private DicomObject toSCN(DicomObject ian) {
DicomObject scn = new BasicDicomObject();
scn.putString(Tag.PatientID, VR.LO, ian.getString(Tag.PatientID));
scn.putString(Tag.PatientName, VR.PN, ian.getString(Tag.PatientName));
scn.putString(Tag.StudyID, VR.SH, ian.getString(Tag.StudyID));
scn.putString(Tag.StudyInstanceUID, VR.UI, ian.getString(Tag.StudyInstanceUID));
DicomElement ianSeriesSeq = ian.get(Tag.ReferencedSeriesSequence);
DicomElement scnSeriesSeq = scn.putSequence(Tag.ReferencedSeriesSequence);
DicomObject ianSeriesItem, scnSeriesItem, scnSOPItem;
DicomElement ianSOPSeq, scnSOPSeq;
for (int i = 0, n = ianSeriesSeq.countItems(); i < n; ++i) {
ianSeriesItem = ianSeriesSeq.getDicomObject(i);
scnSeriesItem = new BasicDicomObject();
scnSeriesItem.putString(
Tag.SeriesInstanceUID, VR.UI, ianSeriesItem.getString(Tag.SeriesInstanceUID));
scnSeriesSeq.addDicomObject(scnSeriesItem);
ianSOPSeq = ianSeriesItem.get(Tag.ReferencedSOPSequence);
scnSOPSeq = scnSeriesItem.putSequence(Tag.ReferencedImageSequence);
for (int j = 0, m = ianSOPSeq.countItems(); j < m; ++j) {
scnSOPItem = new BasicDicomObject();
ianSOPSeq.getDicomObject(j).exclude(INSTANCE_AVAILABILITY).copyTo(scnSOPItem);
scnSOPSeq.addDicomObject(scnSOPItem);
}
}
return scn;
}
private void insertDicomTags(
int dcmobject_id, DicomObject obj, Integer parentId, PreparedStatement stmt)
throws Exception {
for (Iterator<DicomElement> it = obj.iterator(); it.hasNext(); ) {
DicomElement e = it.next();
StringBuffer sb = new StringBuffer();
try {
String[] values = e.getStrings(obj.getSpecificCharacterSet(), false);
sb.append(values[0].replaceAll("\0", ""));
int i;
for (i = 1; i < values.length; i++) {
sb.append("/").append(values[i].replaceAll("\0", ""));
}
} catch (Exception ee) {
try {
sb.append(e.getString(obj.getSpecificCharacterSet(), false));
} catch (Exception e2) {
}
}
stmt.setInt(1, dcmobject_id);
stmt.setString(2, DicomHeader.toTagString(e.tag()));
stmt.setString(3, e.vr().toString());
// only the first 150 chars are saved if the tag-value is longer
if (sb.length() > 150) {
stmt.setString(
4, sb.toString().substring(0, 150).concat("*** end of tag-value not applicable ***"));
} else {
stmt.setString(4, sb.toString());
}
stmt.setInt(5, itemOrder);
if (parentId == null) {
stmt.setNull(6, Types.INTEGER);
} else {
stmt.setInt(6, parentId);
}
stmt.addBatch();
// System.out.println( stmt );
itemOrder++;
if (e.countItems() > 0) {
if (e.hasDicomObjects()) {
for (int i = 0; i < e.countItems(); i++) {
insertDicomTags(dcmobject_id, e.getDicomObject(i), itemOrder - 1, stmt);
}
}
}
}
}
private DicomObject mkStgCmtResult(Association as, DicomObject rqdata) {
DicomObject result = new BasicDicomObject();
result.putString(Tag.TransactionUID, VR.UI, rqdata.getString(Tag.TransactionUID));
DicomElement rqsq = rqdata.get(Tag.ReferencedSOPSequence);
DicomElement resultsq = result.putSequence(Tag.ReferencedSOPSequence);
if (stgcmtRetrieveAET != null) {
result.putString(Tag.RetrieveAETitle, VR.AE, stgcmtRetrieveAET);
}
DicomElement failedsq = null;
File dir = getDir(as);
for (int i = 0, n = rqsq.countItems(); i < n; i++) {
DicomObject rqItem = rqsq.getDicomObject(i);
String uid = rqItem.getString(Tag.ReferencedSOPInstanceUID);
DicomObject resultItem = new BasicDicomObject();
rqItem.copyTo(resultItem);
if (stgcmtRetrieveAETs != null) {
resultItem.putString(Tag.RetrieveAETitle, VR.AE, stgcmtRetrieveAETs);
}
File f = new File(dir, uid);
if (f.isFile()) {
resultsq.addDicomObject(resultItem);
} else {
resultItem.putInt(Tag.FailureReason, VR.US, NO_SUCH_OBJECT_INSTANCE);
if (failedsq == null) {
failedsq = result.putSequence(Tag.FailedSOPSequence);
}
failedsq.addDicomObject(resultItem);
}
}
return result;
}
/**
* insert the given file into the database
*
* @param f
* @param insertDCMSeriesStmt
* @param insertDCMObjectStmt
* @param insertDCMTagsStmt
* @param currentDbConnection
*/
private void insertFile2DB(
File f,
PreparedStatement insertDCMSeriesStmt,
PreparedStatement insertDCMObjectStmt,
PreparedStatement insertDCMTagsStmt,
Connection currentDbConnection) {
logger.info(
" \r\n\r\n"
+ "#######################################################\r\n"
+ "#\r\n"
+ "# STARTING IMPORT FOR "
+ f.getName()
+ "\r\n"
+ "#\r\n"
+ "#######################################################");
used_files++;
long start = System.currentTimeMillis();
boolean importFile = true;
try {
DicomHeader dh = new DicomHeader(f);
DicomObject dcmObjectHeader = dh.getDicomObject();
// if a rule to filter exist -> no import
if (!filterTags.isEmpty()) {
for (Iterator<String> iter = filterTags.keySet().iterator(); iter.hasNext(); ) {
String tag = (String) iter.next();
// check comma separated filter e. g. 0008,0060=MR, UR, NM, US
if (filterTags.get(tag).contains(",")) {
String[] splittedValue = filterTags.get(tag).split(", ");
for (int i = 0; i < splittedValue.length; i++) {
if (splittedValue[i].equals(dh.getHeaderStringValue(tag))) {
importFile = false;
logger.info("NOT importing File, matches Filtertags: " + filterTags.get(tag));
break;
}
}
} else if (dh.getHeaderStringValue(tag).equals(filterTags.get(tag))) {
importFile = false;
logger.info("NOT importing File, matches Filtertags: " + filterTags.get(tag));
break;
}
}
}
// filter the reconstruction-images
if (importFile && CHECK_RECONSTRUCTION) {
importFile = checkRecontruction(currentDbConnection, dh);
}
if (importFile) {
// insert dcmSeries if it not exists
if (!seriesExists(currentDbConnection, dh)) {
try {
int i = 1; // index for database-fields in series
for (Iterator<String> iter = dicomTags.keySet().iterator(); iter.hasNext(); i++) {
String tag = (String) iter.next();
String VR = DicomHeader.getHeaderFieldType(tag);
// if Date
if ("DA".equals(VR)) {
try {
Date d = dh.getHeaderDateValue(tag);
insertDCMSeriesStmt.setDate(i, new java.sql.Date(d.getTime()));
} catch (Exception e) {
insertDCMSeriesStmt.setDate(i, null);
}
// if Time
} else if ("TM".equals(VR)) {
try {
Date d = dh.getHeaderDateValue(tag);
insertDCMSeriesStmt.setTime(i, new java.sql.Time(d.getTime()));
} catch (Exception e) {
insertDCMSeriesStmt.setTime(i, null);
}
// else String
} else {
String s = dh.getHeaderStringValue(tag);
s = s.replaceAll("\0", "");
insertDCMSeriesStmt.setString(i, s);
}
}
insertDCMSeriesStmt.execute();
// Exception if Seriesuid exist
} catch (SQLException sqle) {
if (sqle.getMessage().indexOf("duplicate key") < 0) {
logger.error("Error adding series: ", sqle);
} else {
logger.warn("Series allready in DB");
}
currentDbConnection.rollback();
}
}
// insert the dicom-object and the tags
try {
int j = 1; // index for database-fields in dicom-objects
insertDCMObjectStmt.setString(j++, dh.getDicomObject().getString(Tag.SeriesInstanceUID));
insertDCMObjectStmt.setString(j++, dh.getDicomObject().getString(Tag.SOPInstanceUID));
insertDCMObjectStmt.setTimestamp(j++, new Timestamp(System.currentTimeMillis()));
// storing the md5 of pixel-data in database, if CHECKSUM is true
if (CHECKSUM) {
DicomInputStream dis = new DicomInputStream(f);
DicomObject dcmObj = new BasicDicomObject();
dis.readDicomObject(dcmObj, -1);
DicomElement de = dcmObj.get(Tag.PixelData);
byte[] bytes = de.getBytes();
MessageDigest md = MessageDigest.getInstance("MD5");
md.update(bytes);
byte[] md5 = md.digest();
BigInteger bi = new BigInteger(1, md5);
insertDCMObjectStmt.setString(j++, bi.toString(16));
} else {
insertDCMObjectStmt.setString(j++, null);
}
insertDCMObjectStmt.setString(j++, SOFTWARE_VERSION);
insertDCMObjectStmt.execute();
// currentDbConnection.commit();
int parentID =
getDCMObjectID(
currentDbConnection, dh.getDicomObject().getString(Tag.SOPInstanceUID));
itemOrder = 1;
// recursive insert of dicom-tags
insertDCMTagsStmt.clearBatch();
insertDicomTags(parentID, dcmObjectHeader, null, insertDCMTagsStmt);
insertDCMTagsStmt.executeBatch();
currentDbConnection.commit();
logger.info("File inserted");
imported_files++;
} catch (SQLException sqle) {
currentDbConnection.rollback();
if (sqle.getMessage().indexOf("duplicate key") < 0) {
logger.error("Error importing image: ", sqle);
} else {
logger.warn(
"File with UID="
+ dh.getDicomObject().getString(Tag.SOPInstanceUID)
+ " allready in db");
}
}
}
if (DELETE_FILES_AFTER_IMPORT) {
f.delete();
} else {
boolean success = f.renameTo(new File(OK_DIR, f.getName()));
if (success) {
logger.info("moved file to: " + OK_DIR + File.separator + f.getName());
} else {
logger.warn("unable to move file to: " + OK_DIR + File.separator + f.getName());
}
}
} catch (Exception e) {
boolean success = f.renameTo(new File(ERROR_DIR, f.getName()));
logger.log(
Level.WARN, "Failed to insert file: " + f.getAbsolutePath() + " " + e.getMessage(), e);
if (success) {
logger.info("moved file to: " + ERROR_DIR + File.separator + f.getName());
} else {
logger.warn("unable to move file to: " + ERROR_DIR + File.separator + f.getName());
}
try {
currentDbConnection.rollback();
} catch (SQLException e1) {
logger.log(Level.ERROR, e1.getMessage(), e1);
}
}
logger.info(
"END OF IMPORT FOR "
+ f.getName()
+ " took "
+ (System.currentTimeMillis() - start)
+ "µsec. \r\n"
+ "Files used: "
+ used_files
+ " Files imported: "
+ imported_files
+ " \r\n"
+ "#######################################################");
}
