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S O F T W a R E D E V E L O P E R ' S Q U a R T E R SOFTWARE DEVELOPER’S QUARTERLY Issue 12• Jan 2010 MIDAS 2.4 RELEASED AS OPEN SOURCE Editor’s Note ........................................................................... 1 Kitware is proud to announce the release of MIDAS 2.4, a major release implementing more than 20 new features. We Recent Releases ..................................................................... 1 are also happy to announce that the MIDAS source-code is now freely available under an unrestricted (BSD) license. A Synthetic LiDAR Scanner for VTK ..................................... 3 New Variational Level-Set Classes with Region Fitting Energy in ITK ......................................................................... 6 Alternative Memory Models for ITK..................................... 9 N3 Implementation for MRI Bias Field Correction ............ 11 Exporting Contours to DICOM-RTSTRUCT ......................... 13 Kitware News ...................................................................... 15 Kitware is pleased to present a special edition of the Source which features several of the strongest Insight Journal submissions from 2009. The Insight Journal was designed Improved image gallery with color selection to provide a realistic support system for disseminating sci- entific research in the medical image processing domain. For the past year MIDAS, Kitware’s digital archiving and Recognizing the need for a mechanism whereby the medical distributed processing system, has been generating a lot of image analysis community can collectively share their ideas, interest from the research community and we believe that code, data and results, Dr. Luis Ibàñez has worked with the opening its source code will lead to a better archiving and ISC and championed the open-science cause to make the processing system. We encourage users to download the A Synthetic lidar scanner for vtk Insight Journal a reality. latest release and join the mailing list. By providing a platform for open-access scientific publica- Among the new features of the 2.4 release: tion, Kitware continues to foster its commitment to the • Redesigned image gallery open-science community. To continue celebrating this cause • Improved LDAP support we will annually publish this special Insight Journal Edition • Support for plug-ins of the Source. Anyone may submit their work to the Insight • Improved server-side upload Journal by registering, for free, at insight-journal.org; perhaps your work will be featured here next year! • Custom upload workflows • Better BatchMake integration with custom reporting The Kitware Source is just one of a suite of products and services that Kitware offers to assist developers in getting Kitware’s public instance of MIDAS is available at http:// the most out of its open-source products. Each project’s insight-journal.org/midas, and is currenlty host to hundreds website contains links to free resources including mailing of freely available scientific and medical datasets. lists, documentation, FAQs and Wikis. In addition, Kitware MIDAS can be downloaded from kitware.com/midas. supports its open-source projects with technical books, user’s guides, consulting services, support contracts and training CDASH 1.6 courses. For more information on Kitware’s suite of products CDash, the open-source, web-based software testing server and services, please visit our website at www.kitware.com. has had another major release. CDash aggregates, analyzes and displays the results of software testing processes sub- In contrast to the traditional undo/redo stack, which is mitted from clients around the world, conveying the state cleared whenever new actions are performed, the plugin of a software system to continually improve its quality. This captures the complete exploration trail as a user explores release adds more than 20 new features including: different parameters and visualization techniques. A tree- • Support for persistent login based view of the history of actions allows a user to return • Better database compression to a previous version in an intuitive way, undo bad changes, compare different visualizations, and be reminded of the • New graphs and reports actions that led to a particular result. • Improved coverage visualization • Better CTest communication There is no limit on the number of operations that can be • Expected submission time based on historic average undone, no matter how far back in the history of the visual- ization they are, and the history is persistent across sessions. • Faster load of the main dashboard page • Improved navigation links The VisTrails plugin can save all of the information needed • Remote build management (beta) to restore any state of the visualization in .vt files, which can be reloaded across ParaView sessions and shared among To get started with CDash, host your project for free at collaborators. This also allows multiple visualizations to my.cdash.org. For more info on CDash 1.6 visit cdash.org. be shared with a single file. For more information on the VisTrails Provenenance Explorer Plugin see page 8 of the July ITK 3.18 2009 Kitware Source. ITK 3.18 will be released in early 2010. The main changes in this release include improvements in the following areas: LANL’s cosmo plug-in is now distributed with ParaView. This • Support for mathematical routines in itkMath plug-in allows ParaView to read and process *.cosmo format • Management of integer rounding and casting files, in which particles are described by mass, velocity and identification tags. These particles typically represent stellar • 64-bit platform support, particularly Windows and Mac masses. The halo finder filter is a friend-of-a-friend particle • Consistency in streaming large image files clustering algorithm. It creates groups containing particles • Infrastructure for running many tests in parallel (ctest -jN) that satisfy a tolerance/threshold linking distance criterion. in addition to: The cosmology data format, halo finding algorithm, and related (experimental) filter implementations are made • Added options for installing ITK in a flat directory. This will possible by the LANL cosmology researchers, the LANL visu- facilitate the use of ITK from external projects. alization team, and international collaborators. • Fixes for the Mattes Mutual Information Metric enabling this metric to work on binary images. Mac application bundle and comand line tools are now built as universal binaries (PPC and Intel i386). This simplifies man- For up-to-date information on ITK 3.18, please visit the ITK aging ParaView on Mac as now there is only a single binary mailing lists or search the ITK Wiki for “Release 3.18”. to download for any architecture. PARAVIEW 3.6.2 As always, we rely on your feedback to improve ParaView. Kitware, Sandia National Laboratories and Los Alamos We are experimenting with a new user-feedback mecha- National Lab are proud to announce the release of ParaView nism. Please use http://paraview.uservoice.com/ or click on 3.6.2. The binaries and sources are available for download the “Tell us what you think” link of paraview.org to leave from paraview.org. ParaView 3.6.2 contains the following your feedback and vote for new features. new features and improvements. The Python interface has been revamped, an exciting new extension to the Paraview Python interface is Python trace. The goal of trace is to generate human readable, not overly verbose, Python scripts that mimic a user’s actions in the GUI. See the “Python Trace” article on page 6 of the October 2009 Kitware Source for more details. A collection of statistics algorithms is now available. Using these statistics algortihms, you can compute descriptive statistics (mean, variance, min, max, skewness, kurtosis), compute contingency tables, perform k-means analysis, examine correlations between arrays, and perform princi- pal component analysis on arrays. More information about these filters is available on the ParaView Wiki by searching “Statistical Analysis”. This release also Includes the VisTrails Provenance Explorer plugin in Windows and Linux packages. VisTrails is an open- source, scientific workflow and provenance management ParaView 3.6.2 demonstrating the VisTrails Provenance Explorer system developed at the University of Utah that provides plugin for scientific workflow and provenance management. support for data exploration and visualization. The VisTrails Plug-in brings provenance tracking and the benefits of prov- enance to ParaView users. It automatically and transparently tracks the steps a user follows to create a visualization. 2 vtkRay A SYnthetic lidar scanner This is a container class to hold a point (ray origin) and a FOR VTK vector (ray direction). It also contains functions to: • Get a point along the ray a specified distance from the In recent years, Light Detection and Ranging (LiDAR) scanners origin of the ray have become more prevalent in the scientific community. (double* GetPointAlong(double)) • Determine if a point is in the half-space that the ray is They capture a “2.5-D” image of a scene by sending out pointing “toward“ thousands of laser pulses and using time-of-flight calcula- (bool IsInfront(double*)) • Transform the ray tions to determine the distance to the first reflecting surface (void ApplyTransform in the scene. However, they are still quite expensive, limiting (vtkTransform* Trans)) the availability of the data which they produce. Even if a vtkLidarPoint LiDAR scanner is available to a researcher, it can be quite time consuming to physically
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