Package gov.nih.mipav.model.file

Class FileRaw

java.lang.Object
gov.nih.mipav.model.file.FileBase
gov.nih.mipav.model.file.FileRaw
public class FileRaw extends FileBase
The class reads and writes raw files of all data types: boolean, byte, short, int, long, float, and double. For the read process an offset can be pass as a parameter to identify the location in the file where the data starts. A number of file formats while not "raw" have data at a specific location after a fixed length but unknown header and therefore can be treated as raw.
Version:
0.1 Sept 2, 1997
See Also:

  • Field Details

    • compressionType

      private int compressionType
      DOCUMENT ME!

    • file

      private File file
      DOCUMENT ME!

    • fileInfo

      private FileInfoBase fileInfo
      DOCUMENT ME!

    • fileName

      private String fileName

    • fileRW

      private FileRawChunk fileRW
      DOCUMENT ME!

    • nImages

      private int nImages
      DOCUMENT ME!

    • nTimePeriods

      private int nTimePeriods
      DOCUMENT ME!

    • planarConfig

      private int planarConfig
      DOCUMENT ME!

    • YBR_FULL_422

      private boolean YBR_FULL_422

    • startPosition

      private long startPosition
      DOCUMENT ME!

    • numChannels

      private int numChannels

    • RGBAOrder

      private boolean RGBAOrder
      Allow reading from 4 color files with RGBA order

    • zeroLengthFlag

      private boolean zeroLengthFlag
      flag that indicates if raFile should first be set to length of 0

    • dataFileName

      private String[] dataFileName

    • minimumBitsMinus1

      private int minimumBitsMinus1
      Used in reading and writing boolean

    • shiftToDivide

      private int shiftToDivide
      Used in reading and writing boolean

    • threeByteInteger

      private boolean threeByteInteger

    • bitsAllocated

      private int bitsAllocated

    • bitsStored

      private int bitsStored

    • highBit

      private int highBit

  • Constructor Details

    • FileRaw

      public FileRaw(FileInfoBase fInfo)
      Constructor for Raw Files that will be used to write from 4D to 3D or from 3D to 2D.
      Parameters:
      fInfo - fileinfo

    • FileRaw

      public FileRaw(String fileName, FileInfoBase fInfo, int rwFlag) throws IOException
      Raw reader/writer constructor.
      Parameters:
      fileName - Complete file name
      fInfo - Information that describes the image.
      rwFlag - Read/write flag.
      Throws:
      IOException - if there is an error making the files

    • FileRaw

      public FileRaw(String fileName, String fileDir, FileInfoBase fInfo, int rwFlag) throws IOException
      Raw reader/writer constructor..
      Parameters:
      fileName - File name (no path)
      fileDir - File directory (with trailing file separator).
      fInfo - Information that describes the image.
      rwFlag - Read/write flag.
      showProgressBar - Boolean indicating if progess bar should be displayed.
      Throws:
      IOException - if there is an error making the files

  • Method Details

    • close

      public void close() throws IOException
      Closes random access file associated with this object.
      Throws:
      IOException - DOCUMENT ME!

    • finalize

      public void finalize()
      Prepares this class for cleanup.
      Overrides:
      finalize in class FileBase

    • setThreeByteInteger

      public void setThreeByteInteger(boolean threeByteInteger)

    • setBitsAllocated

      public void setBitsAllocated(int bitsAllocated)

    • setBitsStored

      public void setBitsStored(int bitsStored)

    • setHighBit

      public void setHighBit(int highBit)

    • setMinimumBitsMinus1

      public void setMinimumBitsMinus1(int minimumBitsMinus1)
      Used in reading and writing boolean
      Parameters:
      minimumBitsMinus1 -

    • setShiftToDivide

      public void setShiftToDivide(int shiftToDivide)
      Used in reading and writing boolean
      Parameters:
      shiftToDivide -

    • setYBR_FULL_422

      public void setYBR_FULL_422(boolean YBR_FULL_422)

    • getNImages

      public int getNImages()
      Accessor that returns the number of image slices saved.
      Returns:
      The number of images.

    • getNTimePeriods

      public int getNTimePeriods()
      Accessor that returns the number of time periods saved.
      Returns:
      The number of time periods.

    • getDataFileName

      public String[] getDataFileName()
      Accessor that returns the array of data file names
      Returns:

    • readImage

      public void readImage(ModelImage image, long offset) throws IOException
      This method reads a raw image file (1D - 5D).
      Parameters:
      image - Image model where the data will be stored.
      offset - Points to where the data of the image is located. It is equal to the header length.
      Throws:
      IOException - if there is an error reading the file
      See Also:

    • readFloatImage

      public void readFloatImage(ModelImage image, int originalDataType, float[] scaleFactor, float[] offsetAdjustment, long offset) throws IOException
      This method reads a raw image file (1D - 5D). Then multiplies raw data by a scaleFactor[k] and adds an offsetAdjustment[k], where k is the slice index
      Parameters:
      image - Image model where the data will be stored. Either a ModelStorageBase.FLOAT or a ModelStorageBase.ARGB_FLOAT.
      originalDataType -
      scaleFactor - array with a multiplicative factor for each slice
      offsetAdjustment - array with an additive offset adjustment for each slice
      offset - Points to where the data of the image is located. It is equal to the header length.
      Throws:
      IOException - if there is an error reading the file
      See Also:

    • readImage

      public void readImage(float[] buffer, long offset, int imageType) throws IOException
      This method reads a file and puts the data in the buffer.
      Parameters:
      buffer - float buffer where the data will be stored.
      offset - points to where the data of the image is located. It is equal to the header length.
      imageType - ModelImage type (i.e. boolean, byte ...);
      Throws:
      IOException - if there is an error reading the file
      See Also:

    • readImage

      public void readImage(double[] buffer, long offset) throws IOException
      This method reads a file and puts the data in the buffer.
      Parameters:
      buffer - double buffer where the data will be stored.
      offset - points to where the data of the image is located. It is equal to the header length.
      Throws:
      IOException - if there is an error reading the file
      See Also:

    • readImage

      public void readImage(short[] buffer, long offset, int imageType) throws IOException
      This method reads a file and puts the data in the buffer. Added here to help speed the reading of DICOM images
      Parameters:
      buffer - float buffer where the data will be stored.
      offset - points to where the data of the image is located. It is equal to the header length.
      imageType - ModelImage type (i.e. boolean, byte ...);
      Throws:
      IOException - if there is an error reading the file
      See Also:

    • readImage

      public void readImage(int[] buffer, long offset, int imageType) throws IOException
      This method reads a file and puts the data in the buffer. Added here to help speed the reading of DICOM images
      Parameters:
      buffer - float buffer where the data will be stored.
      offset - points to where the data of the image is located. It is equal to the header length.
      imageType - ModelImage type (i.e. boolean, byte ...);
      Throws:
      IOException - if there is an error reading the file
      See Also:

    • setImageFile

      public void setImageFile(String fileName, String fileDir, FileInfoBase fInfo, int rwFlag) throws IOException
      Sets the name and directory to new values opens the file.
      Parameters:
      fileName - DOCUMENT ME!
      fileDir - File directory.
      fInfo - Information that describes the image.
      rwFlag - Read/write flag.
      Throws:
      IOException - if there is an error making the files

    • setPlanarConfig

      public void setPlanarConfig(int _planarConfig)
      Sets the planar configuration for RGB images.
      Parameters:
      _planarConfig - 0 indicates pixels are RGB, RGB chunky
      1 indicates pixels are RRR, GGG, BBB planar

    • setNumChannels

      public void setNumChannels(int numChannels)
      Sets the number of channels used in RGB files
      Parameters:
      numChannels -

    • setRGBAOrder

      public void setRGBAOrder(boolean RGBAOrder)

    • setStartPosition

      public void setStartPosition(long startPosition)
      DOCUMENT ME!
      Parameters:
      startPosition - starting byte position for writing data

    • writeImage

      public void writeImage(ModelImage image, FileWriteOptions options) throws IOException
      This method writes a raw image file.
      Parameters:
      image - image model where the data is stored.
      options - DOCUMENT ME!
      Throws:
      IOException - if there is an error writing the file

    • writeImage

      public void writeImage(ModelImage image, int beginSlice, int endSlice, int beginTimePeriod, int endTimePeriod) throws IOException
      This method writes a raw image file.
      Parameters:
      image - image model where the data is stored.
      beginSlice -
      endSlice -
      beginTimePeriod -
      endTimePeriod -
      Throws:
      IOException - if there is an error writing the file

    • writeImage3DTo2D

      public void writeImage3DTo2D(ModelImage image, FileWriteOptions options, String suffix) throws IOException
      Method to save 3D images to an array of 2D images. Images will be name sequentially with the given start # and # of digits
      Parameters:
      image - Image to be saved (broken down into 2D images)
      options - File Write options
      suffix - Suffix for file names. Example: ".xml", ".img"
      Throws:
      IOException - DOCUMENT ME!

    • writeImage3DTo2D

      public void writeImage3DTo2D(ModelImage image, FileWriteOptions options, String suffix, long[] finalHeaderPosition) throws IOException
      Method to save 3D images to an array of 2D images. Images will be name sequentially with the given start # and # of digits
      Parameters:
      image - Image to be saved (broken down into 2D images)
      options - File Write options
      suffix - Suffix for file names. Example: ".xml", ".img"
      finalHeaderPosition - starting locations
      Throws:
      IOException - DOCUMENT ME!

    • writeImage4DTo3D

      public void writeImage4DTo3D(ModelImage image, FileWriteOptions options, String suffix) throws IOException
      Method to write 4D images to an array of 3D image files. the files will be named sequentially with the given # of digits and given starting #. This method will save ALL slices and the files will be split up by time-period
      Parameters:
      image - Image that is to be saved
      options - File write options
      suffix - file suffix for saving name-convention example ".raw", ".img"
      Throws:
      IOException - DOCUMENT ME!

    • writeImage4DTo3D

      public void writeImage4DTo3D(ModelImage image, FileWriteOptions options, String suffix, long[] finalHeaderPosition) throws IOException
      Method to write 4D images to an array of 3D image files. the files will be named sequentially with the given # of digits and given starting #. This method will save ALL slices and the files will be split up by time-period
      Parameters:
      image - Image that is to be saved
      options - File write options
      suffix - file suffix for saving name-convention example ".raw", ".img"
      finalHeaderPosition - starting positions
      Throws:
      IOException - DOCUMENT ME!

    • setZeroLengthFlag

      public void setZeroLengthFlag(boolean zeroLengthFlag)
      setZeroLengthFlag
      Parameters:
      zeroLengthFlag -