3D bathymetric surfaces of low- and high-relief sites from the coral reef flat off Waiakane, Molokai

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Frequently anticipated questions:


What does this data set describe?

Title:
3D bathymetric surfaces of low- and high-relief sites from the coral reef flat off Waiakane, Molokai
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].
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.
  1. How might this data set be cited?
    Pomeroy, Andrew W.M., Storlazzi, Curt D., Logan, Joshua B., and Norris, Benjamin K., 20230524, 3D bathymetric surfaces of low- and high-relief sites from the coral reef flat off Waiakane, Molokai: data release DOI: 10.5066/P9HNLI7Y, U.S. Geological Survey, Pacific Coastal and Marine Science Center, Santa Cruz, California.

    Online Links:

  2. What geographic area does the data set cover?
    West_Bounding_Coordinate: -157.1551
    East_Bounding_Coordinate: -157.1551
    North_Bounding_Coordinate: 21.08714
    South_Bounding_Coordinate: 21.08712
  3. What does it look like?
    https://www.sciencebase.gov/catalog/item/6202e938d34e622189dcecf1?name=Coarse_and_fine_scale_3D_bathymetry.PNG (PNG)
    Perspective view of the coarse- and fine-scale 3D bathymetry.
  4. Does the data set describe conditions during a particular time period?
    Calendar_Date: 21-Jun-2018
    Currentness_Reference:
    ground condition at time data were collected
  5. What is the general form of this data set?
    Geospatial_Data_Presentation_Form: point cloud digital data
  6. How does the data set represent geographic features?
    1. How are geographic features stored in the data set?
      This is a Point data set.
    2. What coordinate system is used to represent geographic features?
      This local coordinate system was used: 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.
      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
  7. How does the data set describe geographic features?
    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)

Who produced the data set?

  1. Who are the originators of the data set? (may include formal authors, digital compilers, and editors)
    • Andrew W.M. Pomeroy
    • Curt D. Storlazzi
    • Joshua B. Logan
    • Benjamin K. Norris
  2. Who also contributed to the data set?
  3. To whom should users address questions about the data?
    U.S. Geological Survey, Pacific Coastal and Marine Science Center
    Attn: PCMSC Science Data Coordinator
    2885 Mission Street
    Santa Cruz, CA

    831-427-4747 (voice)
    pcmsc_data@usgs.gov

Why was the data set created?

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.

How was the data set created?

  1. From what previous works were the data drawn?
    coarse (source 1 of 1)
    Logan, Joshua B., and Storlazzi, Curt 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, Pacific Coastal and Marine Science Center, Santa Cruz, California.

    Online Links:

    Type_of_Source_Media: digital .las files
    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
  2. How were the data generated, processed, and modified?
    Date: 08-Feb-2022 (process 1 of 2)
    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.
    Date: 08-Feb-2022 (process 2 of 2)
    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). Data sources used in this process:
    • coarse
  3. What similar or related data should the user be aware of?

How reliable are the data; what problems remain in the data set?

  1. How well have the observations been checked?
    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.
  2. How accurate are the geographic locations?
    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.
  3. How accurate are the heights or depths?
    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.
  4. Where are the gaps in the data? What is missing?
    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.
  5. How consistent are the relationships among the observations, including topology?
    No formal logical accuracy tests were conducted.

How can someone get a copy of the data set?

Are there legal restrictions on access or use of the data?
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.
  1. Who distributes the data set? (Distributor 1 of 1)
    U.S. Geological Survey - ScienceBase
    Denver Federal Center, Building 810, Mail Stop 302
    Denver, CO
    United States

    1-888-275-8747 (voice)
    sciencebase@usgs.gov
  2. What's the catalog number I need to order this data set? The topographic point clouds are available as LAS files.
  3. What legal disclaimers am I supposed to read?
    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.
  4. How can I download or order the data?
  5. What hardware or software do I need in order to use the data set?
    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.

Who wrote the metadata?

Dates:
Last modified: 24-May-2023
Metadata author:
U.S. Geological Survey, Pacific Coastal and Marine Science Center
Attn: PCMSC Science Data Coordinator
2885 Mission Street
Santa Cruz, CA

831-427-4747 (voice)
pcmsc_data@usgs.gov
Metadata standard:
Content Standard for Digital Geospatial Metadata (FGDC-STD-001-1998)

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