Joshua B. Logan
Eric E. Grossman
Nathan R. VanArendonk
Avery F.G. Maverick
20210915
Topographic point cloud for the intertidal zone at West Whidbey Island, WA, 2019-06-04
point cloud digital data
data release
DOI:10.5066/P9R76MVP
Pacific Coastal and Marine Science Center, Santa Cruz, California
U.S. Geological Survey
https://doi.org/10.5066/P9R76MVP
https://www.sciencebase.gov/catalog/item/5ef53efd82ced62aaae6a0c0
Joshua B. Logan
Eric E. Grossman
Nathan R. VanArendonk
Avery F.G. Maverick
2021
Aerial imagery and structure-from-motion data products from UAS survey of the intertidal zone at West Whidbey Island, WA, June 2019
data release
DOI:10.5066/P9R76MVP
Pacific Coastal and Marine Science Center, Santa Cruz, CA
U.S. Geological Survey
https://doi.org/10.5066/P9R76MVP
https://www.sciencebase.gov/catalog/item/5f2c526f82ceae4cb3c2cfd1
This portion of the data release presents a topographic point cloud of the intertidal zone at West Whidbey Island, WA. The point cloud was derived from structure-from-motion (SfM) processing of aerial imagery collected with an unmanned aerial system (UAS) on 2019-06-04. The point cloud has 293,261,002 points with an average point density of 1,063 points per-square meter. The point cloud is tiled to reduce individual file sizes and is grouped within a zip file for downloading. Each point in the point cloud contains an explicit horizontal and vertical coordinate, color, intensity, and classification. Water portions of the point cloud were classified using a polygon digitized from the orthomosaic imagery derived from these surveys (also available in this data release). No other classifications were performed. The raw imagery used to create these point clouds 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 70 percent overlap between images from adjacent lines. The camera was triggered at 1 Hz using a built-in intervalometer. The UAS was flown at an approximate altitude of 70 meters above ground level (AGL), resulting in a nominal ground-sample-distance (GSD) of 1.8 centimeters per pixel. Additional imagery was collected with the camera in an oblique orientation toward the coastal bluff face to image vertical faces. The raw imagery was geotagged using positions from the UAS onboard single-frequency autonomous GPS. Twenty-five temporary ground control points (GCPs) were distributed throughout the survey area to establish survey control. The GCPs consisted of a combination of small square tarps with black-and-white cross patterns and "X" marks placed on the ground using temporary chalk. The GCP positions were measured using post-processed kinematic (PPK) GPS, using corrections from a GPS base station located approximately 7 kilometers from the study area. The point clouds are formatted in LAZ format (LAS 1.2 specification).
These data were collected to characterize the morphology, substrate composition and roughness of intertidal areas to support modeling of coastal storm and wave impacts with sea-level rise as part of the USGS Puget Sound Coastal Storm Modeling System (PS-CoSMoS). The data are also intended to be used to model and evaluate sediment transport and its effects on coastal habitats, a focus of the USGS Coastal Habitats in Puget Sound Project (CHIPS) and its partners to inform resource management and adaptive planning for our Nation's coasts.
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=2019-623-FA
Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
20190604
ground condition at time data were collected
None planned
-122.74790
-122.73654
48.27638
48.26540
ISO 19115 Topic Category
elevation
geoscientificInformation
Data Categories for Marine Planning
Bathymetry and Elevation
USGS Thesaurus
topography
topographic maps
remote sensing
geomorphology
aerial photography
image mosaics
geospatial datasets
structure from motion
Marine Realms Information Bank (MRIB) keywords
photography
remote sensing
aerial and satellite photography
altimetry
orthophotography
coastal processes
None
U.S. Geological Survey
USGS
Coastal and Marine Hazards and Resources Program
CHMRP
Pacific Coastal and Marine Science Center
PCMSC
UAS
Unmanned aerial system
Structure-from-motion
SfM
Hastie Lake County Park
USGS Metadata Identifier
USGS:5ef53efd82ced62aaae6a0c0
Geographic Names Information System (GNIS)
State of Washington
Whidbey Island
Island County
Strait of Juan de Fuca
Salish Sea
None
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.
U.S. Geological Survey, Pacific Coastal and Marine Science Center
PCMSC Science Data Coordinator
mailing and physical
2885 Mission Street
Santa Cruz
CA
95060
831-427-4747
pcmsc_data@usgs.gov
https://www.sciencebase.gov/catalog/file/get/5ef53efd82ced62aaae6a0c0?name=WestWhidbey_2019-06-04_pointcloud_browse.jpg&allow=openTrue
Perspective view of the West Whidbey topographic point cloud from the 2019-06-04 UAS survey.
JPEG
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.
No formal attribute accuracy tests were conducted.
No formal logical accuracy tests were conducted.
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.
Horizontal accuracy was estimated by comparing SfM-derived ground control point (GCP) positions to PPK GPS measurements. Due to the time-intensive process of placing GCPs in the field, all available GCPs were used for registration and camera optimization in the SfM processing workflow during the creation of the final point clouds. To evaluate the horizontal positional accuracy of the point cloud after processing was completed, each GCPs was disabled one-at-a-time using a python script to create a 'temporary check point'. With a single GCP temporarily disabled, camera optimization was performed with all lens parameters fixed, and all other GCPs enabled. The residual errors of the check point relative to its GPS-measured position were recorded. After all temporary check point iterations were complete, the root-mean-square error (RMSE) and mean-absolute error (MAE) were calculated. The resulting horizontal RMSE was 0.043 meters (MAE 0.039 meters). The addition of the estimated horizontal GPS uncertainty (0.020 meters) in quadrature results in a total horizontal accuracy estimate of 0.047 meters for the point cloud. It should be noted that this error estimate is for areas of bare ground or low vegetation where GCPs were placed. Additional sources of error such as poor image-to-image point matching due to vegetation or uniform substrate texture (such as sand) resulting in poor surface reconstruction may cause localized errors in some portions of the point clouds to exceed this estimate.
Vertical accuracy was estimated by comparing SfM-derived ground control point (GCP) positions to PPK GPS measurements. Due to the time-intensive process of placing GCPs in the field, all available GCPs were used for registration and camera optimization in the SfM processing workflow during the creation of the final point cloud. To evaluate the vertical positional accuracy of the point cloud after processing was completed, each GCPs was disabled one-at-a-time using a python script to create a 'temporary check point'. With a single GCP temporarily disabled, camera optimization was performed with all lens parameters fixed, and all other GCPs enabled. The residual errors of the check point relative to its GPS-measured position were recorded. After all temporary check point iterations were complete, the root-mean-square error (RMSE) and mean-absolute error (MAE) were calculated. The resulting vertical RMSE was 0.079 meters (MAE 0.058 meters). The addition of the estimated vertical GPS uncertainty (0.025 meters) in quadrature results in a total vertical accuracy estimate of 0.083 meters for the point cloud. It should be noted that this error estimate is for areas of bare ground or low vegetation where GCPs were placed. Additional sources of error such as poor image-to-image point matching due to vegetation or uniform substrate texture (such as sand) resulting in poor surface reconstruction may cause localized errors in some portions of the point clouds to exceed this estimate.
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. Flights using both a nadir camera orientation and an oblique camera orientation were conducted. For the nadir flights (F04, F05, F06, F07, and F08), the camera was mounted using a fixed mount on the bottom of the UAS and oriented in an approximately nadir orientation. The UAS was flown on pre-programmed autonomous flight lines at an approximate altitude of 70 meters above ground level (AGL), resulting in a nominal ground-sample-distance (GSD) of 1.8 centimeters per pixel. The flight lines were oriented roughly shore-parallel and were spaced to provide approximately 70 percent overlap between images from adjacent lines. For the oblique orientation flights (F03, F09, F10, and F11), the camera was mounted using a fixed mount on the bottom of the UAS and oriented facing forward with a downward tilt. The UAS was flown manually in a sideways-facing orientation with the camera pointed toward the bluff. Before each flight, the camera digital ISO, aperture, and shutter speed were manually set to adjust for ambient light conditions. Although these settings were changed between flights, they were not permitted to change during a flight; thus, the images from each flight were acquired with consistent camera settings.
20190604
Joshua Logan
U.S. Geological Survey, Pacific Coastal and Marine Science Center
Physical Scientist
mailing address
2885 Mission Street
Santa Cruz
CA
95060
US
831-460-7519
831-427-4748
jlogan@usgs.gov
Ground control was established using ground control points (GCPs) consisting of small square tarps with black-and-white cross patterns and temporary chalk 'X' marks placed on the ground surface throughout the survey area. The GCP positions were measured using survey-grade GPS receivers operating in post-processed-kinematic (PPK) mode. The GPS receivers were placed on short fixed-height tripods and set to occupy each GCP for a minimum occupation time of one minute. The PPK corrections were referenced to a Continuously Operating Reference (CORS) GPS base station ('COUP') located approximately 7 kilometers from the study area operated by the Washington State Reference Network (WSRN).
20190604
Joshua Logan
U.S. Geological Survey, Pacific Coastal and Marine Science Center
mailing and physical
2885 Mission Street
Santa Cruz
CA
95060
831-460-7519
jlogan@usgs.gov
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 a custom Python script which processes the GPS data from the UAS telemetry log and calls the command-line 'exiftool' software. 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 corrected 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 intertidal zone on the west side of Whidbey Island, Washington, USA, from USGS survey 2019-623-FA." ^
-Caption-Abstract="Intertidal zone on the west side of Whidbey Island, Washington, USA, from USGS survey 2019-623-FA." ^
-Caption="Aerial image of the intertidal zone on the west side of Whidbey Island, Washington, USA, from USGS survey 2019-623-FA." ^
-sep ", " ^
-keywords="Marine Nearshore Intertidal, Whidbey Island, Strait of Juan de Fuca, Rosario Strait, Washington, 2019-623-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 2019-623-FA." ^
-Credit="U.S. Geological Survey" ^
-Contact="pcmsc_data@usgs.gov" ^
-Artist="U.S. Geological Survey, Pacific Coastal and Marine Science Center" ^
2019
Joshua Logan
U.S. Geological Survey, Pacific Coastal and Marine Science Center
mailing and physical
2885 Mission Street
Santa Cruz
CA
95060
831-460-7519
jlogan@usgs.gov
Structure-from-motion (SfM) processing techniques were used to create the point clouds in the Agisoft Photoscan/Metashape software package using the following workflow:
1. Initial image alignment was performed with the following parameters - Accuracy: 'high'; Pair selection: 'reference', 'generic'; Key point limit: 0 (unlimited); Tie point limit: 0 (unlimited).
2. Sparse point cloud error reduction was performed using an iterative gradual selection and camera optimization process with the following parameters: Reconstruction Uncertainty: 10; Projection Accuracy: 3. Lens calibration parameters f, cx, cy, k1, k2, k3, p1, and p2 were included in the optimization. Additional sparse points obviously above or below the true surface were manually deleted after the last error reduction iteration.
3. Ground control points (GCPs) were automatically detected using the 'Cross (non-coded)' option. False matches were manually removed, and all markers were visually checked and manually placed or adjusted if needed. Markers were manually placed for GCPs that consisted of chalk 'X' marks.
4. Additional sparse point cloud error reduction was performed using an iterative gradual selection and camera optimization process with the following parameters: Reconstruction Error: 0.3. Lens calibration parameters f, cx, cy, k1, k2, k3, p1, and p2 were initially included in the optimization, but additional parameters k4, b1, b2, p3, and p4 were included once Reconstruction Error was reduced below 1 pixel. Additional sparse points obviously above or below the true surface were manually deleted after the last error reduction iteration, and a final optimization was performed.
5. A dense point cloud was created using the 'high' accuracy setting, with 'aggressive' depth filtering.
6. A Digital Surface Model (DSM) with a native resolution of 3.6 centimeters per pixel was created using all points in the dense point cloud, and was exported to a GeoTIFF format with a 4-centimeter pixel resolution.
7. An RGB orthomosaic with a native resolution of 1.8 centimeters per pixel was created using the main DSM as the orthorectification surface, and was exported to a GeoTIFF format with a 2-centimeter pixel resolution.
8. An exterior boundary was digitized using the orthomosaic as a reference and was used as a clipping mask to exclude areas of water, obvious edge artifacts, and large areas of interpolation.
9. The point clouds were exported in LAZ format.
10. LAStools 'lasclip' was used to set the classification of all points falling within the horizontal bounds of the water clipping mask shapefile as Class 9 ('water').
2019
Joshua Logan
U.S. Geological Survey, Pacific Coastal and Marine Science Center
Physical Scientist
mailing address
2885 Mission Street
Santa Cruz
CA
95060
US
831-460-7519
831-427-4748
jlogan@usgs.gov
Performed minor edits to the metadata to correct typos. No data were changed
20211013
U.S. Geological Survey
Susan A. Cochran
Geologist
Mailing and Physical
2885 Mission Street
Santa Cruz
CA
95060
831-460-7545
scochran@usgs.gov
Point
Universal Transverse Mercator
10
0.9996
-123.0
0.0
500000.0
0.0
coordinate pair
0.001
0.001
meters
NAD83 (National Spatial Reference System 2011) (EPSG:1116)
GRS 1980 (EPSG:7019)
6378137.0
298.257222101
North American Vertical Datum of 1988 (EPSG:5703), derived using GEOID12B
0.001
meters
Explicit elevation coordinate included with horizontal coordinates
The attribute information associated with point cloud follows the LAZ file standard. Attributes include location (northing, easting, and elevation in the NAD83(2011)/UTM zone 10N (EPSG:6339) horizontal and NAVD88 vertical coordinate systems), color (red, blue, and green components), intensity, and classification. All points are classified as 0 (unclassified) or 9 (water).
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)
U.S. Geological Survey - ScienceBase
mailing address
Denver Federal Center, Building 810, Mail Stop 302
Denver
CO
80225
United States
1-888-275-8747
sciencebase@usgs.gov
The topographic point clouds are available as LAZ files.
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.
LAZ
LAS 1.2
These zip files contain point cloud data in LAZ format (LAS 1.2 specification).
Zip
2330
https://www.sciencebase.gov/catalog/file/get/5ef53efd82ced62aaae6a0c0?name=WestWhidbey_2019-06-04_pointcloud.zip
https://www.sciencebase.gov/catalog/item/5ef53efd82ced62aaae6a0c0
https://doi.org/10.5066/P9R76MVP
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 LAZ format. The second link points to a landing page with the point cloud, metadata, and a browse image. The third link points to the landing page for the entire data release, including links to pages of the various data files.
None.
This zip file contains point cloud data in LAZ format (LAS 1.2 specification). The user must have software capable of uncompressing the .zip compressed file and displaying or processing the .laz format file.
20211013
U.S. Geological Survey, Pacific Coastal and Marine Science Center
PCMSC Science Data Coordinator
mailing and physical
2885 Mission Street
Santa Cruz
CA
95060
831-427-4747
pcmsc_data@usgs.gov
Content Standard for Digital Geospatial Metadata
FGDC-STD-001-1998