Package com.xinapse.image.template

Class ICBMLabel

java.lang.Object
com.xinapse.image.template.ICBMLabel
All Implemented Interfaces:
Comparable<ICBMLabel>
public class ICBMLabel extends Object implements Comparable<ICBMLabel>
Class for handling the ICBM atlas labels.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    final float
    diceKappa
    The Dice Kappa score for the brain region.
    final short
    labelLeft
    The integer label for the region in the left side of the brain.
    final short
    labelRight
    The integer label for the region in the right side of the brain.
    final short
    mindboggleID
    The Mindboggle ID for the label.
    static final int
    N_COLS
    The number of image columns for the ICBM labels image.
    static final int
    N_ROWS
    The number of image rows for the ICBM labels image.
    static final int
    N_SLICES
    The number of image slices for the ICBM labels image.
    final String
    name
    The label name.
    final String
    note
    Comments about the region label.
    static final float
    PIXEL_X_SIZE
    The pixel width for the ICBM labels image.
    static final float
    PIXEL_Y_SIZE
    The pixel height for the ICBM labels image.
    static final float
    PIXEL_Z_SIZE
    The pixel depth for the ICBM labels image.

  • Method Summary

    Modifier and Type
    Method
    Description
    int
    compareTo(ICBMLabel label)
     
    boolean
    equals(Object o)
     
    static ICBMLabel
    get(int label)
    Returns the ICBMLabel from an integer region label.
    static ICBMLabel
    get(String name)
    Returns the ICBMLabel from a label name.
    static ICBMLabel
    get(org.jogamp.vecmath.Point3f xyz)
    Returns the ICBMLabel at a given image location.
    static ICBMLabel[]
    getAllLabels()
    Returns an array of all known ICBMLabels.
    static int
    getLeftLabel(String labelName)
    Returns the integer code for the region name for the left side of the brain.
    static int
    getRightLabel(String labelName)
    Returns the integer code for the region name for the right side of the brain.
    int
    hashCode()
     
    boolean
    isAccumbens()
    Tests whether this ICBMLabel is Accumbens.
    static boolean
    isAccumbens(org.jogamp.vecmath.Point3f xyz)
    Tests whether the brain region at the given point is Accumbens.
    boolean
    isAmygdala()
    Tests whether this ICBMLabel is amygdala.
    static boolean
    isAmygdala(org.jogamp.vecmath.Point3f xyz)
    Tests whether the brain region at the given point is amygdala.
    boolean
    isBasalGanglia()
    Tests whether this ICBMLabel is part of the basal ganglia.
    static boolean
    isBasalGanglia(org.jogamp.vecmath.Point3f xyz)
    Tests whether the brain region at the given point is part of the basal ganglia.
    boolean
    isCentral()
    Tests whether this ICBMLabel is part of the central.
    static boolean
    isCentral(org.jogamp.vecmath.Point3f xyz)
    Tests whether the brain region at the given point is part of the central.
    boolean
    isCerebellum()
    Tests whether this ICBMLabel is part of the cerebellum.
    static boolean
    isCerebellum(org.jogamp.vecmath.Point3f xyz)
    Tests whether the brain region at the given point is cerebellum.
    boolean
    isCingulate()
    Tests whether this ICBMLabel is part of the cingulate.
    static boolean
    isCingulate(org.jogamp.vecmath.Point3f xyz)
    Tests whether the brain region at the given point is part of the cingulate.
    boolean
    isCSF()
    Tests whether this ICBMLabel is for a region that contains CSF.
    static boolean
    isCSF(org.jogamp.vecmath.Point3f xyz)
    Tests whether the region at the given point contains CSF.
    boolean
    isCuneus()
    Tests whether this ICBMLabel is part of the cuneus.
    static boolean
    isCuneus(org.jogamp.vecmath.Point3f xyz)
    Tests whether the brain region at the given point is part of the cuneus.
    boolean
    isFrontal()
    Tests whether this ICBMLabel is part of the frontal lobe cortex.
    static boolean
    isFrontal(org.jogamp.vecmath.Point3f xyz)
    Tests whether the brain region at the given point is part of the frontal lobe cortex.
    boolean
    isHippocampus()
    Tests whether this ICBMLabel is hippocampus.
    static boolean
    isHippocampus(org.jogamp.vecmath.Point3f xyz)
    Tests whether the brain region at the given point is hippocampus.
    boolean
    isMedioTemporal()
    Tests whether this ICBMLabel is part of the medio-temporal cortex.
    static boolean
    isMedioTemporal(org.jogamp.vecmath.Point3f xyz)
    Tests whether the brain region at the given point is part of the medio-temporal cortex.
    boolean
    isOrbito()
    Tests whether this ICBMLabel is part of the orbito-frontal/lateral cortex.
    static boolean
    isOrbito(org.jogamp.vecmath.Point3f xyz)
    Tests whether the brain region at the given point is part of the orbito-frontal/lateral cortex.
    boolean
    isPallidum()
    Tests whether this ICBMLabel is part of the pallidum.
    static boolean
    isPallidum(org.jogamp.vecmath.Point3f xyz)
    Tests whether the brain region at the given point is part of the pallidum.
    boolean
    isParietal()
    Tests whether this ICBMLabel is part of the parietal.
    static boolean
    isParietal(org.jogamp.vecmath.Point3f xyz)
    Tests whether the brain region at the given point is part of the parietal.
    boolean
    isPutamen()
    Tests whether this ICBMLabel is part of the putamen.
    static boolean
    isPutamen(org.jogamp.vecmath.Point3f xyz)
    Tests whether the brain region at the given point is part of the putamen.
    static boolean
    isSeptum(org.jogamp.vecmath.Point3f xyz)
    Tests whether the region at the given point is septum.
    boolean
    isTemporal()
    Tests whether this ICBMLabel is part of the temporal lobe cortex.
    static boolean
    isTemporal(org.jogamp.vecmath.Point3f xyz)
    Tests whether the brain region at the given point is part of the temporal lobe cortex.
    boolean
    isVermis()
    Tests whether this ICBMLabel is part of the vermis.
    static boolean
    isVermis(org.jogamp.vecmath.Point3f xyz)
    Tests whether the brain region at the given point is vermis.
    static void
    main(String[] args)
    Run the self-test on the ICBMLabel class.
    boolean
    nameContains(String subString)
    Tests whether this ICBMLabel name contains the sub-string, ignoring case.
    String
    toString()
     

    Methods inherited from class java.lang.Object

    clone, finalize, getClass, notify, notifyAll, wait, wait, wait

  • Field Details

    • N_COLS

      public static final int N_COLS
      The number of image columns for the ICBM labels image.

    • N_ROWS

      public static final int N_ROWS
      The number of image rows for the ICBM labels image.

    • N_SLICES

      public static final int N_SLICES
      The number of image slices for the ICBM labels image.

    • PIXEL_X_SIZE

      public static final float PIXEL_X_SIZE
      The pixel width for the ICBM labels image.

    • PIXEL_Y_SIZE

      public static final float PIXEL_Y_SIZE
      The pixel height for the ICBM labels image.

    • PIXEL_Z_SIZE

      public static final float PIXEL_Z_SIZE
      The pixel depth for the ICBM labels image.

    • mindboggleID

      public final short mindboggleID
      The Mindboggle ID for the label.

    • name

      public final String name
      The label name.

    • labelRight

      public final short labelRight
      The integer label for the region in the right side of the brain.

    • labelLeft

      public final short labelLeft
      The integer label for the region in the left side of the brain.

    • note

      public final String note
      Comments about the region label.

    • diceKappa

      public final float diceKappa
      The Dice Kappa score for the brain region.

  • Method Details

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • get

      public static ICBMLabel get(int label)
      Returns the ICBMLabel from an integer region label. The integer label can correspond to either right side or the left side of the brain.
      Parameters:
      label - the integer region label.
      Returns:
      the ICBMLabel corresponding to the supplied integer region label. Returns null if there is no ICBMLabel corresponding to the supplied integer.

    • get

      public static ICBMLabel get(String name) throws InvalidArgumentException
      Returns the ICBMLabel from a label name.
      Parameters:
      name - the name of the ICBM region.
      Returns:
      the ICBMLabel corresponding to the supplied integer name.
      Throws:
      InvalidArgumentException - if no ICBM label exists with the supplied name.

    • getRightLabel

      public static int getRightLabel(String labelName) throws NoSuchFieldError
      Returns the integer code for the region name for the right side of the brain.
      Parameters:
      labelName - the region name.
      Returns:
      the integer code for the region name for the right side of the brain.
      Throws:
      NoSuchFieldError - if there is no region with the supplied name.

    • getLeftLabel

      public static int getLeftLabel(String labelName) throws NoSuchFieldError
      Returns the integer code for the region name for the left side of the brain.
      Parameters:
      labelName - the region name.
      Returns:
      the integer code for the region name for the left side of the brain.
      Throws:
      NoSuchFieldError - if there is no region with the supplied name.

    • nameContains

      public boolean nameContains(String subString)
      Tests whether this ICBMLabel name contains the sub-string, ignoring case.
      Parameters:
      subString - a String against which the ICBMLabel name is tested.
      Returns:
      true if this ICBMLabel name contains the sub-string; false otherwise.

    • isSeptum

      public static boolean isSeptum(org.jogamp.vecmath.Point3f xyz)
      Tests whether the region at the given point is septum.
      Parameters:
      xyz - the position to test.
      Returns:
      true if there is septum at this point; false otherwise.

    • isCSF

      public static boolean isCSF(org.jogamp.vecmath.Point3f xyz)
      Tests whether the region at the given point contains CSF.
      Parameters:
      xyz - the position to test.
      Returns:
      true if there is CSF at this point; false otherwise.

    • isCSF

      public boolean isCSF()
      Tests whether this ICBMLabel is for a region that contains CSF.
      Returns:
      true if this ICBMLabel is contains CSF; false otherwise.

    • isCerebellum

      public static boolean isCerebellum(org.jogamp.vecmath.Point3f xyz)
      Tests whether the brain region at the given point is cerebellum.
      Parameters:
      xyz - the position to test.
      Returns:
      true if there is cerebellum at this point; false otherwise.

    • isCerebellum

      public boolean isCerebellum()
      Tests whether this ICBMLabel is part of the cerebellum.
      Returns:
      true if this ICBMLabel is part of the cerebellum; false otherwise.

    • isVermis

      public static boolean isVermis(org.jogamp.vecmath.Point3f xyz)
      Tests whether the brain region at the given point is vermis.
      Parameters:
      xyz - the position to test.
      Returns:
      true if there is vermis at this point; false otherwise.

    • isVermis

      public boolean isVermis()
      Tests whether this ICBMLabel is part of the vermis.
      Returns:
      true if this ICBMLabel is part of the vermis; false otherwise.

    • isTemporal

      public static boolean isTemporal(org.jogamp.vecmath.Point3f xyz)
      Tests whether the brain region at the given point is part of the temporal lobe cortex.
      Parameters:
      xyz - the position to test.
      Returns:
      true if there is temporal lobe cortex at this point; false otherwise.

    • isTemporal

      public boolean isTemporal()
      Tests whether this ICBMLabel is part of the temporal lobe cortex.
      Returns:
      true if this ICBMLabel is part of the temporal lobe cortex; false otherwise.

    • isFrontal

      public static boolean isFrontal(org.jogamp.vecmath.Point3f xyz)
      Tests whether the brain region at the given point is part of the frontal lobe cortex.
      Parameters:
      xyz - the position to test.
      Returns:
      true if there is frontal lobe cortex at this point; false otherwise.

    • isFrontal

      public boolean isFrontal()
      Tests whether this ICBMLabel is part of the frontal lobe cortex.
      Returns:
      true if this ICBMLabel is part of the frontal lobe cortex; false otherwise.

    • isOrbito

      public static boolean isOrbito(org.jogamp.vecmath.Point3f xyz)
      Tests whether the brain region at the given point is part of the orbito-frontal/lateral cortex.
      Parameters:
      xyz - the position to test.
      Returns:
      true if there is orbito-frontal/lateral cortex at this point; false otherwise.

    • isOrbito

      public boolean isOrbito()
      Tests whether this ICBMLabel is part of the orbito-frontal/lateral cortex.
      Returns:
      true if this ICBMLabel is part of the orbito-frontal/lateral cortex; false otherwise.

    • isHippocampus

      public static boolean isHippocampus(org.jogamp.vecmath.Point3f xyz)
      Tests whether the brain region at the given point is hippocampus.
      Parameters:
      xyz - the position to test.
      Returns:
      true if there is hippocampus at this point; false otherwise.

    • isHippocampus

      public boolean isHippocampus()
      Tests whether this ICBMLabel is hippocampus.
      Returns:
      true if this ICBMLabel is hippocampus; false otherwise.

    • isAmygdala

      public static boolean isAmygdala(org.jogamp.vecmath.Point3f xyz)
      Tests whether the brain region at the given point is amygdala.
      Parameters:
      xyz - the position to test.
      Returns:
      true if there is amygdala at this point; false otherwise.

    • isAmygdala

      public boolean isAmygdala()
      Tests whether this ICBMLabel is amygdala.
      Returns:
      true if this ICBMLabel is amygdala; false otherwise.

    • isAccumbens

      public static boolean isAccumbens(org.jogamp.vecmath.Point3f xyz)
      Tests whether the brain region at the given point is Accumbens.
      Parameters:
      xyz - the position to test.
      Returns:
      true if there is Accumbens at this point; false otherwise.

    • isAccumbens

      public boolean isAccumbens()
      Tests whether this ICBMLabel is Accumbens.
      Returns:
      true if this ICBMLabel is Accumbens; false otherwise.

    • isMedioTemporal

      public static boolean isMedioTemporal(org.jogamp.vecmath.Point3f xyz)
      Tests whether the brain region at the given point is part of the medio-temporal cortex.
      Parameters:
      xyz - the position to test.
      Returns:
      true if there is medio-temporal cortex at this point; false otherwise.

    • isMedioTemporal

      public boolean isMedioTemporal()
      Tests whether this ICBMLabel is part of the medio-temporal cortex.
      Returns:
      true if this ICBMLabel is part of the medio-temporal cortex; false otherwise.

    • isPutamen

      public static boolean isPutamen(org.jogamp.vecmath.Point3f xyz)
      Tests whether the brain region at the given point is part of the putamen.
      Parameters:
      xyz - the position to test.
      Returns:
      true if there is putamen at this point; false otherwise.

    • isPutamen

      public boolean isPutamen()
      Tests whether this ICBMLabel is part of the putamen.
      Returns:
      true if this ICBMLabel is part of the putamen; false otherwise.

    • isPallidum

      public static boolean isPallidum(org.jogamp.vecmath.Point3f xyz)
      Tests whether the brain region at the given point is part of the pallidum.
      Parameters:
      xyz - the position to test.
      Returns:
      true if there is pallidum at this point; false otherwise.

    • isPallidum

      public boolean isPallidum()
      Tests whether this ICBMLabel is part of the pallidum.
      Returns:
      true if this ICBMLabel is part of the pallidum; false otherwise.

    • isBasalGanglia

      public static boolean isBasalGanglia(org.jogamp.vecmath.Point3f xyz)
      Tests whether the brain region at the given point is part of the basal ganglia.
      Parameters:
      xyz - the position to test.
      Returns:
      true if there is basal ganglia at this point; false otherwise.

    • isBasalGanglia

      public boolean isBasalGanglia()
      Tests whether this ICBMLabel is part of the basal ganglia.
      Returns:
      true if this ICBMLabel is part of the basal ganglia; false otherwise.

    • isCingulate

      public static boolean isCingulate(org.jogamp.vecmath.Point3f xyz)
      Tests whether the brain region at the given point is part of the cingulate.
      Parameters:
      xyz - the position to test.
      Returns:
      true if there is cingulate at this point; false otherwise.

    • isCingulate

      public boolean isCingulate()
      Tests whether this ICBMLabel is part of the cingulate.
      Returns:
      true if this ICBMLabel is part of the cingulate; false otherwise.

    • isCuneus

      public static boolean isCuneus(org.jogamp.vecmath.Point3f xyz)
      Tests whether the brain region at the given point is part of the cuneus.
      Parameters:
      xyz - the position to test.
      Returns:
      true if there is cuneus at this point; false otherwise.

    • isCuneus

      public boolean isCuneus()
      Tests whether this ICBMLabel is part of the cuneus.
      Returns:
      true if this ICBMLabel is part of the cuneus; false otherwise.

    • isParietal

      public static boolean isParietal(org.jogamp.vecmath.Point3f xyz)
      Tests whether the brain region at the given point is part of the parietal.
      Parameters:
      xyz - the position to test.
      Returns:
      true if there is parietal at this point; false otherwise.

    • isParietal

      public boolean isParietal()
      Tests whether this ICBMLabel is part of the parietal.
      Returns:
      true if this ICBMLabel is part of the parietal; false otherwise.

    • isCentral

      public static boolean isCentral(org.jogamp.vecmath.Point3f xyz)
      Tests whether the brain region at the given point is part of the central.
      Parameters:
      xyz - the position to test.
      Returns:
      true if there is central at this point; false otherwise.

    • isCentral

      public boolean isCentral()
      Tests whether this ICBMLabel is part of the central.
      Returns:
      true if this ICBMLabel is part of the central; false otherwise.

    • get

      public static ICBMLabel get(org.jogamp.vecmath.Point3f xyz)
      Returns the ICBMLabel at a given image location.
      Parameters:
      xyz - the image location, in standard coordinates with the origin at the centre of the field-of-view.
      Returns:
      the ICBMLabel at the specified image location, or null if there is no lable at that location.

    • getAllLabels

      public static ICBMLabel[] getAllLabels()
      Returns an array of all known ICBMLabels.
      Returns:
      all known ICBMLabels.

    • compareTo

      public int compareTo(ICBMLabel label)
      Specified by:
      compareTo in interface Comparable<ICBMLabel>

    • equals

      public boolean equals(Object o)
      Overrides:
      equals in class Object

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • main

      public static void main(String[] args)
      Run the self-test on the ICBMLabel class.
      Parameters:
      args - ignored.