Reverse Engineering Software Research Articles

A Parallel Implementation of the Network Identification by Multiple Regression (NIR) Algorithm to Reverse-Engineer Regulatory Gene Networks

The reverse engineering of gene regulatory networks using gene expression profile data has become crucial to gain novel biological knowledge. Large amounts of data that need to be analyzed are currently being produced due to advances in microarray technologies. Using current reverse engineering algorithms to analyze large data sets can be very computational-intensive. These emerging computational requirements can be met using parallel computing techniques. It has been shown that the Network Identification by multiple Regression (NIR) algorithm performs better than the other ready-to-use reverse engineering software. However it cannot be used with large networks with thousands of nodes - as is the case in biological networks - due to the high time and space complexity. In this work we overcome this limitation by designing and developing a parallel version of the NIR algorithm. The new implementation of the algorithm reaches a very good accuracy even for large gene networks, improving our understanding of the gene regulatory networks that is crucial for a wide range of biomedical applications.

Reconstruction of a 3-D digital virtual wrist model based on CT images and anatomy

Objective To reconstruct a 3-D digital virtual wrist model based on CT images and anatomy,to explore its feasibility and clinical application,and to provide a pre-processing morphologic moddel for wrist biomechanics analysis.Methods High resolution serial CT images of a young Chinese male volunteer's right forearm were obtained.3-D bone reconstruction was done using Mimics software,Based on wrist anatomy and available data,the triangular fibrocartilage and the important ligaments were outlined on the grey scale areas of the CT images using the 3D-Doctor software.The contours of bones,tringular fibrocartilage and ligaments were then imported into the reverse-engineering software Geomagic to integrate and register into a wrist model. Results A wrist model containing radius,ulna,metacarpals (including cortical bone,cancellous bone and medullay cavity),carpal bones,triangular fibrocartilage complex,dorsal radiocarpal,radioscaphoid,radioscaphocapitate,and radiolunate ligaments was reconstructed.The 3-D digitized measurements of the ligaments of the wrist model were consistent with the anatomical data available in the literature. Conclusion It is feasible to reconstruct a 3-D digitized virtual wrist model based on CT images and anatomy data using medical image management software.This approach may be a pre-processing technique for virtual hand finite element analysis. Key words: Carpal joints; Triangular fibrocagrtilage; Ligaments; 3D-remodeling

Utilizing 3D Laser Scanning Technology for Remodeling Work of Building Inside

Laser scanning technology is a maturing measurement technology which is capable of obtaining 3D measurement data of objects with high-accuracy, high-resolution and in a short time. Laser scanners are used more and more as surveying instruments for various applications. This paper describes the procedure of 3D data acquirement using terrestrial LiDAR and section drawing extraction through a series of processing for remodeling the interior of a department building. Accurate drawings are needed for improvement construction of building interior. However if the design drawings of that time of construction work were lost or damaged or actual dimensions of drawings differ from those of design drawings, the interior should be resurveyed. In this study, the extraction process of interior plane figures were suggested through using laser scanning and related reverse engineering software

Outside In

This article discusses reverse engineering software is slowly changing the way design engineers do their everyday jobs. With the pervasiveness of computer-aided design packages, reverse engineering technology has become a practical tool to create a 3D virtual model of an existing physical part. This model is then available to be used in 3D CAD, computer-aided manufacturing, or other computer-aided engineering applications. The reverse engineering process needs hardware and software that work together. The hardware is used to measure an object, and the software reconstructs it as a 3D model. The physical object can be measured using 3D scanning technologies such as a coordinate measuring machine, laser scanner, structured light digitizer, or computed tomography. The wider accessibility of handheld-laser scanners and portable CMMs like the one used at Excel Foundry means more companies can afford reverse engineering for their own unique ends. The scanner has turned out to be equally useful for engineering and for local archeological and preservation projects; and so far, it has been used to help preserve endangered artifacts.

Rapid prototyping drill guide template for lumbar pedicle screw placement

To develop a novel method of spinal pedical stereotaxy by reverse engineering and rapid prototyping techniques, and to validate its accuracy by experimental and clinical studies. A 3D reconstruction model for the desired lumbar vertebra was generated by using the Mimics 10.11 software, and the optimal screw size and orientation were determined using the reverse engineering software. Afterwards, a drill template was created by reverse engineering principle, whose surface was the antitemplate of the vertebral surface. The drill template and its corresponding vertebra were manufactured using the rapid prototyping technique. The accuracy of the drill template was confirmed by drilling screw trajectory into the vertebral biomodel preoperatively. This method also showed its ability to customize the placement and size of each screw based on the unique morphology of the lumbar vertebra.The drill template fits the postural surface of the vertebra very well in the cadaver experiment. Postoperative CT scans for controlling the pedicle bore showed that the personalized template had a high precision in cadaver experiment and clinical application. No misplacement occurred by using the personalized template. During surgery, no additional computer assistance was needed. The authors have developed a novel drill template for lumbar pedicle screw placement with good applicability and high accuracy. The potential use of drill templates to place lumbar pedicle screws is promising. Our methodology appears to provide an accurate technique and trajectory for pedicle screw placement in the lumbar spine.

Predictive modelling of cervical disc implant wear

This study presents a chain of simulations aimed at estimating the wear in a cervical disc implant and providing insight into the in vivo biomechanical performance of the implant. The simulation chain can start with determining a representative maximum range of motion (ROM) of a person's head. The ROM is used as motion input to a kinematic simulation of the cervical spine containing a disc implant. The cervical spine geometry is obtained from computed tomography (CT) scans and converted to STL format using reverse engineering software. The time histories of the loads imposed by the adjacent vertebrae on the implant, as well as the vertebral relative rotations can be extracted from the kinematic simulation. Alternatively, force and motion profiles prescribed by wear test protocols (e.g. ISO 18192-1 and ASTM F2423-05) can be used. The force and motion profiles are applied as boundary conditions to a non-linear finite element model (FEM) of the implant to determine the time-varying contact stress and slip velocity distributions at the interface between the two halves of the implant. The stresses and slip velocities are used in a linear wear model to estimate the wear rate distribution at the FEM's nodal points where contact occurs. Reverse engineering software is used to triangulate the contact surface so that the total wear volume can be calculated. The simulation chain's predicted wear rate shows good agreement with in vitro results in the literature. The simulation chain is thereby demonstrated to be suitable for comparative pre-experimental studies of spinal implant designs.

Reverse-engineering-based quantitative three-dimensional measurement of facial swelling after administration of Yunnan Baiyao following orthognathic surgery

To evaluate the effects of perioperative oral administration of Yunan Baiyao on reduction of postoperative facial swelling following bimaxillary orthognathic surgery. Patients scheduled for Le Fort I osteotomies and bilateral sagittal split ramus osteotomies were enrolled in the prospective, randomized, double-blind, placebo-controlled clinical study. Patients were orally administrated with Yunnan Baiyao capsules or placebo capsules before 3 days of operation and 5 days post-operation. Three-dimensional face images were recorded with OKIO-SC-400 Scanning System in 40 patients at pre-operation, postoperatively 3 day, 1 week and 1 month. Facial scans from different time periods were registrated to same coordinates and overlaid onto the baseline facial scan. 3D and 2D model deviations were performed with reverse engineering software to compare the differences between each two models and to quantitatively determine the reductions in facial swelling. There were 18 patients in Yunnan Baiyao group and 22 patients in control group. The severe swelling region was in the cheek, followed by the upper and lower lip. The average reduction of swelling thickness in Yunnan Baiyao group and control group from 3 day to 1 week postoperative was 3.6 mm and 2.3 mm respectively; there was significant difference between the two groups. Significant differences were also found in percentage changes of facial morphology from 3 day to 1 week postoperative (49.0% and 38.3% respectively). There were no significant changes in facial volumes of swelling between the two groups. Perioperative oral administration of Yunnan Baiyao capsules can effectively reduce the magnitude of facial swelling in bimaxillary orthognathic surgery. Yunnan Biayao has efficacy of anti-inflammatory response.

A feasibility study on laser rapid forming of a complete titanium denture base plate

This work attempted to integrate the technologies of computer-aided design and computer-aided manufacture (CAD/CAM) and laser rapid forming (LRF) for the fabrication of the titanium plate of a complete denture. By the combination of laser scan and reverse engineering software, the standard triangulation language (STL)-formatted denture base plate was finally designed and sliced into a sequence of numerical controlled codes. The titanium (Ti) complete denture plate was finally built, layer-by-layer, on the LRF system. To evaluate the quality of fit, a virtual adaptation test that measured and compared the profiles of the laser free formed denture plate and those of the edentulous plaster cast had been conducted, and the mean deviation was found to be 0.34 mm. After traditional dental finishing techniques, a complete denture with a Ti base plate was then made and judged to be acceptable. The CAD/CAM/LRF system is a potential candidate and a new platform for the design and manufacture of custom-made Ti denture plates and restorations.

Determination of Average Contour of Thais Skulls for Design of Implants

In this study, 100 dry skulls of Thais collected at the Srinagarind Hospital in Khon Kaen, Thailand were CT scanned and served for the investigation of the geometric average contour of Thais skulls. Moreover, measurements of distances between landmark points on skulls (cranial anthropometry) were made with this set of skulls for future standardization of skull implants. Thus the main purpose of this study was to determine the average contour of Thai skulls using techniques of medical image processing, Computer Aided Design (CAD) and reverse engineering software tools. After obtaining the average contour or the skull template we were able to select a region of interest and cut it for each proper standardized implant. These standardized implants will reduce the time for surgeons in implant preparation process. With their presence there is no longer necessity for CT scanning process and therefore treatment costs for a patient decrease considerably. Therefore, the result will be a good alternative for cranioplasty compared with conventional methods.

Theoretical and Experimental Study on Laser Compound Forming of Plate

An emerging process named laser compound forming of plate was presented by analyzing the advantages of laser thermal-stress forming (LTF) and laser peen forming (LPF) respectively. This technique combined the heat effect of continuous laser and mechanical effect of pulsed laser. Based on introducing the process of laser pre-stressed compound peen forming, the mechanism of plastic deformation and residual stress were analyzed. In order to apply pre-stressed load, a CO2 laser was used to scan SUS304 stainless plate according to the designed tracks firstly, the basic shape were formed and the contours of plate’s surface were measured by the optical scan measuring system, reverse engineering software Imageware was used to establish the virtual models of plate. Then the virtual models were inverted into finite element models by FEM code ABAQUS. The optimum distribution of residual stress field was obtained by adjusting laser parameters and controlling tracks of LPF. Finally, the optimized laser parameters and processing condition were used for LPF experiment. The results indicated that the anticipated shape could be obtained, and both side of the plate hold residual compressive stress after laser compound forming.

The algorithms for trimmed surfaces construction and tool path generation in reverse engineering

In the duplication of a physical part such as die and mold, aerospace part and so on, most of patches are trimmed surfaces resulting from Boolean manipulations. Direct generation of tool paths from the practical parts is a fundamental problem. This paper presents an efficient method for generating NC tool paths from some trimmed surfaces. Three types of control points are determined to construct an underlying NURBS surfaces. NC tool paths are then generated based on these surfaces. The method can deal efficiently with parts composed of trimmed surfaces. It can be considered as a tool for reverse engineering software integration.

Preliminary study on the comparison and analysis of the digital maxillary alveolar casts

To develop a three-dimensional (3-D) comparison and measuring techniques to analyze changes in palatal forms of the serial maxillary alveolar cast and to evaluate the significance of the different reference change indexes. Following digitizing the casts with a 3-D laser scanner and using reverse engineering software Geomagic Studio 7.0 for a pair of 3-D digital maxillary alveolar cast of an infant of UCLP before and after cheiloplasty, a pair of cast surfaces were reconstructed. The reference points and the character lines were extracted. The model coordinate system and the datum planes were established on the basis of reference points extracted. The newly developed analysis technique completed 3-D comparison of palatal forms of UCLP infants before and after cheiloplasty. Distances and volumes changes between the surfaces were determined and expressed graphically. With establishing the model coordinate system and the datum plane, it is possible to visualize the comparison outcome of the reference change indexes longitudinally. The various reference change indexes may reflect the trend of the infant maxillary growth.

Establishment of artificial-tooth three-dimensional coordinates based on dental anatomic concepts

To establish a three-dimensional (3-D) descartes coordinates of artificial teeth based on concepts of dental anatomy and to obtain their geometric parameters. Using the 3-D reverse engineering software, artificial-tooth coordinates were defined based on their anatomic concepts which included long axis, mesiodistal and buccolingual directions, and occlusal plane. Some geometric parameters, such as mesiodistal and buccolingual dimensions, height and obliquity of dental cusp, were measured. The 3-D coordinates of 28 artificial teeth were established and geometric parameters in coordinates were obtained. The definition of artificial-tooth coordinates can be made using mathematic language based on dental anatomic concepts, which is the basal work of complete denture computer-aided design (CAD).

Preliminary study on the reconstruction and analysis of digital maxillary cast of infants with cleft lip and palate

To reconstruct a digital maxillary cast of infants with cleft lip and palate (CLP) by laser scanning and to provide an analysis method for the edentulous cast of CLP. Under general anesthesia, an edentulous cast of one infant with right CLP was made and scanned by laser scanner. Using reverse engineering software, this cast surface was reconstructed. By this method, the digital cast could be observed from each degree and direction, and on this digital cast, the reference landmarks formeasarenment were determined, and the cast was then segmented, measured, and calculated. The 3-D analysis developed is an ideal tool for the examination of 3-D morphological changes in the edentulous maxilla of patients with CLP. This newly developed analysis enables a quantification of the extent and direction of morphological changes in the maxilla of infants with CLP.

Evaluation of object-oriented design patterns in game development

The use of object-oriented design patterns in game development is being evaluated in this paper. Games’ quick evolution, demands great flexibility, code reusability and low maintenance costs. Games usually differentiate between versions, in respect of changes of the same type (additional animation, terrains etc). Consequently, the application of design patterns in them can be beneficial regarding maintainability. In order to investigate the benefits of using design patterns, a qualitative and a quantitative evaluation of open source projects is being performed. For the quantitative evaluation, the projects are being analyzed by reverse engineering techniques and software metrics are calculated.

Feature-based reverse modeling strategies

We presented two integrated solution schemes, sectional feature based strategy and surface feature based strategy, for modeling industrial components from point cloud to surfaces without using triangulation. For the sectional feature based strategy, slicing, curve feature recognition and constrained fitting are introduced. This strategy emphasizes the advanced feature architecture patterns from 2D to 3D in reverse engineering. The surface feature based strategy relies on differential geometric attributes estimation and diverse feature extraction techniques. The methods and algorithms such as attributes estimation based on 4D Shepard surface, symmetry plane extraction, quadric surface recognition and optimization, extruded and rotational surface extraction, and blend feature extraction with probability and statistic theory are proposed. The reliable three-dimensional feature fabricated the valid substratum of B-rep model faultlessly. All the algorithms are implemented in RE-SOFT, a reverse engineering software developed by Zhejiang University. The proposed strategies can be used to capture the original design intention accurately and to complete the reverse modeling process conveniently. Typical industrial components are used to illustrate the validation of our feature-based strategies.

Computer aided design for fixed partial denture framework based on reverse engineering technology

To explore a computer aided design (CAD) route for the framework of domestic fixed partial denture (FPD) and confirm the suitable method of 3-D CAD. The working area of a dentition model was scanned with a 3-D mechanical scanner. Using the reverse engineering (RE) software, margin and border curves were extracted and several reference curves were created to ensure the dimension and location of pontic framework that was taken from the standard database. The shoulder parts of the retainers were created after axial surfaces constructed. The connecting areas, axial line and curving surface of the framework connector were finally created. The framework of a three-unit FPD was designed with RE technology, which showed smooth surfaces and continuous contours. The design route is practical. The result of this study is significant in theory and practice, which will provide a reference for establishing the computer aided design/computer aided manufacture (CAD/CAM) system of domestic FPD.

An empirical examination of the reverse engineering process for binary files

Reverse engineering of binary code file has become increasingly easier to perform. The binary reverse engineering and subsequent software exploitation activities represent a significant threat to the intellectual property content of commercially supplied software products. Protection technologies integrated within the software products offer a viable solution towards deterring the software exploitation threat. However, the absence of metrics, measures, and models to characterize the software exploitation process prevents execution of quantitative assessments to define the extent of protection technology suitable for application to a particular software product. This paper examines a framework for collecting reverse engineering measurements, the execution of a reverse engineering experiment, and the analysis of the findings to determine the primary factors that affect the software exploitation process. The results of this research form a foundation for the specification of metrics, gathering of additional measurements, and development of predictive models to characterize the software exploitation process.

Constrained fitting for 2D profile-based reverse modeling

Profile curve reconstruction is crucial to surface reconstruction in reverse engineering. In this paper, we present a new constrained fitting method involving lines, circular arcs and B-spline curves for profile curve reconstruction. By using similarity transformation, we reduce the condition number of the Hessian matrix involved in the optimization process and, therefore, the numerical stability is significantly improved. Several industrial examples are presented to demonstrate the efficiency of our method. This paper describes a 2D constrained fitting method for profile curve reconstruction in reverse engineering. The method is an extension to the published methods for 2D constrained fitting. Further more, the numerical problem associated with constrained fitting is tackled in our paper. The described method has been implemented in RE-SOFT, which is a feature-based reverse engineering software developed by the CAD/CAE/CAM Lab of Zhejiang University.

頭部固定装置を備えた非接触型三次元計測装置を用いた顎顔面軟組織形状の計測―ソフトウェア上での頭位補正機能の精度検証―

There are many methods of measuring facial configurations, and in recent years, reports and clinical studies on three-dimensional analysis have increased. Especially, the 3D optical scanning system offers not only rapid high-precision measurement but also no radiation exposure.We have newly developed a non-contact 3D optical scanning system (SURFLACER VMH-300F) which is equipped with cephalostats, and investigated the reliability, accuracy and stability of locating specific landmarks on facial soft tissue. We measured and analyzed the facial configurations of 10 adult Japanese, 5 times per subject, using this system and reverse engineering software (Imageware 9).The results were as follows.1. The operation of rectifying a position could be reduce the error to 0.63±0.15mm.2.High-precision Measurement could be performed by using cephalostats, without rectifying a position. However, rectifying increased the accuracy.3. The meanerrorof the measurement datum point was 2.68±0.89mm, the datum point of the foreheadarea had high reproducibility, and the datum point of the angle of mouth and angle of mandible had low reproducibility.