plugin:filter:digital_darkfield_decomposition:start
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+ | ====== Digital Darkfield Decomposition ====== | ||
+ | ===== Introduction ===== | ||
+ | |||
+ | Digital-darkfield analysis involves the spatial mapping of selected frequencies across a digitized image, much as analog (e.g. electron-optical) darkfield-imaging allows one to locate crystals responsible for a given diffraction spot. This analysis involves a type of image decomposition which, like wavelets, is intermediate between direct and reciprocal (spatial-frequency) space [1]. | ||
+ | |||
+ | Digital-darkfield analysis is of particular use on images that have well defined spatial-frequencies in them, like lattice-fringe images of atomic-planes encountered edge-on by high-energy electrons in crystalline materials [2-10]. | ||
+ | |||
+ | More soon on the sections below. | ||
+ | |||
+ | * [[http:// | ||
+ | * [[https:// | ||
+ | * [[http:// | ||
+ | * [[http:// | ||
+ | ===== Author ===== | ||
+ | |||
+ | P. Fraundorf, // | ||
+ | |||
+ | ===== Features ===== | ||
+ | |||
+ | A set of java plugins is provided for this work, along with ImageJ macros for putting them to use. The java plugins include routines for quantitatively converting complex-number arrays to and from RGB images with pixel-intensity proportional to coefficient log-amplitude and pixel-hue linked to coefficient phase. These plugins may also be used by hue-maximization routines, to be described elsewhere. | ||
+ | |||
+ | Some of the routines allow the user to place a circular aperture in the power spectrum of an image, from which periodicity amplitude and phase-gradient (strain) maps are calculated, labeled, and displayed. The periodicity-amplitude map is shown (top right panel) in the figure below, for one of the many periodicities which show up in the power spectrum (top center panel) of the HR-TEM (electron phase-contrast) image of some WC< | ||
+ | |||
+ | {{: | ||
+ | |||
+ | The composite below here shows a log complex-color darkfield (bottom left panel), and log component-color analyses (right-most panels) of isotropic and shear periodicity gradients in a zone-plate calibration image. In the latter, red intensity denotes compression, | ||
+ | |||
+ | {{: | ||
+ | |||
+ | Another set of routines allows the user to tile frequency space with an array of tiny darkfield (plus one brightfield) images, yielding a tableau which contains one direct-space image formed by the spatial-periodicities found in each of the frequency-space tiles. This darkfield-tableau strategy has applications in finding patterns (like icosahedral-twin " | ||
+ | |||
+ | For example in the figure below, the tableau (right panel) can be used to identify which diffraction features (center panel) come from which 2D lattice structures (left panel). One can also check this because the diffraction spots are convolved by the lattice shape transform, which is elongate along directions in which the corresponding lattice is narrow. | ||
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+ | {{: | ||
+ | ===== Description ===== | ||
+ | |||
+ | Images ψ[x,y] drawn from only a subset of spatial frequencies in an input image s[x,y] may be obtained by construction of a Fourier-space window-function W[f< | ||
+ | |||
+ | The foregoing might sound like " | ||
+ | |||
+ | However, the spacing between atoms in solids brings with it a level of frequency-fidelity not common in macroscopic images. | ||
+ | |||
+ | ===== Installation ===== | ||
+ | |||
+ | Download java files listed below to the ImageJ plugins folder (or a subfolder like **ElectronJava**), | ||
+ | |||
+ | Note that more recent versions of these routines are in preparation for linkage to this site, so stay tuned... | ||
+ | ===== Download ===== | ||
+ | |||
+ | The digital darkfield macros we'll be describing are text files that use " | ||
+ | |||
+ | Drafts of additional and/or upgraded plugins and macros are available, if you'd like a preliminary look, in the files section of [[https:// | ||
+ | ===== License ===== | ||
+ | |||
+ | This software will be protected by [[http:// | ||
+ | |||
+ | THIS SOFTWARE IS BEING PROVIDED "AS IS", WITHOUT ANY EXPRESS OR IMPLIED WARRANTY. IN PARTICULAR, THE AUTHOR DOES NOT MAKE ANY REPRESENTATION OR WARRANTY OF ANY KIND CONCERNING THE MERCHANTABILITY OF THIS SOFTWARE OR ITS FITNESS FOR ANY PARTICULAR PURPOSE. | ||
+ | |||
+ | ===== Changelog ===== | ||
+ | |||
+ | Page created 26 Mar 2009, mainly with weblinks to related resources. | ||
+ | |||
+ | Better documentation on this wiki, to introduce improved versions of these ImageJ macros and plugins, began in Jan 2014 and is still in progress. | ||
+ | ===== Known Bugs ===== | ||
+ | |||
+ | The early (2007 vintage) StrainMaps_.txt macro did not work well with the xyColorToXY_.java plugin. Thus the XY gradient stack was generally correct, but the component-color (isotropic and shear strain) breakdown was not. A fix for that is in the works, and is already reflected in the zone-plate analysis above. Abilities to handle non-square images, and to provide periodicity-overlays in the calculated images, is also needed and in the works. | ||
+ | ===== References ===== | ||
+ | |||
+ | - P. Fraundorf (2004) " | ||
+ | - P. Fraundorf and Lu Fei (2004) " | ||
+ | - W. Qin and P. Fraundorf (2005) " | ||
+ | - P. Fraundorf, Jinfeng Wang, Eric Mandell and Martin Rose (2006) Microscopy and Microanalysis 12: Supplement 2, 1010-1011. \\ | ||
+ | - Martin Rose and P. Fraundorf (2006) " | ||
+ | - P. Fraundorf, J. Liu and E. Mandell (2007) " | ||
+ | - P. Fraundorf and Somik Mukherjee (2013) " | ||
+ | - Mukherjee S, Ramalingam B, Griggs L, Hamm S, Baker GA, Fraundorf P, Sengupta S, Gangopadhyay S. (2012) " | ||
+ | - P. Fraundorf, Wentao Qin, P. Moeck and Eric Mandell (2005) " | ||
+ | - P. Wang, A. L. Bleloch, U. Falke and P. J. Goodhew (2006) " | ||
+ | - Wentao Qin and P. Fraundorf (2003) " | ||
+ | - P. Fraundorf, Jinfeng Wang, Eric Mandell and Martin Rose (2006) " | ||
+ | - P. Fraundorf and Chris Bishop (2013) " |
plugin/filter/digital_darkfield_decomposition/start.txt · Last modified: 2019/04/12 13:13 by 127.0.0.1