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: http://www.astro.louisville.edu/software/astroimagej/imagej/api/ij/plugin/filter/EDM.html
Дата изменения: Thu Dec 2 23:03:11 2010 Дата индексирования: Mon Oct 1 23:06:02 2012 Кодировка: Поисковые слова: п п п п п п п п |
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java.lang.Objectij.plugin.filter.EDM
public class EDM
This plugin implements the Euclidean Distance Map (EDM), Watershed, Ultimate Eroded Points and Voronoi commands in the Process/Binary submenu. - Euclidean Distance Map: The value of each pixel is the distance to the nearest background pixel (for background pixels, the EDM is 0) - Ultimate Eroded Points (UEPs) are maxima of the EDM. In the output, the points are assigned the EDM value, which is equal to the radius of the largest circle that fits into the particle, with the UEP as the center. - Watershed segmentation of the EDM splits particles at "necks"; starting at maxima of the EDM. - 'Voronoi' splits the image by lines of points having equal distance to the borders of the two nearest particles. Thus, the Voronoi cell of each particle includes all points that are nearer to this particle than any other particle. For the case of the priticles being single points, this is a Voronoi tessellation (also known as Dirichlet tessellation). In the output, the value inside the Voronoi cells is zero; the pixel values of the dividing lines between the cells are equal to the distance to the two nearest particles. This is similar to a medial axis transform of the background, but there are no lines in inner holes of particles. Watershed, Ultimate Eroded Points and Voronoi are handled by the MaximumFinder plugin applied to the EDM Note: These functions do not take ROIs into account. Setup is called with argument "" (empty string) for EDM, "watershed" for watershed segmentation, "points" for ultimate eroded points and "voronoi" for Voronoi segmentation of the background The EDM algorithm is similar to the 8SSEDT in F. Leymarie, M. D. Levine, in: CVGIP Image Understanding, vol. 55 (1992), pp 84-94 http://dx.doi.org/10.1016/1049-9660(92)90008-Q The algorithm provides a fast approximation of the EDM, with the deviation from a full calculation being between -0.09 and 0. The algorithm is exact for distances<13. For d>=13, deviations from the true result can occur, but are very rare: typically the fraction of pixels deviating from the exact result is in the 10^-5 range, with most deviations between -0.03 and -0.04. Limitations: Maximum image diagonal for EDM: 46340 pixels (sqrt(2^31)); if the particles are dense enough it also works for width, height <=65534. Version 30-Apr-2008 Michael Schmid: more accurate EDM algorithm, 16-bit and float output possible, parallel processing for stacks Voronoi output added
Field Summary | |
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static int |
BYTE
Output type: new 8-bit image |
static int |
BYTE_OVERWRITE
Output type: overwrite current 8-bit image |
static int |
FLOAT
Output type: new 32-bit image |
static int |
ONE
Unit in old make16bitEDM: this pixel value corresponds to a distance of one pixel. |
static int |
SHORT
Output type: new 16-bit image |
static int |
SQRT2
In old make16bitEDM this pixel value corresponds to a pixel distance of sqrt(2) |
static int |
SQRT5
In old make16bitEDM this pixel value corresponds to a pixel distance of sqrt(5) |
Fields inherited from interface ij.plugin.filter.ExtendedPlugInFilter |
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KEEP_PREVIEW |
Fields inherited from interface ij.plugin.filter.PlugInFilter |
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CONVERT_TO_FLOAT, DOES_16, DOES_32, DOES_8C, DOES_8G, DOES_ALL, DOES_RGB, DOES_STACKS, DONE, FINAL_PROCESSING, KEEP_THRESHOLD, NO_CHANGES, NO_IMAGE_REQUIRED, NO_UNDO, PARALLELIZE_STACKS, ROI_REQUIRED, SNAPSHOT, STACK_REQUIRED, SUPPORTS_MASKING |
Constructor Summary | |
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EDM()
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Method Summary | |
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static int |
getOutputType()
Returns the current output type (BYTE_OVERWRITE, BYTE, SHORT or FLOAT) |
ShortProcessor |
make16bitEDM(ImageProcessor ip)
Calculates a 16-bit grayscale Euclidean Distance Map for a binary 8-bit image. |
FloatProcessor |
makeFloatEDM(ImageProcessor ip,
int backgroundValue,
boolean edgesAreBackground)
Creates the Euclidian Distance Map of a (binary) byte image. |
void |
run(ImageProcessor ip)
Called by the PlugInFilterRunner to process the image or one frame of a stack |
void |
setNPasses(int nPasses)
Prepare the progress bar. |
static void |
setOutputType(int type)
Sets the output type (BYTE_OVERWRITE, BYTE, SHORT or FLOAT) |
int |
setup(java.lang.String arg,
ImagePlus imp)
Prepare for processing; also called at the very end with argument 'final' to show any newly created output image. |
int |
showDialog(ImagePlus imp,
java.lang.String command,
PlugInFilterRunner pfr)
Called by the PlugInFilterRunner after setup. |
void |
toEDM(ImageProcessor ip)
Converts a binary image into a 8-bit grayscale Euclidean Distance Map (EDM). |
void |
toWatershed(ImageProcessor ip)
Do watershed segmentation based on the EDM of the foreground objects (nonzero pixels) in an 8-bit image. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final int BYTE_OVERWRITE
public static final int BYTE
public static final int SHORT
public static final int FLOAT
public static final int ONE
public static final int SQRT2
public static final int SQRT5
Constructor Detail |
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public EDM()
Method Detail |
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public int setup(java.lang.String arg, ImagePlus imp)
setup
in interface PlugInFilter
public int showDialog(ImagePlus imp, java.lang.String command, PlugInFilterRunner pfr)
showDialog
in interface ExtendedPlugInFilter
imp
- The active image already passed in the
setup(arg, imp)
call. It will be null, however, if
the NO_IMAGE_REQUIRED
flag has been set.command
- The command that has led to the invocation of
the plugin-filter. Useful as a title for the dialog.pfr
- The PlugInFilterRunner calling this plugin-filter.
It can be passed to a GenericDialog by addPreviewCheckbox
to enable preview by calling the run(ip)
method of this
plugin-filter. pfr
can be also used later for calling back
the PlugInFilterRunner, e.g., to obtain the slice number
currently processed by run(ip)
.
PlugInFilter
and
ExtendedPlugInFilter
.public void run(ImageProcessor ip)
run
in interface PlugInFilter
public void setNPasses(int nPasses)
setNPasses
in interface ExtendedPlugInFilter
nPasses
- Number of images that this EDM will process.public void toEDM(ImageProcessor ip)
public void toWatershed(ImageProcessor ip)
public ShortProcessor make16bitEDM(ImageProcessor ip)
public FloatProcessor makeFloatEDM(ImageProcessor ip, int backgroundValue, boolean edgesAreBackground)
ip
- The input image, not modified; must be a ByteProcessor.backgroundValue
- Pixels in the input with this value are interpreted as background.
Note: for pixel value 255, write either -1 or (byte)255.edgesAreBackground
- Whether out-of-image pixels are considered background
public static void setOutputType(int type)
public static int getOutputType()
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