Module ij
Package ij.process

Class ImageProcessor

    • Constructor Summary

      Constructors 
      Constructor Description
      ImageProcessor()  
    • Method Summary

      All Methods Static Methods Instance Methods Abstract Methods Concrete Methods Deprecated Methods 
      Modifier and Type Method Description
      void abs()
      If this is a 32-bit or signed 16-bit image, performs an absolute value transform, otherwise does nothing.
      void add​(double value)
      Adds 'value' to each pixel in the image or ROI.
      void add​(int value)
      Adds 'value' to each pixel in the image or ROI.
      void and​(int value)
      Binary AND of each pixel in the image or ROI with 'value'.
      void applyMacro​(java.lang.String macro)
      Uses the Process/Math/Macro command to apply macro code to this image.
      abstract void applyTable​(int[] lut)
      Transforms the image or ROI using a lookup table.
      void autoThreshold()
      Converts the image to binary using an automatically determined threshold.
      ImageProcessor bin​(int shrinkFactor)
      Returns a copy of this image that has been reduced in size using binning.
      void blurGaussian​(double sigma)
      Blurs the image by convolving with a Gaussian function.
      java.lang.Object clone()
      Returns a shallow copy of this ImageProcessor, where this image and the copy share pixel data.
      ImageProcessor convertToByte​(boolean doScaling)
      Returns an 8-bit version of this image as a ByteProcessor.
      ByteProcessor convertToByteProcessor()
      Returns an 8-bit version of this image as a ByteProcessor.
      ByteProcessor convertToByteProcessor​(boolean scale)
      Returns an 8-bit version of this image as a ByteProcessor.
      ColorProcessor convertToColorProcessor()
      Returns an RGB version of this image as a ColorProcessor.
      ImageProcessor convertToFloat()
      Returns a 32-bit float version of this image as a FloatProcessor.
      FloatProcessor convertToFloatProcessor()
      Returns a 32-bit float version of this image as a FloatProcessor.
      ImageProcessor convertToRGB()
      Returns an RGB version of this image as a ColorProcessor.
      ImageProcessor convertToShort​(boolean doScaling)
      Returns a 16-bit version of this image as a ShortProcessor.
      ShortProcessor convertToShortProcessor()
      Returns a 16-bit version of this image as a ShortProcessor.
      ShortProcessor convertToShortProcessor​(boolean scale)
      Returns a 16-bit version of this image as a ShortProcessor.
      abstract void convolve​(float[] kernel, int kernelWidth, int kernelHeight)
      Performs a convolution operation using the specified kernel.
      abstract void convolve3x3​(int[] kernel)
      Convolves the image or ROI with the specified 3x3 integer convolution kernel.
      abstract void copyBits​(ImageProcessor ip, int xloc, int yloc, int mode)
      Copies the image contained in 'ip' to (xloc, yloc) using one of the transfer modes defined in the Blitter interface.
      abstract java.awt.Image createImage()
      Returns a copy of this image is the form of an AWT Image.
      ByteProcessor createMask()
      Returns a binary mask, or null if a threshold is not set or this is an RGB image.
      abstract ImageProcessor createProcessor​(int width, int height)
      Returns a new, blank processor with the specified width and height.
      abstract ImageProcessor crop()
      Returns a new processor containing an image that corresponds to the current ROI.
      static double cubic​(double x)  
      abstract void dilate()
      Dilates the image or ROI using a 3x3 minimum filter.
      void draw​(Roi roi)
      Draws the specified ROI on this image using the line width and color defined by ip.setLineWidth() and ip.setColor().
      void drawDot​(int xcenter, int ycenter)
      Draws a dot using the current line width and fill/draw value.
      void drawDot2​(int x, int y)
      Deprecated. 
      void drawLine​(int x1, int y1, int x2, int y2)
      Draws a line from (x1,y1) to (x2,y2).
      void drawLine4​(int x1, int y1, int x2, int y2)  
      void drawOval​(int x, int y, int width, int height)
      Draws an elliptical shape.
      void drawOverlay​(Overlay overlay)
      Draws the specified Overlay on this image.
      abstract void drawPixel​(int x, int y)
      Sets the pixel at (x,y) to the current fill/draw value.
      void drawPolygon​(java.awt.Polygon p)
      Draws a polygon.
      void drawRect​(int x, int y, int width, int height)
      Draws a rectangle.
      void drawRoi​(Roi roi)
      Draws the specified ROI on this image using the stroke width, stroke color and fill color defined by roi.setStrokeWidth, roi.setStrokeColor() and roi.setFillColor().
      void drawString​(java.lang.String s)
      Draws a string at the current drawing location using the current fill/draw value.
      void drawString​(java.lang.String s, int x, int y)
      Draws a string at the specified location using the current fill/draw value.
      void drawString​(java.lang.String s, int x, int y, java.awt.Color background)
      Draws a string at the specified location with a filled background.
      abstract ImageProcessor duplicate()
      Returns a duplicate of this image.
      abstract void erode()
      Erodes the image or ROI using a 3x3 maximum filter.
      void exp()
      Performs a exponential transform on the image or ROI.
      void fill()
      Fills the image or ROI bounding rectangle with the current fill/draw value.
      void fill​(Roi roi)
      Fills the ROI with the current fill/draw value.
      abstract void fill​(ImageProcessor mask)
      Fills pixels that are within the ROI bounding rectangle and part of the mask (i.e.
      void fillOutside​(Roi roi)
      Fills outside an Roi.
      void fillOval​(int x, int y, int width, int height)
      Fills an elliptical shape.
      void fillPolygon​(java.awt.Polygon p)
      Fills a polygon.
      void fillRect​(int x, int y, int width, int height)
      Fills a rectangle.
      boolean fillValueSet()
      Returns 'true' if the fill/draw value has been set.
      abstract void filter​(int type)
      A 3x3 filter operation, where the argument (BLUR_MORE, FIND_EDGES, MEDIAN_FILTER, MIN or MAX) determines the filter type.
      void findEdges()
      Finds edges in the image or ROI using a Sobel operator.
      void flipHorizontal()
      Flips the image or ROI horizontally.
      abstract void flipVertical()
      Flips the image or ROI vertically.
      void gamma​(double value)
      Performs gamma correction of the image or ROI.
      abstract int get​(int index)  
      abstract int get​(int x, int y)
      This is a faster version of getPixel() that does not do bounds checking.
      int getAutoThreshold()
      Returns a pixel value (threshold) that can be used to divide the image into objects and background.
      int getAutoThreshold​(int[] histogram)
      This is a version of getAutoThreshold() that uses a histogram passed as an argument.
      abstract double getBackgroundValue()
      Returns the background fill value.
      int getBestIndex​(java.awt.Color c)
      Returns the LUT index that's the best match for this color.
      double getBicubicInterpolatedPixel​(double x0, double y0, ImageProcessor ip2)
      This method is from Chapter 16 of "Digital Image Processing: An Algorithmic Introduction Using Java" by Burger and Burge (http://www.imagingbook.com/).
      int getBitDepth()
      Returns the bit depth, 8, 16, 24 (RGB) or 32.
      java.awt.image.BufferedImage getBufferedImage()
      Returns this image as a BufferedImage.
      float[] getCalibrationTable()
      Returns the calibration table or null.
      java.awt.image.ColorModel getColorModel()
      Returns this processor's color model.
      float[] getColumn​(int x, int y, float[] data, int length)
      Returns the pixel values down the column starting at (x,y).
      void getColumn​(int x, int y, int[] data, int length)
      Returns the pixel values down the column starting at (x,y).
      java.awt.image.ColorModel getCurrentColorModel()
      Returns the current color model, which may have been modified by setMinAndMax() or setThreshold().
      java.awt.image.IndexColorModel getDefaultColorModel()
      Returns the default grayscale IndexColorModel.
      abstract float getf​(int index)  
      abstract float getf​(int x, int y)
      Returns the value of the pixel at (x,y) as a float.
      float[][] getFloatArray()
      Returns a copy of the pixel data as a 2D float array with dimensions [x=0..width-1][y=0..height-1].
      java.awt.Font getFont()
      Returns the current font.
      java.awt.FontMetrics getFontMetrics()
      Returns the current FontMetrics.
      abstract double getForegroundValue()
      Returns the default fill/draw value.
      int getHeight()
      Returns the height of this image in pixels.
      abstract int[] getHistogram()
      Returns the histogram of the image or ROI.
      int[] getHistogram​(int nBins)
      Returns the histogram of the image or ROI, using the specified number of bins.
      double getHistogramMax()
      Returns the maximum histogram value used for histograms of float images.
      double getHistogramMin()
      Returns the minimum histogram value used for histograms of float images.
      int getHistogramSize()
      Returns the number of float image histogram bins.
      protected java.awt.image.SampleModel getIndexSampleModel()  
      int[][] getIntArray()
      Returns a copy of the pixel data as a 2D int array with dimensions [x=0..width-1][y=0..height-1].
      boolean getInterpolate()
      Returns the value of the interpolate field.
      abstract double getInterpolatedPixel​(double x, double y)
      Uses the current interpolation method (bilinear or bicubic) to find the pixel value at real coordinates (x,y).
      double getInterpolatedValue​(double x, double y)
      Uses bilinear interpolation to find the pixel value at real coordinates (x,y).
      int getInterpolationMethod()
      Returns the current interpolation method (NONE, BILINEAR or BICUBIC).
      static java.lang.String[] getInterpolationMethods()  
      double[] getLine​(double x1, double y1, double x2, double y2)
      Returns an array containing the pixel values along the line starting at (x1,y1) and ending at (x2,y2).
      int getLineWidth()
      Returns the current line width.
      LUT getLut()  
      int getLutUpdateMode()
      Returns the LUT update mode, which can be RED_LUT, BLACK_AND_WHITE_LUT, OVER_UNDER_LUT or NO_LUT_UPDATE.
      ImageProcessor getMask()
      For images with irregular ROIs, returns a mask, otherwise, returns null.
      byte[] getMaskArray()
      Returns a reference to the mask pixel array, or null if there is no mask.
      abstract double getMax()
      Returns the largest displayed pixel value.
      double getMaxThreshold()
      Returns the upper threshold level.
      abstract double getMin()
      Returns the smallest displayed pixel value.
      double getMinThreshold()
      Returns the lower threshold level.
      int getNChannels()
      Returns the number of color channels in the image.
      void getNeighborhood​(int x, int y, double[][] arr)
      Experimental
      Overlay getOverlay()  
      abstract int getPixel​(int x, int y)
      Returns the value of the pixel at (x,y).
      int[] getPixel​(int x, int y, int[] iArray)
      Returns the samples for the pixel at (x,y) in an int array.
      int getPixelCount()  
      abstract int getPixelInterpolated​(double x, double y)
      Uses the current interpolation method to find the pixel value at real coordinates (x,y).
      abstract java.lang.Object getPixels()
      Returns a reference to this image's pixel array.
      abstract java.lang.Object getPixelsCopy()
      Returns a copy of the pixel data.
      abstract float getPixelValue​(int x, int y)
      Returns the value of the pixel at (x,y).
      protected int getProgressIncrement​(int w, int h)  
      java.awt.Rectangle getRoi()
      Returns a Rectangle that represents the current region of interest.
      float[] getRow​(int x, int y, float[] data, int length)
      Returns the pixel values along the horizontal line starting at (x,y).
      void getRow​(int x, int y, int[] data, int length)
      Returns the pixel values along the horizontal line starting at (x,y).
      int getSliceNumber()  
      abstract java.lang.Object getSnapshotPixels()
      Returns a reference to the snapshot (undo) buffer, or null.
      ImageStatistics getStatistics()
      Calculates and returns complete uncalibrated (raw) statistics for this image or ROI but it is up to 70 times slower than getStats().
      ImageStatistics getStats()
      Calculates and returns uncalibrated statistics for this image or ROI, including histogram, area, mean, min and max, standard deviation, and mode.
      java.awt.Rectangle getStringBounds​(java.lang.String s)
      Returns a rectangle enclosing the pixels affected by drawString assuming it is drawn at (x=0, y=0).
      int getStringWidth​(java.lang.String s)
      Returns the width in pixels of the specified string, including any background space (whitespace) between the x drawing coordinate and the string, not necessarily including all whitespace at the right.
      protected java.awt.image.IndexColorModel getThresholdColorModel()  
      double getValue​(int x, int y)
      Returns the value of the pixel at (x,y), a calibrated value from 8-bit and 16-bit images, an intensity value from RGB images and a double value from 32-bit images.
      int getWidth()
      Returns the width of this image in pixels.
      protected void hideProgress()
      Deprecated. 
      void insert​(ImageProcessor ip, int xloc, int yloc)
      Inserts the image contained in 'ip' at (xloc, yloc).
      void invert()
      Inverts the image or ROI.
      void invertLut()
      Inverts the values in this image's LUT (indexed color model).
      boolean isBinary()
      Returns 'true' if this is a binary image (8-bit-image with only 0 and 255).
      boolean isColorLut()
      Returns true if this image uses a color LUT.
      boolean isDefaultLut()
      Returns true if the image is using the default grayscale LUT.
      boolean isGrayscale()
      Returns 'true' if this is an image with a grayscale LUT or an RGB image with identical red, green and blue channels.
      boolean isInvertedLut()
      Returns true if this image uses an inverting LUT that displays zero as white and 255 as black.
      boolean isKillable()
      Deprecated. 
      boolean isPseudoColorLut()
      Returns true if this image uses a pseudocolor or grayscale LUT, in other words, is this an image that can be filtered.
      boolean isSigned16Bit()
      Returns 'true' if this is a signed 16-bit image.
      void lineTo​(int x2, int y2)
      Draws a line from the current drawing location to (x2,y2).
      void ln()
      Does a natural logarithmic (base e) transform of the image or ROI.
      void log()
      Does a natural logarithmic (base e) transform of the image or ROI.
      protected void makeDefaultColorModel()  
      protected java.lang.String maskSizeError​(ImageProcessor mask)  
      void max​(double value)
      Pixels greater than 'value' are set to 'value'.
      double maxValue()
      Returns the maximum possible pixel value.
      abstract void medianFilter()
      A 3x3 median filter.
      void min​(double value)
      Pixels less than 'value' are set to 'value'.
      double minValue()
      Returns the minimum possible pixel value.
      void moveTo​(int x, int y)
      Sets the current drawing location.
      void multiply​(double value)
      Multiplies each pixel in the image or ROI by 'value'.
      abstract void noise​(double standardDeviation)
      Adds pseudorandom, Gaussian ("normally") distributed values, with mean 0.0 and the specified standard deviation, to this image or ROI.
      void or​(int value)
      Binary OR of each pixel in the image or ROI with 'value'.
      void putColumn​(int x, int y, float[] data, int length)
      Inserts the pixels contained in 'data' into a column starting at (x,y).
      void putColumn​(int x, int y, int[] data, int length)
      Inserts the pixels contained in 'data' into a column starting at (x,y).
      abstract void putPixel​(int x, int y, int value)
      Stores the specified value at (x,y).
      void putPixel​(int x, int y, int[] iArray)
      Sets a pixel in the image using an int array of samples.
      abstract void putPixelValue​(int x, int y, double value)
      Stores the specified value at (x,y).
      void putRow​(int x, int y, float[] data, int length)
      Inserts the pixels contained in 'data' into a horizontal line starting at (x,y).
      void putRow​(int x, int y, int[] data, int length)
      Inserts the pixels contained in 'data' into a horizontal line starting at (x,y).
      abstract void reset()
      Restores the pixel data from the snapshot (undo) buffer.
      abstract void reset​(ImageProcessor mask)
      Restores pixels from the snapshot buffer that are within the rectangular roi but not part of the mask.
      void resetBinaryThreshold()
      Resets the threshold if minThreshold=maxThreshold and lutUpdateMode=NO_LUT_UPDATE.
      void resetMinAndMax()
      For short and float images, recalculates the min and max image values needed to correctly display the image.
      void resetRoi()
      Sets the ROI (Region of Interest) and clipping rectangle to the entire image.
      void resetThreshold()
      Disables thresholding.
      ImageProcessor resize​(int dstWidth)
      Returns a new ImageProcessor containing a scaled copy of this image or ROI, with the aspect ratio maintained.
      abstract ImageProcessor resize​(int dstWidth, int dstHeight)
      Returns a new ImageProcessor containing a scaled copy of this image or ROI.
      ImageProcessor resize​(int dstWidth, int dstHeight, boolean useAverging)
      Returns a new ImageProcessor containing a scaled copy of this image or ROI.
      protected ImageProcessor resizeLinearly​(int width2, int height2)
      Use linear interpolation to resize images that have a width or height of one.
      abstract void rotate​(double angle)
      Rotates the image or selection 'angle' degrees clockwise.
      ImageProcessor rotateLeft()
      Rotates the entire image 90 degrees counter-clockwise.
      ImageProcessor rotateRight()
      Rotates the entire image 90 degrees clockwise.
      abstract void scale​(double xScale, double yScale)
      Scales the image by the specified factors.
      void scaleAndSetThreshold​(double lower, double upper, int lutUpdate)
      Set the threshold using a 0-255 range.
      void set​(double value)
      Assigns 'value' to each pixel in the image or ROI.
      abstract void set​(int index, int value)  
      abstract void set​(int x, int y, int value)
      This is a faster version of putPixel() that does not clip out of range values and does not do bounds checking.
      void setAntialiasedText​(boolean antialiasedText)
      Specifies whether or not text is drawn using antialiasing.
      void setAutoThreshold​(int method, int lutUpdate)
      Automatically sets the lower and upper threshold levels, where 'method' must be ISODATA or ISODATA2 and 'lutUpdate' must be RED_LUT, BLACK_AND_WHITE_LUT, OVER_UNDER_LUT or NO_LUT_UPDATE.
      void setAutoThreshold​(AutoThresholder.Method method, boolean darkBackground)  
      void setAutoThreshold​(AutoThresholder.Method method, boolean darkBackground, int lutUpdate)  
      void setAutoThreshold​(java.lang.String method)
      Automatically sets the lower and upper threshold levels, where 'method' must be "Default", "Huang", "Intermodes", "IsoData", "IJ_IsoData", "Li", "MaxEntropy", "Mean", "MinError", "Minimum", "Moments", "Otsu", "Percentile", "RenyiEntropy", "Shanbhag", "Triangle" or "Yen".
      void setAutoThreshold​(java.lang.String mString, boolean darkBackground, int lutUpdate)  
      void setBackgroundColor​(java.awt.Color color)
      Sets the background fill/draw color.
      abstract void setBackgroundValue​(double value)
      Sets the background fill value used by the rotate() and scale() methods.
      void setBinaryThreshold()  
      void setCalibrationTable​(float[] cTable)
      Set a lookup table used by getPixelValue(), getLine() and convertToFloat() to calibrate pixel values.
      void setClipRect​(java.awt.Rectangle clipRect)
      Updates the clipping rectangle used by lineTo(), drawLine(), drawDot() and drawPixel().
      void setColor​(double value)
      Sets the default fill/draw value.
      void setColor​(int value)
      Sets the default fill/draw value.
      abstract void setColor​(java.awt.Color color)
      Sets the default fill/draw value to the pixel value closest to the specified color.
      void setColorModel​(java.awt.image.ColorModel cm)
      Sets the color model.
      abstract void setf​(int index, float value)  
      abstract void setf​(int x, int y, float value)
      Sets the value of the pixel at (x,y) to 'value'.
      void setFloatArray​(float[][] a)
      Replaces the pixel data with contents of the specified 2D float array.
      void setFont​(java.awt.Font font)
      Sets the font used by drawString().
      void setFontSize​(int size)
      Sets the size of the font used by drawString().
      void setGlobalBackgroundColor()
      Sets the global (Color Picker) background color as the fill/draw color.
      void setGlobalForegroundColor()
      Sets the global (Color Picker) foreground color as the fill/draw color.
      void setHistogramRange​(double histMin, double histMax)
      Set the range used for histograms of float images.
      void setHistogramSize​(int size)
      Set the number of bins to be used for histograms of float images.
      void setIntArray​(int[][] a)
      Replaces the pixel data with contents of the specified 2D int array.
      void setInterpolate​(boolean interpolate)
      This method has been replaced by setInterpolationMethod().
      void setInterpolationMethod​(int method)
      Use this method to set the interpolation method (NONE, BILINEAR or BICUBIC) used by scale(), resize() and rotate().
      void setJustification​(int justification)
      Sets the justification used by drawString(), where justification is CENTER_JUSTIFY, RIGHT_JUSTIFY or LEFT_JUSTIFY.
      void setLineWidth​(int width)
      Sets the line width used by lineTo() and drawDot().
      void setLut​(LUT lut)  
      void setLutAnimation​(boolean lutAnimation)
      For 16 and 32 bit processors, set 'lutAnimation' true to have createImage() use the cached 8-bit version of the image.
      void setMask​(ImageProcessor mask)
      Defines a byte mask that limits processing to an irregular ROI.
      abstract void setMinAndMax​(double min, double max)
      This image will be displayed by mapping pixel values in the range min-max to screen values in the range 0-255.
      static void setOverColor​(int red, int green, int blue)
      Sets the upper Over/Under threshold color.
      void setOverlay​(Overlay overlay)
      This method is used to display virtual stack overlays.
      abstract void setPixels​(int channelNumber, FloatProcessor fp)
      Sets the pixels (of one color channel for RGB images) from a FloatProcessor.
      abstract void setPixels​(java.lang.Object pixels)
      Sets a new pixel array for the image.
      void setProgressBar​(ProgressBar pb)
      Assigns a progress bar to this processor.
      static void setRandomSeed​(double randomSeed)  
      void setRoi​(int x, int y, int rwidth, int rheight)
      Defines a rectangular region of interest and sets the mask to null if this ROI is not the same size as the previous one.
      void setRoi​(Roi roi)
      Defines a non-rectangular region of interest that will consist of a rectangular ROI and a mask.
      void setRoi​(java.awt.Polygon roi)
      Defines a polygonal region of interest that will consist of a rectangular ROI and a mask.
      void setRoi​(java.awt.Rectangle roi)
      Defines a rectangular region of interest and sets the mask to null if this ROI is not the same size as the previous one.
      void setSliceNumber​(int slice)
      PlugInFilterRunner uses this method to set the slice number.
      void setSnapshotCopyMode​(boolean b)
      The getPixelsCopy() method returns a reference to the snapshot buffer if it is not null and 'snapshotCopyMode' is true.
      abstract void setSnapshotPixels​(java.lang.Object pixels)
      Sets a new pixel array for the snapshot (undo) buffer.
      void setThreshold​(double minThreshold, double maxThreshold)
      Sets the lower and upper threshold levels using NO_LUT_UPDATE.
      void setThreshold​(double minThreshold, double maxThreshold, int lutUpdate)
      Sets the lower and upper threshold levels.
      static void setUnderColor​(int red, int green, int blue)
      Set the lower Over/Under thresholding color.
      static void setUseBicubic​(boolean b)  
      abstract void setValue​(double value)
      Sets the default fill/draw value.
      void sharpen()
      Sharpens the image or ROI using a 3x3 convolution kernel.
      protected void showProgress​(double percentDone)  
      void smooth()
      Replaces each pixel with the 3x3 neighborhood mean.
      abstract void snapshot()
      Makes a copy of this image's pixel data that can be later restored using reset() or reset(mask).
      void sqr()
      Performs a square transform on the image or ROI.
      void sqrt()
      Performs a square root transform on the image or ROI.
      void subtract​(double value)
      Subtracts 'value' from each pixel in the image or ROI.
      abstract void swapPixelArrays()
      Swaps the pixel and snapshot (undo) buffers.
      abstract void threshold​(int level)
      Sets pixels less than or equal to level to 0 and all other pixels to 255.
      abstract FloatProcessor toFloat​(int channelNumber, FloatProcessor fp)
      Returns a FloatProcessor with the image or one color channel thereof.
      java.lang.String toString()
      Returns a string containing information about this ImageProcessor.
      void translate​(double xOffset, double yOffset)
      Moves the image or selection vertically or horizontally by a specified number of pixels.
      void translate​(int xOffset, int yOffset, boolean eraseBackground)
      Deprecated.
      replaced by translate(x,y)
      void updateComposite​(int[] rgbPixels, int mode)
      This method is used by CompositeImage.updateImage() to create RGB images (for display) of a multi-channel composite images.
      void xor​(int value)
      Binary exclusive OR of each pixel in the image or ROI with 'value'.
      • Methods inherited from class java.lang.Object

        equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
    • Field Detail

      • BLACK

        public static final int BLACK
        Value of pixels included in masks.
        See Also:
        Constant Field Values
      • NO_THRESHOLD

        public static final double NO_THRESHOLD
        Value returned by getMinThreshold() when thresholding is not enabled.
        See Also:
        Constant Field Values
      • CENTER_JUSTIFY

        public static final int CENTER_JUSTIFY
        Center justify text.
        See Also:
        Constant Field Values
      • RIGHT_JUSTIFY

        public static final int RIGHT_JUSTIFY
        Right justify text.
        See Also:
        Constant Field Values
      • ISODATA2

        public static final int ISODATA2
        Modified isodata method used in Image/Adjust/Threshold tool
        See Also:
        Constant Field Values
      • UPDATE_RED

        public static final int UPDATE_RED
        Composite image projection modes.
        See Also:
        Constant Field Values
      • UPDATE_GREEN

        public static final int UPDATE_GREEN
        Composite image projection modes.
        See Also:
        Constant Field Values
      • UPDATE_BLUE

        public static final int UPDATE_BLUE
        Composite image projection modes.
        See Also:
        Constant Field Values
      • SET_FIRST_CHANNEL

        public static final int SET_FIRST_CHANNEL
        Composite image projection modes.
        See Also:
        Constant Field Values
      • SUM_PROJECTION

        public static final int SUM_PROJECTION
        Composite image projection modes.
        See Also:
        Constant Field Values
      • MAX_PROJECTION

        public static final int MAX_PROJECTION
        Composite image projection modes.
        See Also:
        Constant Field Values
      • MIN_PROJECTION

        public static final int MIN_PROJECTION
        Composite image projection modes.
        See Also:
        Constant Field Values
      • INVERT_PROJECTION

        public static final int INVERT_PROJECTION
        Composite image projection modes.
        See Also:
        Constant Field Values
      • NEAREST_NEIGHBOR

        public static final int NEAREST_NEIGHBOR
        Interpolation methods
        See Also:
        Constant Field Values
      • lineWidth

        protected int lineWidth
      • cx

        protected int cx
      • cy

        protected int cy
      • font

        protected java.awt.Font font
      • fontMetrics

        protected java.awt.FontMetrics fontMetrics
      • antialiasedText

        protected boolean antialiasedText
      • boldFont

        protected boolean boldFont
      • width

        protected int width
      • snapshotWidth

        protected int snapshotWidth
      • height

        protected int height
      • snapshotHeight

        protected int snapshotHeight
      • roiX

        protected int roiX
      • roiY

        protected int roiY
      • roiWidth

        protected int roiWidth
      • roiHeight

        protected int roiHeight
      • xMin

        protected int xMin
      • xMax

        protected int xMax
      • yMin

        protected int yMin
      • yMax

        protected int yMax
      • baseCM

        protected java.awt.image.ColorModel baseCM
      • cm

        protected java.awt.image.ColorModel cm
      • rLUT1

        protected byte[] rLUT1
      • gLUT1

        protected byte[] gLUT1
      • bLUT1

        protected byte[] bLUT1
      • rLUT2

        protected byte[] rLUT2
      • gLUT2

        protected byte[] gLUT2
      • bLUT2

        protected byte[] bLUT2
      • interpolate

        protected boolean interpolate
      • interpolationMethod

        protected int interpolationMethod
      • minThreshold

        protected double minThreshold
      • maxThreshold

        protected double maxThreshold
      • histogramSize

        protected int histogramSize
      • histogramMin

        protected double histogramMin
      • histogramMax

        protected double histogramMax
      • cTable

        protected float[] cTable
      • lutAnimation

        protected boolean lutAnimation
      • source

        protected java.awt.image.MemoryImageSource source
      • img

        protected java.awt.Image img
      • newPixels

        protected boolean newPixels
      • drawingColor

        protected java.awt.Color drawingColor
      • clipXMin

        protected int clipXMin
      • clipXMax

        protected int clipXMax
      • clipYMin

        protected int clipYMin
      • clipYMax

        protected int clipYMax
      • justification

        protected int justification
      • lutUpdateMode

        protected int lutUpdateMode
      • raster

        protected java.awt.image.WritableRaster raster
      • image

        protected java.awt.image.BufferedImage image
      • fmImage

        protected java.awt.image.BufferedImage fmImage
      • fmGraphics

        protected java.awt.Graphics2D fmGraphics
      • cm2

        protected java.awt.image.ColorModel cm2
      • sampleModel

        protected java.awt.image.SampleModel sampleModel
      • defaultColorModel

        protected static java.awt.image.IndexColorModel defaultColorModel
      • minMaxSet

        protected boolean minMaxSet
      • seed

        protected static double seed
      • rnd

        protected static java.util.Random rnd
      • fillValueSet

        protected boolean fillValueSet
      • inversionTested

        protected boolean inversionTested
      • invertedLut

        protected boolean invertedLut
    • Constructor Detail

      • ImageProcessor

        public ImageProcessor()
    • Method Detail

      • showProgress

        protected void showProgress​(double percentDone)
      • hideProgress

        protected void hideProgress()
        Deprecated.
      • getWidth

        public int getWidth()
        Returns the width of this image in pixels.
      • getHeight

        public int getHeight()
        Returns the height of this image in pixels.
      • getBitDepth

        public int getBitDepth()
        Returns the bit depth, 8, 16, 24 (RGB) or 32. RGB images actually use 32 bits per pixel.
      • getColorModel

        public java.awt.image.ColorModel getColorModel()
        Returns this processor's color model. For non-RGB processors, this is the base lookup table (LUT), not the one that may have been modified by setMinAndMax() or setThreshold().
      • getCurrentColorModel

        public java.awt.image.ColorModel getCurrentColorModel()
        Returns the current color model, which may have been modified by setMinAndMax() or setThreshold().
      • setColorModel

        public void setColorModel​(java.awt.image.ColorModel cm)
        Sets the color model. Must be an IndexColorModel (aka LUT) for all processors except the ColorProcessor.
      • getLut

        public LUT getLut()
      • setLut

        public void setLut​(LUT lut)
      • makeDefaultColorModel

        protected void makeDefaultColorModel()
      • invertLut

        public void invertLut()
        Inverts the values in this image's LUT (indexed color model). Does nothing if this is a ColorProcessor.
      • getBestIndex

        public int getBestIndex​(java.awt.Color c)
        Returns the LUT index that's the best match for this color.
      • isInvertedLut

        public boolean isInvertedLut()
        Returns true if this image uses an inverting LUT that displays zero as white and 255 as black.
      • isGrayscale

        public boolean isGrayscale()
        Returns 'true' if this is an image with a grayscale LUT or an RGB image with identical red, green and blue channels.
      • isColorLut

        public boolean isColorLut()
        Returns true if this image uses a color LUT.
      • isPseudoColorLut

        public boolean isPseudoColorLut()
        Returns true if this image uses a pseudocolor or grayscale LUT, in other words, is this an image that can be filtered.
      • isDefaultLut

        public boolean isDefaultLut()
        Returns true if the image is using the default grayscale LUT.
      • setColor

        public abstract void setColor​(java.awt.Color color)
        Sets the default fill/draw value to the pixel value closest to the specified color.
      • setBackgroundColor

        public void setBackgroundColor​(java.awt.Color color)
        Sets the background fill/draw color.
      • setColor

        public void setColor​(int value)
        Sets the default fill/draw value.
      • setColor

        public void setColor​(double value)
        Sets the default fill/draw value.
      • setValue

        public abstract void setValue​(double value)
        Sets the default fill/draw value.
      • getForegroundValue

        public abstract double getForegroundValue()
        Returns the default fill/draw value.
      • fillValueSet

        public boolean fillValueSet()
        Returns 'true' if the fill/draw value has been set.
      • setBackgroundValue

        public abstract void setBackgroundValue​(double value)
        Sets the background fill value used by the rotate() and scale() methods.
      • getBackgroundValue

        public abstract double getBackgroundValue()
        Returns the background fill value.
      • getMin

        public abstract double getMin()
        Returns the smallest displayed pixel value.
      • getMax

        public abstract double getMax()
        Returns the largest displayed pixel value.
      • setMinAndMax

        public abstract void setMinAndMax​(double min,
                                          double max)
        This image will be displayed by mapping pixel values in the range min-max to screen values in the range 0-255. For byte images, this mapping is done by updating the LUT. For short and float images, it's done by generating 8-bit AWT images. For RGB images, it's done by changing the pixel values. With signed 16-bit images, use IJ.setMinAndMax(imp,min,max).
        See Also:
        IJ.setMinAndMax(ij.ImagePlus,double,double)
      • resetMinAndMax

        public void resetMinAndMax()
        For short and float images, recalculates the min and max image values needed to correctly display the image. For ByteProcessors, resets the LUT.
      • setThreshold

        public void setThreshold​(double minThreshold,
                                 double maxThreshold)
        Sets the lower and upper threshold levels using NO_LUT_UPDATE.
      • setThreshold

        public void setThreshold​(double minThreshold,
                                 double maxThreshold,
                                 int lutUpdate)
        Sets the lower and upper threshold levels. The 'lutUpdate' argument can be RED_LUT, BLACK_AND_WHITE_LUT, OVER_UNDER_LUT or NO_LUT_UPDATE. Thresholding of RGB images is not supported.
      • setAutoThreshold

        public void setAutoThreshold​(java.lang.String method)
        Automatically sets the lower and upper threshold levels, where 'method' must be "Default", "Huang", "Intermodes", "IsoData", "IJ_IsoData", "Li", "MaxEntropy", "Mean", "MinError", "Minimum", "Moments", "Otsu", "Percentile", "RenyiEntropy", "Shanbhag", "Triangle" or "Yen". The 'method' string may also include the keywords 'dark' (dark background) 'red' (red LUT, the default), 'b&w' (black and white LUT), 'over/under' (over/under LUT) or 'no-lut' (no LUT changes), for example "Huang dark b&w". The display range of 16-bit and 32-bit images is not reset if the 'method' string contains 'no-reset'.
        See Also:
        resetThreshold(), setThreshold(double, double), createMask()
      • setAutoThreshold

        public void setAutoThreshold​(java.lang.String mString,
                                     boolean darkBackground,
                                     int lutUpdate)
      • setAutoThreshold

        public void setAutoThreshold​(AutoThresholder.Method method,
                                     boolean darkBackground,
                                     int lutUpdate)
      • setAutoThreshold

        public void setAutoThreshold​(int method,
                                     int lutUpdate)
        Automatically sets the lower and upper threshold levels, where 'method' must be ISODATA or ISODATA2 and 'lutUpdate' must be RED_LUT, BLACK_AND_WHITE_LUT, OVER_UNDER_LUT or NO_LUT_UPDATE.
      • scaleAndSetThreshold

        public void scaleAndSetThreshold​(double lower,
                                         double upper,
                                         int lutUpdate)
        Set the threshold using a 0-255 range. For 16-bit and 32-bit images, this range is taken as relative with respect to the range between the current display min and max, but lower=0 and upper=255 are set to the full-range limits of 16-bit images and -/+1e30 for float images.
      • resetThreshold

        public void resetThreshold()
        Disables thresholding.
      • getMinThreshold

        public double getMinThreshold()
        Returns the lower threshold level. Returns NO_THRESHOLD if thresholding is not enabled.
      • getMaxThreshold

        public double getMaxThreshold()
        Returns the upper threshold level.
      • getLutUpdateMode

        public int getLutUpdateMode()
        Returns the LUT update mode, which can be RED_LUT, BLACK_AND_WHITE_LUT, OVER_UNDER_LUT or NO_LUT_UPDATE.
      • setBinaryThreshold

        public void setBinaryThreshold()
      • resetBinaryThreshold

        public void resetBinaryThreshold()
        Resets the threshold if minThreshold=maxThreshold and lutUpdateMode=NO_LUT_UPDATE. This removes the invisible threshold set by the MakeBinary and Convert to Mask commands.
        See Also:
        setBinaryThreshold()
      • setRoi

        public void setRoi​(java.awt.Rectangle roi)
        Defines a rectangular region of interest and sets the mask to null if this ROI is not the same size as the previous one.
        See Also:
        resetRoi()
      • setRoi

        public void setRoi​(int x,
                           int y,
                           int rwidth,
                           int rheight)
        Defines a rectangular region of interest and sets the mask to null if this ROI is not the same size as the previous one.
        See Also:
        resetRoi()
      • setRoi

        public void setRoi​(Roi roi)
        Defines a non-rectangular region of interest that will consist of a rectangular ROI and a mask. After processing, call reset(mask) to restore non-masked pixels. Here is an example:
                        ip.setRoi(new OvalRoi(50, 50, 100, 50));
                        ip.fill();
                        ip.reset(ip.getMask());
                        
        The example assumes snapshot() has been called, which is the case for code executed in the run() method of plugins that implement the PlugInFilter interface.
        See Also:
        ImagePlus.getRoi()
      • setRoi

        public void setRoi​(java.awt.Polygon roi)
        Defines a polygonal region of interest that will consist of a rectangular ROI and a mask. After processing, call reset(mask) to restore non-masked pixels. Here is an example:
                        Polygon p = new Polygon();
                        p.addPoint(50, 0); p.addPoint(100, 100); p.addPoint(0, 100);
                        ip.setRoi(triangle);
                        ip.invert();
                        ip.reset(ip.getMask());
                        
        The example assumes snapshot() has been called, which is the case for code executed in the run() method of plugins that implement the PlugInFilter interface.
        See Also:
        Roi.getPolygon(), drawPolygon(java.awt.Polygon), fillPolygon(java.awt.Polygon)
      • resetRoi

        public void resetRoi()
        Sets the ROI (Region of Interest) and clipping rectangle to the entire image.
      • getRoi

        public java.awt.Rectangle getRoi()
        Returns a Rectangle that represents the current region of interest.
      • setMask

        public void setMask​(ImageProcessor mask)
        Defines a byte mask that limits processing to an irregular ROI. Background pixels in the mask have a value of zero.
      • getMask

        public ImageProcessor getMask()
        For images with irregular ROIs, returns a mask, otherwise, returns null. Pixels outside the mask have a value of zero.
      • getMaskArray

        public byte[] getMaskArray()
        Returns a reference to the mask pixel array, or null if there is no mask.
      • setProgressBar

        public void setProgressBar​(ProgressBar pb)
        Assigns a progress bar to this processor. Set 'pb' to null to disable the progress bar.
      • setInterpolate

        public void setInterpolate​(boolean interpolate)
        This method has been replaced by setInterpolationMethod().
      • setInterpolationMethod

        public void setInterpolationMethod​(int method)
        Use this method to set the interpolation method (NONE, BILINEAR or BICUBIC) used by scale(), resize() and rotate().
      • getInterpolationMethod

        public int getInterpolationMethod()
        Returns the current interpolation method (NONE, BILINEAR or BICUBIC).
      • getInterpolationMethods

        public static java.lang.String[] getInterpolationMethods()
      • getInterpolate

        public boolean getInterpolate()
        Returns the value of the interpolate field.
      • isKillable

        public boolean isKillable()
        Deprecated.
      • getLine

        public double[] getLine​(double x1,
                                double y1,
                                double x2,
                                double y2)
        Returns an array containing the pixel values along the line starting at (x1,y1) and ending at (x2,y2). Pixel values are sampled using getInterpolatedValue(double,double) if interpolation is enabled or getPixelValue(int,int) if it is not. For byte and short images, returns calibrated values if a calibration table has been set using setCalibrationTable(). The length of the returned array, minus one, is approximately equal to the length of the line.
        See Also:
        setInterpolate(boolean), getPixelValue(int, int), getInterpolatedValue(double, double)
      • getRow

        public void getRow​(int x,
                           int y,
                           int[] data,
                           int length)
        Returns the pixel values along the horizontal line starting at (x,y).
      • getRow

        public float[] getRow​(int x,
                              int y,
                              float[] data,
                              int length)
        Returns the pixel values along the horizontal line starting at (x,y).
      • getColumn

        public void getColumn​(int x,
                              int y,
                              int[] data,
                              int length)
        Returns the pixel values down the column starting at (x,y).
      • getColumn

        public float[] getColumn​(int x,
                                 int y,
                                 float[] data,
                                 int length)
        Returns the pixel values down the column starting at (x,y).
      • putRow

        public void putRow​(int x,
                           int y,
                           int[] data,
                           int length)
        Inserts the pixels contained in 'data' into a horizontal line starting at (x,y).
      • putRow

        public void putRow​(int x,
                           int y,
                           float[] data,
                           int length)
        Inserts the pixels contained in 'data' into a horizontal line starting at (x,y).
      • putColumn

        public void putColumn​(int x,
                              int y,
                              int[] data,
                              int length)
        Inserts the pixels contained in 'data' into a column starting at (x,y).
      • putColumn

        public void putColumn​(int x,
                              int y,
                              float[] data,
                              int length)
        Inserts the pixels contained in 'data' into a column starting at (x,y).
      • setLineWidth

        public void setLineWidth​(int width)
        Sets the line width used by lineTo() and drawDot().
      • getLineWidth

        public int getLineWidth()
        Returns the current line width.
      • lineTo

        public void lineTo​(int x2,
                           int y2)
        Draws a line from the current drawing location to (x2,y2).
      • drawLine

        public void drawLine​(int x1,
                             int y1,
                             int x2,
                             int y2)
        Draws a line from (x1,y1) to (x2,y2).
      • drawLine4

        public void drawLine4​(int x1,
                              int y1,
                              int x2,
                              int y2)
      • drawRect

        public void drawRect​(int x,
                             int y,
                             int width,
                             int height)
        Draws a rectangle.
      • fillRect

        public void fillRect​(int x,
                             int y,
                             int width,
                             int height)
        Fills a rectangle.
      • drawOval

        public void drawOval​(int x,
                             int y,
                             int width,
                             int height)
        Draws an elliptical shape.
      • fillOval

        public void fillOval​(int x,
                             int y,
                             int width,
                             int height)
        Fills an elliptical shape.
      • drawPolygon

        public void drawPolygon​(java.awt.Polygon p)
        Draws a polygon.
      • fillPolygon

        public void fillPolygon​(java.awt.Polygon p)
        Fills a polygon.
      • drawDot2

        public void drawDot2​(int x,
                             int y)
        Deprecated.
      • drawDot

        public void drawDot​(int xcenter,
                            int ycenter)
        Draws a dot using the current line width and fill/draw value.
      • drawString

        public void drawString​(java.lang.String s)
        Draws a string at the current drawing location using the current fill/draw value. Draws multiple lines if the string contains newline characters. The current x coordinate is the left/center/right end of the string for left/center/right justification. The current y coordinate determines the bottommost position of the string, including the descent of the font (i.e., characters reaching below the baseline) For multi-line strings, the y coordinate applies to the first line. The y of the drawing position is incremented by the height of one text line, i.e. points at the drawing position for the next text line
      • drawString

        public void drawString​(java.lang.String s,
                               int x,
                               int y)
        Draws a string at the specified location using the current fill/draw value. Draws multiple lines if the string contains newline characters. The x coordinate is the left/center/right end of the string for left/center/right justification. The y coordinate determines the bottommost position of the string, including the descent of the font (i.e., characters reaching below the baseline) For multi-line strings, the y coordinate applies to the first line.
      • drawString

        public void drawString​(java.lang.String s,
                               int x,
                               int y,
                               java.awt.Color background)
        Draws a string at the specified location with a filled background. A JavaScript example is available at http://imagej.nih.gov/ij/macros/js/DrawTextWithBackground.js
      • setJustification

        public void setJustification​(int justification)
        Sets the justification used by drawString(), where justification is CENTER_JUSTIFY, RIGHT_JUSTIFY or LEFT_JUSTIFY. The default is LEFT_JUSTIFY.
      • setFont

        public void setFont​(java.awt.Font font)
        Sets the font used by drawString().
      • setFontSize

        public void setFontSize​(int size)
        Sets the size of the font used by drawString().
      • setAntialiasedText

        public void setAntialiasedText​(boolean antialiasedText)
        Specifies whether or not text is drawn using antialiasing. Antialiased test requires an 8 bit or RGB image. Antialiasing does not work with 8-bit images that are not using 0-255 display range.
      • getStringWidth

        public int getStringWidth​(java.lang.String s)
        Returns the width in pixels of the specified string, including any background space (whitespace) between the x drawing coordinate and the string, not necessarily including all whitespace at the right.
      • getStringBounds

        public java.awt.Rectangle getStringBounds​(java.lang.String s)
        Returns a rectangle enclosing the pixels affected by drawString assuming it is drawn at (x=0, y=0). As drawString draws above the drawing location, the y coordinate of the rectangle is negative.
      • getFont

        public java.awt.Font getFont()
        Returns the current font.
      • getFontMetrics

        public java.awt.FontMetrics getFontMetrics()
        Returns the current FontMetrics.
      • smooth

        public void smooth()
        Replaces each pixel with the 3x3 neighborhood mean.
      • sharpen

        public void sharpen()
        Sharpens the image or ROI using a 3x3 convolution kernel.
      • findEdges

        public void findEdges()
        Finds edges in the image or ROI using a Sobel operator.
      • flipVertical

        public abstract void flipVertical()
        Flips the image or ROI vertically.
      • flipHorizontal

        public void flipHorizontal()
        Flips the image or ROI horizontally.
      • rotateRight

        public ImageProcessor rotateRight()
        Rotates the entire image 90 degrees clockwise. Returns a new ImageProcessor that represents the rotated image.
      • rotateLeft

        public ImageProcessor rotateLeft()
        Rotates the entire image 90 degrees counter-clockwise. Returns a new ImageProcessor that represents the rotated image.
      • insert

        public void insert​(ImageProcessor ip,
                           int xloc,
                           int yloc)
        Inserts the image contained in 'ip' at (xloc, yloc).
      • toString

        public java.lang.String toString()
        Returns a string containing information about this ImageProcessor.
        Overrides:
        toString in class java.lang.Object
      • fill

        public void fill()
        Fills the image or ROI bounding rectangle with the current fill/draw value. Use fill(Roi) or fill(ip.getMask()) to fill non-rectangular selections.
        See Also:
        setColor(Color), setValue(double), fill(Roi)
      • fill

        public abstract void fill​(ImageProcessor mask)
        Fills pixels that are within the ROI bounding rectangle and part of the mask (i.e. pixels that have a value=BLACK in the mask array). Use ip.getMask() to acquire the mask. Throws and IllegalArgumentException if the mask is null or the size of the mask is not the same as the size of the ROI.
        See Also:
        setColor(Color), setValue(double), getMask(), fill(Roi)
      • fillOutside

        public void fillOutside​(Roi roi)
        Fills outside an Roi.
      • draw

        public void draw​(Roi roi)
        Draws the specified ROI on this image using the line width and color defined by ip.setLineWidth() and ip.setColor().
        See Also:
        drawRoi(ij.gui.Roi)
      • drawRoi

        public void drawRoi​(Roi roi)
        Draws the specified ROI on this image using the stroke width, stroke color and fill color defined by roi.setStrokeWidth, roi.setStrokeColor() and roi.setFillColor(). Works with RGB images. Does not work with 16-bit and float images.
        See Also:
        draw(ij.gui.Roi), drawOverlay(ij.gui.Overlay)
      • drawOverlay

        public void drawOverlay​(Overlay overlay)
        Draws the specified Overlay on this image. Works best with RGB images. Does not work with 16-bit and float images. Requires Java 1.6.
        See Also:
        drawRoi(ij.gui.Roi)
      • setCalibrationTable

        public void setCalibrationTable​(float[] cTable)
        Set a lookup table used by getPixelValue(), getLine() and convertToFloat() to calibrate pixel values. The length of the table must be 256 for byte images and 65536 for short images. RGB and float processors do not do calibration.
        See Also:
        Calibration.setCTable(float[], java.lang.String)
      • getCalibrationTable

        public float[] getCalibrationTable()
        Returns the calibration table or null.
      • setHistogramSize

        public void setHistogramSize​(int size)
        Set the number of bins to be used for histograms of float images.
      • getHistogramSize

        public int getHistogramSize()
        Returns the number of float image histogram bins. The bin count is fixed at 256 for the other three data types.
      • setHistogramRange

        public void setHistogramRange​(double histMin,
                                      double histMax)
        Set the range used for histograms of float images. The image range is used if both histMin and histMax are zero.
      • getHistogramMin

        public double getHistogramMin()
        Returns the minimum histogram value used for histograms of float images.
      • getHistogramMax

        public double getHistogramMax()
        Returns the maximum histogram value used for histograms of float images.
      • getPixels

        public abstract java.lang.Object getPixels()
        Returns a reference to this image's pixel array. The array type (byte[], short[], float[] or int[]) varies depending on the image type.
      • getPixelsCopy

        public abstract java.lang.Object getPixelsCopy()
        Returns a copy of the pixel data. Or returns a reference to the snapshot buffer if it is not null and 'snapshotCopyMode' is true.
        See Also:
        snapshot(), setSnapshotCopyMode(boolean)
      • getPixel

        public abstract int getPixel​(int x,
                                     int y)
        Returns the value of the pixel at (x,y). For RGB images, the argb values are packed in an int. For float images, the the value must be converted using Float.intBitsToFloat(). Returns zero if either the x or y coodinate is out of range. Use getValue(x,y) to get calibrated values from 8-bit and 16-bit images, to get intensity values from RGB images and to get float values from 32-bit images.
        See Also:
        getValue(int, int)
      • get

        public abstract int get​(int x,
                                int y)
        This is a faster version of getPixel() that does not do bounds checking.
      • get

        public abstract int get​(int index)
      • set

        public abstract void set​(int x,
                                 int y,
                                 int value)
        This is a faster version of putPixel() that does not clip out of range values and does not do bounds checking.
      • set

        public abstract void set​(int index,
                                 int value)
      • getf

        public abstract float getf​(int x,
                                   int y)
        Returns the value of the pixel at (x,y) as a float. Faster than getPixelValue() but does no bounds checking and does not return calibrated values.
      • getf

        public abstract float getf​(int index)
      • setf

        public abstract void setf​(int x,
                                  int y,
                                  float value)
        Sets the value of the pixel at (x,y) to 'value'. Does no bounds checking or clamping, making it faster than putPixel(). Due to the lack of bounds checking, (x,y) coordinates outside the image may cause an exception. Due to the lack of clamping, values outside the 0-255 range (for byte) or 0-65535 range (for short) are not handled correctly.
      • setf

        public abstract void setf​(int index,
                                  float value)
      • getPixelCount

        public int getPixelCount()
      • getIntArray

        public int[][] getIntArray()
        Returns a copy of the pixel data as a 2D int array with dimensions [x=0..width-1][y=0..height-1]. With RGB images, the returned values are in packed ARGB format. With float images, the returned values must be converted to float using Float.intBitsToFloat().
      • setIntArray

        public void setIntArray​(int[][] a)
        Replaces the pixel data with contents of the specified 2D int array.
      • getFloatArray

        public float[][] getFloatArray()
        Returns a copy of the pixel data as a 2D float array with dimensions [x=0..width-1][y=0..height-1].
      • setFloatArray

        public void setFloatArray​(float[][] a)
        Replaces the pixel data with contents of the specified 2D float array.
      • getNeighborhood

        public void getNeighborhood​(int x,
                                    int y,
                                    double[][] arr)
        Experimental
      • getPixel

        public int[] getPixel​(int x,
                              int y,
                              int[] iArray)
        Returns the samples for the pixel at (x,y) in an int array. RGB pixels have three samples, all others have one. Returns zeros if the the coordinates are not in bounds. iArray is an optional preallocated array.
      • putPixel

        public void putPixel​(int x,
                             int y,
                             int[] iArray)
        Sets a pixel in the image using an int array of samples. RGB pixels have three samples, all others have one.
      • getInterpolatedPixel

        public abstract double getInterpolatedPixel​(double x,
                                                    double y)
        Uses the current interpolation method (bilinear or bicubic) to find the pixel value at real coordinates (x,y).
      • getPixelInterpolated

        public abstract int getPixelInterpolated​(double x,
                                                 double y)
        Uses the current interpolation method to find the pixel value at real coordinates (x,y). For RGB images, the argb values are packed in an int. For float images, the value must be converted using Float.intBitsToFloat(). Returns zero if the (x, y) is not inside the image.
      • getInterpolatedValue

        public final double getInterpolatedValue​(double x,
                                                 double y)
        Uses bilinear interpolation to find the pixel value at real coordinates (x,y). Returns zero if the (x, y) is not inside the image.
      • getBicubicInterpolatedPixel

        public double getBicubicInterpolatedPixel​(double x0,
                                                  double y0,
                                                  ImageProcessor ip2)
        This method is from Chapter 16 of "Digital Image Processing: An Algorithmic Introduction Using Java" by Burger and Burge (http://www.imagingbook.com/).
      • cubic

        public static final double cubic​(double x)
      • putPixel

        public abstract void putPixel​(int x,
                                      int y,
                                      int value)
        Stores the specified value at (x,y). Does nothing if (x,y) is outside the image boundary. For 8-bit and 16-bit images, out of range values are clamped. For RGB images, the argb values are packed in 'value'. For float images, 'value' is expected to be a float converted to an int using Float.floatToIntBits().
      • getValue

        public double getValue​(int x,
                               int y)
        Returns the value of the pixel at (x,y), a calibrated value from 8-bit and 16-bit images, an intensity value from RGB images and a double value from 32-bit images. This is an alias for getPixelValue(x,y).
        See Also:
        getPixel(int, int), getPixelValue(int, int), getf(int, int)
      • getPixelValue

        public abstract float getPixelValue​(int x,
                                            int y)
        Returns the value of the pixel at (x,y). For byte and short images, returns a calibrated value if a calibration table has been set using setCalibraionTable(). For RGB images, returns the luminance value.
        See Also:
        getPixel(int, int), getValue(int, int), getf(int, int)
      • putPixelValue

        public abstract void putPixelValue​(int x,
                                           int y,
                                           double value)
        Stores the specified value at (x,y).
      • drawPixel

        public abstract void drawPixel​(int x,
                                       int y)
        Sets the pixel at (x,y) to the current fill/draw value.
      • setPixels

        public abstract void setPixels​(java.lang.Object pixels)
        Sets a new pixel array for the image. The length of the array must be equal to width*height. Use setSnapshotPixels(null) to clear the snapshot buffer.
      • copyBits

        public abstract void copyBits​(ImageProcessor ip,
                                      int xloc,
                                      int yloc,
                                      int mode)
        Copies the image contained in 'ip' to (xloc, yloc) using one of the transfer modes defined in the Blitter interface.
      • applyTable

        public abstract void applyTable​(int[] lut)
        Transforms the image or ROI using a lookup table. The length of the table must be 256 for byte images and 65536 for short images. RGB and float images are not supported.
      • invert

        public void invert()
        Inverts the image or ROI.
      • add

        public void add​(int value)
        Adds 'value' to each pixel in the image or ROI.
      • add

        public void add​(double value)
        Adds 'value' to each pixel in the image or ROI.
      • subtract

        public void subtract​(double value)
        Subtracts 'value' from each pixel in the image or ROI.
      • multiply

        public void multiply​(double value)
        Multiplies each pixel in the image or ROI by 'value'.
      • set

        public void set​(double value)
        Assigns 'value' to each pixel in the image or ROI.
      • and

        public void and​(int value)
        Binary AND of each pixel in the image or ROI with 'value'.
      • or

        public void or​(int value)
        Binary OR of each pixel in the image or ROI with 'value'.
      • xor

        public void xor​(int value)
        Binary exclusive OR of each pixel in the image or ROI with 'value'.
      • gamma

        public void gamma​(double value)
        Performs gamma correction of the image or ROI.
      • log

        public void log()
        Does a natural logarithmic (base e) transform of the image or ROI.
      • ln

        public void ln()
        Does a natural logarithmic (base e) transform of the image or ROI.
      • exp

        public void exp()
        Performs a exponential transform on the image or ROI.
      • sqr

        public void sqr()
        Performs a square transform on the image or ROI.
      • sqrt

        public void sqrt()
        Performs a square root transform on the image or ROI.
      • abs

        public void abs()
        If this is a 32-bit or signed 16-bit image, performs an absolute value transform, otherwise does nothing.
      • min

        public void min​(double value)
        Pixels less than 'value' are set to 'value'.
      • max

        public void max​(double value)
        Pixels greater than 'value' are set to 'value'.
      • createImage

        public abstract java.awt.Image createImage()
        Returns a copy of this image is the form of an AWT Image.
      • getBufferedImage

        public java.awt.image.BufferedImage getBufferedImage()
        Returns this image as a BufferedImage.
      • createProcessor

        public abstract ImageProcessor createProcessor​(int width,
                                                       int height)
        Returns a new, blank processor with the specified width and height.
      • snapshot

        public abstract void snapshot()
        Makes a copy of this image's pixel data that can be later restored using reset() or reset(mask).
        See Also:
        reset(), reset(ImageProcessor)
      • reset

        public abstract void reset()
        Restores the pixel data from the snapshot (undo) buffer.
      • swapPixelArrays

        public abstract void swapPixelArrays()
        Swaps the pixel and snapshot (undo) buffers.
      • reset

        public abstract void reset​(ImageProcessor mask)
        Restores pixels from the snapshot buffer that are within the rectangular roi but not part of the mask.
      • setSnapshotPixels

        public abstract void setSnapshotPixels​(java.lang.Object pixels)
        Sets a new pixel array for the snapshot (undo) buffer.
      • getSnapshotPixels

        public abstract java.lang.Object getSnapshotPixels()
        Returns a reference to the snapshot (undo) buffer, or null.
      • convolve3x3

        public abstract void convolve3x3​(int[] kernel)
        Convolves the image or ROI with the specified 3x3 integer convolution kernel.
      • filter

        public abstract void filter​(int type)
        A 3x3 filter operation, where the argument (BLUR_MORE, FIND_EDGES, MEDIAN_FILTER, MIN or MAX) determines the filter type.
      • medianFilter

        public abstract void medianFilter()
        A 3x3 median filter. Requires 8-bit or RGB image.
      • noise

        public abstract void noise​(double standardDeviation)
        Adds pseudorandom, Gaussian ("normally") distributed values, with mean 0.0 and the specified standard deviation, to this image or ROI.
      • crop

        public abstract ImageProcessor crop()
        Returns a new processor containing an image that corresponds to the current ROI.
      • threshold

        public abstract void threshold​(int level)
        Sets pixels less than or equal to level to 0 and all other pixels to 255. Only works with 8-bit and 16-bit images.
      • duplicate

        public abstract ImageProcessor duplicate()
        Returns a duplicate of this image.
      • scale

        public abstract void scale​(double xScale,
                                   double yScale)
        Scales the image by the specified factors. Does not change the image size.
        See Also:
        setInterpolate(boolean), resize(int, int)
      • resize

        public abstract ImageProcessor resize​(int dstWidth,
                                              int dstHeight)
        Returns a new ImageProcessor containing a scaled copy of this image or ROI.
        See Also:
        setInterpolate(boolean)
      • resize

        public ImageProcessor resize​(int dstWidth)
        Returns a new ImageProcessor containing a scaled copy of this image or ROI, with the aspect ratio maintained.
      • resize

        public ImageProcessor resize​(int dstWidth,
                                     int dstHeight,
                                     boolean useAverging)
        Returns a new ImageProcessor containing a scaled copy of this image or ROI.
        Parameters:
        dstWidth - Image width of the resulting ImageProcessor
        dstHeight - Image height of the resulting ImageProcessor
        useAverging - True means that the averaging occurs to avoid aliasing artifacts; the kernel shape for averaging is determined by the interpolationMethod. False if subsampling without any averaging should be used on downsizing. Has no effect on upsizing.
        See Also:
        Author: Michael Schmid
      • resizeLinearly

        protected ImageProcessor resizeLinearly​(int width2,
                                                int height2)
        Use linear interpolation to resize images that have a width or height of one.
      • bin

        public ImageProcessor bin​(int shrinkFactor)
        Returns a copy of this image that has been reduced in size using binning.
      • translate

        public void translate​(double xOffset,
                              double yOffset)
        Moves the image or selection vertically or horizontally by a specified number of pixels. Positive x values move the image or selection to the right, negative values move it to the left. Positive y values move the image or selection down, negative values move it up.
      • translate

        public void translate​(int xOffset,
                              int yOffset,
                              boolean eraseBackground)
        Deprecated.
        replaced by translate(x,y)
      • getHistogram

        public abstract int[] getHistogram()
        Returns the histogram of the image or ROI. Returns a luminosity histogram for RGB images and null for float images.

        For 8-bit and 16-bit images, returns an array with one entry for each possible value that a pixel can have, from 0 to 255 (8-bit image) or 0-65535 (16-bit image). Thus, the array size is 256 or 65536, and the bin width in uncalibrated units is 1.

        For RGB images, the brightness is evaluated using the color weights (which would result in a float value) and rounded to an int. This gives 256 bins. FloatProcessor.getHistogram is not implemented (returns null).

      • getHistogram

        public int[] getHistogram​(int nBins)
        Returns the histogram of the image or ROI, using the specified number of bins.
      • erode

        public abstract void erode()
        Erodes the image or ROI using a 3x3 maximum filter. Requires 8-bit or RGB image.
      • dilate

        public abstract void dilate()
        Dilates the image or ROI using a 3x3 minimum filter. Requires 8-bit or RGB image.
      • setLutAnimation

        public void setLutAnimation​(boolean lutAnimation)
        For 16 and 32 bit processors, set 'lutAnimation' true to have createImage() use the cached 8-bit version of the image.
      • convertToByte

        public ImageProcessor convertToByte​(boolean doScaling)
        Returns an 8-bit version of this image as a ByteProcessor.
      • convertToShort

        public ImageProcessor convertToShort​(boolean doScaling)
        Returns a 16-bit version of this image as a ShortProcessor.
      • convertToFloat

        public ImageProcessor convertToFloat()
        Returns a 32-bit float version of this image as a FloatProcessor. For byte and short images, converts using a calibration function if a calibration table has been set using setCalibrationTable().
      • convertToRGB

        public ImageProcessor convertToRGB()
        Returns an RGB version of this image as a ColorProcessor.
      • convertToByteProcessor

        public ByteProcessor convertToByteProcessor()
        Returns an 8-bit version of this image as a ByteProcessor. 16-bit and 32-bit pixel data are scaled from min-max to 0-255.
      • convertToByteProcessor

        public ByteProcessor convertToByteProcessor​(boolean scale)
        Returns an 8-bit version of this image as a ByteProcessor. 16-bit and 32-bit pixel data are scaled from min-max to 0-255 if 'scale' is true.
      • convertToShortProcessor

        public ShortProcessor convertToShortProcessor()
        Returns a 16-bit version of this image as a ShortProcessor. 32-bit pixel data are scaled from min-max to 0-255.
      • convertToShortProcessor

        public ShortProcessor convertToShortProcessor​(boolean scale)
        Returns a 16-bit version of this image as a ShortProcessor. 32-bit pixel data are scaled from min-max to 0-255 if 'scale' is true.
      • convertToFloatProcessor

        public FloatProcessor convertToFloatProcessor()
        Returns a 32-bit float version of this image as a FloatProcessor. For byte and short images, converts using a calibration function if a calibration table has been set using setCalibrationTable().
      • convertToColorProcessor

        public ColorProcessor convertToColorProcessor()
        Returns an RGB version of this image as a ColorProcessor.
      • convolve

        public abstract void convolve​(float[] kernel,
                                      int kernelWidth,
                                      int kernelHeight)
        Performs a convolution operation using the specified kernel. KernelWidth and kernelHeight must be odd.
      • autoThreshold

        public void autoThreshold()
        Converts the image to binary using an automatically determined threshold. For byte and short images, converts to binary using an automatically determined threshold. For RGB images, converts each channel to binary. For float images, does nothing.
      • getAutoThreshold

        public int getAutoThreshold()
        Returns a pixel value (threshold) that can be used to divide the image into objects and background. It does this by taking a test threshold and computing the average of the pixels at or below the threshold and pixels above. It then computes the average of those two, increments the threshold, and repeats the process. Incrementing stops when the threshold is larger than the composite average. That is, threshold = (average background + average objects)/2. This description was posted to the ImageJ mailing list by Jordan Bevic.
      • getAutoThreshold

        public int getAutoThreshold​(int[] histogram)
        This is a version of getAutoThreshold() that uses a histogram passed as an argument.
      • setClipRect

        public void setClipRect​(java.awt.Rectangle clipRect)
        Updates the clipping rectangle used by lineTo(), drawLine(), drawDot() and drawPixel(). The clipping rectangle is reset by passing a null argument or by calling resetRoi().
      • maskSizeError

        protected java.lang.String maskSizeError​(ImageProcessor mask)
      • getIndexSampleModel

        protected java.awt.image.SampleModel getIndexSampleModel()
      • getDefaultColorModel

        public java.awt.image.IndexColorModel getDefaultColorModel()
        Returns the default grayscale IndexColorModel.
      • setSnapshotCopyMode

        public void setSnapshotCopyMode​(boolean b)
        The getPixelsCopy() method returns a reference to the snapshot buffer if it is not null and 'snapshotCopyMode' is true.
        See Also:
        getPixelsCopy(), snapshot()
      • getNChannels

        public int getNChannels()
        Returns the number of color channels in the image. The color channels can be accessed by toFloat(channelNumber, fp) and written by setPixels(channelNumber, fp).
        Returns:
        1 for grayscale images, 3 for RGB images
      • toFloat

        public abstract FloatProcessor toFloat​(int channelNumber,
                                               FloatProcessor fp)
        Returns a FloatProcessor with the image or one color channel thereof. The roi and mask are also set for the FloatProcessor.
        Parameters:
        channelNumber - Determines the color channel, 0=red, 1=green, 2=blue. Ignored for grayscale images.
        fp - Here a FloatProcessor can be supplied, or null. The FloatProcessor is overwritten when converting data (re-using its pixels array improves performance).
        Returns:
        A FloatProcessor with the converted image data of the color channel selected
      • setPixels

        public abstract void setPixels​(int channelNumber,
                                       FloatProcessor fp)
        Sets the pixels (of one color channel for RGB images) from a FloatProcessor.
        Parameters:
        channelNumber - Determines the color channel, 0=red, 1=green, 2=blue.Ignored for grayscale images.
        fp - The FloatProcessor where the image data are read from.
      • minValue

        public double minValue()
        Returns the minimum possible pixel value.
      • maxValue

        public double maxValue()
        Returns the maximum possible pixel value.
      • updateComposite

        public void updateComposite​(int[] rgbPixels,
                                    int mode)
        This method is used by CompositeImage.updateImage() to create RGB images (for display) of a multi-channel composite images.
      • setOverColor

        public static void setOverColor​(int red,
                                        int green,
                                        int blue)
        Sets the upper Over/Under threshold color. Can be called from a macro, e.g., call("ij.process.ImageProcessor.setOverColor", 0,255,255).
      • setUnderColor

        public static void setUnderColor​(int red,
                                         int green,
                                         int blue)
        Set the lower Over/Under thresholding color.
      • isBinary

        public boolean isBinary()
        Returns 'true' if this is a binary image (8-bit-image with only 0 and 255).
      • isSigned16Bit

        public boolean isSigned16Bit()
        Returns 'true' if this is a signed 16-bit image.
      • setUseBicubic

        public static void setUseBicubic​(boolean b)
      • blurGaussian

        public void blurGaussian​(double sigma)
        Blurs the image by convolving with a Gaussian function.
      • applyMacro

        public void applyMacro​(java.lang.String macro)
        Uses the Process/Math/Macro command to apply macro code to this image.
      • getSliceNumber

        public int getSliceNumber()
      • setSliceNumber

        public void setSliceNumber​(int slice)
        PlugInFilterRunner uses this method to set the slice number.
      • clone

        public java.lang.Object clone()
        Returns a shallow copy of this ImageProcessor, where this image and the copy share pixel data. Use the duplicate() method to create a copy that does not share the pixel data.
        Overrides:
        clone in class java.lang.Object
        See Also:
        duplicate()
      • setOverlay

        public void setOverlay​(Overlay overlay)
        This method is used to display virtual stack overlays.
      • getOverlay

        public Overlay getOverlay()
      • getProgressIncrement

        protected int getProgressIncrement​(int w,
                                           int h)
      • setRandomSeed

        public static void setRandomSeed​(double randomSeed)
      • getThresholdColorModel

        protected java.awt.image.IndexColorModel getThresholdColorModel()