The book is an introduction to the idea of design patterns in software engineering, and a catalog of twenty-three common patterns. The nice thing is, most experienced OOP designers will find out they've known about patterns all along. It's just that they've never considered them as such, or tried to centralize the idea behind a given pattern so that it will be easily reusable.

Design Patterns: Elements of Reusable Object-Oriented Software

scikit-image is an image processing library that implements algorithms and utilities for use in research, education and industry applications. It is released under the liberal Modified BSD open source license, provides a well-documented API in the Python programming language, and is developed by an active, international team of collaborators. In this paper we highlight the advantages of open source to achieve the goals of the scikit-image library, and we showcase several real-world image processing applications that use scikit-image. More information can be found on the project homepage, http://scikit-image.org.

/pdf/scikit-image-image-processing-in-python-3tlzmiwc32.pdf

scikit-image: Image processing in Python

Several existing volume rendering algorithms operate by factoring the viewing transformation into a 3D shear parallel to the data slices, a projection to form an intermediate but distorted image, and a 2D warp to form an undistorted final image. We extend this class of algorithms in three ways. First, we describe a new object-order rendering algorithm based on the factorization that is significantly faster than published algorithms with minimal loss of image quality. Shear-warp factorizations have the property that rows of voxels in the volume are aligned with rows of pixels in the intermediate image. We use this fact to construct a scanline-based algorithm that traverses the volume and the intermediate image in synchrony, taking advantage of the spatial coherence present in both. We use spatial data structures based on run-length encoding for both the volume and the intermediate image. Our implementation running on an SGI Indigo workstation renders a 2563 voxel medical data set in one second. Our second extension is a shear-warp factorization for perspective viewing transformations, and we show how our rendering algorithm can support this extension. Third, we introduce a data structure for encoding spatial coherence in unclassified volumes (i.e. scalar fields with no precomputed opacity). When combined with our shear-warp rendering algorithm this data structure allows us to classify and render a 2563 voxel volume in three seconds. The method extends to support mixed volumes and geometry and is parallelizable.

/pdf/fast-volume-rendering-using-a-shear-warp-factorization-of-11o5tav1m5.pdf

Fast volume rendering using a shear-warp factorization of the viewing transformation

Mathematica--A System for Doing Mathematics by Computer.

AutoDock 2.4 predicts the bound conformations of a small, flexible ligand to a nonflexible macromolecular target of known structure. The technique combines simulated annealing for conformation searching with a rapid grid-based method of energy evaluation based on the AMBER force field. AutoDock has been optimized in performance without sacrificing accuracy; it incorporates many enhancements and additions, including an intuitive interface. We have developed a set of tools for launching and analyzing many independent docking jobs in parallel on a heterogeneous network of UNIX-based workstations. This paper describes the current release, and the results of a suite of diverse test systems. We also present the results of a systematic investigation into the effects of varying simulated-annealing parameters on molecular docking. We show that even for ligands with a large number of degrees of freedom, root-mean-square deviations of less than 1 A from the crystallographic conformation are obtained for the lowest-energy dockings, although fewer dockings find the crystallographic conformation when there are more degrees of freedom.

https://link.springer.com/content/pdf/10.1007/BF00124499.pdf

Distributed automated docking of flexible ligands to proteins: parallel applications of AutoDock 2.4.

From the Publisher:
"The GRAPHICS GEMS Series" was started in 1990 by Andrew Glassner. The vision and purpose of the Series was - and still is - to provide tips, techniques, and algorithms for graphics programmers. All of the gems are written by programmers who work in the field and are motivated by a common desire to share interesting ideas and tools with their colleagues. Each volume provides a new set of innovative solutions to a variety of programming problems

Graphics gems

A method of rendering a color image on a designated output medium is disclosed which maps colors to the gamut of the designated output medium while preserving the semantic consistency of the object color and illumination information in the image The method performs gamut mapping earlier in the image synthesis process than current gamut method methods, at the point where information about object primitives and their spectral attributes in a scene description is available, but after the fixed scene geometry has been determined by the rendering system The method makes use of the output of a symbolic rendering system which produces symbolic pixel expressions, having basis spectra variables which represent the interplay of light and object primitives in the scene description, and spectral data having color information about the light and object primitives in the scene, and which is indexed to the basis spectra variables The method performs spectral change calculations using the symbolic pixel expressions, the spectral data, and spectral information about the gamut of the specific output medium to determine the modifications to the original spectral data that need to be made to the individual object primitives in the scene in order to produce image pixel colors which are in the gamut of the output medium The resulting image colors are locally and globally consistent with the semantics of the image, make effective use of as much of the available gamut of the display device as is possible, and require no further post-rendering gamut mapping prior to display or reproduction on the designated medium

Method of rendering a color image for an output medium from symbolic image data

If you are indoors and reading this document on paper, then the page may be lit by a fluorescent light bulb. The gases inside the bulb absorb high-energy electrons, and then fluoresce, or re-radiate that absorbed energy at a different frequency. The particular gases in common fluorescent bulbs are chosen to be efficient at re-radiating this energy in the visible wavelengths. If you are reading this document on-line, then you’re probably reading it on a cathode-ray tube (CRT). The face of the CRT is lined with phosphors, which absorb the high-energy electrons directed at them, and gradually release that energy over time in the visible band. The two phenomena of fluorescence and phosphorescence are not as common as simple reflection and transmission, but do have an important part to play in the complete description of macroscopic physical behavior that should be modeled by image synthesis programs. This paper presents a mathematical model for global energy balancing which includes these phenomena.

A Model for Fluorescence and Phosphorescence

Publisher Summary This chapter analyzes winged-edge models. The winged-edge data structure is a powerful mechanism for manipulating polyhedral models. The basic idea rests on the idea of an edge and its adjacent polygons. The name is derived by imagining the two polygons as a butterfly's wings, and the edge as the butterfly's body separating them. This simple concept provides a basis for implementing a variety of powerful tools for performing high-level operations on models. There are several fundamental operations that a winged-edge library must support. Each operation requires carefully moving and adjusting a variety of pointers. This chapter describes solution of some tricky pointer-stitching problems in implementing a winged-edge library. It suggests a general architecture and data structures, and gives recipes for performing those basic mechanisms that require some care to implement correctly. The architecture suggested by Pat Hanrahan is discussed. The general structure in this architecture is that faces, edges, and vertices each are stored in a ring.

Maintaining winged-edge models

Rendering systems can produce images that include the entire range of visible colors. Imaging hardware, however, can reproduce only a subset of these colors: the device gamut. An image can only be correctly displayed if all of its colors lie inside of the gamut of the target device. Current solutions to this problem are either to correct the scene colors by hand, or to apply gamut mapping techniques to the final image. We propose a methodology called device-directed rendering that performs scene color adjustments automatically. Device-directed rendering applies classic minimization techniques to a symbolic representation of the image that describes the relationship of the scene lights and surfaces to the pixel colors. This representation can then be evaluated to produce an image that is guaranteed to be in gamut. Although our primary application has been correcting out-of-gamut colors, this methodology can be generally applied to the problem of adjusting a scene description to accommodate constraints on the output image pixel values.

Andrew S. Glassner

Papers

Graphics gems

Method of rendering a color image for an output medium from symbolic image data

A Model for Fluorescence and Phosphorescence

Maintaining winged-edge models

Device-directed rendering