Module org.hdfgroup.hdfview
Package hdf.view

Class Tools

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 Details

  • Constructor Details

  • Method Details

    • convertUINT64toBigInt

      public static BigInteger convertUINT64toBigInt​(Long l)
      Converts unsigned 64-bit integer data to a BigInteger since Java does not have unsigned types.
      Parameters:
      l - The long value to convert to a BigInteger
      Returns:
      A BigInteger representing the unsigned value of the given long.

    • 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 IOException
      Save a BufferedImage into an image file.
      Parameters:
      image - the BufferedImage to save.
      file - the image file.
      type - the image type.
      Throws:
      IOException - 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, long w, long 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, long w, long 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 interlace.
      w - the width of the image.
      h - the height of the image.
      Returns:
      the image.

    • toBufferedImage

      public static BufferedImage toBufferedImage​(Image image)
      This method returns a buffered image with the contents of an image.
      Parameters:
      image - the plain image object.
      Returns:
      buffered image for the given image.

    • getBytes

      public static byte[] getBytes​(Object rawData, double[] minmax, long w, long 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, long w, long h, boolean isTransposed, List<Number> invalidValues, byte[] byteData)

    • getBytes

      public static byte[] getBytes​(Object rawData, double[] minmax, long w, long h, boolean isTransposed, List<Number> invalidValues, boolean convertByteData, byte[] byteData)

    • getBytes

      public static byte[] getBytes​(Object rawData, double[] minmax, long w, long 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 dataIN, Object dataOUT, double[] params, double[] minmax, boolean isUnsigned)
      Apply autocontrast parameters to the original data in place (destructive)
      Parameters:
      dataIN - the original data array of signed/unsigned integers
      dataOUT - 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

    • saveAsBinary

      public static void saveAsBinary​(DataOutputStream out, Object data, ByteOrder order) throws Exception
      Throws:
      Exception

    • getBinaryDataFromFile

      public static boolean getBinaryDataFromFile​(Object dataOut, String fileName, ByteOrder order)
      Reads data from a binary file into a buffer.
      Parameters:
      dataOut - the output stream
      fileName - the file to read binary data from
      order - the new byte order, either BIG_ENDIAN or LITTLE_ENDIAN
      Returns:
      true if successful; otherwise, false.

    • 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).

    • toBinaryString

      public static final String toBinaryString​(BigDecimal v, int nbytes)

    • toBinaryString

      public static final String toBinaryString​(BigInteger v, int nbytes)

    • 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).

    • toHexString

      public static final String toHexString​(BigInteger v, int nbytes)
      Returns a string representation of the BigInteger argument as an unsigned integer in base 16. This is different from BigInteger.toString(16). This function adds 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 BigInteger 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).

    • toHexString

      public static final String toHexString​(BigDecimal v, int nbytes)

    • 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 successfully; otherwise, false.

    • getHDF5UserBlock

      public static byte[] getHDF5UserBlock​(String filename)
      Read HDF5 user block data into byte array.
      Parameters:
      filename - the HDF5 file from which to get the user block
      Returns:
      a byte array of user block, or null if there is user data.

    • setHDF5UserBlock

      public static boolean setHDF5UserBlock​(String fin, String fout, byte[] buf)
      Write HDF5 user block data into byte array.
      Parameters:
      fin - the input filename
      fout - the output filename
      buf - the data to write into the user block
      Returns:
      a byte array of user block, or null if there is user data.

    • isHDF4

      public static boolean isHDF4​(String filename)
      look at the first 4 bytes of the file to see if it is an HDF4 file. byte[0]=14, byte[1]=3, byte[2]=19, byte[3]=1 or if it is a netCDF file byte[0]=67, byte[1]=68, byte[2]=70, byte[3]=1
      Parameters:
      filename - the file to test if HDF4
      Returns:
      true if the file is of type HDF4

    • isHDF5

      public static boolean isHDF5​(String filename)
      look at the first 8 bytes of the file to see if it is an HDF5 file. byte[0]=-199 which is 137 in unsigned byte, byte[1]=72, byte[2]=68, byte[3]=70, byte[4]=13, byte[5]=10, byte[6]=26, byte[7]=10
      Parameters:
      filename - the file to test if HDF5
      Returns:
      true if the file is of type HDF5

    • isNetcdf

      public static boolean isNetcdf​(String filename)
      look at the first 4 bytes of the file to see if it is a netCDF file byte[0]=67, byte[1]=68, byte[2]=70, byte[3]=1 or
      Parameters:
      filename - the file to test if netcdf
      Returns:
      true if the file is of type netcdf

    • 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

    • createNewFile

      public static FileFormat createNewFile​(String filename, String dir, String type, List<FileFormat> openFiles) throws Exception
      Create a new HDF file with default file creation properties
      Parameters:
      filename - the file to create
      dir - the directory for file
      type - the type of the file
      openFiles - the list of already opened files
      Returns:
      the FileFormat instance of the newly created file
      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 number to be checked
      Returns:
      true if the number is Nan or INF; otherwise, false.

    • checkValidJavaArrayIndex

      public static boolean checkValidJavaArrayIndex​(long value)
      Since Java does not allow array indices to be larger than int type, check the given value to see if it is within the valid range of a Java int.
      Parameters:
      value - The value to check
      Returns:
      false if the value is outside the range of a Java int, true otherwise.

    • showError

      public static void showError​(org.eclipse.swt.widgets.Shell parent, String title, String errorMsg)
      Show an SWT error dialog with the given error message.
      Parameters:
      parent - The parent Shell of the MessageDialog
      title - The title to set for the MessageDialog
      errorMsg - The error message to display in the MessageDialog

    • showInformation

      public static void showInformation​(org.eclipse.swt.widgets.Shell parent, String title, String infoMsg)
      Show an SWT Information dialog with the given message.
      Parameters:
      parent - The parent Shell of the MessageDialog
      title - The title to set for the MessageDialog
      infoMsg - The message to display in the MessageDialog

    • showConfirm

      public static boolean showConfirm​(org.eclipse.swt.widgets.Shell parent, String title, String confMsg)
      Show an SWT Confirm dialog with the given message.
      Parameters:
      parent - The parent Shell of the MessageDialog
      title - The title to set for the MessageDialog
      confMsg - The message to display in the MessageDialog
      Returns:
      The status of the dialog after closing

    • showWarning

      public static void showWarning​(org.eclipse.swt.widgets.Shell parent, String title, String warnMsg)
      Show an SWT Warning dialog with the given message.
      Parameters:
      parent - The parent Shell of the MessageDialog
      title - The title to set for the MessageDialog
      warnMsg - The message to display in the MessageDialog