protected void ensureContentAvailable() {
if (!isContentAvailable()) {
DicomInputStream dis = null;
try {
List<org.dcm4chee.archive.entity.File> files =
((TCQueryLocal) JNDIUtils.lookup(TCQueryLocal.JNDI_NAME))
.findInstanceByUID(getSOPInstanceUID())
.getFiles();
String fsId = files.get(0).getFileSystem().getDirectoryPath();
String fileId = files.get(0).getFilePath();
dis =
new DicomInputStream(
fsId.startsWith("tar:")
? TarRetrieveDelegate.getInstance().retrieveFileFromTar(fsId, fileId)
: FileUtils.resolve(new File(fsId, fileId)));
metaData = dis.readDicomObject();
} catch (Exception e) {
log.error("Unable to retrieve instance!", e); // $NON-NLS-1$
} finally {
if (dis != null) {
try {
dis.close();
} catch (Exception e2) {
}
}
}
}
}
private void fixRecursive(File source, File target, int[] counts) {
if (!source.exists()) {
System.err.println("no such file or directory `" + source + "'");
} else if (source.isDirectory()) {
if (!target.exists()) {
if (!target.mkdir()) System.err.println("failed to create directory `" + target + "'");
}
if (target.isFile()) {
System.err.println(
"cannot overwrite non-directory `" + target + "' with directory `" + source + "'");
return;
}
String[] ss = source.list();
for (String s : ss) {
fixRecursive(new File(source, s), new File(target, s), counts);
}
} else if (target.isDirectory()) {
System.err.println(
"cannot overwrite directory `" + target + "' with non-directory `" + source + "'");
} else {
Replacements replacements = new Replacements();
try {
counts[0]++;
DicomInputStream din = new DicomInputStream(source);
try {
din.setHandler(replacements);
din.readDicomObject();
} finally {
try {
din.close();
} catch (IOException ignore) {
}
}
if (replacements.numItems == 0) throw new NoFixException("no Pixel Data Fragments");
replacements.applyTo(source, target);
counts[1]++;
System.out.println(
"PATCHED " + source + ": JPEG-LS " + replacements.bitsStored + "-bit -> " + target);
} catch (Exception e) {
System.out.println("skipped " + source + ": " + e.getMessage());
}
}
}
private byte[] getDocumentContent() {
if (data != null) {
return data;
} else if (dicomFile != null) {
DicomInputStream dis = null;
try {
dis = new DicomInputStream(dicomFile);
return dis.readDicomObject().getBytes(Tag.EncapsulatedDocument);
} catch (Exception e) {
log.error("Unable to get content of encapsulated document!", e);
} finally {
if (dis != null) {
try {
dis.close();
} catch (Exception e) {
log.error(null, e);
}
}
}
}
return null;
}
public boolean readValue(DicomInputStream in) throws IOException {
int tag = in.tag();
int len = in.valueLength();
long pos = in.getStreamPosition();
DicomObject attrs = in.getDicomObject();
String uid;
if (fmi && tag >= 0x00080000) {
if (replacements == null)
throw new NoFixException("File Meta Information (0002,eeee) is missing");
if (FixJpegLS.this.implClassUID != null) {
uid = attrs.getString(Tag.ImplementationClassUID);
if (!FixJpegLS.this.implClassUID.equals(uid))
throw new NoFixException("Implementation Class UID (0002,0012) = " + uid);
}
fmi = false;
}
switch (tag) {
case Tag.FileMetaInformationGroupLength:
case Tag.ItemDelimitationItem:
case Tag.SequenceDelimitationItem:
return in.readValue(in);
case Tag.TransferSyntaxUID:
in.readValue(in);
uid = attrs.getString(Tag.TransferSyntaxUID);
if (!UID.JPEGLSLossless.equals(uid))
throw new NoFixException("Transfer Syntax UID (0002,0010) = " + DICT.prompt(uid));
replacements = new ArrayList<Replacement>();
return true;
case Tag.ImplementationClassUID:
if (replacements == null)
throw new NoFixException("File Meta Information (0002,eeee) is missing");
in.readValue(in);
if (FixJpegLS.this.newImplClassUID != null)
addImplClassUIDReplacements(pos, len, (int) in.getEndOfFileMetaInfoPosition());
return true;
case Tag.PixelData:
if (in.level() == 0) {
if (len != -1)
throw new NoFixException("Pixel Data is not encapsulated into Data Fragments");
pixelData = true;
}
return in.readValue(in);
case Tag.Item:
if (pixelData) {
if (len == 0) return true;
byte[] jpegheader = new byte[17];
in.readFully(jpegheader);
byte[] lse = selectLSE(jpegheader);
in.skipFully(len - 18);
addItemReplacements(pos, len, lse, in.read() == 0);
numItems++;
return true;
}
}
pixelData = false;
if (len == -1) return in.readValue(in);
in.skipFully(len);
return true;
}
/**
* 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"
+ "#######################################################");
}
