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

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Metadata:

Identification_Information:
Citation:
Citation_Information:
Originator: Joshua B. Logan
Originator: Curt D. Storlazzi
Publication_Date: 20220321
Title:
Orthomosaic imagery from the UAS survey of the coral reef off Waiakane, Molokai, Hawaii, 24 June 2018
Geospatial_Data_Presentation_Form: GeoTIFF
Series_Information:
Series_Name: data release
Issue_Identification: DOI:10.5066/P9XZT1FK
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
Online_Linkage: Larger_Work_Citation:
Citation_Information:
Originator: Joshua B. Logan
Originator: Curt D. Storlazzi
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
Series_Information:
Series_Name: data release
Issue_Identification: DOI:10.5066/P9XZT1FK
Publication_Information:
Publication_Place: Pacific Coastal and Marine Science Center, Santa Cruz, CA
Publisher: U.S. Geological Survey
Online_Linkage: https://doi.org/10.5066/P9XZT1FK
Online_Linkage:
Description:
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.
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. The orthomosaic images can be used with geographic information systems (GIS) software for research purposes.
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.
Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 20180624
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: -157.15679
East_Bounding_Coordinate: -157.15388
North_Bounding_Coordinate: 21.09352
South_Bounding_Coordinate: 21.08451
Keywords:
Theme:
Theme_Keyword_Thesaurus: ISO 19115 Topic Category
Theme_Keyword: imageryBaseMapsEarthCover
Theme:
Theme_Keyword_Thesaurus: Data Categories for Marine Planning
Theme_Keyword: Substrate
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_Keyword: structure from motion
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_Keyword: reef
Theme_Keyword: fringing reef
Theme_Keyword: coral reefs
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: UAS
Theme_Keyword: Unmanned aerial system
Theme_Keyword: Structure-from-motion
Theme_Keyword: SfM
Theme:
Theme_Keyword_Thesaurus: USGS Metadata Identifier
Theme_Keyword: USGS:61ae9e45d34eb622f69a732b
Place:
Place_Keyword_Thesaurus: Geographic Names Information System (GNIS)
Place_Keyword: State of Hawaii
Place_Keyword: Molokai
Place_Keyword: Maui County
Place_Keyword: Waiakane
Place_Keyword: Kalohi Channel
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: Browse_Graphic_File_Description:
Orthomosaic image from the UAS survey of the coral reef off Waiakane, Molokai, HI.
Browse_Graphic_File_Type: JPEG
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 3.16, and GDAL 3.1.0.
Data_Quality_Information:
Attribute_Accuracy:
Attribute_Accuracy_Report: No formal attribute accuracy tests were conducted.
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:
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.
Vertical_Positional_Accuracy:
Vertical_Positional_Accuracy_Report:
Vertical positional accuracy was not evaluated for this data product.
Lineage:
Process_Step:
Process_Description:
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.
Process_Date: 20180624
Process_Contact:
Contact_Information:
Contact_Person_Primary:
Contact_Person: Joshua Logan
Contact_Organization:
U.S. Geological Survey, Pacific Coastal and Marine Science Center
Contact_Position: Physical Scientist
Contact_Address:
Address_Type: mailing address
Address: 2885 Mission Street
City: Santa Cruz
State_or_Province: CA
Postal_Code: 95060
Country: US
Contact_Voice_Telephone: 831-460-7519
Contact_Facsimile_Telephone: 831-427-4748
Contact_Electronic_Mail_Address: jlogan@usgs.gov
Process_Step:
Process_Description:
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).
Process_Date: 20180624
Process_Contact:
Contact_Information:
Contact_Person_Primary:
Contact_Person: Joshua Logan
Contact_Organization:
U.S. Geological Survey, Pacific Coastal and Marine Science Center
Contact_Address:
Address_Type: mailing and physical
Address: 2885 Mission Street
City: Santa Cruz
State_or_Province: CA
Postal_Code: 95060
Contact_Voice_Telephone: 831-460-7519
Contact_Electronic_Mail_Address: jlogan@usgs.gov
Process_Step:
Process_Description:
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"
Process_Date: 2018
Process_Contact:
Contact_Information:
Contact_Person_Primary:
Contact_Person: Joshua Logan
Contact_Organization:
U.S. Geological Survey, Pacific Coastal and Marine Science Center
Contact_Address:
Address_Type: mailing and physical
Address: 2885 Mission Street
City: Santa Cruz
State_or_Province: CA
Postal_Code: 95060
Contact_Voice_Telephone: 831-460-7519
Contact_Electronic_Mail_Address: jlogan@usgs.gov
Process_Step:
Process_Description:
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.
Process_Date: 2018
Process_Contact:
Contact_Information:
Contact_Person_Primary:
Contact_Person: Joshua Logan
Contact_Organization:
U.S. Geological Survey, Pacific Coastal and Marine Science Center
Contact_Position: Physical Scientist
Contact_Address:
Address_Type: mailing address
Address: 2885 Mission Street
City: Santa Cruz
State_or_Province: CA
Postal_Code: 95060
Country: US
Contact_Voice_Telephone: 831-460-7519
Contact_Facsimile_Telephone: 831-427-4748
Contact_Electronic_Mail_Address: jlogan@usgs.gov
Spatial_Data_Organization_Information:
Direct_Spatial_Reference_Method: Raster
Raster_Object_Information:
Raster_Object_Type: Grid Cell
Spatial_Reference_Information:
Horizontal_Coordinate_System_Definition:
Planar:
Grid_Coordinate_System:
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_Coordinate_Information:
Planar_Coordinate_Encoding_Method: row and column
Coordinate_Representation:
Abscissa_Resolution: 0.025
Ordinate_Resolution: 0.025
Planar_Distance_Units: meters
Geodetic_Model:
Horizontal_Datum_Name: NAD83 (National Spatial Reference System PA11) (EPSG:6322)
Ellipsoid_Name: GRS 1980 (EPSG:7019)
Semi-major_Axis: 6378137.0
Denominator_of_Flattening_Ratio: 298.257222101
Entity_and_Attribute_Information:
Detailed_Description:
Entity_Type:
Entity_Type_Label: GeoTIFF
Entity_Type_Definition: GeoTIFF containing RGB color bands.
Entity_Type_Definition_Source: Producer defined
Attribute:
Attribute_Label: Band_1
Attribute_Definition: Red band
Attribute_Definition_Source: Producer defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 0
Range_Domain_Maximum: 255
Attribute:
Attribute_Label: Band_2
Attribute_Definition: Green band
Attribute_Definition_Source: Producer defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 0
Range_Domain_Maximum: 255
Attribute:
Attribute_Label: Band_3
Attribute_Definition: Blue band
Attribute_Definition_Source: Producer defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 0
Range_Domain_Maximum: 255
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 orthomosaic image is available as a cloud-optimized GeoTIFF file (Waiakane_2018-06-24_orthomosaic_25mm.tif).
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: GeoTIFF
Format_Version_Number: GDAL 3.1.0dev
Format_Information_Content:
cloud-optimized GeoTIFF contains a three-band RGB orthomosaic with 8-bit unsigned integer values stored with high quality JPEG compression
File_Decompression_Technique: none
Transfer_Size: 80
Digital_Transfer_Option:
Online_Option:
Computer_Contact_Information: Access_Instructions:
Data can be downloaded using the Network_Resource_Name links. The first link is a direct link to download the 2.5centimeter resolution orthomosaic image. The second link is for accessing the orthomosaic image on cloud-based storage and can be used for cloud-based queries or viewing. The third link points to a landing page with the orthomosaic image, metadata, and a browse image. The fourth link points to the landing page for the entire data release, including links to pages of the various data files.
Fees: None.
Technical_Prerequisites:
These data can be viewed with GIS software or other software capable of displaying geospatial raster data.
Metadata_Reference_Information:
Metadata_Date: 20231114
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

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