Package gov.nih.mipav.model.file

Class FileDicomTag

java.lang.Object
gov.nih.mipav.model.structures.ModelSerialCloneable
gov.nih.mipav.model.file.FileDicomTag
All Implemented Interfaces:
Serializable, Cloneable, Comparable<FileDicomTag>
public class FileDicomTag extends ModelSerialCloneable implements Comparable<FileDicomTag>
This class holds all the important information about each DICOM tag. As the parser reads the DICOM dictionary file, it stores new DicomTags in a standard Hashtable. Then when the DICOM file reader reads a new file, it sets the value attribute of the DicomTag. The other constructor is used for private tags, because private tags do not have unique attributes. Thus, the reader can read and display all the tags in a file, but may not read the data properly and does not know the significance of the data. If the user wishes to know more information about the file that is encoded in the private tags, then he or she needs to edit the DICOM dictionary file to include the necessary private tags.
Author:
Neva Cherniavsky, David Parsons
See Also:

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    private int
    element
    Integer element word (in hexadecimal).
    private int
    group
    Integer group word (in hexadecimal).
    private int
    length
    Length of the tag as defined in the input image.
    private static final long
    serialVersionUID
    Use serialVersionUID for interoperability.
    private final FileDicomTagInfo
    tagInfo
    Pointer to more information about this tag, read in and contained within the dicom dictionary.
    private Object
    value
    Actual value of the tag (may be an array of elements).
    private FileDicomTagInfo.VR
    valueRepresentation
    Value representation for this tag, if the tags in this dicom file have explicit VRs.

  • Constructor Summary

    Constructors
    Constructor
    Description
    FileDicomTag(FileDicomTagInfo info)
    Constructor that creates a DicomTag empty except for the group and element fields.
    FileDicomTag(FileDicomTagInfo info, Object value)
    Constructor that creates a DicomTag empty except for the name field. this is used for private tags and the name field is the supposed value of the tag.

  • Method Summary

    Modifier and Type
    Method
    Description
    int
    compareTo(FileDicomTag toCompare)
     
    boolean
    equals(Object obj)
    Tests whether a tag contains the same information as this tag.
    void
    finalize()
    Prepares this class for cleanup.
    private String
    fromAStoVisibleString()
    From age string to something that makes more sense. ages are DICOM as nnnT.
    private String
    fromDAtoVisibleString()
    parses the DICOM v3 format tag to make a mm/dd/yyyy formatted date.
    private String
    fromPatientOrientationToVisibleString()
    DOCUMENT ME!
    private String
    fromPatientSexToVisibleString()
    Converts a DICOM patient sex tag (eg, "M") into a more understandable value (eg, "Male").
    private String
    fromTMtoVisibleString()
    Takes a DICOM tag with a TM value representation and returns it in the format HH:MM:SS.frac, or as much as is available to convert (ie, HH:MM could be all that is currently stored).
    private String
    fromVisibleStringToAS(String tempValue)
    Converts the given readable string to a DICOM compliant age string.
    private String
    fromVisibleStringToDA(String tempValue)
    Converts the given string into a DICOM-legal value for a DA value-representation (VR) tag. places a date (yyyymmdd) into value that is in either yyyymmdd (DICOM v3) or yyyy.mm.dd (invalid input: '<' DICOM v3) or mm/dd/yyyy format.
    private String
    fromVisibleStringToDS(String tempValue)
    Takes the input string and forms a DICOM compliant decimal string out of it.
    private String
    fromVisibleStringToDT(String tempValue)
    setVisibleStringToDT.
    private String
    fromVisibleStringToPatientOrientation(String tmpValue)
    DOCUMENT ME!
    private String
    fromVisibleStringToPatientSex(String tempValue)
    Converts patient sex (eg, "Male") into a valid DICOM value (eg, "M").
    private String
    fromVisibleStringToPN(String tmpValue)
    Converts a DICOM person's name ("PN") tag into a more understandable value.
    private String
    fromVisibleStringToTM(String tempValue)
    setVisibleStringToTM.
    final int
    getDataLength()
    Calculates the number of bytes that the data (the object value) will take to be stored.
    final int
    getElement()
    Accessor that returns the element word of the tag (hex).
    final int
    getGroup()
    Accessor that returns the group word of the tag (hex).
    final FileDicomTagInfo
    getInfo()
    Return a reference to information about this tag in the dicom dictionary.
    final FileDicomKey
    getKey()
    Return the key object (group,element info) for this tag.
    final String
    getKeyword()
    Return the keyword for this tag.
    final int
    getLength()
    Returns the length of this tag.
    final String
    getName()
    Return the name of this tag.
    int
    getNumberOfValues()
    Provides the number of items held by the tag, as opposed the value specified by Value Multiplicity(VM).
    final FileDicomTagInfo.VR
    getType()
    Return the type of this tag (determined from its value representation (vr)).
    Object
    getValue(boolean parse)
    Translates the tag value into an understandable string so no other class need understand how to parse this information.
    Object[]
    getValueList()
    Returns the value(s) as an array so that each tag with a value multiplicity of more than 1 -- ie, TypeString items separated by '\' -- is its own element in the array.
    final int
    getValueMultiplicity()
    Accessor that returns the value multiplicity of the tag.
    final FileDicomTagInfo.VR
    getValueRepresentation()
    Return the value representation (vr) of this tag.
    final int
    hashCode()
    Returns the unique identifier's hash code.
    final void
    setElement(int element)
    Sets the Element of this DICOM tag as read in by FileDicom.
    final void
    setGroup(int group)
    Sets the Group of this DICOM tag as read in by FileDicom.
    final void
    setLength(int length)
    Sets the length of this DICOM tag as read in by FileDicom.
    void
    setValue(Object value)
    Sets the value and length attributes of the DicomTag.
    private final void
    setValue(Object value, int length)
    Sets the value attribute of the DicomTag.
    final void
    setValueRepresentation(FileDicomTagInfo.VR vr)
    Sets the value representation (vr) of this tag.
    int
    sizeof()
    Gets the data size in bytes of the units held in this class.
    static final Double[]
    toDouble(byte[] b, int vm, boolean endianess)
    Converts a little-endian byte array into an array of Doubles with length equal to the tag vm.
    static final Float[]
    toFloat(byte[] b, int vm, boolean endianess)
    Converts a little-endian byte array into an array of Floats with length equal to the tag vm.
    static final Integer[]
    toInt(byte[] b, int vm, boolean endianess)
    Converts a little-endian byte array into an array of Integers with length equal to the tag vm.
    static final Integer[]
    toShort(byte[] b, int vm, boolean endianess)
    Converts a little-endian byte array into an array of Integers with length equal to the tag vm.
    String
    toString()
    Used for debugging so that the information contained in the tag can be converted to a readable form.
    static final Long[]
    toUInt(byte[] b, int vm, boolean endianess)
    Converts a little-endian byte array into an array of Longs with length equal to the tag vm.
    static final Integer[]
    toUShort(byte[] b, int vm, boolean endianess)
    Converts a little-endian byte array into an array of Integers with length equal to the tag vm.

    Methods inherited from class gov.nih.mipav.model.structures.ModelSerialCloneable

    clone, nativeClone

    Methods inherited from class java.lang.Object

    getClass, notify, notifyAll, wait, wait, wait

  • Field Details

    • serialVersionUID

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

    • element

      private int element
      Integer element word (in hexadecimal).

    • group

      private int group
      Integer group word (in hexadecimal).

    • length

      private int length
      Length of the tag as defined in the input image.

    • tagInfo

      private final FileDicomTagInfo tagInfo
      Pointer to more information about this tag, read in and contained within the dicom dictionary.

    • value

      private Object value
      Actual value of the tag (may be an array of elements).

    • valueRepresentation

      private FileDicomTagInfo.VR valueRepresentation
      Value representation for this tag, if the tags in this dicom file have explicit VRs. If the dicom tags have implicit VRs, then the DicomDictionary VR is used.

  • Constructor Details

    • FileDicomTag

      public FileDicomTag(FileDicomTagInfo info)
      Constructor that creates a DicomTag empty except for the group and element fields.
      Parameters:
      info - information about this tag

    • FileDicomTag

      public FileDicomTag(FileDicomTagInfo info, Object value)
      Constructor that creates a DicomTag empty except for the name field. this is used for private tags and the name field is the supposed value of the tag.
      Parameters:
      info - information about this tag
      value - the object to be stored

  • Method Details

    • equals

      public boolean equals(Object obj)
      Tests whether a tag contains the same information as this tag.
      Overrides:
      equals in class Object
      Parameters:
      obj - A object (hopefully a non-null FileDicomTag, but not required).
      Returns:
      Whether all of the tag data (group, element, tag info, value, length) in the other tag is the same as this one. False if the tag is null or not a FileDicomTag.

    • finalize

      public void finalize()
      Prepares this class for cleanup.
      Overrides:
      finalize in class Object

    • getDataLength

      public final int getDataLength()
      Calculates the number of bytes that the data (the object value) will take to be stored. This method returns the number of data items times the sizeof the data type. This may be different from the previously stored length of the tag.
      Returns:
      size of the value in bytes

    • getElement

      public final int getElement()
      Accessor that returns the element word of the tag (hex).
      Returns:
      the element word

    • getGroup

      public final int getGroup()
      Accessor that returns the group word of the tag (hex).
      Returns:
      the group word

    • getInfo

      public final FileDicomTagInfo getInfo()
      Return a reference to information about this tag in the dicom dictionary.
      Returns:
      Information about this tag.

    • getKey

      public final FileDicomKey getKey()
      Return the key object (group,element info) for this tag.
      Returns:
      This tag's key.

    • getKeyword

      public final String getKeyword()
      Return the keyword for this tag.
      Returns:
      The tag keyword.

    • getLength

      public final int getLength()
      Returns the length of this tag.
      Returns:
      the length

    • getName

      public final String getName()
      Return the name of this tag.
      Returns:
      The tag name.

    • getNumberOfValues

      public int getNumberOfValues()
      Provides the number of items held by the tag, as opposed the value specified by Value Multiplicity(VM). While a VM may specify an unlimited number of values, this represents the number of values actually held. This is numerically equivalent to the value of getValueList().length. Formerly getMultiplicity().
      Returns:
      DOCUMENT ME!

    • getType

      public final FileDicomTagInfo.VR getType()
      Return the type of this tag (determined from its value representation (vr)).
      Returns:
      The tag type.

    • getValue

      public Object getValue(boolean parse)
      Translates the tag value into an understandable string so no other class need understand how to parse this information. However, values with more than one multiple (vm > 1) are still encoded with "\" (as in unprocessable DICOM tags) or " \ " as separators. A single value may then be de-coded using StringBuffer(str, "\"), and ...nextToken().

      Eg., The age is encoded as '014Y', so getValue() returns '14 Years'. Coded strings such as patient sex is 'F', which returns 'Female'

      An additional note: in order to write a DICOM image correctly, the value should NOT be parsed into readable form.

      Parameters:
      parse - boolean indicating if we should parse (translate) the value or just return the value as-is
      Returns:
      the value

    • getValueList

      public Object[] getValueList()
      Returns the value(s) as an array so that each tag with a value multiplicity of more than 1 -- ie, TypeString items separated by '\' -- is its own element in the array. This method will be so much simpler when (if) the tags are seperated out as individual classes.
      Returns:
      DOCUMENT ME!

    • getValueMultiplicity

      public final int getValueMultiplicity()
      Accessor that returns the value multiplicity of the tag. The value multiplicity is how many instances of this value representation (VR) there can be in one tag.
      Returns:
      the value multiplicity

    • getValueRepresentation

      public final FileDicomTagInfo.VR getValueRepresentation()
      Return the value representation (vr) of this tag. If the tag VR for this dicom are implicit, then the VR is retrieved from the DicomDictionary.
      Returns:
      The tag vr.

    • hashCode

      public final int hashCode()
      Returns the unique identifier's hash code.
      Overrides:
      hashCode in class Object
      Returns:
      The hash code.

    • setElement

      public final void setElement(int element)
      Sets the Element of this DICOM tag as read in by FileDicom.
      Parameters:
      element - element to set to

    • setGroup

      public final void setGroup(int group)
      Sets the Group of this DICOM tag as read in by FileDicom.
      Parameters:
      group - group to set to

    • setLength

      public final void setLength(int length)
      Sets the length of this DICOM tag as read in by FileDicom.
      Parameters:
      length - length to set to

    • setValue

      public void setValue(Object value)
      Sets the value and length attributes of the DicomTag. Parses value so the stored value is converted from a standard, English-readable string to a DICOM v3 form. If the parsing routine is unavailable, the value gets stored as is. Sending strings to set the value of tags of other types (eg., short) will attempt to convert the string to the correct type. Attempting to store a value which is too large for the given type will throw an exception. In any case, the proper size is used.

      For tags with neither value representation nor keyword (a private tag), this method ignores the value. To add, the user class must use setValue(). typeSequence and typeUnknown must also explicitly use setValue().

      Parameters:
      value - the value to store

    • setValue

      private final void setValue(Object value, int length)
      Sets the value attribute of the DicomTag. Does NOT parse so stored value is the same as the one read in. getValue does parse.

      NOTE: DICOM compliant codes will be accepted.

      Parameters:
      value - the value to store
      length - length of the tag

    • setValueRepresentation

      public final void setValueRepresentation(FileDicomTagInfo.VR vr)
      Sets the value representation (vr) of this tag. This method should only be used when a dicom's tag VRs are explicit. Otherwise, the DicomDictionary VR should be used (implicit).
      Parameters:
      vr - The tag's explicit value representation.

    • sizeof

      public int sizeof()
      Gets the data size in bytes of the units held in this class.
      Returns:
      DOCUMENT ME!

    • toString

      public String toString()
      Used for debugging so that the information contained in the tag can be converted to a readable form.
      Overrides:
      toString in class Object
      Returns:
      The tag in readable form

    • fromAStoVisibleString

      private String fromAStoVisibleString()
      From age string to something that makes more sense. ages are DICOM as nnnT. That is, three digits preceeeding a letter indicating the time unit; valid units are D (day), M (month), and Y (year).

      This method translates the unit into the word, and drops leading zeros.

      Returns:
      DOCUMENT ME!

    • fromDAtoVisibleString

      private String fromDAtoVisibleString()
      parses the DICOM v3 format tag to make a mm/dd/yyyy formatted date.
      Returns:
      DOCUMENT ME!

    • fromPatientOrientationToVisibleString

      private String fromPatientOrientationToVisibleString()
      DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • fromPatientSexToVisibleString

      private String fromPatientSexToVisibleString()
      Converts a DICOM patient sex tag (eg, "M") into a more understandable value (eg, "Male"). "M", "F", and "O" are valid inputs. Any other value representation (VR) is converted to "Other" but an empty string (which is valid, since the Patient Sex tag is Type 2, that is, required to exist, but no value is required) returns an empty string.
      Returns:
      DOCUMENT ME!

    • fromTMtoVisibleString

      private String fromTMtoVisibleString()
      Takes a DICOM tag with a TM value representation and returns it in the format HH:MM:SS.frac, or as much as is available to convert (ie, HH:MM could be all that is currently stored).
      Returns:
      String HH:MM:SS.fraction

    • fromVisibleStringToAS

      private String fromVisibleStringToAS(String tempValue)
      Converts the given readable string to a DICOM compliant age string. The following limitations apply: has to start with numbers, then follow-up with the word 'days', 'months', 'years' irrespective of capitalization; a number may be no larger than 3 digits, or only the top three digits are accepted.
      Parameters:
      tempValue - Original (readable) string value.
      Returns:
      Dicom string version of age.

    • fromVisibleStringToDA

      private String fromVisibleStringToDA(String tempValue)
      Converts the given string into a DICOM-legal value for a DA value-representation (VR) tag. places a date (yyyymmdd) into value that is in either yyyymmdd (DICOM v3) or yyyy.mm.dd (invalid input: '<' DICOM v3) or mm/dd/yyyy format. Assumes that the date is reasonable okay to begin with. Saves value in DICOM v3 format as a yyyymmdd (DICOM v3).
      Parameters:
      tempValue - -- the string that represents the date. In American std mm/dd/yyyy or DIOCM's yyyymmdd or yyyy.mm.dd
      Returns:
      String a date in yyyymmdd DICOM v3 format

    • fromVisibleStringToDS

      private String fromVisibleStringToDS(String tempValue)
      Takes the input string and forms a DICOM compliant decimal string out of it. Allows multiple values (separated by the '\' character.)
      Parameters:
      tempValue - DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • fromVisibleStringToDT

      private String fromVisibleStringToDT(String tempValue)
      setVisibleStringToDT.
      Parameters:
      tempValue - DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • fromVisibleStringToPatientOrientation

      private String fromVisibleStringToPatientOrientation(String tmpValue)
      DOCUMENT ME!
      Parameters:
      tmpValue - DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • fromVisibleStringToPatientSex

      private String fromVisibleStringToPatientSex(String tempValue)
      Converts patient sex (eg, "Male") into a valid DICOM value (eg, "M"). "Male", "M", "Female","F", "Other" and "O" are valid inputs. Any other input is converted to an empty string (which is valid, since the Patient Sex tag is Type 2, that is, required to exist, but no value is required) and returned.
      Parameters:
      tempValue - DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • fromVisibleStringToPN

      private String fromVisibleStringToPN(String tmpValue)
      Converts a DICOM person's name ("PN") tag into a more understandable value. Used so the '^' word-separation character isn't mistakenly removed.
      Parameters:
      tmpValue - DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • fromVisibleStringToTM

      private String fromVisibleStringToTM(String tempValue)
      setVisibleStringToTM.
      Parameters:
      tempValue - DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • toInt

      public static final Integer[] toInt(byte[] b, int vm, boolean endianess)
      Converts a little-endian byte array into an array of Integers with length equal to the tag vm.
      Parameters:
      b - The byte array.
      vm - The tag VM.
      endianess - True indicates big endian, false indicates little endian.
      Returns:
      An Integer array with length vm.

    • toUInt

      public static final Long[] toUInt(byte[] b, int vm, boolean endianess)
      Converts a little-endian byte array into an array of Longs with length equal to the tag vm.
      Parameters:
      b - The byte array.
      vm - The tag VM.
      endianess - True indicates big endian, false indicates little endian.
      Returns:
      A Long array with length vm.

    • toShort

      public static final Integer[] toShort(byte[] b, int vm, boolean endianess)
      Converts a little-endian byte array into an array of Integers with length equal to the tag vm.
      Parameters:
      b - The byte array.
      vm - The tag VM.
      endianess - True indicates big endian, false indicates little endian.
      Returns:
      An Integer array (storing short values) with length vm.

    • toUShort

      public static final Integer[] toUShort(byte[] b, int vm, boolean endianess)
      Converts a little-endian byte array into an array of Integers with length equal to the tag vm.
      Parameters:
      b - The byte array.
      vm - The tag VM.
      endianess - True indicates big endian, false indicates little endian.
      Returns:
      An Integer array (storing short values) with length vm.

    • toFloat

      public static final Float[] toFloat(byte[] b, int vm, boolean endianess)
      Converts a little-endian byte array into an array of Floats with length equal to the tag vm.
      Parameters:
      b - The byte array.
      vm - The tag VM.
      endianess - True indicates big endian, false indicates little endian.
      Returns:
      An Float array with length vm.

    • toDouble

      public static final Double[] toDouble(byte[] b, int vm, boolean endianess)
      Converts a little-endian byte array into an array of Doubles with length equal to the tag vm.
      Parameters:
      b - The byte array.
      vm - The tag VM.
      endianess - True indicates big endian, false indicates little endian.
      Returns:
      An Double array with length vm.

    • compareTo

      public int compareTo(FileDicomTag toCompare)
      Specified by:
      compareTo in interface Comparable<FileDicomTag>