Methods in Oceanography最新文献

Loss of live coral and declines in the structural complexity of reef habitats affects ecosystem-level processes such as energy flow, nutrient cycling, and community dynamics. Scleractinian corals are the primary contributor to the biological and physical three-dimensional (3D) structure of coral reef ecosystems. Disturbance events that induce coral mortality can alter the 3D structure of reefs habitats and lead to disruptions in trophic structure and organismal relationships that drive ecological processes. The coral reef ecosystem at Wai‘ōpae, southeast Hawai‘i Island, experienced several acute disturbance events in 2014, including a hurricane, tropical storms, and a severe coral bleaching event. This study utilized innovative 3D reconstruction techniques to create high-resolution models of the coral reef habitat and quantify structural metrics known to affect the biodiversity and abundance of associated reef organisms. A volumetric analysis was applied to the reconstructed 3D point clouds to determine the precise loss of habitat that occurred throughout the surveyed reef area. Conducting a temporal analysis using 3D reconstructions enabled us to test the hypothesis that volume and 3D architectural complexity of the coral community at Wai‘ōpae was significantly impacted by the acute disturbance events.

Two calibration rigs for controlling the movement of a reference target during a field calibration of multi-beam fishery sonars are described. The first rig was designed to be firmly mounted on the vessel hull and position the reference target inside a single beam, or a few selected sonar beams, with a specified spatial precision. This rig was also used for developing within-beam positioning algorithms, based upon the split-beam principle, using data from individual transducer elements. The size and weight of this rig limited its capacity to calibrate multiple sonar beams. A second rig was therefore designed for swifter movement of the target through multiple beams from each rig-mounting location. The position of the reference target inside each beam was now directly computed from the measured target echo. The rig designs, operation and the experiences of using them, along with comparative performance tests are presented along with some examples of field calibrations.

We present a complete set of freely available MATLAB/Octave scripts called the SOCIB Glider Toolbox (https://github.com/socib/glider_toolbox). This new toolbox automates glider data processing functions, including thermal lag correction, quality control and graphical outputs. While the scientific value of the glider platform has been proven, the experience for the glider data user is far from perfect or routine. Over the last 10 years, ocean gliders have evolved such that they are now considered as a core component of multi-platform observing systems and multi-disciplinary process studies; we now have a generic processing system that appropriately complements glider capability.

In an ideal world, a simple connection to a glider would provide oceanographic data ready for scientific application in an intuitive, familiar format; the reality has been somewhat different. Up till now users have faced several time-consuming tasks that prevent them from directly and efficiently extracting new oceanographic knowledge from the acquired data. The SOCIB glider toolbox covers all stages of the data management process, including: metadata aggregation, raw data download, data processing, data correction and the automatic generation of data products and figures. It is designed to be operated either in real-time or in delayed mode, and to process data from two of the most widely used and commercially exploited glider platforms, Slocum gliders and SeaGliders. The SOCIB glider toolbox is ready to accelerate glider data integration and promote oceanographic discovery.

Reynolds-averaged Navier–Stokes (RANS) and large eddy simulation (LES) are two schemes for modeling turbulent flows. Here they are compared for modeling flow distortion over the oceanographic research vessel R/V Knorr, which is important for correcting observations from sonic anemometers. Using the OpenFOAM RANS solver SimpleFOAM and the LES solver PisoFOAM, computations are compared with experimental data taken from various anemometer sites on-board the research vessel. The LES showed mean accuracy levels of ∼3% of the wind speed bias whereas the RANS simulations showed mean accuracies of ∼7%. A LES analysis of the wind speed vector pitch and yaw was also conducted. The dominant forcing was found to be the pitch, which gave a 7% increase to overall magnitude of the wind vector. It was also found that the pitch of the wind speed was the main component responsible for the horizontal flow distortions, found to be due to flow separation in the 10–20  $m{s}^{-1}$ range. We also use the LES simulations over a range of orientations from $-60°$ to $+60°$, in increments of $10°$. The numerical analysis showed close agreement to experimental measurements with a 6% mean difference prediction due to flow distortion effects. We also explore two different methods to define a wave induced flow distortion correction and when finally added to the air-flow distortion correction, improved the overall accuracy of the models by 3%.

Here we describe the configuration, calibration, and initial results from the combination of two recently developed underwater instruments that measure acoustic reflectivity and, simultaneously, the location, pose and size of millimeter-sized plankton relative to the sonar beam. The acoustic system, ZOOPS (ZOOPlankton Sonar), uses a broadband chirp signal that operates with a single monostatically configured transducer in the 1.5–2.5 MHz frequency range. We demonstrate that the system can record, with adequate signal-to-noise levels, identifiable reflections from single copepods with lengths as small as 360 $\mu$m. To simultaneously identify taxa and measure orientation, a pair of “O-Cam” microscopes were stereoscopically calibrated and geometrically co-registered with the orientation and range-resolved acoustic transmissions of the sonar beam. The system’s capability is demonstrated via the in situ measurement of acoustic reflectivity as a function of orientation for 224 individual pelagic copepods comprising three orders of free-living taxa. Comparison with a well-known model, the Distorted Wave Born Approximation (DWBA), using a spheroidal formulation, yields both differences and similarities between the in situ field data and the model’s predictions.

Groundfish that associate with rugged seafloor types are difficult to assess with bottom-trawl sampling gear. Simrad ME70 multibeam echosounder (MBES) data and video imagery were collected to characterize trawlable and untrawlable areas, and to ultimately improve efforts to determine habitat-specific groundfish biomass. The data were collected during two acoustic-trawl surveys of the Gulf of Alaska (GOA) during 2011 and 2012 by NOAA Alaska Fisheries Science Center (AFSC) researchers. MBES data were collected continuously along the trackline, which included parallel transects (1–20 nmi spacing) and fine-scale survey locations in 2011. Video data were collected at camera stations using a deployed camera system. Multibeam-derived seafloor metrics were overlaid with the locations of previously conducted AFSC bottom-trawl (BT) survey hauls and 2011 camera stations. Generalized linear models were used to identify the best combination of multibeam metrics to discriminate between trawlable and untrawlable seafloor for the region of overlap between the camera stations or haul paths and the MBES data. The two best models were developed using data collected at camera stations with either oblique incidence backscatter strength $\left(S_b\right)$ or mosaic $S_b$ in combination with bathymetric position index and seafloor ruggedness; these described over 54% of the variation between trawlable and untrawlable seafloor types. A map of predicted seafloor trawlability produced from the model using mosaic $S_b$ and benthic-terrain metrics demonstrated that 58% of the area mapped ($5987{\mathrm{km}}^2$) had $\ge 50\%$ probability of being trawlable and 42% of being untrawlable. The model correctly predicted 69% of trawlable and untrawlable haul locations. Successful hauls occurred in areas with 62% probability of being trawlable and gear damage occurred in areas with a 38% probability of being trawlable. This model and map produced from multibeam-derived seafloor metrics may be used to refine seafloor interpretation for the AFSC BT surveys and to advance efforts to develop habitat-specific biomass estimates for GOA groundfish populations.

Optical signal transmission is an important component of numerous underwater applications, including visibility and electro-optical (EO) communication. In addition to the well-studied effect of particle backscatter, underwater optical signal transmission can be limited by changes in the index of refraction (IOR) due to small-scale variations in temperature and salinity, sometimes called “optical turbulence”. These variations in IOR, which are associated with oceanic turbulence, can lead to the blurring of an underwater optical target, particularly at high spatial frequencies, thus reducing target detail. The 2011 Bahamas Optical Turbulence Experiment (BOTEX) was conducted to investigate this impact of turbulence on underwater optical signal transmission. Investigating naturally occurring “optical turbulence” requires a platform held at depth, capable of concurrent measurements of optical impairment by turbulence, which requires a significant optical path length, as well as associated physical and optical background conditions of the ambient environment. Our novel platform consisted of a high-speed camera and optical target mounted on a $5m$-long frame, along with several Nortek Vector Acoustic Doppler Velocimeter (ADV) and PME Conductivity–Temperature (CT) probes, to estimate turbulent kinetic energy and temperature variance dissipation rates experienced by the frame. Data on the background turbulence was collected with a Rockland Oceanographic Vertical Microstructure Profiler, to aid in analysis and guide error estimates of the ADV/CT measurements. This study was the first effort attempting to collect turbulence measurements on a frame designed for the investigation of the effect of density microstructure variations on optical signal transmission in the open ocean. Our results highlight the numerous challenges associated with studying this phenomenon in the dynamic oceanic environment. Here, we present the interpretation of the high-resolution velocity and temperature measurements collected on the frame and discuss the associated difficulties. Despite the numerous challenges, the investigation of the effect of microstructure on underwater optics is needed for efforts aimed at mitigating the impact of “optical turbulence” on underwater EO signal transmission and may help advance optical methods to quantify oceanic microstructure.

This paper describes the design and deployment of a new type of underwater stereo camera capable of triggering when animals are present in the field of view. Unobtrusive evaluation of the camera view field for potential targets is achieved using far-red illumination invisible to most fishes. The triggered camera (TrigCam) system is designed to be low cost by incorporating off-the-shelf commercial camera and computer components. It also incorporates several novel software and hardware developments such as the Cannon Hackers Development Kit which provides a high degree of control over the cameras, and a Raspberry Pi computer-on-board module for low-power, cost-efficient computing. The innovative triggering algorithm for fine control of the size and intensity of targets necessary to trigger an image is described in detail. Stereo image analysis provides estimates of fish size, position, and orientation to provide quantitative data from images. Test field deployments demonstrate operational capacity and illustrate potential applications for sampling marine organisms through example descriptions of analytical methods, including the trigger process and stereo image analysis. The TrigCam is intended to be an open source project to encourage continued development within the marine research community, with design information available through internet posts.

Seabeds with different physical and biological properties (for example, mud, sand, gravel, rock, seagrass, shell beds) generally produce differently shaped echoes in response to echosounder pings. After allowance for propagation losses and for artefacts caused by sampling at equal time intervals, instead of equi-angular spacing, geometrical (i.e. shape based) estimates of the similarity of echo envelopes may be used to geographically segment the seabed into areas with similar acoustic responses. Post-processing of entire echoes by direct clustering provides a statistically and geometrically optimal method of segmentation which in itself does not need ground truthing, since it is based on the actual seabed acoustic response. However, real-time processing allows sampling strategies to be adapted in response to findings during survey. A real-time segmentation method is presented which uses only two simple echo parameters. Classes formed by direct clustering of actual echoes map to unique areas of the 2-parameter space in a very simple and regular fashion, fully validating its use as a segmentation scheme. Groundtruth (seabed samples or video) must be taken if descriptions (labels) are to be assigned to the 2-parameter segmentations (the segmentation becomes a classification). However, the relation to direct clustering results means that in principle groundtruth is not needed to validate the segmentations. In contrast it has never been shown that echo features used by existing real-time schemes contain sufficient information to adequately characterize seabeds.

We estimated the detonation depth and net explosive weight for a very shallow underwater explosion using cutoff frequencies and spectral analysis. With detonation depth and a bubble pulse the net explosive weight for a shallow underwater explosion could simply be determined. The ray trace modeling confirms the detonation depth as a source of the hydroacoustic wave propagation in a shallow channel. We found cutoff frequencies of the reflection off the ocean bottom to be 8.5 Hz, 25 Hz, and 43 Hz while the cutoff frequency of the reflection off the free surface to be 45 Hz including 1.01 Hz for the bubble pulse, and also found the cutoff frequency of surface reflection to well fit the ray-trace modeling. We also attempted to corroborate our findings using a 3D bubble shape modeling and boundary element method. Our findings led us to the net explosive weight of the underwater explosion offshore of Baengnyeong-do for the ROKS Cheonan sinking to be approximately 136 kg TNT at a depth of about 8 m within an ocean depth of around 44 m.