Package gov.nih.mipav.model.file

Class FileInterfile

java.lang.Object
gov.nih.mipav.model.file.FileBase
gov.nih.mipav.model.file.FileInterfile
public class FileInterfile extends FileBase
Author:
William Gandler
See Also:

  • Field Details

    • SIGNED_INTEGER

      private static final int SIGNED_INTEGER
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    • UNSIGNED_INTEGER

      private static final int UNSIGNED_INTEGER
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    • LONG_FLOAT

      private static final int LONG_FLOAT
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    • SHORT_FLOAT

      private static final int SHORT_FLOAT
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    • BIT

      private static final int BIT
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    • ASCII

      private static final int ASCII
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    • bufferSize

      private int bufferSize
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    • bytesPerPixel

      private int bytesPerPixel
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    • dataByteOffset

      private long dataByteOffset
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    • dataFile

      private File dataFile
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    • dataFileName

      private String dataFileName
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    • headerFileName

      private String headerFileName

    • dataStartingBlock

      private int dataStartingBlock
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    • endianess

      private boolean endianess
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    • file

      private File file
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    • fileDir

      private String fileDir
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    • fileInfo

      private FileInfoInterfile fileInfo
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    • fileInfoCopy

      private FileInfoInterfile fileInfoCopy

    • fileLength

      private long fileLength
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    • fileName

      private String fileName
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    • fileRW

      private FileRawChunk fileRW
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    • foundEOF

      private boolean foundEOF
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    • haveBytesPerPixel

      private boolean haveBytesPerPixel
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    • haveDataByteOffset

      private boolean haveDataByteOffset
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    • haveDataStartingBlock

      private boolean haveDataStartingBlock
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    • haveDecayCorrected

      private boolean haveDecayCorrected
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    • haveDetectorHeadNumber

      private boolean haveDetectorHeadNumber
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    • haveEndianess

      private boolean haveEndianess
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    • haveEnergyWindowsNumber

      private boolean haveEnergyWindowsNumber
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    • haveFileName

      private boolean haveFileName
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    • haveFloodCorrected

      private boolean haveFloodCorrected
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    • haveImagesPerEWindow

      private boolean haveImagesPerEWindow
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    • haveNumberFormat

      private boolean haveNumberFormat
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    • haveOrientation

      private boolean haveOrientation
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    • haveReconstructed

      private boolean haveReconstructed
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    • haveReferenceFrameNumber

      private boolean haveReferenceFrameNumber
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    • haveResolsT

      private boolean haveResolsT
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    • haveResolsX

      private boolean haveResolsX
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    • haveResolsY

      private boolean haveResolsY
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    • haveResolsZ

      private boolean haveResolsZ
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    • haveSliceThickness

      private boolean haveSliceThickness
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    • haveTDim

      private boolean haveTDim

    • haveTomographic

      private boolean haveTomographic
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    • haveTotalImageNumber

      private boolean haveTotalImageNumber
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    • haveXDim

      private boolean haveXDim
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    • haveYDim

      private boolean haveYDim
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    • haveZDim

      private boolean haveZDim
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    • image

      private ModelImage image
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    • imageOrientation

      private int imageOrientation
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    • imgBuffer

      private float[] imgBuffer
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    • imgDBuffer

      private double[] imgDBuffer
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    • imgExtents

      private int[] imgExtents
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    • imgLBuffer

      private long[] imgLBuffer
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    • imgResols

      private float[] imgResols
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    • isotopeNumber

      private String isotopeNumber
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    • LUT

      private ModelLUT LUT
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    • numberFormat

      private int numberFormat
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    • numberSlices

      private int numberSlices
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    • orientation

      private int orientation
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    • originalFileName

      private String originalFileName
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    • resXUnit

      private int resXUnit
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    • resYUnit

      private int resYUnit
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    • resZUnit

      private int resZUnit
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    • scalingFactor1

      private float scalingFactor1
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    • scalingFactor2

      private float scalingFactor2
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    • scalingFactor3

      private float scalingFactor3
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    • scalingFactor4

      private float scalingFactor4
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    • tDim

      private int tDim
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    • timeFrame

      private String timeFrame
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    • totalImageNumber

      private int totalImageNumber
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    • type

      private int type
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    • windowNumber

      private String windowNumber
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    • xDim

      private int xDim
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    • xResol

      private float xResol
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    • yResol

      private float yResol
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    • zResol

      private float zResol
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    • yDim

      private int yDim
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    • zDim

      private int zDim
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    • haveStaticStudy

      private boolean haveStaticStudy

  • Constructor Details

    • FileInterfile

      public FileInterfile(String originalFileName, String fileDir) throws IOException
      Interfile reader/writer constructor.
      Parameters:
      originalFileName - file name
      fileDir - file directory
      Throws:
      IOException - if there is an error making the file

  • Method Details

    • finalize

      public void finalize()
      Prepares this class for cleanup. Calls the finalize method for existing elements, closes any open files and sets other elements to null.
      Overrides:
      finalize in class FileBase

    • isInterfile

      public static String isInterfile(String fName, String fDir)
      Method to test to determine if the image format is Cheshire, so appropriate read method may be called.
      Parameters:
      fName - File name of image.
      fDir - Directory.
      Returns:
      true if Cheshire file, false otherwise.

    • getFileInfo

      public FileInfoInterfile getFileInfo()
      Returns the file info.
      Returns:
      FileInfoBase containing the file info

    • getImageBuffer

      public float[] getImageBuffer()
      Returns the image buffer.
      Returns:
      buffer of image.

    • getModelLUT

      public ModelLUT getModelLUT()
      Returns LUT if defined.
      Returns:
      the LUT if defined else it is null

    • readImage

      public ModelImage readImage(boolean one, boolean readData) throws IOException
      Reads the image.
      Parameters:
      one - Flag for only reading one image of dataset.
      readData -
      Returns:
      returns the image
      Throws:
      IOException - if there is an error reading the file

    • setFileName

      public void setFileName(String fName)
      Sets the file name (used when reading TIFF multiFile).
      Parameters:
      fName - file name of image to read.

    • writeImage

      public void writeImage(ModelImage image, FileWriteOptions options) throws IOException
      Writes an Interfile format type image.
      Parameters:
      image - Image model of data to write.
      options - options such as starting and ending slices and times
      Throws:
      IOException - if there is an error writing the file

    • removeChars

      private static String removeChars(String inString)
      Removes white space and exclamation marks.
      Parameters:
      inString - String to remove characters from.
      Returns:
      new String with removed white space.

    • returnKey

      private static String returnKey(String inString)
      Returns the key found in the string.
      Parameters:
      inString - String to search for key in.
      Returns:
      Key, or null if not found

    • readBBuffer

      private void readBBuffer(int slice, float[] buffer) throws IOException
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      Parameters:
      slice - DOCUMENT ME!
      buffer - DOCUMENT ME!
      Throws:
      IOException - DOCUMENT ME!

    • readBuffer

      private void readBuffer(int slice, float[] buffer) throws IOException
      Reads a slice of data at a time and stores the results in the buffer.
      Parameters:
      slice - offset into the file stored in the dataOffset array
      buffer - buffer where the info is stored
      Throws:
      IOException - if there is an error reading the file

    • readDBuffer

      private void readDBuffer(int slice, double[] buffer) throws IOException
      Reads a slice of data at a time and stores the results in the buffer.
      Parameters:
      slice - offset into the file stored in the dataOffset array
      buffer - buffer where the info is stored
      Throws:
      IOException - if there is an error reading the file

    • readLBuffer

      private void readLBuffer(int slice, long[] buffer) throws IOException
      Reads a slice of data at a time and stores the results in the buffer.
      Parameters:
      slice - offset into the file stored in the dataOffset array
      buffer - buffer where the info is stored
      Throws:
      IOException - if there is an error reading the file

    • readLine

      private String readLine() throws IOException
      Reads lines of the file and strips comments indicated by the ; symbol until a nonnull String results or the end of the file is reached.
      Returns:
      the line read in
      Throws:
      IOException - if there is an error reading the file

    • returnValue

      private String returnValue(String inString)
      Returns the value found in the string.
      Parameters:
      inString - String to search for value in.
      Returns:
      Value, or null if not found