Tools (HDFView 2.14)

Object
- hdf.view.Tools

```
public final class Tools
extends Object
```
The "Tools" class contains various tools for HDF files such as jpeg to HDF converter.

Version:

2.4 9/6/2007

Author:

Peter X. Cao

Field Summary

Fields
Modifier and Type	Field and Description
`static String`	`FILE_TYPE_BMP` Key for BMP image file type.
`static String`	`FILE_TYPE_GIF` Key for GIF image file type.
`static String`	`FILE_TYPE_IMAGE` Key for all image file type.
`static String`	`FILE_TYPE_JPEG` Key for JPEG image file type.
`static String`	`FILE_TYPE_PNG` Key for PNG image file type.
`static String`	`FILE_TYPE_TIFF` Key for TIFF image file type.
`(package private) static char[]`	`HEXCHARS`
`static long`	`MAX_INT16`
`static long`	`MAX_INT32`
`static long`	`MAX_INT64`
`static long`	`MAX_INT8`
`static long`	`MAX_UINT16`
`static long`	`MAX_UINT32`
`static BigInteger`	`MAX_UINT64`
`static long`	`MAX_UINT8`

Constructor Summary

Constructors
Constructor and Description

Tools()

Constructors
Constructor and Description
`Tools()`

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static boolean`	`applyBitmask(Object theData, BitSet theMask, ViewProperties.BITMASK_OP op)` Apply bitmask to a data array.
`static Object`	`autoContrastApply(Object data_in, Object data_out, double[] params, double[] minmax, boolean isUnsigned)` Apply autocontrast parameters to the original data in place (destructive)
`static int`	`autoContrastCompute(Object data, double[] params, boolean isUnsigned)` Computes autocontrast parameters (gain equates to contrast and bias equates to brightness) for integers.
`static int`	`autoContrastComputeMinMax(Object data, double[] minmax)` Computes autocontrast parameters by
`static int`	`autoContrastConvertImageBuffer(Object src, byte[] dst, boolean isUnsigned)` Converts image raw data to bytes.
`static File`	`checkNewFile(String path, String ext)` Check and find a non-exist file.
`static int`	`computeStatistics(Object data, double[] avgstd, Object fillValue)` Computes mean and standard deviation of a data array
`static void`	`convertImageToHDF(String imgFileName, String hFileName, String fromType, String toType)` Converts an image file into HDF4/5 file.
`static byte[][]`	`createGrayPalette()` Creates the gray palette of the indexed 256-color table.
`static byte[][]`	`createGrayWavePalette()` Creates the gray wave palette of the indexed 256-color table.
`static Image`	`createIndexedImage(BufferedImage bufferedImage, byte[] imageData, byte[][] palette, int w, int h)` Creates a RGB indexed image of 256 colors.
`static byte[][]`	`createNaturePalette()` Creates the nature palette of the indexed 256-color table.
`static byte[][]`	`createRainbowPalette()` Creates the rainbow palette of the indexed 256-color table.
`static byte[][]`	`createReverseGrayPalette()` Creates the reverse gray palette of the indexed 256-color table.
`static Image`	`createTrueColorImage(byte[] imageData, boolean planeInterlace, int w, int h)` Creates a true color image.
`static byte[][]`	`createWavePalette()` Creates the wave palette of the indexed 256-color table.
`static void`	`debug(Object caller, Object msg)` Print out debug information
`static int`	`findDataDist(Object data, int[] dataDist, double[] minmax)` Finds the distribution of data values
`static int`	`findMinMax(Object data, double[] minmax, Object fillValue)` Finds the min and max values of the data array
`static byte[]`	`getBytes(Object rawData, double[] minmax, int w, int h, boolean isTransposed, byte[] byteData)` Convert an array of raw data into array of a byte data.
`static byte[]`	`getBytes(Object rawData, double[] minmax, int w, int h, boolean isTransposed, List<Number> invalidValues, boolean convertByteData, byte[] byteData)`
`static byte[]`	`getBytes(Object rawData, double[] minmax, int w, int h, boolean isTransposed, List<Number> invalidValues, boolean convertByteData, byte[] byteData, List<Integer> list)` Convert an array of raw data into array of a byte data.
`static byte[]`	`getBytes(Object rawData, double[] minmax, int w, int h, boolean isTransposed, List<Number> invalidValues, byte[] byteData)`
`static boolean`	`hasAlpha(Image image)` This method returns true if the specified image has transparent pixels.
`static boolean`	`isNaNINF(double val)` Check if a given number if NaN or INF.
`static void`	`launchBrowser(String url)` Launch default browser for a given URL.
`static Object`	`newInstance(Class<?> cls, Object[] initargs)` Create and initialize a new instance of the given class.
`static byte[][]`	`readPalette(String filename)` read an image palette from a file.
`static void`	`saveImageAs(BufferedImage image, File file, String type)` Save a BufferedImage into an image file.
`static String`	`toBinaryString(long v, int nbytes)` Returns a string representation of the long argument as an unsigned integer in base 2.
`static String`	`toHexString(long v, int nbytes)` Returns a string representation of the long argument as an unsigned integer in base 16.

Methods inherited from class Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - MAX_INT8
```
public static final long MAX_INT8
```
    See Also:
    
    Constant Field Values
  - MAX_UINT8
```
public static final long MAX_UINT8
```
    See Also:
    
    Constant Field Values
  - MAX_INT16
```
public static final long MAX_INT16
```
    See Also:
    
    Constant Field Values
  - MAX_UINT16
```
public static final long MAX_UINT16
```
    See Also:
    
    Constant Field Values
  - MAX_INT32
```
public static final long MAX_INT32
```
    See Also:
    
    Constant Field Values
  - MAX_UINT32
```
public static final long MAX_UINT32
```
    See Also:
    
    Constant Field Values
  - MAX_INT64
```
public static final long MAX_INT64
```
    See Also:
    
    Constant Field Values
  - MAX_UINT64
```
public static final BigInteger MAX_UINT64
```
  - FILE_TYPE_JPEG
```
public static final String FILE_TYPE_JPEG
```
    Key for JPEG image file type.
    
    See Also:
    
    Constant Field Values
  - FILE_TYPE_TIFF
```
public static final String FILE_TYPE_TIFF
```
    Key for TIFF image file type.
    
    See Also:
    
    Constant Field Values
  - FILE_TYPE_PNG
```
public static final String FILE_TYPE_PNG
```
    Key for PNG image file type.
    
    See Also:
    
    Constant Field Values
  - FILE_TYPE_GIF
```
public static final String FILE_TYPE_GIF
```
    Key for GIF image file type.
    
    See Also:
    
    Constant Field Values
  - FILE_TYPE_BMP
```
public static final String FILE_TYPE_BMP
```
    Key for BMP image file type.
    
    See Also:
    
    Constant Field Values
  - FILE_TYPE_IMAGE
```
public static final String FILE_TYPE_IMAGE
```
    Key for all image file type.
    
    See Also:
    
    Constant Field Values
  - HEXCHARS
```
static final char[] HEXCHARS
```
- Constructor Detail
  - Tools
```
public Tools()
```
- Method Detail
  - debug
```
public static final void debug(Object caller,
                               Object msg)
```
    Print out debug information
    
    Parameters:
    
    caller - the caller object.
    
    msg - the message to be displayed.
  - convertImageToHDF
```
public static void convertImageToHDF(String imgFileName,
                                     String hFileName,
                                     String fromType,
                                     String toType)
                              throws Exception
```
    Converts an image file into HDF4/5 file.
    
    Parameters:
    
    imgFileName - the input image file.
    
    hFileName - the name of the HDF4/5 file.
    
    fromType - the type of image.
    
    toType - the type of file converted to.
    
    Throws:
    
    Exception - if a failure occurred
  - saveImageAs
```
public static void saveImageAs(BufferedImage image,
                               File file,
                               String type)
                        throws Exception
```
    Save a BufferedImage into an image file.
    
    Parameters:
    
    image - the BufferedImage to save.
    
    file - the image file.
    
    type - the image type.
    
    Throws:
    
    Exception - if a failure occurred
  - createGrayPalette
```
public static final byte[][] createGrayPalette()
```
    Creates the gray palette of the indexed 256-color table.
    The palette values are stored in a two-dimensional byte array and arrange by color components of red, green and blue. palette[][] = byte[3][256], where, palette[0][], palette[1][] and palette[2][] are the red, green and blue components respectively.
    
    Returns:
    
    the gray palette in the form of byte[3][256]
  - createReverseGrayPalette
```
public static final byte[][] createReverseGrayPalette()
```
    Creates the reverse gray palette of the indexed 256-color table.
    The palette values are stored in a two-dimensional byte array and arrange by color components of red, green and blue. palette[][] = byte[3][256], where, palette[0][], palette[1][] and palette[2][] are the red, green and blue components respectively.
    
    Returns:
    
    the gray palette in the form of byte[3][256]
  - createGrayWavePalette
```
public static final byte[][] createGrayWavePalette()
```
    Creates the gray wave palette of the indexed 256-color table.
    The palette values are stored in a two-dimensional byte array and arrange by color components of red, green and blue. palette[][] = byte[3][256], where, palette[0][], palette[1][] and palette[2][] are the red, green and blue components respectively.
    
    Returns:
    
    the gray palette in the form of byte[3][256]
  - createRainbowPalette
```
public static final byte[][] createRainbowPalette()
```
    Creates the rainbow palette of the indexed 256-color table.
    The palette values are stored in a two-dimensional byte array and arrange by color components of red, green and blue. palette[][] = byte[3][256], where, palette[0][], palette[1][] and palette[2][] are the red, green and blue components respectively.
    
    Returns:
    
    the rainbow palette in the form of byte[3][256]
  - createNaturePalette
```
public static final byte[][] createNaturePalette()
```
    Creates the nature palette of the indexed 256-color table.
    The palette values are stored in a two-dimensional byte array and arrange by color components of red, green and blue. palette[][] = byte[3][256], where, palette[0][], palette[1][] and palette[2][] are the red, green and blue components respectively.
    
    Returns:
    
    the nature palette in the form of byte[3][256]
  - createWavePalette
```
public static final byte[][] createWavePalette()
```
    Creates the wave palette of the indexed 256-color table.
    The palette values are stored in a two-dimensional byte array and arrange by color components of red, green and blue. palette[][] = byte[3][256], where, palette[0][], palette[1][] and palette[2][] are the red, green and blue components respectively.
    
    Returns:
    
    the wave palette in the form of byte[3][256]
  - readPalette
```
public static final byte[][] readPalette(String filename)
```
    read an image palette from a file. A palette file has format of (value, red, green, blue). The color value in palette file can be either unsigned char [0..255] or float [0..1]. Float value will be converted to [0..255]. The color table in file can have any number of entries between 2 to 256. It will be converted to a color table of 256 entries. Any missing index will calculated by linear interpolation between the neighboring index values. For example, index 11 is missing in the following table 10 200 60 20 12 100 100 60 Index 11 will be calculated based on index 10 and index 12, i.e. 11 150 80 40
    
    Parameters:
    
    filename - the name of the palette file.
    
    Returns:
    
    the wave palette in the form of byte[3][256]
  - hasAlpha
```
public static boolean hasAlpha(Image image)
```
    This method returns true if the specified image has transparent pixels.
    
    Parameters:
    
    image - the image to be check if has alpha.
    
    Returns:
    
    true if the image has alpha setting.
  - createIndexedImage
```
public static Image createIndexedImage(BufferedImage bufferedImage,
                                       byte[] imageData,
                                       byte[][] palette,
                                       int w,
                                       int h)
```
    Creates a RGB indexed image of 256 colors.
    
    Parameters:
    
    bufferedImage - the target image.
    
    imageData - the byte array of the image data.
    
    palette - the color lookup table.
    
    w - the width of the image.
    
    h - the height of the image.
    
    Returns:
    
    the image.
  - createTrueColorImage
```
public static Image createTrueColorImage(byte[] imageData,
                                         boolean planeInterlace,
                                         int w,
                                         int h)
```
    Creates a true color image.
    DirectColorModel is used to construct the image from raw data. The DirectColorModel model is similar to an X11 TrueColor visual, which has the following parameters:
```
 Number of bits:        32
             Red mask:              0x00ff0000
             Green mask:            0x0000ff00
             Blue mask:             0x000000ff
             Alpha mask:            0xff000000
             Color space:           sRGB
             isAlphaPremultiplied:  False
             Transparency:          Transparency.TRANSLUCENT
             transferType:          DataBuffer.TYPE_INT
 
```
    The data may be arranged in one of two ways: by pixel or by plane. In both cases, the dataset will have a dataspace with three dimensions, height, width, and components.
    For HDF4, the interlace modes specify orders for the dimensions as:
```
 INTERLACE_PIXEL = [width][height][pixel components]
            INTERLACE_PLANE = [pixel components][width][height]
 
```
    For HDF5, the interlace modes specify orders for the dimensions as:
```
 INTERLACE_PIXEL = [height][width][pixel components]
            INTERLACE_PLANE = [pixel components][height][width]
 
```
    Parameters:
    
    imageData - the byte array of the image data.
    
    planeInterlace - flag if the image is plane intelace.
    
    w - the width of the image.
    
    h - the height of the image.
    
    Returns:
    
    the image.
  - getBytes
```
public static byte[] getBytes(Object rawData,
                              double[] minmax,
                              int w,
                              int h,
                              boolean isTransposed,
                              byte[] byteData)
```
    Convert an array of raw data into array of a byte data.
    
    Parameters:
    
    rawData - The input raw data.
    
    minmax - the range of the raw data.
    
    w - the width of the raw data.
    
    h - the height of the raw data.
    
    isTransposed - if the data is transposed.
    
    byteData - the data in.
    
    Returns:
    
    the byte array of pixel data.
  - getBytes
```
public static byte[] getBytes(Object rawData,
                              double[] minmax,
                              int w,
                              int h,
                              boolean isTransposed,
                              List<Number> invalidValues,
                              byte[] byteData)
```
  - getBytes
```
public static byte[] getBytes(Object rawData,
                              double[] minmax,
                              int w,
                              int h,
                              boolean isTransposed,
                              List<Number> invalidValues,
                              boolean convertByteData,
                              byte[] byteData)
```
  - getBytes
```
public static byte[] getBytes(Object rawData,
                              double[] minmax,
                              int w,
                              int h,
                              boolean isTransposed,
                              List<Number> invalidValues,
                              boolean convertByteData,
                              byte[] byteData,
                              List<Integer> list)
```
    Convert an array of raw data into array of a byte data.
    
    Parameters:
    
    rawData - The input raw data.
    
    minmax - the range of the raw data.
    
    w - the width of the raw data.
    
    h - the height of the raw data.
    
    isTransposed - if the data is transposed.
    
    invalidValues - the list of invalid values.
    
    convertByteData - the converted data out.
    
    byteData - the data in.
    
    list - the list of integers.
    
    Returns:
    
    the byte array of pixel data.
  - newInstance
```
public static Object newInstance(Class<?> cls,
                                 Object[] initargs)
                          throws Exception
```
    Create and initialize a new instance of the given class.
    
    Parameters:
    
    cls - the class of the instance
    
    initargs - array of objects to be passed as arguments.
    
    Returns:
    
    a new instance of the given class.
    
    Throws:
    
    Exception - if a failure occurred
  - autoContrastCompute
```
public static int autoContrastCompute(Object data,
                                      double[] params,
                                      boolean isUnsigned)
```
    Computes autocontrast parameters (gain equates to contrast and bias equates to brightness) for integers.
    The computation is based on the following scaling
```
      int_8       [0, 127]
      uint_8      [0, 255]
      int_16      [0, 32767]
      uint_16     [0, 65535]
      int_32      [0, 2147483647]
      uint_32     [0, 4294967295]
      int_64      [0, 9223372036854775807]
      uint_64     [0, 18446744073709551615] // Not supported.
 
```
    Parameters:
    
    data - the raw data array of signed/unsigned integers
    
    params - the auto gain parameter. params[0]=gain, params[1]=bias,
    
    isUnsigned - the flag to indicate if the data array is unsigned integer.
    
    Returns:
    
    non-negative if successful; otherwise, returns negative
  - autoContrastApply
```
public static Object autoContrastApply(Object data_in,
                                       Object data_out,
                                       double[] params,
                                       double[] minmax,
                                       boolean isUnsigned)
```
    Apply autocontrast parameters to the original data in place (destructive)
    
    Parameters:
    
    data_in - the original data array of signed/unsigned integers
    
    data_out - the converted data array of signed/unsigned integers
    
    params - the auto gain parameter. params[0]=gain, params[1]=bias
    
    minmax - the data range. minmax[0]=min, minmax[1]=max
    
    isUnsigned - the flag to indicate if the data array is unsigned integer
    
    Returns:
    
    the data array with the auto contrast conversion; otherwise, returns null
  - autoContrastConvertImageBuffer
```
public static int autoContrastConvertImageBuffer(Object src,
                                                 byte[] dst,
                                                 boolean isUnsigned)
```
    Converts image raw data to bytes. The integer data is converted to byte data based on the following rule
```
         uint_8       x
         int_8       (x & 0x7F) << 1
         uint_16     (x >> 8) & 0xFF
         int_16      (x >> 7) & 0xFF
         uint_32     (x >> 24) & 0xFF
         int_32      (x >> 23) & 0xFF
         uint_64     (x >> 56) & 0xFF
         int_64      (x >> 55) & 0xFF
 
```
    Parameters:
    
    src - the source data array of signed integers or unsigned shorts
    
    dst - the destination data array of bytes
    
    isUnsigned - the flag to indicate if the data array is unsigned integer.
    
    Returns:
    
    non-negative if successful; otherwise, returns negative
  - autoContrastComputeMinMax
```
public static int autoContrastComputeMinMax(Object data,
                                            double[] minmax)
```
    Computes autocontrast parameters by
```
    min = mean - 3 * std.dev
    max = mean + 3 * std.dev
 
```
    Parameters:
    
    data - the raw data array
    
    minmax - the min and max values.
    
    Returns:
    
    non-negative if successful; otherwise, returns negative
  - findMinMax
```
public static int findMinMax(Object data,
                             double[] minmax,
                             Object fillValue)
```
    Finds the min and max values of the data array
    
    Parameters:
    
    data - the raw data array
    
    minmax - the mmin and max values of the array.
    
    fillValue - the missing value or fill value. Exclude this value when check for min/max
    
    Returns:
    
    non-negative if successful; otherwise, returns negative
  - findDataDist
```
public static int findDataDist(Object data,
                               int[] dataDist,
                               double[] minmax)
```
    Finds the distribution of data values
    
    Parameters:
    
    data - the raw data array
    
    dataDist - the data distirbution.
    
    minmax - the data range
    
    Returns:
    
    non-negative if successful; otherwise, returns negative
  - computeStatistics
```
public static int computeStatistics(Object data,
                                    double[] avgstd,
                                    Object fillValue)
```
    Computes mean and standard deviation of a data array
    
    Parameters:
    
    data - the raw data array
    
    avgstd - the statistics: avgstd[0]=mean and avgstd[1]=stdev.
    
    fillValue - the missing value or fill value. Exclude this value when compute statistics
    
    Returns:
    
    non-negative if successful; otherwise, returns negative
  - toBinaryString
```
public static final String toBinaryString(long v,
                                          int nbytes)
```
    Returns a string representation of the long argument as an unsigned integer in base 2. This is different from Long.toBinaryString(long i). This function add padding (0's) to the string based on the nbytes. For example, if v=15, nbytes=1, the string will be "00001111".
    
    Parameters:
    
    v - the long value
    
    nbytes - number of bytes in the integer
    
    Returns:
    
    the string representation of the unsigned long value represented by the argument in binary (base 2).
  - toHexString
```
public static final String toHexString(long v,
                                       int nbytes)
```
    Returns a string representation of the long argument as an unsigned integer in base 16. This is different from Long.toHexString(long i). This function add padding (0's) to the string based on the nbytes. For example, if v=42543, nbytes=4, the string will be "0000A62F".
    
    Parameters:
    
    v - the long value
    
    nbytes - number of bytes in the integer
    
    Returns:
    
    the string representation of the unsigned long value represented by the argument in hexadecimal (base 16).
  - applyBitmask
```
public static final boolean applyBitmask(Object theData,
                                         BitSet theMask,
                                         ViewProperties.BITMASK_OP op)
```
    Apply bitmask to a data array.
    
    Parameters:
    
    theData - the data array which the bitmask is applied to.
    
    theMask - the bitmask to be applied to the data array.
    
    op - the bitmask op to be applied
    
    Returns:
    
    true if bitmask is applied successfuly; otherwise, false.
  - launchBrowser
```
public static final void launchBrowser(String url)
                                throws Exception
```
    Launch default browser for a given URL.
    
    Parameters:
    
    url - the URL to open.
    
    Throws:
    
    Exception - if a failure occurred
  - checkNewFile
```
public static final File checkNewFile(String path,
                                      String ext)
```
    Check and find a non-exist file.
    
    Parameters:
    
    path - -- the path that the new file will be checked.
    
    ext - -- the extention of the new file.
    
    Returns:
    
    -- the new file.
  - isNaNINF
```
public static final boolean isNaNINF(double val)
```
    Check if a given number if NaN or INF.
    
    Parameters:
    
    val - the nubmer to be checked
    
    Returns:
    
    true if the number is Nan or INF; otherwise, false.

Class Tools

Field Summary

Constructor Summary

Method Summary

Methods inherited from class Object

Field Detail

MAX_INT8

MAX_UINT8

MAX_INT16

MAX_UINT16

MAX_INT32

MAX_UINT32

MAX_INT64

MAX_UINT64

FILE_TYPE_JPEG

FILE_TYPE_TIFF

FILE_TYPE_PNG

FILE_TYPE_GIF

FILE_TYPE_BMP

FILE_TYPE_IMAGE

HEXCHARS

Constructor Detail

Tools

Method Detail

debug

convertImageToHDF

saveImageAs

createGrayPalette

createReverseGrayPalette

createGrayWavePalette

createRainbowPalette

createNaturePalette

createWavePalette

readPalette

hasAlpha

createIndexedImage

createTrueColorImage

getBytes

getBytes

getBytes

getBytes

newInstance

autoContrastCompute

autoContrastApply

autoContrastConvertImageBuffer

autoContrastComputeMinMax

findMinMax

findDataDist

computeStatistics

toBinaryString

toHexString

applyBitmask

launchBrowser

checkNewFile

isNaNINF