Package gov.nih.mipav.model.structures

Class ModelSimpleImage

java.lang.Object
gov.nih.mipav.model.structures.ModelSerialCloneable
gov.nih.mipav.model.structures.ModelSimpleImage
All Implemented Interfaces:
Serializable, Cloneable
public class ModelSimpleImage extends ModelSerialCloneable
This is very simple class to store a float type image of up to four dimensions. For speed all class variables are public. This class is used extensively in Registration algorithms where we needs many copies of the image where the data does not need to be visible to the UserInterface. With the data array as public speed is achieved but at a cost that the buffer is always of the type float.
See Also:

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    float
    cMassX
    X coordinate value of the center of mass for the image.
    float
    cMassY
    Y coordinate value of the center of mass for the image.
    float
    cMassZ
    Z coordinate value of the center of mass for the image.
    float[]
    data
    Data buffer that is used to store the image.
    int
    dataSize
    Size of the data buffer (number of pixels in image).
    int[]
    extents
    The dimensionality of the dataset.
    boolean
    isColor
    Indicates whether is image is a color image or not.
    float
    max
    Maximum intensity values of image.
    float
    maxB
    Maximum intensity values of image.
    float
    maxG
    Maximum intensity values of image.
    float
    maxR
    Maximum intensity values of image.
    float
    min
    Minimum intensity values of image.
    float
    minB
    Minimum intensity values of image.
    float
    minG
    Minimum intensity values of image.
    float
    minR
    Minimum intensity values of image.
    String
    name
    add simple image name for AAM model only.
    int
    nDims
    Number of dimensions of the image.
    float[]
    resolutions
    Voxel resolutions (typically x,y,z(slice spacing),t).
    private static final long
    serialVersionUID
    Use serialVersionUID for interoperability.
    int
    tDim
    Number of volumes in the dataset.
    float
    tRes
    Resolution in the time dimension.
    int
    xDim
    Number of pixels in x dimension.
    float
    xRes
    X pixel resolution.
    int
    yDim
    Number of pixels in y dimension.
    float
    yRes
    Y pixel resolution.
    int
    zDim
    Number of pixels in z dimension.
    float
    zRes
    Z voxel resolution.

  • Constructor Summary

    Constructors
    Constructor
    Description
    ModelSimpleImage()
    Add the empty default contructor.
    ModelSimpleImage(int[] dimExtents)
    Creates a class to hold the minimum information about an image - the extents with the resolutions defaulted to 1.
    ModelSimpleImage(int[] dimExtents, float[] voxRes)
    Creates a class to hold the minimum information about an image - the extents and the resolutions.
    ModelSimpleImage(int[] dimExtents, float[] voxRes, boolean isColor)
    Creates a class to hold the minimum information about an image - the extents, the resolutions.
    ModelSimpleImage(int[] dimExtents, float[] voxRes, ModelImage image)
    Creates a class to hold the minimum information about an image - the extents, the resolutions, and optionally, the image data.
    ModelSimpleImage(int[] dimExtents, float[] voxRes, ModelImage image, int timeSlice)
    Creates a class to hold the minimum information about an image - the extents, the resolutions, and the image data.
    ModelSimpleImage(ModelImage image)
    Creates a class to hold the minimum information about an image - the extents, the resolutions, and optionall, the image data.
    ModelSimpleImage(ModelImage image, int timeSlice)
    Creates a class to hold the minimum information about an image - the extents, the resolutions, and the image data.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    calcMinMax()
    Calculates the min and max values for the image array.
    void
    calculateCenterOfMass2D(boolean voxelResol)
    Calculates the center of mass (gravity) of a 2D image using the intensity of each pixel as a weighting value.
    void
    calculateCenterOfMass3D(boolean voxelResol)
    Calculates the center of mass (gravity) of a 3D image.
    void
    CB(double y1, double y2, double d, double[] result)
    Binary interpolation call
    ModelSimpleImage
    createIntensityImage()
    Create a new image with the same dimensions as this image which contains the intensity value from this image if it is a color image or which contains the same values if the image is already an intensity image.
    ModelSimpleImage
    createIntensityImage(float fScaleR, float fScaleG, float fScaleB)
    Create a new image with the same dimensions as this image which contains the intensity value from this image if it is a color image or which contains the same values if the image is already an intensity image.
    ModelSimpleImage
    createMappedImage2d(ModelSimpleImage kImageMapX, ModelSimpleImage kImageMapY)
    Create a mapping of this image.
    ModelSimpleImage
    createMappedImage3d(ModelSimpleImage kImageMapX, ModelSimpleImage kImageMapY, ModelSimpleImage kImageMapZ)
    Create a mapping of this image.
    int
    Depth()
    Used by AAM appearance model to get dimension
    void
    disposeLocal(boolean gcFlag)
    Nulls the data fields so that memory can be recovered.
    void
    exportData(float[] buffer, int start, int end)
    Simple accessor to copy data from this class's data buffer.
    final void
    FillPixels(float value)
    In model simple image, fill pixel with given intensity value.
    protected void
    finalize()
    Calls disposeLocal of this class to ensure this class nulls the references to global class variables so that memory will be recovered.
    final float
    getBiLinear(float x, float y)
    Version of get that performs bi-linear interpoloation.
    String
    getName()
    Get the simple image name
    final float
    getTriLinear(float x, float y, float z)
    Version of get that performs tri-linear interpoloation.
    final float
    getValue(int x, int y)
    Get the value at the x, y position of the data array.
    int
    Height()
    Used by AAM appearance model to get dimension
    void
    importData(float[] buffer, int start, int end)
    For AAM model only, import buffer to the simple image data.
    double
    Pixel1(float x, float y)
    Used by AAM appearance model to get bilinear interpolation.
    ModelSimpleImage
    ReadBandedFile(String szFilename)
    Temporary function to handle AAM image file IO for AAM own testing cases.
    ModelSimpleImage
    ReadFile(String szFileName)
    Temporary function to handle AAM image file IO for AAM own testing cases.
    void
    SetName(String _name)
    Set the simple image name
    final void
    setValue(int x, int y, float value)
    Set the value at the x, y position of the data array.
    ModelSimpleImage
    subSample2dBy2()
    Takes a simple image and subsamples it by 2.
    ModelSimpleImage
    subSample2dBy2(boolean isColor)
    Takes a simple image and subsamples it by 2.
    ModelSimpleImage
    subSample2dBy2(ModelSimpleImage resultImage)
    Takes a simple image and subsamples it by 2.
    ModelSimpleImage
    subSample2dBy2(ModelSimpleImage resultImage, boolean isColor)
    Takes a simple image and subsamples it by 2.
    ModelSimpleImage
    subsample3dBy2()
    Takes a simple image and subsamples it by 2.
    ModelSimpleImage
    subsample3dBy2(boolean isColor)
    Takes a simple 3D image and subsamples it by 2.
    ModelSimpleImage
    subsample3dBy2XY()
    Takes a simple 3D image and subsamples each image plane (XY) by 2.
    ModelSimpleImage
    subsample3dBy2XY(boolean isColor)
    Takes a simple 3D image and subsamples each image plane (XY) by 2.
    ModelSimpleImage
    subSample3dBy2XY(ModelSimpleImage resultImage)
    Takes a simple image and subsamples XY by 2, interpolating so that the new XY values are averages.
    ModelSimpleImage
    subSample3dBy2XY(ModelSimpleImage resultImage, boolean isColor)
    Takes a simple image and subsamples XY by 2, interpolating so that the new XY values are averages.
    String
    toString()
    Returns a readable representation of this simple image.
    int
    Width()
    Used by AAM appearance model to get dimension

    Methods inherited from class gov.nih.mipav.model.structures.ModelSerialCloneable

    clone, nativeClone

    Methods inherited from class java.lang.Object

    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

  • Field Details

    • serialVersionUID

      private static final long serialVersionUID
      Use serialVersionUID for interoperability.
      See Also:

    • cMassX

      public float cMassX
      X coordinate value of the center of mass for the image.

    • cMassY

      public float cMassY
      Y coordinate value of the center of mass for the image.

    • cMassZ

      public float cMassZ
      Z coordinate value of the center of mass for the image.

    • data

      public float[] data
      Data buffer that is used to store the image.

    • dataSize

      public int dataSize
      Size of the data buffer (number of pixels in image).

    • extents

      public int[] extents
      The dimensionality of the dataset.

    • isColor

      public boolean isColor
      Indicates whether is image is a color image or not.

    • max

      public float max
      Maximum intensity values of image.

    • maxR

      public float maxR
      Maximum intensity values of image.

    • maxG

      public float maxG
      Maximum intensity values of image.

    • maxB

      public float maxB
      Maximum intensity values of image.

    • min

      public float min
      Minimum intensity values of image.

    • minR

      public float minR
      Minimum intensity values of image.

    • minG

      public float minG
      Minimum intensity values of image.

    • minB

      public float minB
      Minimum intensity values of image.

    • nDims

      public int nDims
      Number of dimensions of the image.

    • resolutions

      public float[] resolutions
      Voxel resolutions (typically x,y,z(slice spacing),t).

    • tDim

      public int tDim
      Number of volumes in the dataset. Typically t represents time.

    • tRes

      public float tRes
      Resolution in the time dimension.

    • xDim

      public int xDim
      Number of pixels in x dimension.

    • xRes

      public float xRes
      X pixel resolution.

    • yDim

      public int yDim
      Number of pixels in y dimension.

    • yRes

      public float yRes
      Y pixel resolution.

    • zDim

      public int zDim
      Number of pixels in z dimension.

    • zRes

      public float zRes
      Z voxel resolution.

    • name

      public String name
      add simple image name for AAM model only.

  • Constructor Details

    • ModelSimpleImage

      public ModelSimpleImage()
      Add the empty default contructor. AAM appearance model needs to call the default one for local image processing.

    • ModelSimpleImage

      public ModelSimpleImage(ModelImage image)
      Creates a class to hold the minimum information about an image - the extents, the resolutions, and optionall, the image data.
      Parameters:
      image - ModelImage structure where the input image data is stored. In this particular constructor, this parameter must not be null as the extents and resolutions are derived from the input image.

    • ModelSimpleImage

      public ModelSimpleImage(int[] dimExtents)
      Creates a class to hold the minimum information about an image - the extents with the resolutions defaulted to 1. A data array of float type will be allocated where the size is defined by the dimExtents[].
      Parameters:
      dimExtents - Extents of the image; must be non null.

    • ModelSimpleImage

      public ModelSimpleImage(ModelImage image, int timeSlice)
      Creates a class to hold the minimum information about an image - the extents, the resolutions, and the image data. A data array of float type will be allocated where the size is defined by the ModelImage. Used for a 4D image to make a 3D ModelSimpleImage.
      Parameters:
      image - ModelImage Structure where the input image data is stored. In this particular call, this parameter must not be null as the extents and resolutions are derived from the input image.
      timeSlice - Time slice to export.

    • ModelSimpleImage

      public ModelSimpleImage(int[] dimExtents, float[] voxRes)
      Creates a class to hold the minimum information about an image - the extents and the resolutions. A data array of float type will be allocated where the size is defined by the dimExtents[].
      Parameters:
      dimExtents - Extents of the image; must be non null.
      voxRes - Resolutions of the image; must be non null.

    • ModelSimpleImage

      public ModelSimpleImage(int[] dimExtents, float[] voxRes, ModelImage image)
      Creates a class to hold the minimum information about an image - the extents, the resolutions, and optionally, the image data. A data array of float type will be allocated where the size is defined by the dimExtents[].
      Parameters:
      dimExtents - Extents of the image; must be non null.
      voxRes - Resolutions of the image; must be non null.
      image - Structure where image data is stored; can be null. If it is null, the buffer associated with this class will be empty. The ModelImage is not otherwise saved or referenced within this class.

    • ModelSimpleImage

      public ModelSimpleImage(int[] dimExtents, float[] voxRes, boolean isColor)
      Creates a class to hold the minimum information about an image - the extents, the resolutions. A data array of float type will be allocated where the size is defined by the dimExtents[].
      Parameters:
      dimExtents - Extents of the image; must be non null.
      voxRes - Resolutions of the image; must be non null.
      isColor - If true, indicates that this image is a color image (i.e. ARGB).

    • ModelSimpleImage

      public ModelSimpleImage(int[] dimExtents, float[] voxRes, ModelImage image, int timeSlice)
      Creates a class to hold the minimum information about an image - the extents, the resolutions, and the image data. A data array of float type will be allocated where the size is defined by the dimExtents[]. Used for a 4D image to make a 3D ModelSimpleImage.
      Parameters:
      dimExtents - Extents of the image; must be non null.
      voxRes - Resolutions of the image; must be non null.
      image - Structure where image data is stored; can be null. If it is null, the buffer associated with this class will be empty. The ModelImage is not otherwise saved within this class.
      timeSlice - Time slice to export into the 3D data array.

  • Method Details

    • calcMinMax

      public void calcMinMax()
      Calculates the min and max values for the image array.

    • calculateCenterOfMass2D

      public void calculateCenterOfMass2D(boolean voxelResol)
      Calculates the center of mass (gravity) of a 2D image using the intensity of each pixel as a weighting value.
      Parameters:
      voxelResol - if true multiply the center of mass by voxel resolutions.

    • calculateCenterOfMass3D

      public void calculateCenterOfMass3D(boolean voxelResol)
      Calculates the center of mass (gravity) of a 3D image. In image space where the upper left hand corner of the image is 0,0,0. The x axis goes left to right, y axis goes top to bottom and z axis goes into the screen. (i.e. the right hand rule). The intensity of each voxel is used as a weighting value.
      Parameters:
      voxelResol - if true multiply the center of mass by voxel resolutions.

    • createIntensityImage

      public ModelSimpleImage createIntensityImage()
      Create a new image with the same dimensions as this image which contains the intensity value from this image if it is a color image or which contains the same values if the image is already an intensity image. Scale factors are equally weighted for each of the RGB channels.
      Returns:
      ModelSimpleImage New instance created with intensity values only.

    • createIntensityImage

      public ModelSimpleImage createIntensityImage(float fScaleR, float fScaleG, float fScaleB)
      Create a new image with the same dimensions as this image which contains the intensity value from this image if it is a color image or which contains the same values if the image is already an intensity image. Scale factors are specified for how to compute the intensity image as a linear combination of the RGB channels.
      Parameters:
      fScaleR - Scale factor to apply to the red color channel.
      fScaleG - Scale factor to apply to the green color channel.
      fScaleB - Scale factor to apply to the blue color channel.
      Returns:
      ModelSimpleImage New instance created with intensity values only.

    • createMappedImage2d

      public ModelSimpleImage createMappedImage2d(ModelSimpleImage kImageMapX, ModelSimpleImage kImageMapY)
      Create a mapping of this image. The mapping is defined by a set of floating point coordinates for each sample in the image. The coordinates are actually stored in separate images, one for each dimension. The number dimensions and the resolutions of these coordinate images must be the same so that either one can be used to determine the dimensions and resolutions of the new image where the mapped source image values will be stored using bilinear interpolation.
      Parameters:
      kImageMapX - ModelSimpleImage Image contains the x coordinate for the mapping. Each value in the image must be in the range [0,1].
      kImageMapY - ModelSimpleImage Image contains the y coordinate for the mapping. Each value in the image must be in the range [0,1].
      Returns:
      ModelSimpleImage A new instance created with the mapping of this image.

    • createMappedImage3d

      public ModelSimpleImage createMappedImage3d(ModelSimpleImage kImageMapX, ModelSimpleImage kImageMapY, ModelSimpleImage kImageMapZ)
      Create a mapping of this image. The mapping is defined by a set of floating point coordinates for each sample in the image. The coordinates are actually stored in separate images, one for each dimension. The number dimensions and the resolutions of these coordinate images must be the same so that either one can be used to determine the dimensions and resolutions of the new image where the mapped source image values will be stored using trilinear interpolation.
      Parameters:
      kImageMapX - ModelSimpleImage Image contains the x coordinate for the mapping. Each value in the image must be in the range [0,1].
      kImageMapY - ModelSimpleImage Image contains the y coordinate for the mapping. Each value in the image must be in the range [0,1].
      kImageMapZ - ModelSimpleImage Image contains the z coordinate for the mapping. Each value in the image must be in the range [0,1].
      Returns:
      ModelSimpleImage A new instance created with the mapping of this image.

    • disposeLocal

      public void disposeLocal(boolean gcFlag)
      Nulls the data fields so that memory can be recovered.
      Parameters:
      gcFlag - if true the garbage collector is called.

    • exportData

      public void exportData(float[] buffer, int start, int end)
      Simple accessor to copy data from this class's data buffer.
      Parameters:
      buffer - destination buffer
      start - the starting pointer where data is to be copy from the source buffer
      end - the ending pointer where in the source buffer

    • getValue

      public final float getValue(int x, int y)
      Get the value at the x, y position of the data array.
      Parameters:
      x - input x pixel coordinate
      y - input y pixel coordinate
      Returns:
      data value at the given position.

    • setValue

      public final void setValue(int x, int y, float value)
      Set the value at the x, y position of the data array.
      Parameters:
      x - input x pixel coordinate.
      y - input y pixel coordinate
      value - data value.

    • getBiLinear

      public final float getBiLinear(float x, float y)
      Version of get that performs bi-linear interpoloation. Note - does NOT perform bounds checking
      Parameters:
      x - input x coordinate
      y - input y coordinate
      Returns:
      the bilinear interpolated value for x,y.

    • getTriLinear

      public final float getTriLinear(float x, float y, float z)
      Version of get that performs tri-linear interpoloation. Note - does NOT perform bounds checking
      Parameters:
      x - x coordinate
      y - y coordinate
      z - z coordinate
      Returns:
      the trilinear interpolated value for x,y,z.

    • subSample2dBy2

      public ModelSimpleImage subSample2dBy2()
      Takes a simple image and subsamples it by 2. Linear interpolation is used.
      Returns:
      Subsampled image.

    • subSample2dBy2

      public ModelSimpleImage subSample2dBy2(boolean isColor)
      Takes a simple image and subsamples it by 2. Linear interpolation is used.
      Parameters:
      isColor - If true, indicates that this image is a color image (i.e. ARGB).
      Returns:
      Subsampled image.

    • subSample2dBy2

      public ModelSimpleImage subSample2dBy2(ModelSimpleImage resultImage)
      Takes a simple image and subsamples it by 2. Linear interpolation is used.
      Parameters:
      resultImage - The subsampled data will be stored in this object.
      Returns:
      Subsampled image.

    • subSample2dBy2

      public ModelSimpleImage subSample2dBy2(ModelSimpleImage resultImage, boolean isColor)
      Takes a simple image and subsamples it by 2. Linear interpolation is used.
      Parameters:
      resultImage - The subsampled data will be stored in this object.
      isColor - If true, indicates that this image is a color image (i.e. ARGB).
      Returns:
      Subsampled image.

    • subsample3dBy2

      public ModelSimpleImage subsample3dBy2()
      Takes a simple image and subsamples it by 2. Linear interpolation is used.
      Returns:
      Subsampled image.

    • subsample3dBy2

      public ModelSimpleImage subsample3dBy2(boolean isColor)
      Takes a simple 3D image and subsamples it by 2. Linear interpolation is used.
      Parameters:
      isColor - If true, indicates that this image is a color image (i.e. ARGB).
      Returns:
      Subsampled image.

    • subsample3dBy2XY

      public ModelSimpleImage subsample3dBy2XY()
      Takes a simple 3D image and subsamples each image plane (XY) by 2. Linear interpolation is used.
      Returns:
      Subsampled image.

    • subsample3dBy2XY

      public ModelSimpleImage subsample3dBy2XY(boolean isColor)
      Takes a simple 3D image and subsamples each image plane (XY) by 2. Linear interpolation is used.
      Parameters:
      isColor - If true, indicates that this image is a color image (i.e. ARGB).
      Returns:
      Subsampled image.

    • subSample3dBy2XY

      public ModelSimpleImage subSample3dBy2XY(ModelSimpleImage resultImage)
      Takes a simple image and subsamples XY by 2, interpolating so that the new XY values are averages.
      Parameters:
      resultImage - The subsampled data will be stored in this object.
      Returns:
      Subsampled image.

    • subSample3dBy2XY

      public ModelSimpleImage subSample3dBy2XY(ModelSimpleImage resultImage, boolean isColor)
      Takes a simple image and subsamples XY by 2, interpolating so that the new XY values are averages.
      Parameters:
      resultImage - The subsampled data will be stored in this object.
      isColor - If true, indicates that this image is a color image (i.e. ARGB).
      Returns:
      Subsampled image.

    • toString

      public String toString()
      Returns a readable representation of this simple image.
      Overrides:
      toString in class Object
      Returns:
      Representation containing extents and resolutions.

    • finalize

      protected void finalize() throws Throwable
      Calls disposeLocal of this class to ensure this class nulls the references to global class variables so that memory will be recovered.
      Overrides:
      finalize in class Object
      Throws:
      Throwable - Throws an error if there is a problem with the finalization of this object.

    • Width

      public int Width()
      Used by AAM appearance model to get dimension
      Returns:
      x dimension

    • Height

      public int Height()
      Used by AAM appearance model to get dimension
      Returns:
      y dimension

    • Depth

      public int Depth()
      Used by AAM appearance model to get dimension
      Returns:
      z dimension

    • CB

      public void CB(double y1, double y2, double d, double[] result)
      Binary interpolation call
      Parameters:
      y1 -
      y2 -
      d -
      result -

    • Pixel1

      public double Pixel1(float x, float y)
      Used by AAM appearance model to get bilinear interpolation.
      Returns:
      interpolation value.

    • SetName

      public void SetName(String _name)
      Set the simple image name
      Parameters:
      _name -

    • getName

      public String getName()
      Get the simple image name
      Returns:

    • FillPixels

      public final void FillPixels(float value)
      In model simple image, fill pixel with given intensity value.
      Parameters:
      value -

    • importData

      public void importData(float[] buffer, int start, int end)
      For AAM model only, import buffer to the simple image data.
      Parameters:
      buffer -
      start -
      end -

    • ReadBandedFile

      public ModelSimpleImage ReadBandedFile(String szFilename)
      Temporary function to handle AAM image file IO for AAM own testing cases. Lately this function will be removed.
      Parameters:
      szFilename -
      Returns:

    • ReadFile

      public ModelSimpleImage ReadFile(String szFileName)
      Temporary function to handle AAM image file IO for AAM own testing cases. Lately this function will be removed.
      Parameters:
      szFilename -
      Returns: