Orthomosaic imagery from the UAS survey of the coral reef off Waiakane, Molokai, Hawaii, 24 June 2018

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Frequently anticipated questions:


What does this data set describe?

Title:
Orthomosaic imagery from the UAS survey of the coral reef off Waiakane, Molokai, Hawaii, 24 June 2018
Abstract:
This portion of the data release presents a high-resolution orthomosaic image of the coral reef off Waiakane, Molokai, Hawaii. The orthomosaic has a resolution of 2.5 centimeters (cm) per pixel and was derived from structure-from-motion (SfM) processing of aerial imagery collected with an unoccupied aerial system (UAS) on 24 June 2018. The raw imagery used to create the orthomosaic was acquired using a UAS fitted with a Ricoh GR II digital camera featuring a global shutter. The UAS was flown on pre-programmed autonomous flight lines spaced to provide approximately 75 percent overlap between images from adjacent lines. The UAS was flown at an approximate altitude of 100 meters above ground level (AGL), resulting in a nominal ground-sample-distance (GSD) of 2.6 centimeters per pixel. The camera was triggered at 1 Hz using a built-in intervalometer. The raw imagery was geotagged using positions from the UAS onboard single-frequency autonomous GPS. Although imagery was collected using both a circular polarizing filter and with no polarizing filter, only the non-polarized imagery was used for the creation of the orthomosaic. SfM photogrammetry was used to derive a preliminary digital surface model (DSM) from this imagery which was used as a surface for orthorectification and mosaicking. The orthomosaic image is provided in a three-band RGB format, with 8-bit unsigned integer values compressed using high-quality JPEG compression. The image has been formatted as a cloud-optimized GeoTIFF with internal overviews and masks to facilitate cloud-based queries and display.
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.
  1. How might this data set be cited?
    Logan, Joshua B., and Storlazzi, Curt D., 20220321, Orthomosaic imagery from the UAS survey of the coral reef off Waiakane, Molokai, Hawaii, 24 June 2018: data release DOI:10.5066/P9XZT1FK, U.S. Geological Survey, Pacific Coastal and Marine Science Center, Santa Cruz, California.

    Online Links:

    This is part of the following larger work.

    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: data release DOI:10.5066/P9XZT1FK, U.S. Geological Survey, Pacific Coastal and Marine Science Center, Santa Cruz, CA.

    Online Links:

  2. What geographic area does the data set cover?
    West_Bounding_Coordinate: -157.15679
    East_Bounding_Coordinate: -157.15388
    North_Bounding_Coordinate: 21.09352
    South_Bounding_Coordinate: 21.08451
  3. What does it look like?
    https://www.sciencebase.gov/catalog/file/get/61ae9e45d34eb622f69a732b?name=Waiakane_2018-06-24_orthomosaic_25mm_browse.jpg&allowOpen=true (JPEG)
    Orthomosaic image from the UAS survey of the coral reef off Waiakane, Molokai, HI.
  4. Does the data set describe conditions during a particular time period?
    Calendar_Date: 24-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: GeoTIFF
  6. How does the data set represent geographic features?
    1. How are geographic features stored in the data set?
      This is a Raster data set. It contains the following raster data types:
      • Dimensions, type Grid Cell
    2. What coordinate system is used to represent geographic features?
      Grid_Coordinate_System_Name: Universal Transverse Mercator
      Universal_Transverse_Mercator:
      UTM_Zone_Number: 4
      Transverse_Mercator:
      Scale_Factor_at_Central_Meridian: 0.9996
      Longitude_of_Central_Meridian: -159.0
      Latitude_of_Projection_Origin: 0.0
      False_Easting: 500000.0
      False_Northing: 0.0
      Planar coordinates are encoded using row and column
      Abscissae (x-coordinates) are specified to the nearest 0.025
      Ordinates (y-coordinates) are specified to the nearest 0.025
      Planar coordinates are specified in meters
      The horizontal datum used is NAD83 (National Spatial Reference System PA11) (EPSG:6322).
      The ellipsoid used is GRS 1980 (EPSG:7019).
      The semi-major axis of the ellipsoid used is 6378137.0.
      The flattening of the ellipsoid used is 1/298.257222101.
  7. How does the data set describe geographic features?
    GeoTIFF
    GeoTIFF containing RGB color bands. (Source: Producer defined)
    Band_1
    Red band (Source: Producer defined)
    Range of values
    Minimum:0
    Maximum:255
    Band_2
    Green band (Source: Producer defined)
    Range of values
    Minimum:0
    Maximum:255
    Band_3
    Blue band (Source: Producer defined)
    Range of values
    Minimum:0
    Maximum:255

Who produced the data set?

  1. Who are the originators of the data set? (may include formal authors, digital compilers, and editors)
    • Joshua B. Logan
    • Curt D. Storlazzi
  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 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. The orthomosaic images can be used with geographic information systems (GIS) software for research purposes.

How was the data set created?

  1. From what previous works were the data drawn?
  2. How were the data generated, processed, and modified?
    Date: 24-Jun-2018 (process 1 of 4)
    Aerial imagery was collected 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 above ground level (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 reduced reflections and provide improved imaging of the seafloor through the water surface. Only the images collected without the polarizing filter (F02 and F03) were used for the creation of the orthomosaic presented in this data release. Person who carried out this activity:
    Joshua Logan
    U.S. Geological Survey, Pacific Coastal and Marine Science Center
    Physical Scientist
    2885 Mission Street
    Santa Cruz, CA
    US

    831-460-7519 (voice)
    831-427-4748 (FAX)
    jlogan@usgs.gov
    Date: 24-Jun-2018 (process 2 of 4)
    Survey control was established using twenty temporary ground control points (GCPs) distributed throughout the survey area. 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 during the survey; 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 submitted to the National Geodetic Survey Online Positioning User Service (NGS OPUS). Person who carried out this activity:
    Joshua Logan
    U.S. Geological Survey, Pacific Coastal and Marine Science Center
    2885 Mission Street
    Santa Cruz, CA

    831-460-7519 (voice)
    jlogan@usgs.gov
    Date: 2018 (process 3 of 4)
    The image files were renamed using a custom python script. The file names were formed using the following pattern Fx-YYYYMMDDThhmmssZ_Ryz.*, where: - Fx = Flight number - YYYYMMDDThhmmssZ = date and time in the ISO 8601 standard, where 'T' separates the date from the time, and 'Z' denotes UTC ('Zulu') time. - Ry = RA or RB to distinguish camera 'RicohA' from 'RicohB' - z = original image name assigned by camera during acquisition - * = file extension (JPG or DNG)
    The approximate image acquisition coordinates were added to the image metadata (EXIF) ('geotagged') using the image timestamp and the telemetry logs from the UAS onboard single-frequency 1-Hz autonomous GPS. The geotagging process was done using the GeoSetter software package. To improve timestamp accuracy, the image acquisition times were adjusted to true ('corrected') UTC time by comparing the image timestamps with several images taken of a smartphone app ('Emerald Time') showing accurate time from Network Time Protocol (NTP) servers. For this survey, + 00:00:02 (2 seconds) were added to the image timestamp to synchronize with UTC time. The positions stored in the EXIF are in geographic coordinates referenced to the WGS84(G1150) coordinate reference system (EPSG:7660), with elevation in meters relative to the WGS84 ellipsoid.
    Additional information was added to the EXIF using the command-line 'exiftool' software with the following command: exiftool ^ -P ^ -Copyright="Public Domain. Please credit U.S. Geological Survey." ^ -CopyrightNotice="Public Domain. Please credit U.S. Geological Survey." ^ -ImageDescription="Low-altitude aerial image of the shallow coral reef off Waiakane, Molokai, HI, USA, from USGS Unmanned Aircraft System (UAS) survey 2018-617-FA." ^ -Caption-Abstract="Coral reef off Waiakane, Molokai, HI, USA, from USGS survey 2018-617-FA." ^ -Caption="Aerial image of the shallow coral reef off Waiakane, Molokai, HI, USA, from USGS Unmanned Aircraft System (UAS) survey 2018-617-FA." ^ -sep ", " ^ -keywords="coral reef, Molokai, Maui County, Hawaii, Waiakane, 2018-617-FA, Unmanned Aircraft System, UAS, drone, aerial imagery, U.S. Geological Survey, USGS, Pacific Coastal and Marine Science Center" ^ -comment="Low-altitude aerial image from USGS Unmanned Aircraft System (UAS) survey 2018-617-FA." ^ -Credit="U.S. Geological Survey" ^ -Contact="pcmsc_data@usgs.gov" ^ -Artist="U.S. Geological Survey, Pacific Coastal and Marine Science Center" Person who carried out this activity:
    Joshua Logan
    U.S. Geological Survey, Pacific Coastal and Marine Science Center
    2885 Mission Street
    Santa Cruz, CA

    831-460-7519 (voice)
    jlogan@usgs.gov
    Date: 2018 (process 4 of 4)
    Structure-from-motion (SfM) processing techniques were used to create the point clouds in the Agisoft Photoscan/Metashape software package using the following workflow with the JPG images from F02 and F03 (images collected without a polarizing filter): 1. Preliminary image alignment and sparse point cloud error reduction was performed using shoreline imagery to develop an a priori camera lens model. The lens model was then fixed for the subsequent SfM processing steps. 2. Additional image alignment for all the images was performed with the following parameters - Accuracy: 'high'; Pair selection: 'reference', 'generic'; Key point limit: 0 (unlimited); Tie point limit: 0 (unlimited). 3. Sparse point cloud error reduction was performed using an iterative gradual selection and camera optimization process in which all sparse points exceeding a Reconstruction Uncertainty of 10 were removed from the sparse point cloud. Additional sparse points obviously above or below the true surface were manually deleted after the last error reduction iteration, and a final camera optimization was performed. 4. Ground control points (GCPs) were manually marked for all GCPs. All submerged GCPs were disabled in subsequent processing steps to serve as validation check points. 5. A final camera optimization was performed, and a dense point cloud was created using the 'high' accuracy setting, with 'aggressive' depth filtering. 6. A preliminary Digital Surface Model (DSM) with a native resolution of 5.3 centimeters per pixel was created using the dense point cloud. This DSM was used only for orthorectification of imagery. 7. An RGB orthomosaic with a native resolution of 2.5 centimeters per pixel was created using the DSM as the orthorectification surface. 8. The orthomosaic was clipped using a manually digitized clipping mask to exclude areas on the perimeter of the survey which suffered from obvious off-nadir edge effects. 9. The orthomosaic was exported to a GeoTIFF format with a 2.5-centimeter pixel resolution and converted to a cloud-optimized GeoTIFF formats (using internal JPEG compression with a quality of 90) for compatibility with cloud storage services using the GDAL software package. Person who carried out this activity:
    Joshua Logan
    U.S. Geological Survey, Pacific Coastal and Marine Science Center
    Physical Scientist
    2885 Mission Street
    Santa Cruz, CA
    US

    831-460-7519 (voice)
    831-427-4748 (FAX)
    jlogan@usgs.gov
  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?
    No formal attribute accuracy tests were conducted.
  2. How accurate are the geographic locations?
    Horizontal accuracy was estimated by using 8 submerged ground control points (GCPs) as check points. During acquisition, both submerged and sub-aerial GCPs were deployed near one another. Sub-aerial GCPs were deployed on vertical stakes to provide sufficient elevation to maintain the GCP above the water surface elevation. Submerged GCPs were deployed nearby on the seafloor in water generally less than 1 meter deep. The sub-aerial GCPs were used in the SfM processing and the submerged GCPs were withheld to serve as check points to evaluate the accuracy of the SfM products. The horizontal RMSE for the SfM derived positions of the submerged GCPs relative to their PPK GPS-measured positions was 0.111 meters. The addition of the estimated horizontal GPS accuracy (0.050 meters) in quadrature results in a total horizontal accuracy estimate of 0.122 meters for the orthomosaic. It should be noted that this error estimate is for areas near where GCPs were placed and in similar water depths. The effects of refraction at the air-water interface were likely to have caused significant displacement of the apparent position of objects relative to their true position, especially in deep water, or near the edges of the orthomosaic where the position of objects was likely derived from off-nadir sectors of the raw imagery. Additional sources of error such as poor image-to-image point matching due poor water clarity (such as on the shallow reef flat neat the shoreline), uniform substrate texture (such as mud and sand near the shoreline), or greater water depths resulting in poor surface reconstruction likely caused additional localized errors in some portions of the imagery which exceed this estimate.
  3. How accurate are the heights or depths?
    Vertical positional accuracy was not evaluated for this data product.
  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 orthomosaic image is available as a cloud-optimized GeoTIFF file (Waiakane_2018-06-24_orthomosaic_25mm.tif).
  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?
    These data can be viewed with GIS software or other software capable of displaying geospatial raster data.

Who wrote the metadata?

Dates:
Last modified: 21-Mar-2022
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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