Aerial imagery and structure-from-motion-derived shallow water bathymetry from a UAS survey of the coral reef off Waiakane, Molokai, Hawaii, June 2018

Dates

Acquisition: 2018-06-24
Publication Date: 2022-03-21

Citation

Logan, J.B., and Storlazzi, C.D., 2022, Aerial imagery and structure-from-motion-derived shallow water bathymetry from a UAS survey of the coral reef off Waiakane, Molokai, Hawaii, June 2018: U.S. Geological Survey data release, https://doi.org/10.5066/P9XZT1FK.

Summary

An unoccupied aerial system (UAS) was used to acquire high-resolution imagery of the shallow fringing coral reef at Waiakane, Molokai, Hawaii, on 24 June 2018. Imagery was acquired over an area between the shoreline and approximately 900 meters offshore, covering approximately 16 hectares. The imagery was processed using structure-from-motion (SfM) photogrammetric techniques with additional refraction correction post-processing performed to derive a high-resolution bathymetric digital surface model (DSM), orthomosaic imagery, and a bathymetric point cloud. Field data acquisition The image acquisition was conducted using a Department of Interior-owned 3DR Solo quadcopter fitted with a Ricoh GR II digital camera featuring a global [...]

Summary

An unoccupied aerial system (UAS) was used to acquire high-resolution imagery of the shallow fringing coral reef at Waiakane, Molokai, Hawaii, on 24 June 2018. Imagery was acquired over an area between the shoreline and approximately 900 meters offshore, covering approximately 16 hectares. The imagery was processed using structure-from-motion (SfM) photogrammetric techniques with additional refraction correction post-processing performed to derive a high-resolution bathymetric digital surface model (DSM), orthomosaic imagery, and a bathymetric point cloud.

Field data acquisition
The image acquisition was conducted using a Department of Interior-owned 3DR Solo quadcopter fitted with a Ricoh GR II digital camera featuring a global shutter. The UAS was flown on pre-programmed autonomous flight lines which were oriented roughly shore-normal and were spaced to provide approximately 75 percent overlap between images from adjacent lines, at an approximate altitude of 100 meters above ground level (AGL). The camera was triggered at 1 Hz using a built-in intervalometer. Before each flight, the camera’s digital ISO, aperture, and shutter speed were adjusted for ambient light conditions.

A total of five flights were conducted for the survey between 16:40 and 17:45 UTC (06:40 and 07:45 HST). Flight F01 was a reconnaissance flight, and no mapping imagery was collected during the flight. Flights F02 and F03 were conducted at an approximate altitude of 100 meters AGL, resulting in complete coverage of the mapping area with a nominal ground-sample-distance (GSD) of approximately 2.5 centimeters per pixel. Flights F04 and F05 were conducted using the same flight lines and altitudes of F02 and F03, but the camera was fitted with a circular polarizing filter to reduce reflections and provide improved imaging of the seafloor through the water surface. After the survey, all imagery was geotagged using position data from the UAS onboard single-frequency GPS.

Twenty temporary ground control points (GCPs) were distributed throughout the area to establish survey control. The GCPs were placed using a combination of kayaking, wading, and snorkeling. The GCPs consisted of: nine submerged targets consisting of small (80 centimeter X 80 centimeter) square tarps with black-and-white cross patterns anchored to the shallow (less than 1.5 meters deep) seafloor using 0.9 kilogram fishing weights; nine sub-aerial targets consisting of orange plastic five-gallon bucket lids (32 centimeter diameter) painted with a black “X” pattern and affixed in a horizontal orientation to vertical rebar stakes placed in areas of reef rubble to provide the targets with sufficient elevation to remain above the water surface; and two sub-aerial ground targets consisting of small (80 centimeter X 80 centimeter) square tarps with black-and-white cross patterns placed in the sand at the shoreline. Two of the submerged targets were disturbed by waves or currents during the survey and were not used for SfM processing.

All GCP positions were measured using post-processed kinematic (PPK) GPS, using corrections from a GPS base station on a temporary benchmark (“MK02”) located approximately 1 kilometer away from the study area. Reference coordinates for MK02 were established using the mean position derived from four static GPS occupations with durations greater than 4 hours each submitted to the National Geodetic Survey Online Positioning User Service (NGS OPUS).

Water surface elevation
A pressure sensor was temporarily deployed at a central location within the mapping area, approximately 450 meters offshore, to measure water surface elevations during the survey. Water depths were recorded at 1 Hz and were adjusted to compensate for atmospheric pressure using an atmospheric pressure sensor concurrently deployed nearby. The elevation of the pressure sensor port was measured using the same PPK GPS used for the GCPs. The water surface elevation (WSE) was calculated using the sum of the measured ellipsoidal height of the sensor and the mean water depth measured during the duration of the UAS flights.

To correct for potential low-frequency water level fluctuations during the survey (such as those caused by tidal fluctuation, or wind and wave setup), separate WSE were calculated for flights F02 – F03 (unfiltered, “non-polarized” imagery) and F04 – F05 (imagery collected with a circular polarizing filter). Wave action was minimal during both time periods: depths varied by 0.138 meters with a standard deviation of 0.021 meters, and 0.170 meters with a standard deviation of 0.020 meters during the acquisition of the non-polarized and polarized imagery, respectively. Longer-frequency water level changes were also found to be minimal during the time period. Despite the different time periods, the resulting final mean WSE of the time periods for F02 and F03, and F04 and F05 differed by less than 0.001 meters. The final mean WSE for both time periods was calculated as 16.327 meters above the NAD83 GRS80 ellipsoid.

Data processing
To create the final products presented in this data release, structure-from-motion photogrammetric processing was performed separately on the polarized and the non-polarized imagery using the Agisoft Photoscan/Metashape software package.

The non-polarized imagery, which had brighter exposure than the polarized imagery, was used to create the digital orthomosaic which is presented in this data release. To create the orthomosaic, image alignment and sparse point cloud error reduction were performed, and a provisional dense point cloud was created using the sparse points. Point cloud classification was performed to identify low noise and ground points. The ground points were used to create a provisional DSM, which was then used as a surface to derive the final orthomosaic image.

The polarized imagery was used to create the dense point cloud and final refraction-corrected bathymetric DSM that are presented in this data release. To create the refraction-corrected DSM, a dense point cloud was derived using the same steps as those used to create the orthomosaic. The dense point cloud ground points were then exported to an LAZ file to be used as an input for performing multi-view refraction correction using the techniques described in Dietrich (2017).

Prior to refraction correction, the point cloud was thinned to a nominal 5-centimeter point spacing using the ‘lasthin’ utility in the LAStools software package using the ‘lowest’ point operator. The file was exported to a comma-delimited text file and the water surface elevation was added as a field. This file, along with the estimated aligned camera positions and orientation angles, were used as inputs for the ‘py_sfm_depth.py’ script presented in Dietrich (2017) to derive refraction-corrected depths from the SfM-derived apparent water depths. The resulting point cloud with refraction-corrected depths was used to create the final bathymetric DSM using the ‘lasgrid’ command in the LAStools software package.

Data availability
This data release presents five data products derived from these surveys that are available for download: 1) An orthomosaic image with a resolution of 2.5 centimeters per pixel, 2) a refraction-corrected digital surface model (DSM) with a resolution of 10 centimeters per pixel, 3) the refraction-corrected bathymetric point clouds in LAZ format 4) the geographic positions of the ground control points, and 5) the raw aerial imagery in JPG format.

References
Dietrich, J.T., 2017, Bathymetric Structure-from-Motion: extracting shallow stream bathymetry from multi-view stereo photogrammetry: Earth Surface Processes and Landforms, v. 42, p. 355–364, https://doi.org/10.1002/esp.4060

Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

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Contacts

Point of Contact :: PCMSC Science Data Coordinator
Originator :: Joshua Logan, Curt D Storlazzi
Metadata Contact :: PCMSC Science Data Coordinator
Publisher :: U.S. Geological Survey
Distributor :: U.S. Geological Survey - ScienceBase
SDC Data Owner :: Pacific Coastal and Marine Science Center
USGS Mission Area :: Natural Hazards

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Waiakane_2018-06-24_ortho_DSM_browse.jpg “Orthomosaic image and bathymetric digital surface model from the UAS survey.”		415.16 KB	image/jpeg

Related External Resources

Type: Mapping Application

Online view of the orthomosaic image presented as part of this data release	https://www.cogeo.org/map/#/url/https%3A%2F%2Fprod-is-usgs-sb-prod-publish.s3.amazonaws.com%2F61ae9e45d34eb622f69a732b%2FWaiakane_2018-06-24_orthomosaic_25mm.tif/center/-157.15533,21.0883/zoom/17

Type: Related Primary Publication

Norris, B.K., Storlazzi, C.D., Pomeroy, A.W.M., Rosenberger, K.J., Logan, J.B., and Cheriton, O.M., 2023, Combining field observations and high-resolution numerical modeling to demonstrate the effect of coral reef roughness on turbulence and its implications for reef restoration design: Coastal Engineering, v. 184, p. 104331, https://doi.org/10.1016/j.coastaleng.2023.104331 .	https://doi.org/10.1016/j.coastaleng.2023.104331

Purpose

These data were collected to characterize the morphology and rugosity of the shallow fringing coral reef off Waiakane, Molokai, Hawaii, as part of a larger USGS study of nearshore circulation and hydrodynamic properties of coral reefs.

Aerial imagery and structure-from-motion-derived shallow water bathymetry from a UAS survey of the coral reef off Waiakane, Molokai, Hawaii, June 2018

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