Spatial Compression Research Articles

Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection

BackgroundMolecular dynamics (MD) simulations offer the ability to observe the dynamics and interactions of both whole macromolecules and individual atoms as a function of time. Taken in context with experimental data, atomic interactions from simulation provide insight into the mechanics of protein folding, dynamics, and function. The calculation of atomic interactions or contacts from an MD trajectory is computationally demanding and the work required grows exponentially with the size of the simulation system. We describe the implementation of a spatial indexing algorithm in our multi-terabyte MD simulation database that significantly reduces the run-time required for discovery of contacts. The approach is applied to the Dynameomics project data. Spatial indexing, also known as spatial hashing, is a method that divides the simulation space into regular sized bins and attributes an index to each bin. Since, the calculation of contacts is widely employed in the simulation field, we also use this as the basis for testing compression of data tables. We investigate the effects of compression of the trajectory coordinate tables with different options of data and index compression within MS SQL SERVER 2008.ResultsOur implementation of spatial indexing speeds up the calculation of contacts over a 1 nanosecond (ns) simulation window by between 14% and 90% (i.e., 1.2 and 10.3 times faster). For a 'full' simulation trajectory (51 ns) spatial indexing reduces the calculation run-time between 31 and 81% (between 1.4 and 5.3 times faster). Compression resulted in reduced table sizes but resulted in no significant difference in the total execution time for neighbour discovery. The greatest compression (~36%) was achieved using page level compression on both the data and indexes.ConclusionsThe spatial indexing scheme significantly decreases the time taken to calculate atomic contacts and could be applied to other multidimensional neighbor discovery problems. The speed up enables on-the-fly calculation and visualization of contacts and rapid cross simulation analysis for knowledge discovery. Using page compression for the atomic coordinate tables and indexes saves ~36% of disk space without any significant decrease in calculation time and should be considered for other non-transactional databases in MS SQL SERVER 2008.

On three-dimensional spherical acoustic cloaking

Transformation acoustics opens a new avenue towards the design of acoustic metamaterials, which are materials engineered at the subwavelength scale in order to mimic the parameters in wave equations. The design of the acoustic cloaking is based on the property of equations being invariant under a coordinate transformation, i.e. a specific spatial compression is equivalent to a variation of the material parameters in the original space. In this paper, the sound invisibility performance is discussed for spherical cloaks. The original domain consists of alternating concentric layers made from piezoelectric ceramics and epoxy resin, following a triadic Cantor sequence. The spatial compression, obtained by applying the concave-down transformation, leads to an equivalent domain with an inhomogeneous and anisotropic distribution of the material parameters.

Space-time focusing of multimode beams in oceanic waveguides

The quasioptical theory is generalized for approximate analytical description of refraction and diffraction focusing of multimode beams of narrowband pulse radiation in oceanic waveguides stratified over depth. General regularities of joint manifestation of spatial focusing and dispersion-induced compression of frequency-modulated pulsed signals during propagation of multimode beams are analyzed.

A Spatial Correlation-Based Image Compression Framework for Wireless Multimedia Sensor Networks

Data redundancy caused by correlation has motivated the application of collaborative multimedia in-network processing for data filtering and compression in wireless multimedia sensor networks (WMSNs). This paper proposes an information theoretic image compression framework with an objective to maximize the overall compression of the visual information gathered in a WMSN. The novelty of this framework relies on its independence of specific image types and coding algorithms, thereby providing a generic mechanism for image compression under different coding solutions. The proposed framework consists of two components. First, an entropy-based divergence measure (EDM) scheme is proposed to predict the compression efficiency of performing joint coding on the images collected by spatially correlated cameras. The EDM only takes camera settings as inputs without requiring statistics of real images. Utilizing the predicted results from EDM, a distributed multi-cluster coding protocol (DMCP) is then proposed to construct a compression-oriented coding hierarchy. The DMCP aims to partition the entire network into a set of coding clusters such that the global coding gain is maximized. Moreover, in order to enhance decoding reliability at data sink, the DMCP also guarantees that each sensor camera is covered by at least two different coding clusters. Experiments on H.264 standards show that the proposed EDM can effectively predict the joint coding efficiency from multiple sources. Further simulations demonstrate that the proposed compression framework can reduce 10%–23% total coding rate compared with the individual coding scheme, i.e., each camera sensor compresses its own image independently.

Focused visual attention distorts distance perception away from the attentional locus

Several lines of evidence show that visual perception is altered at the locus of visual attention: detection is faster, performance better and spatial resolution increased. It is however not known whether attention can affect visual perception further away from its locus. In the present study, we specifically question whether and how visual attention influences spatial perception away from its locus, independently from any saccadic preparation. We use a landmark task in which subjects have to estimate the location of a bisection stimulus relative to two landmark stimuli 15° apart, while fixating one of them. This task is combined with a highly demanding discrimination task performed on one of the two landmarks. This allows us to test for the effect of spatial attention allocation on distance perception, as measured by the subject estimation of the landmarks midpoint. We show that the estimated midpoint is displaced towards the attentional locus, both when attention is instructed on the central landmark or on the peripheral landmark. These results suggest an overrepresentation of space around the attentional locus that can affect perception up to 8° away, and question the existence of an objective spatial representation. They are in line with reports of spatial distortion in hemineglect patients while they strikingly contrast with the spatial compression reported around the time of saccadic execution.

An arbitrarily shaped cloak with nonsingular and homogeneous parameters designed usinga twofold transformation

An arbitrarily asymmetrical cloak with nonsingular andhomogeneous parameters is obtained by dividing an arbitraryN-sided polygonalregion into N triangular regions, applying an independent twofold spatial compression, and smoothingthe inner boundary of the polygonal cloak. In each triangular region, a small line segmentis first stretched along one side of the triangle; this is followed by a second transformationalong the other side which is carried out to create a pairing triangle. The inner boundarywill thus be continuous and take a shape similar to the outer boundary. The proposed cloakis nonsingular and moreover each region of the cloak is composed of homogeneousmaterials.

Real-time and low-power processing of 3D direct/inverse discrete cosine transform for low-complexity video codec

The 3D discrete cosine transform and its inverse (3D DCT/IDCT) extend the spatial compression properties of conventional 2D DCT to the spatio-temporal coding of 2D videos. The 3D DCT/IDCT transform is particularly suited for embedded systems needing the low-complexity implementation of both video encoder and decoder, such as mobile terminals with video-communication capabilities. This paper addresses the problem of real-time and low-power 3D DCT/IDCT processing by presenting a context-aware fast transform algorithm and a family of VLSI architectures characterized by different levels of parallelism. Implemented in submicron CMOS technology, the proposed hardware macrocells support the real-time processing of main video formats (up to high definition ones with an input rate of tens of Mpixels/s) with different trade-offs between circuit complexity, power consumption and computational throughput. Voltage scaling and adaptive clock-gating strategies are applied to reduce the power consumption versus the state of the art.

Effect of spatial separation, extended bandwidth, and compression speed on intelligibility in a competing-speech task

The benefit for speech intelligibility of extending the bandwidth of hearing aids was assessed when the target speech (sentences) and background (two talkers) were co-located or spatially separated. Also, the relative benefits of slow and fast compression were assessed. Sixteen hearing-impaired (HI) subjects with mild-to-moderate high-frequency hearing loss and eight normal-hearing (NH) subjects were tested. The target and interfering sounds were recorded using a KEMAR manikin and were located at +/-60 degrees azimuth, either co-located or spatially separated. Simulated binaural hearing-aid processing using five-channel slow or fast compression was performed offline, with gains set individually for each HI subject. Upper cutoff frequencies were 5, 7.5, or 10 kHz. Processed stimuli were presented via headphones. For both NH (unaided) and HI subjects, there was no significant effect of cutoff frequency for the co-located condition, but a small but significant benefit from increasing the cutoff frequency from 5 to 7.5 kHz for the spatially separated condition. For the HI subjects, slow compression gave slightly but significantly higher scores than fast compression for the spatially separated but not for the co-located condition. There were marked individual differences both in the benefit from extended bandwidth and in the relative benefit of slow and fast compression.

Improved DNA electrophoresis in conditions favoring polyborates and lewis acid complexation.

Spatial compression among the longer DNA fragments occurs during DNA electrophoresis in agarose and non-agarose gels when using certain ions in the conductive buffer, impairing the range of fragment sizes resolved well in a single gel. Substitutions using various polyhydroxyl anions supported the underlying phenomenon as the complexation of Lewis acids to DNA. We saw significant improvements using conditions (lithium borate 10 mM cations, pH 6.5) favoring the formation of borate polyanions and having lower conductance and Joule heating, delayed electrolyte exhaustion, faster electrophoretic run-speed, and sharper separation of DNA bands from 100bp to 12 kb in a single run.

Experimental Investigation on Time Reversal Precoding for Space–Time Focusing in Wireless Communications

This paper presents the results of indoor wideband measurements investigating the space-time properties of wireless signal transmission with online time-reversal (TR) precoding. The measurements were conducted using a new TR wideband multiple-input-multiple-output (MIMO) channel sounder operating at 2.45 GHz with a bandwidth of 240 MHz. Both line-of-sight (LOS) and non-line-of-sight (NLOS) propagation conditions were investigated. Spatial focusing and temporal compression can clearly be seen with TR precoding, which may be useful for future wireless system applications. Channel hardening due to TR is also observed under both LOS and NLOS conditions.

A One-dimensional Linear Regression Model Based Spatial and Temporal Data Compression Algorithm for Wireless Sensor Networks

A One-dimensional Linear Regression Model Based Spatial and Temporal Data Compression Algorithm for Wireless Sensor Networks

Spatial compression produced by a stationary telescope

Spatial compression produced by a stationary telescope

Improved content aware scene retargeting for retinitis pigmentosa patients

BackgroundIn this paper we present a novel scene retargeting technique to reduce the visual scene while maintaining the size of the key features. The algorithm is scalable to implementation onto portable devices, and thus, has potential for augmented reality systems to provide visual support for those with tunnel vision. We therefore test the efficacy of our algorithm on shrinking the visual scene into the remaining field of view for those patients.MethodsSimple spatial compression of visual scenes makes objects appear further away. We have therefore developed an algorithm which removes low importance information, maintaining the size of the significant features. Previous approaches in this field have included seam carving, which removes low importance seams from the scene, and shrinkability which dynamically shrinks the scene according to a generated importance map. The former method causes significant artifacts and the latter is inefficient. In this work we have developed a new algorithm, combining the best aspects of both these two previous methods. In particular, our approach is to generate a shrinkability importance map using as seam based approach. We then use it to dynamically shrink the scene in similar fashion to the shrinkability method. Importantly, we have implemented it so that it can be used in real time without prior knowledge of future frames.ResultsWe have evaluated and compared our algorithm to the seam carving and image shrinkability approaches from a content preservation perspective and a compression quality perspective. Also our technique has been evaluated and tested on a trial included 20 participants with simulated tunnel vision. Results show the robustness of our method at reducing scenes up to 50% with minimal distortion. We also demonstrate efficacy in its use for those with simulated tunnel vision of 22 degrees of field of view or less.ConclusionsOur approach allows us to perform content aware video resizing in real time using only information from previous frames to avoid jitter. Also our method has a great benefit over the ordinary resizing method and even over other image retargeting methods. We show that the benefit derived from this algorithm is significant to patients with fields of view 20° or less.

Performance analysis for automated gait extraction and recognition in multi-camera surveillance

Many studies have confirmed that gait analysis can be used as a new biometrics. In this research, gait analysis is deployed for people identification in multi-camera surveillance scenarios. We present a new method for viewpoint independent markerless gait analysis that does not require camera calibration and works with a wide range of walking directions. These properties make the proposed method particularly suitable for gait identification in real surveillance scenarios where people and their behaviour need to be tracked across a set of cameras. Tests on 300 synthetic and real video sequences, with subjects walking freely along different walking directions, have been performed. Since the choice of the cameras’ characteristics is a key-point for the development of a smart surveillance system, the performance of the proposed approach is measured with respect to different video properties: spatial resolution, frame-rate, data compression and image quality. The obtained results show that markerless gait analysis can be achieved without any knowledge of camera’s position and subject’s pose. The extracted gait parameters allow recognition of people walking from different views with a mean recognition rate of 92.2% and confirm that gait can be effectively used for subjects’ identification in a multi-camera surveillance scenario.

Green light emission in silicon through slow-light enhanced third-harmonic generation in photonic-crystal waveguides

Slow light has attracted significant interest recently as a potential solution for optical delay lines and time-domain optical signal processing1,2. Perhaps even more significant is the possibility of dramatically enhancing nonlinear optical effects3,4 due to the spatial compression of optical energy5,6,7. Two-dimensional silicon photonic-crystal waveguides have proven to be a powerful platform for realizing slow light, being compatible with on-chip integration and offering wide-bandwidth and dispersion-free propagation2. Here, we report the slow-light enhancement of a nonlinear optical process in a two-dimensional silicon photonic-crystal waveguide. We observe visible third-harmonic-generation at a wavelength of 520 nm with only a few watts of peak power, and demonstrate strong third-harmonic-generation enhancement due to the reduced group velocity of the near-infrared pump signal. This demonstrates yet another unexpected nonlinear function realized in a CMOS-compatible silicon waveguide.

A Moment's Daydreaming

A Moment's Daydreaming

Investigations of Three-Dimensional Concentrators Based on the Analytical Field-Transformation Theory

We have investigated the electromagnetic properties of arbitrarily-shaped three-dimensional concentrators based on the field-transformation theory for the first time. Up to now, many researchers are inclined to investigate the characteristics of the two dimensional optical-transformation devices instead of the three-dimensional (3D) ones due to the huge simulation burden for the commercial electromagnetic softwares. The field transformation theory has provided us a smart and powerful way to study such 3D problems. Analytical expressions for the fields and power flows inside the concentrators have been presented accurately, which have never been considered before. As examples, the spherical and cubic concentrators are discussed in more details. The study shows that the magnification of fields and power-flow densities inside the central parts of concentrators is only dependent upon the spatial compression ratio in the transformation equations, which gives a theoretical proof to the numerical simulations.

Spatial soliton tunneling, compression and splitting

We numerically investigate the tunneling of spatial solitons through a focusing Kerr nonlinear optical lattice with longitudinal potential barrier, and find that the position of input beams apparently affects the tunneling behaviors of spatial solitons, which exhibit compression or splitting when passing through the barrier, and that the transverse modulation frequency of lattice and the intensity of input beams strongly affect the ability of tunneling. Based on these properties, we present a scheme for compressing soliton and splitting soliton into stable twin beams. The obtained results may have promising applications in all-optical devices based on spatial solitons.

Approximation approach of designing practical cloaks with arbitrary shapes

The approach of designing cloaks with arbitrary shapes was investigated. The coordinate transformation was considered as a homeomorphous topological mapping and the related geometrical description was proposed by introducing position surfaces and tracing lines. Then an approximation approach was presented, which considers a close shape as a polyhedron and performs the spatial compression in a general method. As an example of this approach, we deduced the material parameter equations for two-dimensional polygon cloaks and confirmed the results through numerical simulations. Our approach opens up possibilities of designing practical cloaks with arbitrary shapes through numerical or/and semi-analytical methods.

Psychoacoustic-based quantisation of spatial audio cues

The derivation of spatial cues representing source localisation information is a typical component of multichannel spatial audio coders. Efficient compression of spatial cues based on psychoacoustic localisation features is investigated. Results show that the proposed quantisation approach for spatial cue compression achieves bit-rates of less than 6 kbit/s while preserving critical source localisation information.