Package gov.nih.mipav.model.file

Class FileInfoMinc

java.lang.Object
gov.nih.mipav.model.structures.ModelSerialCloneable
gov.nih.mipav.model.file.FileInfoBase
gov.nih.mipav.model.file.FileInfoMinc
All Implemented Interfaces:
Serializable, Cloneable
public class FileInfoMinc extends FileInfoBase
This class holds all the file information for a MINC file. In addition, it has three classes to organize the data.

MINC headers have three main parts: the dimensions, the global attributes, and the variables. There are typically three dimensions, representing the x, y, and z dimensions of the image. There is usually one global attribute, the history. There can be any number of variables.

Variables have within them any number of attributes. So for example, "rootvariable", the first variable in all the MINC files I have seen so far, has the following attributes: varid (= "MINC standard variable"), vartype (= "group________"), version (= "MINC version 1.0"), parent (blank), and children (image). Usually there is a variable for each dimension, a variable for the image, a variable for image min, and a variable for image max. There can also be variables containing patient information or anything else useful.

See the documentation for the classes MincDimElem, MincAttElem, and MincVarElem for further information. The classes are structured exactly like a MINC file.

Version:
1.0 July 1, 2000
See Also:

  • Field Details

    • serialVersionUID

      private static final long serialVersionUID
      Use serialVersionUID for interoperability.
      See Also:

    • NC_BYTE

      public static final int NC_BYTE
      NetCDF defined data type - byte.
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    • NC_CHAR

      public static final int NC_CHAR
      NetCDF defined data type - character.
      See Also:

    • NC_SHORT

      public static final int NC_SHORT
      NetCDF defined data type - short.
      See Also:

    • NC_INT

      public static final int NC_INT
      NetCDF defined data type - integer.
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    • NC_FLOAT

      public static final int NC_FLOAT
      NetCDF defined data type - float.
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    • NC_DOUBLE

      public static final int NC_DOUBLE
      NetCDF defined data type - double.
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    • NC_DIMENSION

      public static final int NC_DIMENSION
      NetCDF defined data type - dimension.
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    • NC_VARIABLE

      public static final int NC_VARIABLE
      NetCDF defined data type - variable.
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    • NC_ATTRIBUTE

      public static final int NC_ATTRIBUTE
      NetCDF defined data type - attribute.
      See Also:

    • dicomToMincVarMap

      public static final String[] dicomToMincVarMap
      Minc var equivalents to anonymizable Dicom tags. Must be in the same order as FileInfoDicom.anonymizeTagIDs.
      See Also:

    • numrecs

      public int numrecs
      DOCUMENT ME!

    • vmax

      public double vmax
      Valid image maximum value. Default = -1.

    • vmin

      public double vmin
      Valid image minimum value. Default = -1.

    • dimArray

      private FileMincDimElem[] dimArray
      DOCUMENT ME!

    • gattArray

      private FileMincAttElem[] gattArray
      DOCUMENT ME!

    • varArray

      private FileMincVarElem[] varArray
      DOCUMENT ME!

  • Constructor Details

    • FileInfoMinc

      public FileInfoMinc(String name, String directory, int format)
      MINC file information constructor.
      Parameters:
      name - file name
      directory - file directory
      format - format (in this case, MINC)

  • Method Details

    • addAttValue

      public void addAttValue(FileMincAttElem elem, Object value, int index)
      Sets the value of the attribute element; used for setting attribute of variables. A MincVarElem has an array of attributes and this method is called on those attributes.
      Parameters:
      elem - the attribute element to add the value to.
      value - the value to set the element to.
      index - the index into the value array to set this value at.
      See Also:

    • addDimElem

      public void addDimElem(String name, int length, int index)
      Puts a new dimension element with the specified parameters into the dimension array at the gievn index. The name is usually xspace, yspace, or zspace; the length is the corresponding size of that dimension.
      Parameters:
      name - the name of the dimension element
      length - the length of the dimension element
      index - the index to put this element into the array

    • addGattElem

      public void addGattElem(String name, int type, int length, int index)
      Puts a new global attribute array element with the specified parameters into the global attribute array at the given index. Usually there is only one element in the global attribute array: the history.
      Parameters:
      name - the name of the global attribute element
      type - the data type, i.e. byte, char, int, etc (see statically defined types)
      length - the length of the element
      index - the index into the array to put this element at

    • addVarElem

      public void addVarElem(String name, int nelems, int[] dimid, int index)
      Puts a new variable element with the specified paramenters into the array at the given index. There are other attributes to set for variables, in particular the attribute array, but that gets set in a different place.
      Parameters:
      name - the name of this variable element
      nelems - the number of elements in the attribute array
      dimid - the dimension id array, usually empty but for "image" containing information about the dimensions
      index - index into the variable array to put this variable
      See Also:

    • anonymize

      public final void anonymize(boolean[] list)
      Removes requested identifying info. Can remove info stored in the minc header in a dicom-like structure and in a more minc-like info structure.
      Parameters:
      list - the list of tags to remove; it MUST correspond to anonymizeTagIDs list (or spurious errors result), and it must be of the same length, or this will throw an IllegalArgumentException.
      Throws:
      IllegalArgumentException - DOCUMENT ME!

    • calculateIntercept

      public static final double calculateIntercept(double min, double slope, double validMin)
      Calculates rescale intercept given a min and a slope value.
      Parameters:
      min - Min value.
      slope - Slope value.
      Returns:
      Rescale intercept.

    • calculateRescaleIntercept

      public void calculateRescaleIntercept(double[] rescaleIntercept, double[] rescaleSlope)
      In MINC images, "real" values for pixels are calculated by taking the given image min and image max and rescaling the data accordingly. Image min and image max are given per slice.
      Parameters:
      rescaleIntercept - Array of rescale intercepts to set
      rescaleSlope - Array of rescale slopes to set

    • calculateSlope

      public static final double calculateSlope(double max, double min, double validMax, double validMin)
      Calculates rescale slope given a min and a max value.
      Parameters:
      max - Max value.
      min - Min value.
      Returns:
      Rescale slope

    • convertTagsToTable

      public Hashtable<String,String> convertTagsToTable()
      Returns all of the dicom-converted tags in the minc header as a tag-value hashtable.
      Returns:
      a tag-value hashtable

    • createDimArray

      public final void createDimArray(int length)
      Constructs the dimension array with the specified length.
      Parameters:
      length - the length of the array

    • createGattArray

      public final void createGattArray(int length)
      Constructs the global attribute array with the specified length.
      Parameters:
      length - the length of the array

    • createVarArray

      public final void createVarArray(int length)
      Constructs the variable array with the specified length.
      Parameters:
      length - the length of the array

    • displayAboutInfo

      public void displayAboutInfo(JDialogBase dlog, TransMatrix matrix)
      Displays important information about the image.
      Specified by:
      displayAboutInfo in class FileInfoBase
      Parameters:
      dlog - where to display the info
      matrix - the transformation matrix

    • getConvertStartLocationsToDICOM

      public final double[] getConvertStartLocationsToDICOM(int slice, int time)
      Accessor that gets the "start" variable values, adjusted so that [0] holds the image x axis value, [1] the image y axis value, and [2] the image z axis value.

      MINC positive axis is left to right; positive axis is posterior to anterior; postive axis is inferior to superior

      DICOM positive axis is right to left; positive axis is anterior to posterior; postive axis is inferior to superior

      If the space's alignment attribute has the value 'centre', then subtract half the space's step value (doesn't seem to apply to zspace for some reason..). Then transform the point by the inverse of the direction_cosines matrix (extracted from the spaces). The result then has some of the signs of its components flipped (which is determined by the image orientation) to get it from minc to dicom orientation.

      Parameters:
      slice - slice to begin the start variable on.
      timeSlice - time to begin the start variable on
      Returns:
      The slice position in dicom (and mipav) space.

    • getDicomValue

      public String getDicomValue(String dicomTag)
      Get the value from the minc info based on a given dicom tag id.
      Parameters:
      dicomTag - dicom tag (group,elem)
      Returns:
      the value stored in the info (or null if it doesn't exist)

    • getDimArray

      public final FileMincDimElem[] getDimArray()
      Gets the array with the dimension information.
      Returns:
      the array

    • getDimElem

      public final FileMincDimElem getDimElem(int index)
      Accessor that returns the dimension element at the indicated index in the dimension array.
      Parameters:
      index - index where the dimension element is located
      Returns:
      dimArray[index]

    • getGattArray

      public final FileMincAttElem[] getGattArray()
      Gets the array with the attribute information.
      Returns:
      the array

    • getGattElem

      public final FileMincAttElem getGattElem(int index)
      Accessor that returns the global attribute element at the indicated index in the global attribute array.
      Parameters:
      index - index where the global attribute element is located
      Returns:
      gattArray[index]

    • getStartLocations

      public final float[] getStartLocations()
      Accessor that gets the "start" variable values, with the "xspace" in 0, "yspace" in 1, and "zspace" in 2. This differs from the other methods because it doesn't place the values so that they correspond to image x, y, and z. Gets values as stored in MINC header, not modified to account for the different origin.
      Returns:
      The "start" values for the image.

    • getVarArray

      public final FileMincVarElem[] getVarArray()
      Gets the array with the variable information.
      Returns:
      the array

    • getVarElem

      public final FileMincVarElem getVarElem(int index)
      Accessor that returns the variable element at the indicated index in the variable array.
      Parameters:
      index - index where the variable element is located
      Returns:
      varArray[index]

    • setImportantImageInfo

      public final void setImportantImageInfo()
      Sets necessary image information.

    • setModality

      public void setModality()
      Sets the image modality based on the.

    • setResolutions

      public void setResolutions(int orientation)
      Sets the resolutions from the variable array based on the orientation of the image. The "zspace" in MINC refers to the inferior-superior axis, whereas in MIPAV the z resolution variable is the slices (space between slices) regardless of the orientation. Therefore for proper display we must convert between them.
      Parameters:
      orientation - The orientation of the image (sagittal, coronal, or axial).

    • setStartLocations

      public final void setStartLocations(double[] origin)
      Sets start locations of each axis.
      Parameters:
      origin - the image origin

    • setUnits

      public final void setUnits()
      Sets the units of the dimensions, as in millimeters, inches, etc. Called after the header has been read in so the values within the varArray have been set properly already.

    • getTagElem

      private static String getTagElem(String fullTag)
      Extract the element identifier (removing the group id).
      Parameters:
      fullTag - the full element identitfier
      Returns:
      the element id

    • getTagGroup

      private static String getTagGroup(String fullTag)
      Extract the group to which a dicom or minc element belongs to.
      Parameters:
      fullTag - the full element identitfier
      Returns:
      the element group

    • getAxisOrientation

      public static int[] getAxisOrientation(TransMatrix mat)
      Return the 3 axis orientation codes that correspond to the closest standard anatomical orientation of the (i,j,k) axes.
      Parameters:
      mat - 4x4 matrix that transforms (i,j,k) indexes to x,y,z coordinates where +x = Right, +y = Anterior, +z = Superior Only the upper-left 3x3 corner of the matrix is used This routine finds the permutation of (x,y,z) which has the smallest angle to the (i,j,k) axes directions, which are columns of the input matrix Errors: The codes returned will be zero.
      Returns:
      codes

    • getMincSliceThickness

      private double getMincSliceThickness()
      Return the slice thickness value stored in the minc header (var = 'acquisition', attrib = 'slice_thickness').
      Returns:
      The slice thickness, if it is stored in the minc header (0 otherwise).

    • setOrientType

      public static int setOrientType(String space, boolean positive)
      Helper method to set the axis orientations.
      Parameters:
      space - The space - "xspace", "yspace", or "zspace".
      positive - Flag indicating if the space is moving in a positive direction.
      Returns:
      The proper axis orientation for that space.

    • setStartLocation

      private void setStartLocation(double originCoord, int axis)
      Sets the start location of the specified axis.
      Parameters:
      originCoord - origin coord.
      axis - Axis of orientation; x is 0, y is 1, z is 2.