Metadata: Identification_Information: Citation: Citation_Information: Originator: Andrew W.M. Pomeroy Originator: Curt D. Storlazzi Originator: Joshua B. Logan Originator: Benjamin K. Norris Publication_Date: 20230524 Title: 3D bathymetric surfaces of low- and high-relief sites from the coral reef flat off Waiakane, Molokai Geospatial_Data_Presentation_Form: point cloud digital data Series_Information: Series_Name: data release Issue_Identification: DOI: 10.5066/P9HNLI7Y Publication_Information: Publication_Place: Pacific Coastal and Marine Science Center, Santa Cruz, California Publisher: U.S. Geological Survey Online_Linkage: https://doi.org/10.5066/P9HNLI7Y Online_Linkage: https://www.sciencebase.gov/catalog/item/6202e938d34e622189dcecf1 Description: Abstract: 3D bathymetric surfaces of low- and high-relief sites from the coral reef flat off Waiakane, Molokai, were created using structure-from-motion (SfM) techniques. The two study sites are located approximately 640 m from shore and approximately 20 m apart in the alongshore direction. At each site, an approximate 12-meter diameter area was imaged in three passes by a swimmer using a handheld digital camera. These images were fed into Structure-from-Motion (SfM) software to produce high-resolution (fine-scale), accurate, and precise topographic point clouds with sub-centimeter accuracy for both the low- and high-relief sites. In addition, a subset of a previously published (Logan and Storlazzi, 2022), coarser-scale, 3D bathymetric surface of the reef flat immediately surrounding the two study sites is included. The point clouds are formatted in LAS (.las) format. These data accompany a manuscript by Norris and others (2023) [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, https://doi.org/10.1016/j.coastaleng.2023.104331]. Purpose: These data were collected as a part of a USGS effort to understand the geologic and oceanographic processes of coral reef systems in the United States of America and its Pacific Island Trust Territories. It is intended to provide a representation of coral reef bathymetry, including benthic habitat resources, Molokai’s southern fringing reef. These data may be used by scientists, managers, and the general public. Supplemental_Information: Additional information about the field activity from which these data were derived is available online at: https://cmgds.marine.usgs.gov/fan_info.php?fan=2018-617-FA Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government. These data are not to be used for navigational purposes. Time_Period_of_Content: Time_Period_Information: Single_Date/Time: Calendar_Date: 20180621 Currentness_Reference: ground condition at time data were collected Status: Progress: Complete Maintenance_and_Update_Frequency: None planned Spatial_Domain: Bounding_Coordinates: West_Bounding_Coordinate: -157.1551 East_Bounding_Coordinate: -157.1551 North_Bounding_Coordinate: 21.08714 South_Bounding_Coordinate: 21.08712 Keywords: Theme: Theme_Keyword_Thesaurus: ISO 19115 Topic Category Theme_Keyword: elevation Theme_Keyword: geoscientificInformation Theme: Theme_Keyword_Thesaurus: Data Categories for Marine Planning Theme_Keyword: Bathymetry and Elevation Theme: Theme_Keyword_Thesaurus: USGS Thesaurus Theme_Keyword: topography Theme_Keyword: topographic maps Theme_Keyword: remote sensing Theme_Keyword: geomorphology Theme_Keyword: aerial photography Theme_Keyword: image mosaics Theme_Keyword: geospatial datasets Theme: Theme_Keyword_Thesaurus: Marine Realms Information Bank (MRIB) keywords Theme_Keyword: photography Theme_Keyword: remote sensing Theme_Keyword: aerial and satellite photography Theme_Keyword: altimetry Theme_Keyword: orthophotography Theme_Keyword: coastal processes Theme: Theme_Keyword_Thesaurus: None Theme_Keyword: U.S. Geological Survey Theme_Keyword: USGS Theme_Keyword: Coastal and Marine Hazards and Resources Program Theme_Keyword: CHMRP Theme_Keyword: Pacific Coastal and Marine Science Center Theme_Keyword: PCMSC Theme_Keyword: Unmanned aerial system Theme_Keyword: UAS Theme_Keyword: Structure-from-motion Theme_Keyword: SfM Theme: Theme_Keyword_Thesaurus: USGS Metadata Identifier Theme_Keyword: USGS:6202e938d34e622189dcecf1 Place: Place_Keyword_Thesaurus: Geographic Names Information System (GNIS) Place_Keyword: State of Hawaii Place_Keyword: Molokai Place_Keyword: Waiakane Access_Constraints: None Use_Constraints: USGS-authored or produced data and information are in the public domain from the U.S. Government and are freely redistributable with proper metadata and source attribution. Please recognize and acknowledge the U.S. Geological Survey as the originator(s) of the dataset and in products derived from these data. This information is not intended for navigation purposes. Point_of_Contact: Contact_Information: Contact_Organization_Primary: Contact_Organization: U.S. Geological Survey, Pacific Coastal and Marine Science Center Contact_Person: PCMSC Science Data Coordinator Contact_Address: Address_Type: mailing and physical Address: 2885 Mission Street City: Santa Cruz State_or_Province: CA Postal_Code: 95060 Contact_Voice_Telephone: 831-427-4747 Contact_Electronic_Mail_Address: pcmsc_data@usgs.gov Browse_Graphic: Browse_Graphic_File_Name: https://www.sciencebase.gov/catalog/item/6202e938d34e622189dcecf1?name=Coarse_and_fine_scale_3D_bathymetry.PNG Browse_Graphic_File_Description: Perspective view of the coarse- and fine-scale 3D bathymetry. Browse_Graphic_File_Type: PNG Native_Data_Set_Environment: Microsoft Windows 10, Agisoft PhotoScan version 1.4.4 through Agisoft Metashape 1.5.3, ESRI ArcGIS 10.6 through 10.7, Exiftool, Geosetter 3.4.16, QGIS 3.04 through 3.12, and LAStools ver. 190417. CloudCompare ver. 2.11.2 Data_Quality_Information: Attribute_Accuracy: Attribute_Accuracy_Report: SfM points with high reconstruction uncertainties (a non-dimensional parameter that relates to directional uncertainties in the point position) and those with high re-projection errors (a metric of the local accuracy of each key point in pixels) were removed from further analysis. Through iteration, it was determined that a reconstruction uncertainty of greater or equal to 30 (which removed a total of 5.7 percent of tie points) and a re-projection error of greater than or equal to 1.0 pixels (3.6 percent of the key points) was appropriate for the data analysis. The resulting key points were the basis for determining camera and scene geometries using photogrammetric principals. Ultimately, the mean error in the camera positions was reported to be plus or minus 0.1 m, and RMSE of the key-point cloud was less than 40 pixels. Logical_Consistency_Report: No formal logical accuracy tests were conducted. Completeness_Report: Dataset is considered complete for the information presented, as described in the abstract. Users are advised to read the rest of the metadata record carefully for additional details. Positional_Accuracy: Horizontal_Positional_Accuracy: Horizontal_Positional_Accuracy_Report: Due to the location of these study sites, it was not possible to obtain precise georeferenced control points thus the point clouds were defined by a local reference system. Vertical_Positional_Accuracy: Vertical_Positional_Accuracy_Report: Due to the location of these study sites, it was not possible to obtain precise georeferenced control points thus the point clouds were defined by a local reference system. Lineage: Source_Information: Source_Citation: Citation_Information: Originator: Logan, Joshua B. Originator: Storlazzi, Curt D. Publication_Date: 2022 Title: Aerial imagery and structure-from-motion-derived shallow water bathymetry from a UAS survey of the coral reef off Waiakane, Molokai, Hawaii, June 2018 Publication_Information: Publication_Place: Pacific Coastal and Marine Science Center, Santa Cruz, California Publisher: U.S. Geological Survey Online_Linkage: https://doi.org/10.5066/P9XZT1FK Type_of_Source_Media: digital .las files Source_Time_Period_of_Content: Time_Period_Information: Single_Date/Time: Calendar_Date: 20180624 Source_Currentness_Reference: ground condition at time data were collected Source_Citation_Abbreviation: coarse Source_Contribution: coarser-scale 3D bathymetry data of the surrounding reef flat immediately surrounding the two study sites are included with the finer-scale data presented in this data release Process_Step: Process_Description: Images of two study sites (approximately 640 m from the shoreline and approximately 20 m apart in the alongshore direction), representing low- and high-relief of the seabed, were collected at 1 Hz in RAW format by a swimmer using a Sony a6300 Camera fitted with a Sony SEL2418Z lens. The camera was mounted inside an underwater casing fitted with a 15.2 cm dome and a 2.5 cm extension ring. This dome and extension ring arrangement was determined with laboratory testing to identify the precise location of the image sensor within the camera and lens setup. This testing was necessary to ensure that the focal length of the camera was constant during the entire image capture process. To provide scale for the images, 15 rulers were distributed throughout both sample areas. Each ruler was affixed with two targets (one at either end of the ruler separated by a known distance), which were used as control points in the three-dimensional (3D) point clouds. To ensure sufficient coverage of the study sites, a swimmer spooled a 6 m line from a fixed central point that was marked by a 1.2 m vertical pole with a 12 cm diameter. Three sweeps of the area were conducted with the camera positioned at three different angles to fully resolve the 3D bottom roughness. Unique points in each image (key points) were identified and matched across each set of images by the SfM software. The overarching goal was to produce several thousand key points per image that were well-distributed within and throughout the image dataset. The total limit of tie points and key points was set to be 4,000 and 40,000 per image, respectively. To minimize errors in the photogrammetry solutions, inaccurate and poorly resolved key points that were positioned well above, below, or beyond the reef bathymetry were removed. Points that had high reconstruction uncertainties (a non-dimensional parameter relate directional uncertainties in the point position) and high re-projection errors were identified and removed. Through iteration, it was determined that a reconstruction uncertainty of greater or equal to 30 (which removed a total of 8,737 or approximately 5.7 percent of the tie points) and a re-projection error of greater than or equal to 1.0 pixels (which removed an addition 5,507 points or approximately 3.6 percent of the key points) was appropriate. These resulting key points were the basis for determining camera and scene geometries using photogrammetric principles. Optimal camera-calibration parameters were calculated from the remaining key points, which solved for the focal length (f), the optical center of the image (cx, cy), the radial distortion factors (k1, k2, k3), the tangential distortion factors (p1, p2), pixel-aspect ratio (aspect), and pixel skew of the lens. Because the key point locations were also recomputed by the software during this step, an additional 5 percent of key points that did not meet the key point threshold requirements were identified. A subsequent camera-calibration was then conducted by removing these points and resolving for the camera-lens parameters. The mean error in the camera positions was reported to be plus or minus 0.1 m, and RMSE of the key-point cloud was less than 40 pixels. Following the image-alignment step, control points were added to improve the camera calibrations. The camera-calibration parameters were then re-optimized using uncertainty settings to match the data and the camera parameters described above. Finally, dense topographic point clouds were generated for the low and high relief sites each with sub-centimeter densities. Both point clouds contain 5 to 10 million topographic points, where each point includes 8-bit red, green, and blue (RGB) color values sampled from the original images. Error analysis conducted using Cloud Compare indicated that the model had a slight concave form, but the displacement at the outer edge of the model, when compared to the middle of the model was small (less than 1 cm) relative to the roughness variability at both sites. The coarse scale cloud contains about 300K topographic points and does not have RBG color values associated with the points. Process_Date: 20220208 Process_Step: Process_Description: Coarser-scale point-cloud data immediately surrounding the two study sites were merged with these new finer-scale data for presentation purposes. Data collection, processing, and error analysis information for the coarse-scale point-cloud data can be found in Logan and Storlazzi, (2022). Source_Used_Citation_Abbreviation: coarse Process_Date: 20220208 Spatial_Data_Organization_Information: Direct_Spatial_Reference_Method: Point Spatial_Reference_Information: Horizontal_Coordinate_System_Definition: Local: Local_Description: To provide scale for the images, 15 rulers were distributed throughout both sample areas. Each ruler was affixed with two targets (one at either end of the ruler separated by a known distance), which were used as control points in the three-dimensional (3D) point clouds. Therefore, points are scaled relative to one another but not a geographic coordinate system. Local_Georeference_Information: Points in the LAS files are relative to an arbitrary center point, but all points are scaled appropriately relative to this center. Box dimensions (x, y, z) have units in meters. Vertical_Coordinate_System_Definition: Altitude_System_Definition: Altitude_Datum_Name: Local Altitude_Resolution: 0.001 Altitude_Distance_Units: meters Altitude_Encoding_Method: Explicit elevation coordinate included with horizontal coordinates Entity_and_Attribute_Information: Overview_Description: Entity_and_Attribute_Overview: The attribute information associated with point cloud follows the LAS file standard. Attributes include location referenced to a local coordinate system. CoarseScale_3D_Surface box center: X: 17.95 Y: -44.60 Z: 114.22 FineScale_HighRelief_3D_Surface box center: X: 12.03 Y: -18.07 Z: 113.70 FineScale_LowRelief_3D_Surface box center: X: 23.38 Y: -20.61 Z: 113.25 Entity_and_Attribute_Detail_Citation: American Society for Photogrammetry and Remote Sensing (ASPRS; 2013, https://www.asprs.org/committee-general/laser-las-file-format-exchange-activities.html) and Isenburg (2013, https://doi.org/10.14358/PERS.79.2.209) Distribution_Information: Distributor: Contact_Information: Contact_Organization_Primary: Contact_Organization: U.S. Geological Survey - ScienceBase Contact_Address: Address_Type: mailing address Address: Denver Federal Center, Building 810, Mail Stop 302 City: Denver State_or_Province: CO Postal_Code: 80225 Country: United States Contact_Voice_Telephone: 1-888-275-8747 Contact_Electronic_Mail_Address: sciencebase@usgs.gov Resource_Description: The topographic point clouds are available as LAS files. Distribution_Liability: Unless otherwise stated, all data, metadata and related materials are considered to satisfy the quality standards relative to the purpose for which the data were collected. Although these data and associated metadata have been reviewed for accuracy and completeness and approved for release by the U.S. Geological Survey (USGS), no warranty expressed or implied is made regarding the display or utility of the data on any other system or for general or scientific purposes, nor shall the act of distribution constitute any such warranty. Standard_Order_Process: Digital_Form: Digital_Transfer_Information: Format_Name: LASer file Format_Version_Number: LAS 1.2 Format_Information_Content: These zip files contain point cloud data in LAS format (LAS 1.2 specification). File_Decompression_Technique: Zip Transfer_Size: 201.17 Digital_Transfer_Option: Online_Option: Computer_Contact_Information: Network_Address: Network_Resource_Name: https://www.sciencebase.gov/catalog/item/6202e938d34e622189dcecf1?name=Coarse_and_fine_scale_3D_surface.zip Network_Resource_Name: https://www.sciencebase.gov/catalog/item/6202e938d34e622189dcecf1 Network_Resource_Name: https://doi.org/10.5066/P9HNLI7Y Access_Instructions: Data can be downloaded using the Network_Resource_Name links. The first link is a direct link to a zip file containing the main survey area point clouds in LAS format. The second link points to a landing page with the point cloud, metadata, and browse image. Fees: None. Technical_Prerequisites: This zip file contains point cloud data in LAS format (LAS 1.2 specification). The user must have software capable of uncompressing the .zip compressed file and displaying or processing the .las format file. It is recommended to use the freeware CloudCompare or Blender to view and manipulate the LAS files. Metadata_Reference_Information: Metadata_Date: 20230524 Metadata_Contact: Contact_Information: Contact_Organization_Primary: Contact_Organization: U.S. Geological Survey, Pacific Coastal and Marine Science Center Contact_Person: PCMSC Science Data Coordinator Contact_Address: Address_Type: mailing and physical Address: 2885 Mission Street City: Santa Cruz State_or_Province: CA Postal_Code: 95060 Contact_Voice_Telephone: 831-427-4747 Contact_Electronic_Mail_Address: pcmsc_data@usgs.gov Metadata_Standard_Name: Content Standard for Digital Geospatial Metadata Metadata_Standard_Version: FGDC-STD-001-1998