DEIReconstructor:a software for diffraction enhanced imaging processing and tomography reconstruction

Diffraction enhanced imaging (DEI) has been widely applied in many fields, especially when imaging low-Z samples or when the difference in the attenuation coefficient between different regions in the sample is too small to be detected. Recent developments of this technique have presented a need for a new software package for data analysis. Here, the Diffraction Enhanced Image Reconstructor (DEIReconstructor), developed in Matlab, is presented. DEIReconstructor has a user-friendly graphical user interface and runs under any of the 32-bit or 64-bit Microsoft Windows operating systems including XP and Win7. Many of its features are integrated to support imaging preprocessing, extract absorption, refractive and scattering information of diffraction enhanced imaging and allow for parallel-beam tomography reconstruction for DEI-CT. Furthermore, many other useful functions are also implemented in order to simplify the data analysis and the presentation of results. The compiled software package is freely available.     

The optical near-field speckles and their first order statistics on the basis of the integral equations of electromagnetic field

Speckle fields are the random light wave distributions produced when the light fields are scattered from random surfaces or a random medium. They appear in many optical phenomena that are related to light propagations[1,2] and have found wide appli-cations in a variety of scientific and technical fields. The examples of the recent impor-tant applications of speckles include the analysis of the movement of the granules[3], the three-dimensional imaging for the microstructures of metal nanocryst…     

Putting It All Together：Experience and Challenges at the DELPHI off—line Processing Farm

After over 10 years of existence,DELPHI off-line software counts altogether over 1500k lines.Being written by multitude of authorsk,many of them having already left,it is very incoherent and extremely difficult to maintain:it is written in Fortran,it relies on obsolete tools and it has to run in a distributed multi-os computing environment.Still.as the analysis of LEP data will continue during the next 5-6 years,this code will have to be used and be ported to yet another platforms.In order to ensure high efficiency in use of our resources,we have developed several tools which hide from the user most of the intricaices of the operating system,batch system and data access.These tools are well integrated and easy to maintain.As the problems are quite typical for the High Energy Physics software,we believe that the ideas we have implemented can be useful also for the next generation of experiments.     

Dynamic control of retrieval contrast in a ∧-type atomic system

We propose an efficient scheme for optimizing the optical memory of a sequence of signal light pulses in a system of ultracold atoms in ∧ configuration.The memory procedure consists of write-in,storage,and retrieval phases.By applying a weak microwave field in the storage stage,additional phase-dependent terms are included,and the contrast of the output signal pulses can be dynamically controlled（enhanced or suppressed） through manipulating the relative phase φ between optical and microwave fields.Our numerical analysis shows that the contrast is enhanced to the most extent when φ = 1.5π.In addition,the contrast is in proportion to the Rabi frequency of the microwave field with a certain relative phase.     

Reduced aliasing artifacts using shaking projection k-space sampling trajectory

Radial imaging techniques, such as projection-reconstruction （PR）, are used in magnetic resonance imaging （MRI） for dynamic imaging, angiography, and short-T2 imaging. They are less sensitive to flow and motion artifacts, and support fast imaging with short echo times. However, aliasing and streaking artifacts are two main sources which degrade radial imaging quality. For a given fixed number of k-space projections, data distributions along radial and angular directions will influence the level of aliasing and streaking artifacts. Conventional radial k-space sampling trajectory introduces an aliasing artifact at the first principal ring of point spread function （PSF）. In this paper, a shaking projection （SP） k-space sampling trajectory was proposed to reduce aliasing artifacts in MR images. SP sampling trajectory shifts the projection alternately along the k-space center, which separates k-space data in the azimuthal direction. Simulations based on conventional and SP sampling trajectories were compared with the same number projections. A significant reduction of aliasing artifacts was observed using the SP sampling trajectory. These two trajectories were also compared with different sampling frequencies. ASP trajectory has the same aliasing character when using half sampling frequency （or half data） for reconstruction. SNR comparisons with different white noise levels show that these two trajectories have the same SNR character. In conclusion, the SP trajectory can reduce the aliasing artifact without decreasing SNR and also provide a way for undersampling recon- struction. Furthermore, this method can be applied to three-dimensional （3D） hybrid or spherical radial k-space sampling for a more efficient reduction of aliasing artifacts.     

The BEPCⅡ Data Production and BESⅢ offline Analysis Software System

The BES detector has operated for about 12 years,and the BES offline data analysis environment also has been developed and upgraded along with developments of the BES hardware and software.The BESⅢ software system will operate for many years.Thus they should meet developments of the new technology in software,It should be highly flexible,Powerful,stable and easy for maintenance.And following points should be taken into account:1) To benefit the collaboration and make better exchanges with the international HEP experiments this system shoule be set up by adopting or referring the newest technology in the software from advanced experiments in the world.2).It should support hundreds of the existing BES software packages and serve for both old experts who familiar with BESII software and computing environment and new members who is going to benefit from the new system.3).The most BESII existing packages will be modified or re-designed according to the hardware changes.     

Data Preprocessing in Cluster Analysis of Gene Expression

Considering that the DNA microarray technology has generated explosive gene expression data and that it is urgent to analyse and to visualize such massive datasets with efficient methods,we investigate the data preprocessing methods used in cluster analysis,normalization or logarithm of the matrix,by using hierarchical clustering,principal component analysis(PCA) and self-organizing maps(SOMs).The results illustrate that when using the Euclidean distance as measuring metrics,logarithm of relative expression level is the best preprocessing method,while data preprocessed by normalization cannot attain the expected results because the data structure is ruined.If there are only a few principal components,the PCA is an effective method to extract the frame structure,while SOMs are more suitalbe for a specific structure.     

Preliminary attempt on maximum likelihood tomosynthesis reconstruction of DEI data

Tomosynthesis is a three-dimension reconstruction method that can remove the effect of superim- position with limited angle projections. It is especially promising in mammography where radiation dose is concerned. In this paper, we propose a maximum likelihood tomosynthesis reconstruction algorithm （ML-TS） on the apparent absorption data of diffraction enhanced imaging （DEI）. The motivation of this contribution is to develop a tomosynthesis algorithm in low-dose or noisy circumstances and make DEI get closer to clinic application. The theoretical statistical models of DEI data in physics are analyzed and the proposed algorithm is validated with the experimental data at the Beijing Synchrotron Radiation Facility （BSRF）. The results of ML-TS have better contrast compared with the well known ＇shift-and-add＇ algorithm and FBP algorithm.     

Go4：Multithreaded Inter—Task Communication with ROOT—writing non—blocking GUIs

The future GSI Online-Offline-Object-Oriented analysis framework Go4 based on ROOT[CERN,R.Brun et al] provides a mechanism to monitor and control an analuysis at any time.This is achieved by running the GUI and the analysis in different tasks.To control these tasks by one non-lbocking GUI,the Go4TaskHandler package was developed.It offers an asynchronous inter task communication via independent channels for commands,data,and status information,Each channel is processed by a dedicated thread and has a buffer queue as interface to the working thread.The threads are controlled by the Go4ThreadMAanager package,based on the ROOT TThread package,In parallel to the GUI actions,the analysis tasks can display objects like histograms in the GUI.A test GUI was implemented using the Qt widget library(Trolltech Inc.).A Qt to ROOT interface has been developed.The Go4 packages may be utilized for any ROOT application that requires to control independent data processing or monitoring tasks from a non-blocking GUI.     

Flow Reversal of Fully-Developed Mixed MHD Convection in Vertical Channels

The present analysis is concerned with flow reversal phenomena of the fully-developed laminar combined free and forced MHD convection in a vertical parallel-plate channel. The effect of viscous dissipation is taken into account. Flow reversal adjacent to the cold （or hot） wall is found to exist within the channel as Gr/Re is above （or below） a threshold value. Parameter zones for the occurrence of reversed flow are presented.     

Laser-induced breakdown spectroscopy in China

Laser-induced breakdown spectroscopy （LIBS） has been regarded as a future superstar for chemical analysis for years due to its unique features such as little or no sample preparation, remote sensing, and fast and multi-element analysis. Chinese LIBS comnmnity is one of the most dynamically developing communities in the World. The aim of the work is to inspect what have been done in China for LIBS development and, based on the understanding of the overall status, to identify the challenges and opportunities for the future development. In this paper, the scientific contributions from Chinese LIBS comlnunity are reviewed for the following four aspects： fimdamentals, instrumentation, data processing and modeling, and applications; and the driving force of LIBS development in China is analyzed, the critical issues for successful LIBS application are discussed, and in our opinion, the potential direction to improve the technology and to realize large scale commercialization in China is proposed.     

Phase Locking and Chaos in a Josephson Junction Array Shunted by a Common Resistance

The dynamics of a Josephson junction array shunted by a common resistance are investigated by using numerical methods. Coexistence of phase locking and chaos is observed in the system when the resistively and capacitively shunted junction model is adopted. The corresponding parameter ranges for phase locking and chaos are presented. When there are three resistively shunted junctions in the array, chaos is found for the first time and the parameter range for chaos is also presented. According to the theory of Chernikov and Schmidt, when there are four or more junctions in the array, the system exhibits chaotic behavior. Our results indicate that the theory of Chernikov and Schmidt is not exactly appropriate.     

Identifying the temperature distribution in a parabolice quation with overspecified data using a multiquadric quasi-interpolation method

In this paper, we use a kind of univariate multiquadric quasi-interpolation to solve a parabolic equation with overspecified data, which has arisen in many physical phenomena. We obtain the numerical scheme by using the derivative of the quasi-interpolation to approximate the spatial derivative of the dependent variable and a simple forward difference to approximate the temporal derivative of the dependent variable. The advantage of the presented scheme is that the algorithm is very simple so it is very easy to implement. The results of the numerical experiment are presented and are compared with the exact solution to confirm the good accuracy of the presented scheme.     

基本参数法在地面验证实验中的的应用

As the nearest celestial body to the earth, the moon has become a hot spot again in astronomy field recently. The element analysis is a much important subject in many lunar projects. Remote X-ray spectrometry plays an important role in the geochemical exploration of the solar bodies. Because of the quasi-vacuum atmosphere on the moon, which has no absorption of X-ray, the X-ray fluorescence analysis is an effective way to determine the elemental abundance of lunar surface. The CE-1 X-ray fluorescence spectrometer （CE-1/XFS） aims to map the major elemental compositions on the lunar surface. This paper describes a method for quantitative analysis of elemental compositions. A series of ground base experiments are done to examine the capability of XFS. The obtained results, which show a reasonable agreement with the certified values at a 30% uncertainty level for major elements, are presented.     

Operation and Optimization of a Linux PC farm for Physics Analysis in the ZEUS Experiment

The ZEUS experiment has migrated its reconstruction and analysis farms to a PC-based environment.More than one year of experience has been acquired with successful operation of an analysis farm designed for several hundred users.Specially designed software has been used to proveide fast and reliable access to large amounts of data (30 TB in total),After the ongoing upgrade of the HERA luminosity,higher requirements will arise in terms of data storage capacity and throughput rate,The necessity of a bigger disk cache has led to consideration of solutions based on commodity technology,PC-based file servers are being tested as a cost-effective storage system,In this article we present the hardware and software solutions deplogyed and discuss their performance.scalability and maintenance issues.     

An acoustic imaging system of migration technique used in borehole

In order to detect the damage of casing boreholes, an acoustic imaging method with a two-dimensional ultrasonic array was presented. Each element of the array independently emits down ultrasonic waves, the echoes received by all elements are sampled and transmitted to a computer on ground surface, where the dynamic migration method is used to form a 2 or 3-dimensional image of the situation in the borehole. The numerical simulation and experiment are conducted that demonstrate a high imaging accuracy with a small number of elements used in array. Since the delay circuits used in the traditional phased array imaging system is not needed in this system, and all data process could be completed in a ground system. the complexity and the volume of system in borehole may be significantly simplified, which is critical to the borehole instrument.     

Medical ultrasound imaging method combining minimum variance beamforming and general coherence factor

In medical ultrasound imaging field,in order to obtain high resolution and correct the phase errors induced by the velocity in-homogeneity of the tissue,a high-resolution medical ultrasound imaging method combining minimum variance beamforming and general coherence factor was presented.First,the data from the elements is delayed for focusing;then the multi-channel data is used for minimum variance beamforming;at the same time,the data is transformed from array space to beam space to calculate the general coherence factor;in the end, the general coherence factor is used to weight the results of minimum variance beamforming. The medical images are gotten by the imaging system.Experiments based on point object and anechoic cyst object are used to verify the proposed method.The results show the proposed method in the aspects of resolution,contrast and robustness is better than minimum variance beamforming and conventional beamforming.     

An ART iterative reconstruction algorithm for computed tomography of diffraction enhanced imaging

X-ray diffraction enhanced imaging （DEI） has extremely high sensitivity for weakly absorbing low- Z samples in medical and biological fields. In this paper, we propose an Algebra Reconstruction Technique （ART） iterative reconstruction algorithm for computed tomography of diffraction enhanced imaging （DEI-CT）. An Ordered Subsets （OS） technique is used to accelerate the ART reconstruction. Few-view reconstruction is also studied, and a partial differential equation （PDE） type filter which has the ability of edge-preserving and denoising is used to improve the image quality and eliminate the artifacts. The proposed algorithm is validated with both the numerical simulations and the experiment at the Beijing synchrotron radiation facility （BSRF）.     

The complex variable reproducing kernel particle method for two-dimensional elastodynamics

On the basis of the reproducing kernel particle method (RKPM), a new meshless method, which is called the complex variable reproducing kernel particle method (CVRKPM), for two-dimensional elastodynamics is presented in this paper. The advantages of the CVRKPM are that the correction function of a two-dimensional problem is formed with one-dimensional basis function when the shape function is obtained. The Galerkin weak form is employed to obtain the discretised system equations, and implicit time integration method, which is the Newmark method, is used for time history analysis. And the penalty method is employed to apply the essential boundary conditions. Then the corresponding formulae of the CVRKPM for two-dimensional elastodynamics are obtained. Three numerical examples of two-dimensional elastodynamics are presented, and the CVRKPM results are compared with the ones of the RKPM and analytical solutions. It is evident that the numerical results of the CVRKPM are in excellent agreement with the analytical solution, and that the CVRKPM has greater precision than the RKPM.     

KID－KLOE Integrated Dataflow

KLOEis acquiring and analyzing hundreds of terabytes of data,stored as tens of millons of files,In order to simplify the access to these data,a URI-based mechanism has been put in plase,The KID package is an implementation of that mechanism and is presented in this paper.