java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.ContourPlot

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class ContourPlot
extends AlgorithmBase
```
The Contours class provides methods to compute contour lines and contour bands from a 2D regular grid of scalar values. See computeContourLines(double[][], double, int) and computeContourBands(double[][], double, double, int, int)

Author:

hageldave

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`static interface`	`ContourPlot.AdaptableView`	The AdaptableView interface defines the `ContourPlot.AdaptableView.setView(Rectangle2D)` method.
`class`	`ContourPlot.BarycentricGradientPaint`	The BarycentricGradientPaint class provides a way to fill a `Shape` with a triangular color gradient.
`class`	`ContourPlot.BarycentricGradientPaintContext`	This class is implements the `PaintContext` for `ContourPlot.BarycentricGradientPaint`.
`class`	`ContourPlot.BlankCanvasFallback`	Fallback implementation for `BlankCanvas` for systems that do not support OpenGL 3 through `org.lwjgl.opengl.awt.AWTGLCanvas` (e.g. macOS).
`static class`	`ContourPlot.BufferedImageFactory`	Class providing convenience methods for converting Images to BufferedImages.
`static class`	`ContourPlot.CharacterAtlas`	The CharacterAtlas class is a texture atlas for looking up character textures.
`static interface`	`ContourPlot.ColorMap`	The ColorMap interface defines discrete mapping from a fixed integer interval [0..N-1] to colors through the `ContourPlot.ColorMap.getColor(int)` method.
`static class`	`ContourPlot.ColorOperations`	The ColorOperations class contains methods for manipulating 32bit ARGB color values.
`class`	`ContourPlot.ColorScheme`	The ColorScheme is responsible for storing and providing color information, which other components can use.
`class`	`ContourPlot.CompleteRenderer`	The `ContourPlot.CompleteRenderer` comprises a `ContourPlot.LinesRenderer`, a `PointsRenderer`, a `ContourPlot.TextRenderer` and a `ContourPlot.TrianglesRenderer`.
`static interface`	`ContourPlot.CoordinateViewListener`	The CoordinateViewListener is a listener that listens on changes to a `ContourPlot.CoordSysRenderer`'s coordinate view (i.e.
`class`	`ContourPlot.CoordSysPanning`	The CoordSysPanning class implements a `MouseListener` and `MouseMotionListener` that realize panning functionality for the coordinate view of the `ContourPlot.CoordSysRenderer`.
`class`	`ContourPlot.CoordSysRenderer`	The CoordSysRenderer is a `ContourPlot.Renderer` that displays a coordinate system.
`class`	`ContourPlot.CoordSysScrollZoom`	The CoordSysScrollZoom class implements a `MouseWheelListener` that realize zooming functionality for the coordinate view of the `ContourPlot.CoordSysRenderer`.
`static class`	`ContourPlot.DefaultColorMap`
`static class`	`ContourPlot.DefaultColorScheme`	Enum containing predefined `ContourPlot.ColorScheme`s, which can be accessed through `ContourPlot.DefaultColorScheme.get()`.
`static class`	`ContourPlot.ExtendedWilkinson`	Implementation of the extended Wilkinson algorithm for tick label positioning.
`static class`	`ContourPlot.FontProvider`
`class`	`ContourPlot.GenericKey`	The GenericKey class can be used as key in `HashMap`s when multiple objects should be combined to a single key.
`class`	`ContourPlot.GenericRenderer<T extends ContourPlot.Renderable>`
`static interface`	`ContourPlot.Glyph`	The Glyph interface has to be implemented by a class that realizes a graphical representation of a 2D point (e.g. a cross or a circle).
`static class`	`ContourPlot.ImageSaver`	Class providing convenience methods for saving Images to file.
`class`	`ContourPlot.Img`	Image class with data stored in an int array.
`static interface`	`ContourPlot.ImgBase<P extends ContourPlot.PixelBase>`	Base interface for imagingkit's Img classes.
`static interface`	`ContourPlot.InteractionConstants`
`static class`	`ContourPlot.Iterators`	Class holding all of the `Iterator` and `Spliterator` classes used in the `ContourPlot.ImgBase` interface.
`static interface`	`ContourPlot.JPlotterCanvas`	This interface defines the methods required by an implementation of a canvas `Component` for use with JPlotter `ContourPlot.Renderer`s such as `BlankCanvas` or `ContourPlot.BlankCanvasFallback`.
`static class`	`ContourPlot.Legend`	The Legend class is `ContourPlot.Renderable` and its own `ContourPlot.Renderer` at once.
`class`	`ContourPlot.Lines`	The Lines class is a collection of linear line segments.
`class`	`ContourPlot.LinesRenderer`	The LinesRenderer is an implementation of the `ContourPlot.GenericRenderer` for `ContourPlot.Lines`.
`static class`	`ContourPlot.Pair<T1,T2>`	Pair class.
`class`	`ContourPlot.ParallelForEachExecutor<T>`	CountedCompleter class for multithreaded execution of a Consumer on a Spliterator.
`static interface`	`ContourPlot.PDFRenderer`	The PDFRenderer interface defines the method `ContourPlot.PDFRenderer.renderPDF(PDDocument, PDPage, int, int, int, int)` which 'renders' the PDFRenderers's content as pdf objects in content streams, i.e. fills content streams with elements and appends them to the specified page.
`class`	`ContourPlot.Pixel`	Pixel class for retrieving a value from an `ContourPlot.Img`.
`static interface`	`ContourPlot.PixelBase`	Basic interface for Pixel classes of `ContourPlot.ImgBase` implementations.
`static class`	`ContourPlot.PixelConvertingSpliterator<P extends ContourPlot.PixelBase,T>`	The PixelConvertingSpliterator enables iterating an `ContourPlot.Img` with a different datatype than `ContourPlot.Pixel` (`ContourPlot.ImgBase.spliterator()`).
`static interface`	`ContourPlot.PixelManipulator<P extends ContourPlot.PixelBase,T>`	The PixelManipulator interface defines an action to be performed on a pixel.
`static class`	`ContourPlot.PointDetails`	Class for storing all the details of a single point to be rendered.
`class`	`ContourPlot.PointeredPoint2D`	The PointeredPoint2D class is an implementation of the `Point2D` class that uses two double arrays of size 1 to store its x and y coordinate.
`class`	`ContourPlot.Points`	The Points class is a collection of 2D points that are to be represented using the same `ContourPlot.Glyph` (the graphical representation of a point).
`static interface`	`ContourPlot.Renderable`	Interface for an object that can be rendered by a `ContourPlot.Renderer` e.g. the `ContourPlot.GenericRenderer`.
`static interface`	`ContourPlot.Renderer`	The Renderer interface defines methods to initialize the renderer, execute a rendering pass, close the renderer.
`class`	`ContourPlot.SegmentDetails`	Specification of a line segment which comprises vertex locations, colors, picking color, and thicknesses.
`static class`	`ContourPlot.SignedDistanceCharacters`	The SignedDistanceCharacters class comprises signed distance fields of a set of characters.
`class`	`ContourPlot.SimpleColorMap`	Implementation of the `ContourPlot.ColorMap` interface.
`class`	`ContourPlot.Text`	Abstract class for `ContourPlot.Renderable`s representing text that can be rendered using the `ContourPlot.TextRenderer`.
`class`	`ContourPlot.TextRenderer`	The TrianglesRenderer is an implementation of the `ContourPlot.GenericRenderer` for `ContourPlot.Text`.
`static interface`	`ContourPlot.TickMarkGenerator`	The TickMarkGenerator interface provides the `ContourPlot.TickMarkGenerator.genTicksAndLabels(double, double, int, boolean)` method.
`class`	`ContourPlot.TranslatedPoint2D`	The TranslatedPoint2D is an implementation of `Point2D` that references another Point2D and has a certain fixed translation from that point.
`class`	`ContourPlot.TriangleDetails`	Specification of a triangle which comprises vertex locations, colors and picking color.
`class`	`ContourPlot.Triangles`	The Triangles class is a collection of 2D triangles.
`class`	`ContourPlot.TrianglesRenderer`	The TrianglesRenderer is an implementation of the `ContourPlot.GenericRenderer` for `ContourPlot.Triangles`.
`static class`	`ContourPlot.Utils`	Class containing utility methods

Nested classes/interfaces inherited from class java.lang.Thread
java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Field Summary

Fields
Modifier and Type Field Description

private static ContourPlot cp
Example from source ContourPlot.java draws contour plot of function surface correctly.
- Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
  destFlag, destImage, image25D, mask, maxProgressValue, minProgressValue, multiThreadingEnabled, nthreads, progress, progressModulus, progressStep, runningInSeparateThread, separable, srcImage, threadStopped
- Fields inherited from class java.lang.Thread
  MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors
Constructor Description

ContourPlot()

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`static int`	`a(int color)`
`static double`	`a_normalized(int color)`
`static int`	`argb_bounded(int a, int r, int g, int b)`	Packs 8bit ARGB color components into a single 32bit integer value.
`static int`	`argb_fast(int a, int r, int g, int b)`	Packs 8bit ARGB color components into a single 32bit integer value.
`static int`	`argb_fromNormalized(double a, double r, double g, double b)`	Packs normalized ARGB color components (values in [0.0 .. 1.0]) into a single 32bit integer value.
`static int`	`b(int color)`
`static double`	`b_normalized(int color)`
`(package private) static int`	`celltype(boolean v1, boolean v2, boolean v3)`
`(package private) static int`	`celltype(boolean v11, boolean v21, boolean v31, boolean v12, boolean v22, boolean v32)`
`static double`	`clamp_0_1(double val)`	Clamps a value to the range [0.0, 1.0].
`int`	`clamp_0_255(int val)`	Clamps a value to the range [0,255].
`static java.util.List<ContourPlot.TriangleDetails>`	`computeContourBands(double[][] X, double[][] Y, double[][] Z, double isoValue1, double isoValue2, int c1, int c2)`	Computes the contour bands from the grid samples of a bivariate function z(x,y).
`static java.util.List<ContourPlot.TriangleDetails>`	`computeContourBands(double[][] uniformGridSamples, double isoValue1, double isoValue2, int c1, int c2)`	Computes the contour bands from the grid samples of a bivariate function z(x,y) with implicit integer valued (x,y) = (i,j). The resulting triangles are solutions to the equation { (x,y) \| iso1 < z(x,y) < iso2 } within the grid.
`static java.util.List<ContourPlot.SegmentDetails>`	`computeContourLines(double[][] X, double[][] Y, double[][] Z, double isoValue, int color)`	Computes the contour lines from the grid samples of a bivariate function z(x,y).
`static java.util.List<ContourPlot.SegmentDetails>`	`computeContourLines(double[][] uniformGridSamples, double isoValue, int color)`	Computes the contour lines from the grid samples of a bivariate function z(x,y) with implicit integer valued (x,y) = (i,j). The resulting line segments are solutions to the equation { (x,y) \| z(x,y)=iso } within the grid.
`static int`	`g(int color)`
`static double`	`g_normalized(int color)`
`static int`	`interpolateColor(int c1, int c2, double m)`	Linearly interpolates between the two specified colors. c = c1(1-m) + c2m
`(package private) static double`	`interpolateToValue(double lower, double upper, double iso)`	Returns m of the equation: iso = lower(1-m) + upperm which is: m = (iso-lower)/(upper-lower)
`static int`	`r(int color)`
`static double`	`r_normalized(int color)`
`static void`	`requireAreaInImageBounds(int xStart, int yStart, int width, int height, ContourPlot.ImgBase<?> img)`	Throws an `IllegalArgumentException` when the specified area is not within the bounds of the specified image, or if the area is not positive.
`static int`	`rgb_bounded(int r, int g, int b)`	Packs 8bit RGB color components into a single 32bit ARGB integer value with alpha=255 (opaque).
`static int`	`rgb_fast(int r, int g, int b)`	Packs 8bit RGB color components into a single 32bit ARGB integer value with alpha=255 (opaque).
`static int`	`rgb_fromNormalized(double r, double g, double b)`	Packs normalized ARGB color components (values in [0.0 .. 1.0]) into a single 32bit integer value with alpha=255 (opaque).
`void`	`runAlgorithm()`	Actually runs the algorithm.
`void`	`testContourPlot()`
`void`	`testIsolinesViz()`

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
actionPerformed, addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, finalize, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, generateProgressValues, getDestImage, getElapsedTime, getMask, getMaxProgressValue, getMinProgressValue, getNumberOfThreads, getProgress, getProgressChangeListener, getProgressChangeListeners, getProgressModulus, getProgressStep, getProgressValues, getSrcImage, isCompleted, isImage25D, isMultiThreadingEnabled, isRunningInSeparateThread, isThreadStopped, linkProgressToAlgorithm, linkProgressToAlgorithm, makeProgress, notifyListeners, removeListener, removeProgressChangeListener, run, setCompleted, setImage25D, setMask, setMaxProgressValue, setMinProgressValue, setMultiThreadingEnabled, setNumberOfThreads, setProgress, setProgressModulus, setProgressStep, setProgressValues, setProgressValues, setRunningInSeparateThread, setSrcImage, setStartTime, setThreadStopped, startMethod, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened

Methods inherited from class java.lang.Thread
activeCount, checkAccess, clone, countStackFrames, currentThread, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, suspend, toString, yield

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - cp
```
private static ContourPlot cp
```
    Example from source ContourPlot.java draws contour plot of function surface correctly. Need to work on example in IsolinesViz.java.
- Constructor Detail
  - ContourPlot
```
public ContourPlot()
```
- Method Detail
  - testIsolinesViz
```
public void testIsolinesViz()
```
  - testContourPlot
```
public void testContourPlot()
```
  - runAlgorithm
```
public void runAlgorithm()
```
    Description copied from class: AlgorithmBase
    
    Actually runs the algorithm. Implemented by inheriting algorithms.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
  - b
```
public static final int b(int color)
```
    Parameters:
    
    color - ARGB(32bit) or RGB(24bit) value
    
    Returns:
    
    blue component(8bit) of specified color.
    
    Since:
    
    1.0
    
    See Also:
    
    a(int), r(int), g(int), #argb(int, int, int, int), #rgb(int, int, int)
  - g
```
public static final int g(int color)
```
    Parameters:
    
    color - ARGB(32bit) or RGB(24bit) value
    
    Returns:
    
    green component(8bit) of specified color.
    
    Since:
    
    1.0
    
    See Also:
    
    a(int), r(int), b(int), #argb(int, int, int, int), #rgb(int, int, int)
  - r
```
public static final int r(int color)
```
    Parameters:
    
    color - ARGB(32bit) or RGB(24bit) value
    
    Returns:
    
    red component(8bit) of specified color.
    
    Since:
    
    1.0
    
    See Also:
    
    a(int), g(int), b(int), #argb(int, int, int, int), #rgb(int, int, int)
  - a
```
public static final int a(int color)
```
    Parameters:
    
    color - ARGB(32bit) value
    
    Returns:
    
    alpha component(8bit) of specified color.
    
    Since:
    
    1.0
    
    See Also:
    
    r(int), g(int), b(int), #argb(int, int, int, int), #rgb(int, int, int)
  - b_normalized
```
public static final double b_normalized(int color)
```
    Parameters:
    
    color - ARGB(32bit) or RGB(24bit) value
    
    Returns:
    
    normalized blue component of specified color
    (value in [0.0 .. 1.0]).
    
    Since:
    
    1.2
    
    See Also:
    
    #b(), r_normalized(int), g_normalized(int), a_normalized(int)
  - g_normalized
```
public static final double g_normalized(int color)
```
    Parameters:
    
    color - ARGB(32bit) or RGB(24bit) value
    
    Returns:
    
    normalized green component of specified color
    (value in [0.0 .. 1.0]).
    
    Since:
    
    1.2
    
    See Also:
    
    #g(), r_normalized(int), b_normalized(int), a_normalized(int)
  - r_normalized
```
public static final double r_normalized(int color)
```
    Parameters:
    
    color - ARGB(32bit) or RGB(24bit) value
    
    Returns:
    
    normalized red component of specified color
    (value in [0.0 .. 1.0]).
    
    Since:
    
    1.2
    
    See Also:
    
    #r(), b_normalized(int), g_normalized(int), a_normalized(int)
  - a_normalized
```
public static final double a_normalized(int color)
```
    Parameters:
    
    color - ARGB(32bit) value
    
    Returns:
    
    normalized alpha component of specified color
    (value in [0.0 .. 1.0]).
    
    Since:
    
    1.2
    
    See Also:
    
    #a(), r_normalized(int), g_normalized(int), a_normalized(int)
  - argb_fast
```
public static final int argb_fast(int a,
                                  int r,
                                  int g,
                                  int b)
```
    Packs 8bit ARGB color components into a single 32bit integer value. Components larger than 8bit are NOT truncated and will result in a broken, malformed value.
    
    Parameters:
    
    a - alpha
    
    r - red
    
    g - green
    
    b - blue
    
    Returns:
    
    packed ARGB value
    
    Since:
    
    1.0
    
    See Also:
    
    #argb(int, int, int, int), argb_bounded(int, int, int, int), rgb_bounded(int, int, int), #rgb(int, int, int), rgb_fast(int, int, int), a(int), r(int), g(int), b(int)
  - argb_bounded
```
public static final int argb_bounded(int a,
                                     int r,
                                     int g,
                                     int b)
```
    Packs 8bit ARGB color components into a single 32bit integer value. Components are clamped to [0,255].
    
    Parameters:
    
    a - alpha
    
    r - red
    
    g - green
    
    b - blue
    
    Returns:
    
    packed ARGB value
    
    Since:
    
    1.0
    
    See Also:
    
    #argb(int, int, int, int), argb_fast(int, int, int, int), rgb_bounded(int, int, int), #rgb(int, int, int), rgb_fast(int, int, int), a(int), r(int), g(int), b(int)
  - argb_fromNormalized
```
public static final int argb_fromNormalized(double a,
                                            double r,
                                            double g,
                                            double b)
```
    Packs normalized ARGB color components (values in [0.0 .. 1.0]) into a single 32bit integer value. Component values less than 0 or greater than 1 are clamped to fit the range.
    
    Parameters:
    
    a - alpha
    
    r - red
    
    g - green
    
    b - blue
    
    Returns:
    
    packed ARGB value
    
    Since:
    
    1.2
    
    See Also:
    
    rgb_fromNormalized(double, double, double), #argb(int, int, int, int), a_normalized(int), r_normalized(int), g_normalized(int), b_normalized(int)
  - rgb_fast
```
public static final int rgb_fast(int r,
                                 int g,
                                 int b)
```
    Packs 8bit RGB color components into a single 32bit ARGB integer value with alpha=255 (opaque). Components larger than 8bit are NOT truncated and will result in a broken, malformed value.
    
    Parameters:
    
    r - red
    
    g - green
    
    b - blue
    
    Returns:
    
    packed ARGB value
    
    Since:
    
    1.0
    
    See Also:
    
    #argb(int, int, int, int), argb_bounded(int, int, int, int), argb_fast(int, int, int, int), rgb_bounded(int, int, int), #rgb(int, int, int), a(int), r(int), g(int), b(int)
  - rgb_bounded
```
public static final int rgb_bounded(int r,
                                    int g,
                                    int b)
```
    Packs 8bit RGB color components into a single 32bit ARGB integer value with alpha=255 (opaque). Components are clamped to [0,255].
    
    Parameters:
    
    r - red
    
    g - green
    
    b - blue
    
    Returns:
    
    packed ARGB value
    
    Since:
    
    1.0
    
    See Also:
    
    #argb(int, int, int, int), argb_bounded(int, int, int, int), argb_fast(int, int, int, int), #rgb(int, int, int), rgb_fast(int, int, int), a(int), r(int), g(int), b(int)
  - rgb_fromNormalized
```
public static final int rgb_fromNormalized(double r,
                                           double g,
                                           double b)
```
    Packs normalized ARGB color components (values in [0.0 .. 1.0]) into a single 32bit integer value with alpha=255 (opaque). Component values less than 0 or greater than 1 clamped to fit the range.
    
    Parameters:
    
    r - red
    
    g - green
    
    b - blue
    
    Returns:
    
    packed ARGB value
    
    Since:
    
    1.2
    
    See Also:
    
    argb_fromNormalized(double, double, double, double), #rgb(int, int, int), a_normalized(int), r_normalized(int), g_normalized(int), b_normalized(int)
  - interpolateColor
```
public static int interpolateColor(int c1,
                                   int c2,
                                   double m)
```
    Linearly interpolates between the two specified colors.
    c = c1*(1-m) + c2*m
    
    Parameters:
    
    c1 - integer packed ARGB color value
    
    c2 - integer packed ARGB color value, e.g. 0xff00ff00 for opaque green
    
    m - in [0,1]
    
    Returns:
    
    interpolated color
  - computeContourLines
```
public static java.util.List<ContourPlot.SegmentDetails> computeContourLines(double[][] X,
                                                                             double[][] Y,
                                                                             double[][] Z,
                                                                             double isoValue,
                                                                             int color)
```
    Computes the contour lines from the grid samples of a bivariate function z(x,y). The resulting line segments are solutions to the equation { (x,y) | z(x,y)=iso } within the grid.
    About indices For cartesian or rectilinear grids, x varies with the inner index of the 2D array, y with the outer index:
    X_ij=X[i][j]=X[?][j].
    Y_ij=Y[i][j]=Y[i][?]
    
    Parameters:
    
    X - x-coordinates of the grid points ( (x,y,z)_ij = (X_ij,Y_ij,Z_ij) )
    
    Y - y-coordinates of the grid points ( (x,y,z)_ij = (X_ij,Y_ij,Z_ij) )
    
    Z - z-coordinates of the grid points ( (x,y,z)_ij = (X_ij,Y_ij,Z_ij) )
    
    isoValue - the iso value for which the contour (iso) lines should be computed
    
    color - integer packed ARGB color value the returned line segments should have, e.g. 0xff00ff00 for opaque green.
    
    Returns:
    
    list of line segments that form the contour lines. There is no particular order so subsequent segments are not necessarily adjacent.
  - computeContourBands
```
public static java.util.List<ContourPlot.TriangleDetails> computeContourBands(double[][] X,
                                                                              double[][] Y,
                                                                              double[][] Z,
                                                                              double isoValue1,
                                                                              double isoValue2,
                                                                              int c1,
                                                                              int c2)
```
    Computes the contour bands from the grid samples of a bivariate function z(x,y). The resulting triangles are solutions to the equation { (x,y) | iso1 < z(x,y) < iso2 } within the grid.
    About indices For cartesian or rectilinear grids, x varies with the inner index of the 2D array, y with the outer index:
    X_ij=X[i][j]=X[?][j].
    Y_ij=Y[i][j]=Y[i][?]
    
    Parameters:
    
    X - x-coordinates of the grid points ( (x,y,z)_ij = (X_ij,Y_ij,Z_ij) )
    
    Y - y-coordinates of the grid points ( (x,y,z)_ij = (X_ij,Y_ij,Z_ij) )
    
    Z - z-coordinates of the grid points ( (x,y,z)_ij = (X_ij,Y_ij,Z_ij) )
    
    isoValue1 - the lower bound for values of the iso bands
    
    isoValue2 - the upper bound for values of the iso bands
    
    c1 - color for the isoValue1
    
    c2 - color for the isoValue2, values in between iso1 and iso2 will have their color linearly interpolated
    
    Returns:
    
    list of triangles that form the iso bands. The order of triangles does NOT imply any adjacency between them.
  - computeContourLines
```
public static java.util.List<ContourPlot.SegmentDetails> computeContourLines(double[][] uniformGridSamples,
                                                                             double isoValue,
                                                                             int color)
```
    Computes the contour lines from the grid samples of a bivariate function z(x,y)
    with implicit integer valued (x,y) = (i,j).
    The resulting line segments are solutions to the equation { (x,y) | z(x,y)=iso } within the grid.
    The lines are computed using the Meandering Triangles algorithm which divides each square cell of the grid into 2 triangle cells first before computing isovalue intersections on the triangle sides. The more well known Marching Squares algorithm has significantly more cell cases to check, which is why Meandering Triangles was preferred here.
    
    Parameters:
    
    uniformGridSamples - z-coordinates of the grid points ( (x,y,z)_ij = (i,j,Z_ij) )
    
    isoValue - the iso value for which the contour (iso) lines should be computed
    
    color - integer packed ARGB color value the returned line segments should have, e.g. 0xff00ff00 for opaque green.
    
    Returns:
    
    list of line segments that form the contour lines. There is no particular order so subsequent segments are not necessarily adjacent.
  - computeContourBands
```
public static java.util.List<ContourPlot.TriangleDetails> computeContourBands(double[][] uniformGridSamples,
                                                                              double isoValue1,
                                                                              double isoValue2,
                                                                              int c1,
                                                                              int c2)
```
    Computes the contour bands from the grid samples of a bivariate function z(x,y)
    with implicit integer valued (x,y) = (i,j).
    The resulting triangles are solutions to the equation { (x,y) | iso1 < z(x,y) < iso2 } within the grid.
    The triangles are computed using the Meandering Triangles algorithm which divides each square cell of the grid into 2 triangle cells first before computing isovalue intersections on the triangle sides. The more well known Marching Squares algorithm has significantly more cell cases to check, which is why Meandering Triangles was preferred here.
    
    Parameters:
    
    uniformGridSamples - z-coordinates of the grid points ( (x,y,z)_ij = (i,j,Z_ij) )
    
    isoValue1 - the lower bound for values of the iso bands
    
    isoValue2 - the upper bound for values of the iso bands
    
    c1 - color for the isoValue1
    
    c2 - color for the isoValue2, values in between iso1 and iso2 will have their color linearly interpolated
    
    Returns:
    
    list of triangles that form the iso bands. The order of triangles does NOT imply any adjacency between them.
  - celltype
```
static int celltype(boolean v1,
                    boolean v2,
                    boolean v3)
```
  - celltype
```
static int celltype(boolean v11,
                    boolean v21,
                    boolean v31,
                    boolean v12,
                    boolean v22,
                    boolean v32)
```
  - interpolateToValue
```
static double interpolateToValue(double lower,
                                 double upper,
                                 double iso)
```
    Returns m of the equation: iso = lower*(1-m) + upper*m
    which is: m = (iso-lower)/(upper-lower)
    
    Parameters:
    
    lower - value
    
    upper - value
    
    iso - value in between lower and upper
    
    Returns:
    
    m
  - clamp_0_255
```
public final int clamp_0_255(int val)
```
    Clamps a value to the range [0,255]. Returns 0 for values less than 0, 255 for values greater than 255, and the value it self when in range.
    
    Parameters:
    
    val - value to be clamped
    
    Returns:
    
    value clamped to [0,255]
  - clamp_0_1
```
public static double clamp_0_1(double val)
```
    Clamps a value to the range [0.0, 1.0]. Returns 0.0 for values less than 0, 1.0 for values greater than 1.0, and the value it self when in range.
    
    Parameters:
    
    val - value to be clamped
    
    Returns:
    
    value clamped to [0.0, 1.0]
  - requireAreaInImageBounds
```
public static void requireAreaInImageBounds(int xStart,
                                            int yStart,
                                            int width,
                                            int height,
                                            ContourPlot.ImgBase<?> img)
```
    Throws an IllegalArgumentException when the specified area is not within the bounds of the specified image, or if the area is not positive. This is used for parameter evaluation.
    
    Parameters:
    
    xStart - left boundary of the area
    
    yStart - top boundary of the area
    
    width - of the area
    
    height - of the area
    
    img - the area has to fit in.
    
    Throws:
    
    java.lang.IllegalArgumentException - when area not in image bounds or not area not positive

Class ContourPlot

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread

Field Summary

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

Fields inherited from class java.lang.Thread

Constructor Summary

Method Summary

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

Methods inherited from class java.lang.Thread

Methods inherited from class java.lang.Object

Field Detail

cp

Constructor Detail

ContourPlot

Method Detail

testIsolinesViz

testContourPlot

runAlgorithm

b

g

r

a

b_normalized

g_normalized

r_normalized

a_normalized

argb_fast

argb_bounded

argb_fromNormalized

rgb_fast

rgb_bounded

rgb_fromNormalized

interpolateColor

computeContourLines

computeContourBands

computeContourLines

computeContourBands

celltype

celltype

interpolateToValue

clamp_0_255

clamp_0_1

requireAreaInImageBounds