Field Detail

• mediaDirectoryPath

  protected java.lang.String mediaDirectoryPath

• logger

  protected java.io.PrintWriter logger

• onlyDirectoriesFileFilter

  protected ConvertAmicasJPEG2000FilesetToDicom.OnlyDirectoriesFileFilter onlyDirectoriesFileFilter

• onlyXMLFilenameFilter

  protected ConvertAmicasJPEG2000FilesetToDicom.OnlySuffixFilenameFilter onlyXMLFilenameFilter

• specificCharacterSet

  protected SpecificCharacterSet specificCharacterSet

• dictionary

  protected static DicomDictionary dictionary

• uidGenerator

  protected static UIDGenerator uidGenerator

Constructor Detail

• ConvertAmicasJPEG2000FilesetToDicom

  public ConvertAmicasJPEG2000FilesetToDicom()

  Construct an converter that will looked for files in the system default path.

• ConvertAmicasJPEG2000FilesetToDicom

  public ConvertAmicasJPEG2000FilesetToDicom​(java.lang.String mediaDirectoryPath)

  Construct an converter that will looked for files in the specified path.

  Parameters:

  mediaDirectoryPath - where to begin looking for the amicas-patients folder

Method Detail

• setLogger

  public void setLogger​(java.io.PrintWriter logger)

• setLogger

  public void setLogger​(java.io.OutputStream stream)

• setLogger

  public void setLogger​(javax.swing.JFrame content,
                        int width,
                        int height)

• choosePathsAndConvertAmicasFiles

  public void choosePathsAndConvertAmicasFiles()
                                        throws java.io.IOException,
                                               DicomException,
                                               javax.xml.parsers.ParserConfigurationException,
                                               org.xml.sax.SAXException

  Pop up folder chooser dialogs that allow the user to specify the location of the amicas-patients folder, or the parent folder (for example, the drive or volume) in which the amicas-patients folder is located, and the output folder to store the converted DICOM files, and then perform the conversion.

  Throws:

  java.io.IOException

  DicomException

  javax.xml.parsers.ParserConfigurationException

  org.xml.sax.SAXException

• newAttribute

  protected Attribute newAttribute​(AttributeTag tag)
                            throws DicomException

  Throws:

  DicomException

• getNamedAttributeValue

  protected java.lang.String getNamedAttributeValue​(org.w3c.dom.NamedNodeMap xmlAttributes,
                                                    java.lang.String xmlAttributeName)

• makeDicomAttributeFromXmlAttribute

  protected Attribute makeDicomAttributeFromXmlAttribute​(AttributeTag tag,
                                                         java.lang.String xmlAttributeName,
                                                         org.w3c.dom.NamedNodeMap xmlAttributes,
                                                         int type,
                                                         java.lang.String defaultValue)
                                                  throws DicomException

  Throws:

  DicomException

• addDicomAttributeFromXmlAttribute

  protected void addDicomAttributeFromXmlAttribute​(AttributeList list,
                                                   AttributeTag tag,
                                                   java.lang.String xmlAttributeName,
                                                   org.w3c.dom.NamedNodeMap xmlAttributes,
                                                   int type,
                                                   java.lang.String defaultValueForType1)
                                            throws DicomException

  Throws:

  DicomException

• makeAttributeListForPatient

  protected AttributeList makeAttributeListForPatient​(org.w3c.dom.NamedNodeMap xmlAttributes)
                                               throws DicomException

  Throws:

  DicomException

• makeAttributeListForStudy

  protected AttributeList makeAttributeListForStudy​(org.w3c.dom.NamedNodeMap xmlAttributes)
                                             throws DicomException

  Throws:

  DicomException

• makeAttributeListForSeries

  protected AttributeList makeAttributeListForSeries​(org.w3c.dom.NamedNodeMap xmlAttributes)
                                              throws DicomException

  Throws:

  DicomException

• makeAttributeListForImage

  protected AttributeList makeAttributeListForImage​(org.w3c.dom.NamedNodeMap xmlAttributes)
                                             throws DicomException

  Throws:

  DicomException

• setSpecificCharacterSetFromDocumentEncoding

  protected static SpecificCharacterSet setSpecificCharacterSetFromDocumentEncoding​(org.w3c.dom.Document document)

• createDicomImageFileFromAmicasImageFile

  protected void createDicomImageFileFromAmicasImageFile​(java.io.File amicasFolder,
                                                         java.lang.String amicasFileName,
                                                         java.lang.String dicomOutputFolder,
                                                         java.lang.String storingAETitle,
                                                         AttributeList patientList,
                                                         AttributeList studyList,
                                                         AttributeList seriesList,
                                                         AttributeList imageList)
                                                  throws java.io.IOException,
                                                         DicomException

  Throws:

  java.io.IOException

  DicomException

• convertAmicasFiles

  public void convertAmicasFiles​(java.lang.String pathName,
                                 java.lang.String dicomOutputFolder)
                          throws java.io.IOException,
                                 DicomException,
                                 javax.xml.parsers.ParserConfigurationException,
                                 org.xml.sax.SAXException

  Read an amicas-patients folder, and then convert any image files within.

  Parameters:

  pathName - the path name to an amicas-patients folder or folder containing an amicas-patients folder

  dicomOutputFolder - the path name to where to write the DICOM files

  Throws:

  java.io.IOException

  DicomException

  javax.xml.parsers.ParserConfigurationException

  org.xml.sax.SAXException

• main

  public static void main​(java.lang.String[] arg)

  Convert a set of Amicas JPEG 2000 files to DICOM.

  Parameters:

  arg - array of two strings - the path to the media or folder containing the files to convert, and the path to the folder to stored the converted images, or else will pop up file chooser dialogs to select these and create a frame to show the progress.