Array Files Research Articles

Towards online patient imaging during helical radiotherapy.

Exit-detector data from helical radiation therapy have been studied extensively for delivery verification and dose reconstruction. Since the same radiation source is used for both imaging and treatment, this work investigates the possibility of utilising exit-detector raw data for imaging purposes. This gives rise to potential clinical applications such as retrospective daily setup verification and inter-fractional setup error detection. The exit-detector raw data were acquired and independently analysed using Python programming language. The raw data were extracted from the treatment machine's onboard computer, and converted into 2D array files. The contours of objects (phantom or patient) were acquired by applying a logarithmic function to the ratio of two sinograms, one with the object in the beam and one without. The setup variation between any two treatment deliveries can be detected by applying the same function to their corresponding exit-detector sinograms. The contour of the object was well defined by the secondary radiation from the treatment beam and validated with the imaging beam, although no internal structures were discernible due to the interference from the primary radiation. The sensitivity of the setup variation detection was down to 2 mm, which was mainly limited by the resolution of the exit-detector itself. The exit-detector data from treatment procedures contain valuable photon exit fluence maps which can be utilised for contour definition and verification of patient alignment without reconstruction.

Chunked extendible dense arrays for scientific data storage

Several meetings of the Extremely Large Databases Community for large scale scientific applications advocate the use of multidimensional arrays as the appropriate model for representing scientific databases. Scientific databases gradually grow to massive sizes of the order of terabytes and petabytes. As such, the storage of such databases require efficient dynamic storage schemes where the array is allowed to arbitrarily extend the bounds of the dimensions. Conventional multidimensional array representations cannot extend or shrink their bounds without relocating elements of the data-set. In general, extendibility of the bounds of the dimensions, is limited to only one dimension. This paper presents a technique for storing dense multidimensional arrays by chunks such that the array can be extended along any dimension without compromising the access time for an element. This is done with a computed access mapping function, that maps the k-dimensional index onto a linear index of the storage locations. This concept forms the basis for the implementation of an array file of any number of dimensions, where the bounds of the array dimension can be extended arbitrarily. Such a feature currently exists in the Hierarchical Data Format version 5 (HDF5). However, extending the bound of a dimension in the HDF5 array file can be unusually expensive in time. Such extensions, in our storage scheme for dense array files, can still be performed while still accessing elements of the array at orders of magnitude faster than in HDF5 or conventional arrays-files. We also present theoretical and experimental analysis of our scheme with respect to access time and storage overhead. Such mapping scheme can be readily integrated into existing PGAS models for parallel processing in a cluster networked computing environment.

The inter‐ and intrafraction reproducibilities of three common IMRT delivery techniques

Intensity modulated radiation therapy (IMRT) treatment delivery requires higher precision than conventional 3D treatment delivery because of the sensitivity of the resulting dose to small geometric misalignment of the modulated beamlets. The chosen treatment delivery technique will affect the treatment precision in different ways, based on the characteristics of the delivery method. Delivery using a multileaf collimator (MLC) can reduce treatment time and therapist workload, but typically requires a greater number of monitor units and the fields are prone to both systematic and random leaf positioning errors. An alternative to MLC-based fields, patient specific brass compensators, do not suffer from these leaf positioning errors. In our study, we set out to investigate which delivery method will provide the highest levels of dosimetric reproducibility and the minimum amount of interfraction variability. In our study, a seven field IMRT plan for a head and neck treatment was created using the Pinnacle3 treatment planning system and the intensity maps for each field were obtained. The intensity maps of the fields were delivered with a Varian 2100C/D linear accelerator, using solid compensators and sliding window (SW) and step-and-shoot (SS) MLC segments. Three fields were selected from the seven-beam IMRT plan for comparison. Analysis was carried out using the MatriXX ion chamber array, radiochromic film, and Varian dynalog files. Our results show that the error in MLC leaf positioning has no gantry angle dependence. The compensator and SW deliveries showed excellent agreement, even when stricter than usual gamma criteria were applied. However, we noted that under these strict conditions, the SS field had at least ten times more pixels out of range than did the compensators. When using step-and-shoot MLC fields, it was observed that the increase in dose rate or the increase of MU/segment degrades the quality of the plan. Analysis of the dynalog files showed that while each individual field had its own propensity for error, all fields showed the same trend: a greater percentage of time the leaves are out of position as dose rate increases, MUs decrease, or both. The compensator-based field and both types of MLC-based fields have MatriXX results that are within the clinically acceptable tolerance of 3% dose difference and 2 mm DTA. However, when the criteria are tightened, it becomes evident that the compensators have a definite advantage over their comparable MLC-based competitors in terms of interfraction reproducibility. Fewer monitor units are required to deliver each portal, potentially improving patient outcomes and reducing unwanted side effects to both patients and therapists. In centers without MLC, compensators represent a simple and cost effective way to offer patients state of the art treatment. Based on the results of this study, compensator-based IMRT is a reliable, viable option for use in clinics both with and without MLC-equipped linacs.

Efficient Parallel Implementation of the CCSD External Exchange Operator and the Perturbative Triples (T) Energy Calculation.

A new, efficient parallel algorithm is presented for the most expensive step in coupled cluster singles and doubles (CCSD) energy calculations, the external exchange operator (EEO). The new implementation requires much less input/output than our previous algorithm and takes better advantage of integral screening. It is formulated as a series of matrix multiplications. Both the atomic orbital integrals and the corresponding CC coefficients are broken up into smaller blocks to diminish the memory requirement. Integrals are presorted to make their sparsity pattern more regular. This allows the simultaneous use of two normally conflicting techniques for speeding up the CCSD procedure: the use of highly efficient dense matrix multiplication routines and the efficient utilization of sparsity. We also describe an efficient parallel implementation of the perturbative triples correction to CCSD and related methods. Using the Array Files tool for distributed filesystems, parallelization is straightforward and does not compromise efficiency. Representative timings are shown for calculations with 282-1528 atomic orbitals, 68-228 correlated electrons, and various symmetries, C1 to C2h.

Parallel Calculation of Coupled Cluster Singles and Doubles Wave Functions Using Array Files.

A new parallel implementation of the Coupled Cluster Singles and Doubles (CCSD) and related wave functions (e.g Quadratic Configuration Interaction, QCI, and Coupled Electron Pair, CEPA) is described, based on the Array Files middleware. The program can handle large basis sets, even without utilizing symmetry, on modest distributed memory workstation clusters. High computational efficiency is achieved by formulating all major operations in terms of matrix multiplications. Timings are provided for systems with 50-228 valence electrons and up to 1144 basis functions, with little or no symmetry. Our largest calculation (QCISD/aug-cc-pVQZ for the parallel displaced benzene dimer) uses 1512 basis functions. Calculations on the benzene dimer show that the usual procedure of estimating the effect of basis set enlargement from second-order Møller-Plesset (MP2) calculations is less reliable than previously assumed. Replacing the weak pair amplitudes in CCSD/QCISD calculations by MP2 amplitudes affects the calculated energy only slightly.

Array files for computational chemistry: MP2 energies

A simple message-passing implementation for distributed disk storage, called array files (AF), is described. It is designed primarily for parallelizing computational chemistry applications but it should be useful for any application that handles large amounts of data stored on disk. AF allows transparent distributed storage and access of large data files. An AF consists of a set of logically related records, i.e., blocks of data. It is assumed that the records have the typical dimension of matrices in quantum chemical calculations, i.e., they range from 0.1 to approximately 32 MB in size. The individual records are not striped over nodes; each record is stored on a single node. As a simple application, second-order Møller-Plesset (MP2) energies have been implemented using AF. The AF implementation approaches the efficiency of the hand-coded program. MP2 is relatively simple to parallelize but for more complex applications, such as Coupled Cluster energies, the AF system greatly simplifies the programming effort.