool Bathymetric High; (iv) Contour Tool Bathymetric High; and (v) Pseudo Contour Tool Bathymetric High.


2. The BathymetricLow.pyt toolbox is used to map bathymetric low features, and includes five tools: (i) TPI Tool Bathymetric Low; (ii) TPI CI Tool Bathymetric Low; (iii) Openness Tool Bathymetric Low; (iv) Contour Tool Bathymetric Low; and (v) Pseudo Contour 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 performance advantage (over the AddAttributes.pyt toolbox) of applying multiprocessing capabilities. This version of the toolbox contains six tools: (i) Add Shape Attributes High Tool Fast; (ii) Add Shape Attributes Low Tool Fast; (iii) Add Topographic Attributes Low Tool Fast; (iv) Add Topographic Attributes High Tool Fast; (v) Add Profile Attributes High Tool Fast; and (vi) Add Profile Attributes Low Tool Fast.


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 three tools: (i) Classify Bathymetric High Features Tool; (ii) Classify Bathymetric Low Features Tool; and (iii) Verify Depression Features Tool.


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.

References:
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

Nanson, R., Arosio, R., Gafeira, J., McNeil, M., Dove, D., Bjarnadóttir, L. R., Dolan, M. F. J., Post, A., Nichol, S., Huang, Z., Guinan, J., Bialik, O. M., Webb, J., Wells, J., & Carroll, A. G. (2026). Coastal to deep-marine geomorphic classification: A standardised framework and review of terms to support globally consistent mapping. Earth-Science Reviews, 276, Article 105439. https://doi.org/10.1016/j.earscirev.2026.105439.

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 3 (GA-SaMMT v3.0) update previous versions (GA-SaMMT v2.0 and GA-SaMMT v1.2); all these 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; Nanson et al., 2026). This new version has implemented the following bug fixes, improvements and new tools/features. Future updates can be accessed from the following GitHub site: https://github.com/GeoscienceAustralia/GA-SaMMT. Bugs Fixing and Improvements This current version fixed a number of bugs/limitations in the Python code, as well as fool-proved some issues generated by unusual user inputs. They are listed as follows:

1. Issue when there are duplicated featID values in the input featureclass when running the add attributes tools. Some codes were added to identify duplicated featID values then to exit gracefully (with informative error message) when this occurs.
2. Issue when multiple outputs were given the same name. Some codes were added to identify this issue then to exit gracefully (with informative error message) when this occurs.
3. Issue when the STD scale parameter values assigned are too high which results in the threshold values being out of the range of the corresponding grid (e.g., TPI, NO, PO, LMI and CI). Some codes were added to identify this issue then to exit gracefully (with informative error message) when this occurs.
4. Issue when the number of input features is smaller than the number of CPUs nominated when running the add attributes fast tools. Some codes were added to identify this issue then to exit gracefully (with informative error message) when this occurs.
5. Issue when the bathymetric grid and input featureclass are not from the same file geodatabase when running the add attributes fast tools. Some codes were added to remove the need of the two inputs being from the same file geodatabase.

The current version also implemented the following improvements:

1. Significant coding restructure. Helper functions used across multiple toolboxes (.pyt files) and other important functions have been extracted from the .pyt files, and organised as local Python modules (.py files). These local modules are then called in the .pyt files. This has significantly improved the readability of the Python codes and aligns with the best coding practices.
2. Significant changes to the arcpy syntax. The syntax of the arcpy functions have been updated according to the latest versions of ArcGIS Pro (v3.4 and beyond). This aligns the GA-SaMMT tools with the latest updates of ArcGIS Pro, while maintaining backward compatibility to older versions of ArcGIS Pro.
3. Minor changes to the classification tools. Minor changes to the classification tools regarding the “unclassified” class have been implemented.

New topographic attributes In this version, the following new attributes were added to the Add Topographic Attributes tools:

• relativeHeight,
• relativeDepth,
• surfaceArea,
• volume, and
• sArea.

The relativeHeight and relativeDepth attributes represent the vertical relief of a seabed feature. The surfaceArea, sArea and volume attributes represent the 3-D surface area and 3-D volume of a seabed feature. They are often more time-consuming to calculate. Therefore, two new tools, Add Topographic Attributes High Fast tool and Add Topographic Attributes Low Fast tool, were added to the AddAttributesFast toolbox to improve computing performance (see below for details). New Add Topographic Attributes Fast tools In this version, two new tools, Add Topographic Attributes High Fast tool and Add Topographic Attributes Low Fast tool, were added to the AddAttributesFast toolbox. The Add Topographic Attributes High Tool Fast offers multiprocessing capability and thus is more efficient in generating topographic attributes for each bathymetric high feature. The Add Topographic Attributes Low Tool Fast offers multiprocessing capability and thus is more efficient in generating topographic attributes for each bathymetric low feature. New contour-based mapping tools In this version, two new mapping tools, Contour Tool Bathymetric High and Pseudo Contour Tool Bathymetric High, were added to the BathymetricHigh toolbox. The Contour Tool Bathymetric High maps bathymetric high features from a bathymetric data using a Contour based method. The Pseudo Contour Tool Bathymetric High maps bathymetric high features from a bathymetric data using a pseudo Contour based method. Two additional new mapping tools, Contour Tool Bathymetric Low and Pseudo Contour Tool Bathymetric Low, were added to the BathymetricLow toolbox. The Contour Tool Bathymetric Low maps bathymetric low features from a bathymetric data using a Contour based method. The Pseudo Contour Tool Bathymetric Low maps bathymetric low features from a bathymetric data using a pseudo Contour based method. These new tools are suitable for the mapping of seabed features that are enclosed by bathymetric contours. New Verify Depression Feature Tool In this version, a new classification tool, Verify Depression Feature Tool, was added to the ClassificationFeature toolbox. The classification rule for the Depression Feature in the "Classify Bathymetric Low Features Tool" does not apply the "closed-contour" criterion defined in the Dove et al. (2020) morphology scheme. This new tool uses the "closed-contour" criterion to verify whether a bathymetric low feature originally classified as Depression is indeed a proper Depression.

Notes

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