Package gov.nih.mipav.model.file

Class FileLIFF

java.lang.Object
gov.nih.mipav.model.file.FileBase
gov.nih.mipav.model.file.FileLIFF
public class FileLIFF extends FileBase

  • Field Details

  • Constructor Details

    • FileLIFF

      public FileLIFF(String fileName, String fileDir) throws IOException
      LIFF reader/writer 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

    • readCString

      private String readCString() throws IOException
      Throws:
      IOException

    • setFileName

      public void setFileName(String fName)
      Accessor to set the file name (used for reading COR multiFile).
      Parameters:
      fName - file name of image to read.