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: http://www.astro.louisville.edu/software/astroimagej/imagej/api/ij/plugin/filter/ParticleAnalyzer.html
Дата изменения: Thu Dec 2 23:03:10 2010 Дата индексирования: Mon Oct 1 23:57:50 2012 Кодировка: Поисковые слова: п п п п п п п п п п п п п п п п п п п п п п п п п п |
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java.lang.Objectij.plugin.filter.ParticleAnalyzer
public class ParticleAnalyzer
Implements ImageJ's Analyze Particles command.
for each line do for each pixel in this line do if the pixel value is "inside" the threshold range then trace the edge to mark the object do the measurement fill the object with a color outside the threshold range else continue the scan
Field Summary | |
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static int |
ADD_TO_MANAGER
Add particles to ROI Manager. |
protected boolean |
addToManager
|
protected Analyzer |
analyzer
|
static int |
CLEAR_WORKSHEET
Clear ImageJ console before starting. |
static int |
DISPLAY_SUMMARY
Display a summary. |
protected boolean |
displaySummary
|
protected static int |
ELLIPSES
|
static int |
EXCLUDE_EDGE_PARTICLES
Do not measure particles touching edge of image. |
protected boolean |
excludeEdgeParticles
|
protected boolean |
floodFill
|
static int |
FOUR_CONNECTED
Use 4-connected particle tracing. |
protected ImagePlus |
imp
|
static int |
INCLUDE_HOLES
Flood fill to ignore interior holes. |
protected static int |
MASKS
|
protected static int |
NOTHING
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protected static int |
OUTLINES
|
protected boolean |
processStack
|
static int |
RECORD_STARTS
Record starting coordinates so outline can be recreated later using doWand(x,y). |
protected boolean |
recordStarts
|
protected boolean |
resetCounter
|
protected static int |
ROI_MASKS
|
protected ResultsTable |
rt
|
static int |
SHOW_MASKS
Display image containing binary masks of measured particles. |
static int |
SHOW_NONE
Do not display particle outline image. |
static int |
SHOW_OUTLINES
Display image containing outlines of measured particles. |
static int |
SHOW_PROGRESS
Display a progress bar. |
static int |
SHOW_RESULTS
Display results in the ImageJ console. |
static int |
SHOW_ROI_MASKS
Display image containing grayscales masks that identify measured particles. |
static int |
SHOW_SUMMARY
Obsolete |
protected static int |
showChoice
|
protected boolean |
showProgress
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protected boolean |
showResults
|
protected boolean |
showSizeDistribution
|
protected int |
slice
|
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 |
Fields inherited from interface ij.measure.Measurements |
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AREA, AREA_FRACTION, CENTER_OF_MASS, CENTROID, CIRCULARITY, ELLIPSE, FERET, INTEGRATED_DENSITY, INVERT_Y, KURTOSIS, LABELS, LIMIT, MAX_STANDARDS, MEAN, MEDIAN, MIN_MAX, MODE, PERIMETER, RECT, SCIENTIFIC_NOTATION, SHAPE_DESCRIPTORS, SKEWNESS, SLICE, STACK_POSITION, STD_DEV |
Constructor Summary | |
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ParticleAnalyzer()
Default constructor |
|
ParticleAnalyzer(int options,
int measurements,
ResultsTable rt,
double minSize,
double maxSize)
Constructs a ParticleAnalyzer using the default min and max circularity values (0 and 1). |
|
ParticleAnalyzer(int options,
int measurements,
ResultsTable rt,
double minSize,
double maxSize,
double minCirc,
double maxCirc)
Constructs a ParticleAnalyzer. |
Method Summary | |
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boolean |
analyze(ImagePlus imp)
Performs particle analysis on the specified image. |
boolean |
analyze(ImagePlus imp,
ImageProcessor ip)
Performs particle analysis on the specified ImagePlus and ImageProcessor. |
protected void |
drawParticle(ImageProcessor drawIP,
Roi roi,
ImageStatistics stats,
ImageProcessor mask)
Draws a selected particle in a separate image. |
ImagePlus |
getOutputImage()
Returns the "Outlines", "Masks", "Elipses" or "Count Masks" image, or null if "Nothing" is selected in the "Show:" menu. |
void |
run(ImageProcessor ip)
Filters use this method to process the image. |
static void |
savePreferences(java.util.Properties prefs)
Called once when ImageJ quits. |
protected void |
saveResults(ImageStatistics stats,
Roi roi)
Saves statistics for one particle in a results table. |
void |
setHideOutputImage(boolean hideOutputImage)
Set 'hideOutputImage' true to not display the "Show:" image. |
int |
setup(java.lang.String arg,
ImagePlus imp)
This method is called once when the filter is loaded. |
boolean |
showDialog()
Displays a modal options dialog. |
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 SHOW_RESULTS
public static final int SHOW_SUMMARY
public static final int SHOW_OUTLINES
public static final int EXCLUDE_EDGE_PARTICLES
public static final int SHOW_ROI_MASKS
public static final int SHOW_PROGRESS
public static final int CLEAR_WORKSHEET
public static final int RECORD_STARTS
public static final int DISPLAY_SUMMARY
public static final int SHOW_NONE
public static final int INCLUDE_HOLES
public static final int ADD_TO_MANAGER
public static final int SHOW_MASKS
public static final int FOUR_CONNECTED
protected static final int NOTHING
protected static final int OUTLINES
protected static final int MASKS
protected static final int ELLIPSES
protected static final int ROI_MASKS
protected static int showChoice
protected ImagePlus imp
protected ResultsTable rt
protected Analyzer analyzer
protected int slice
protected boolean processStack
protected boolean showResults
protected boolean excludeEdgeParticles
protected boolean showSizeDistribution
protected boolean resetCounter
protected boolean showProgress
protected boolean recordStarts
protected boolean displaySummary
protected boolean floodFill
protected boolean addToManager
Constructor Detail |
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public ParticleAnalyzer(int options, int measurements, ResultsTable rt, double minSize, double maxSize, double minCirc, double maxCirc)
options
- a flag word created by Oring SHOW_RESULTS, EXCLUDE_EDGE_PARTICLES, etc.measurements
- a flag word created by ORing constants defined in the Measurements interfacert
- a ResultsTable where the measurements will be storedminSize
- the smallest particle size in pixelsmaxSize
- the largest particle size in pixelsminCirc
- minimum circularitymaxCirc
- maximum circularitypublic ParticleAnalyzer(int options, int measurements, ResultsTable rt, double minSize, double maxSize)
public ParticleAnalyzer()
Method Detail |
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public int setup(java.lang.String arg, ImagePlus imp)
PlugInFilter
For Plugin-filters specifying the FINAL_PROCESSING flag, the setup method will be called again, this time with arg = "final" after all other processing is done.
setup
in interface PlugInFilter
public void run(ImageProcessor ip)
PlugInFilter
null
.
run
in interface PlugInFilter
public boolean showDialog()
public boolean analyze(ImagePlus imp)
public boolean analyze(ImagePlus imp, ImageProcessor ip)
protected void saveResults(ImageStatistics stats, Roi roi)
protected void drawParticle(ImageProcessor drawIP, Roi roi, ImageStatistics stats, ImageProcessor mask)
public ImagePlus getOutputImage()
public void setHideOutputImage(boolean hideOutputImage)
public static void savePreferences(java.util.Properties prefs)
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