Package gov.nih.mipav.model.file

Class FileZVI

java.lang.Object
gov.nih.mipav.model.file.FileBase
gov.nih.mipav.model.file.FileZVI
public class FileZVI extends FileBase
Documentation used was the ZVI Format Specification V 2.0.5 - August, 2010. The following email was sent to Zeiss support: Here are problems I spotted in ZVI Format Specification V 2.0.5 - August, 2010: 2.1.1 stream of the container image: TypeDescription is VT_EMPTY rather than VT_BSTR FileName is VT_EMPTY rather than VT_BSTR m_PluginCLSID is VT_BLOB rather than VT_CLSID The {Tags} VT_STORED_OBJECT that goes between the {Layers} and {Scaling} VT_STORED_OBJECTs is missing. 2.2.1 stream of the image item: Version is used rather than unused with minor = 1003 hex and major = 3000 hex. TypeDescription is VT_EMPTY rather than VT_BSTR. FileName is VT_EMPTY rather than VT_BSTR m_PluginCLSID is VT_BLOB rather than VT_CLSID Items after the {Others} VT_BLOB are completely different from what's listed. I find: VT_DISPATCH VT_STORED_OBJECT with a string = Tags VT_DISPATCH VT_DISPATCH VT_DISPATCH RAW pixel data 3.3 Coordinate ID for Image Dimensions: Index should be 0 1 2 3 4 5 6 7 instead of the existing 0 1 3 4 5 6 7 8. 3.4 Tag IDs ID 301 is used for both ImageBaseTimeFirst and ImageBaseTime1. I suspect the ImageBaseTimeFirst entry should be deleted. The following tags show up in .ZVI files but are not listed in your table: 2071, 20478. What is the info for these tags? 65781 has both AuroxCamRes6 and AuroxCamCFactor. Information for decoding the 64-bit VT_DATE structure is missing. Is it available somewhere? Is it possible for me to obtain sample .ZVI files so I can improve the ZVI file read in the MIPAV image processing program? Sincerely, William Gandler

  • Field Details

    • VT_EMPTY

      private static final short VT_EMPTY
      See Also:

    • VT_BOOL

      private static final short VT_BOOL
      See Also:

    • VT_I2

      private static final short VT_I2
      See Also:

    • VT_I4

      private static final short VT_I4
      See Also:

    • VT_R8

      private static final short VT_R8
      See Also:

    • VT_BSTR

      private static final short VT_BSTR
      See Also:

    • VT_STORED_OBJECT

      private static final short VT_STORED_OBJECT
      See Also:

    • VT_DATE

      private static final short VT_DATE
      See Also:

    • VT_DISPATCH

      private static final short VT_DISPATCH
      See Also:

    • VT_BLOB

      private static final short VT_BLOB
      See Also:

    • file

      private File file
      DOCUMENT ME!

    • fileDir

      private String fileDir
      DOCUMENT ME!

    • fileInfo

      private FileInfoZVI fileInfo
      DOCUMENT ME!

    • fileName

      private String fileName
      DOCUMENT ME!

    • image

      private ModelImage image
      DOCUMENT ME!

    • imageExtents

      private int[] imageExtents
      DOCUMENT ME!

    • imgBuffer

      private float[] imgBuffer
      DOCUMENT ME!

    • imgResols

      private float[] imgResols
      DOCUMENT ME!

    • LUT

      private ModelLUT LUT
      DOCUMENT ME!

    • endianess

      private boolean endianess

    • sectorSize

      private int sectorSize

    • shortSectorSize

      private int shortSectorSize

    • shortSectorTable

      private int[] shortSectorTable

    • shortStreamStartSect

      private int shortStreamStartSect

    • totalShortStreamSize

      private long totalShortStreamSize

    • imageWidth

      private int imageWidth

    • imageHeight

      private int imageHeight

    • imageCount

      private int imageCount

    • imagePixelFormat

      private int imagePixelFormat

    • zDim

      private int zDim

    • backupZDim

      private int backupZDim

    • tDim

      private int tDim

    • channelNumber

      private int channelNumber

    • positionNumber

      private int positionNumber

    • zArray

      private int[] zArray

    • cArray

      private int[] cArray

    • tArray

      private int[] tArray

    • positionArray

      private int[] positionArray

    • startSectorArray

      private int[] startSectorArray

    • offsetArray

      private int[] offsetArray

    • ap

      private int ap

    • imageFocusPositionArray

      private double[] imageFocusPositionArray

    • imageStagePositionXArray

      private double[] imageStagePositionXArray

    • imageZXArray

      private int[] imageZXArray

    • imageZYArray

      private int[] imageZYArray

    • imageStagePositionYArray

      private double[] imageStagePositionYArray

    • imageOriginalStagePositionXArray

      private double[] imageOriginalStagePositionXArray

    • imageOriginalZXArray

      private int[] imageOriginalZXArray

    • imageOriginalZYArray

      private int[] imageOriginalZYArray

    • imageOriginalStagePositionYArray

      private double[] imageOriginalStagePositionYArray

    • imageZArray

      private int[] imageZArray

    • imageZ2Array

      private int[] imageZ2Array

    • imageC2Array

      private int[] imageC2Array

    • imageT2Array

      private int[] imageT2Array

    • imageBlackValueArray

      private double[] imageBlackValueArray

    • imageZ3Array

      private int[] imageZ3Array

    • imageC3Array

      private int[] imageC3Array

    • imageT3Array

      private int[] imageT3Array

    • imageWhiteValueArray

      private double[] imageWhiteValueArray

    • imageRelFocusPosition1Array

      private double[] imageRelFocusPosition1Array

    • imageZ4Array

      private int[] imageZ4Array

    • imageRelFocusPosition2Array

      private double[] imageRelFocusPosition2Array

    • imageZ5Array

      private int[] imageZ5Array

    • cameraImageAcquisitionTime

      private double[] cameraImageAcquisitionTime

    • imageZ6Array

      private int[] imageZ6Array

    • imageC6Array

      private int[] imageC6Array

    • imageT6Array

      private int[] imageT6Array

    • imageRelativeTime

      private double[] imageRelativeTime

    • imageZ7Array

      private int[] imageZ7Array

    • imageC7Array

      private int[] imageC7Array

    • imageT7Array

      private int[] imageT7Array

    • icp

      private int icp

    • icp2

      private int icp2

    • icp3

      private int icp3

    • icp4

      private int icp4

    • icp5

      private int icp5

    • icp6

      private int icp6

    • icp7

      private int icp7

    • icpX

      private int icpX

    • icpY

      private int icpY

    • icpOriginalX

      private int icpOriginalX

    • icpOriginalY

      private int icpOriginalY

    • sat

      private int[] sat

    • add128

      private boolean add128

    • minC

      private int minC

    • maxC

      private int maxC

    • minZ

      private int minZ

    • maxZ

      private int maxZ

    • minT

      private int minT

    • maxT

      private int maxT

    • minPosition

      private int minPosition

    • maxPosition

      private int maxPosition

  • Constructor Details

    • FileZVI

      public FileZVI(String fileName, String fileDir) throws IOException
      ZVI reader constructor.
      Parameters:
      fileName - 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

    • getFileInfo

      public FileInfoBase getFileInfo()
      Accessor that returns the file info.
      Returns:
      FileInfoBase containing the file info

    • getImageBuffer

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

    • getModelLUT

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

    • readImage

      public ModelImage readImage(boolean multiFile, boolean one) throws IOException
      Reads the LIFF header which indicates endianess, the TIFF magic number, and the offset in bytes of the first IFD. It then reads all the IFDs. This method then opens a Model of an image and imports the the images one slice at a time. Image slices are separated by an IFD.
      Parameters:
      multiFile - true if a set of files each containing a separate 2D image is present false if one file with either a 2D image or a stack of 2D images
      one - true if only want to read in one image of the 3D set
      Returns:
      returns the image
      Throws:
      IOException - if there is an error reading the file

    • readHeader

      public boolean readHeader() throws IOException
      Throws:
      IOException

    • zviToMipavMeasurementUnits

      private int zviToMipavMeasurementUnits(int zviScalingUnit)

    • displayPixelFormat

      private void displayPixelFormat(int pixelFormat)

    • calculateTimeStampString

      String calculateTimeStampString(long timeStamp)

    • calculateVTDateTimeString

      private String calculateVTDateTimeString(double dateTime)

    • calculateRelativeTime

      private String calculateRelativeTime(double relativeTime)