/**
* Update the indexes for this object. This stage tracks the following data:
*
* <ul>
* <li>Processing date (today)
* <li>PatientID
* <li>StudyInstanceUID
* <li>SeriesInstanceUID
* <li>SOPInstanceUID
* </ul>
*
* It creates table entries for the values in this object. IDs which are not unique may be
* overwritten by subsequent objects (e.g. duplicates). Thus, the tables contain only records of
* unique objects that have been processed.
*
* @param fileObject the object to process.
* @return the same FileObject if the result is true; otherwise null.
*/
public FileObject process(FileObject fileObject) {
lastFileIn = new File(fileObject.getFile().getAbsolutePath());
lastTimeIn = System.currentTimeMillis();
try {
if (fileObject instanceof DicomObject) {
DicomObject dob = (DicomObject) fileObject;
String date = StringUtil.getDate("");
String patientID = dob.getPatientID();
String studyInstanceUID = dob.getStudyInstanceUID();
String seriesInstanceUID = dob.getSeriesInstanceUID();
String sopInstanceUID = dob.getSOPInstanceUID();
index(dateIndex, date, patientID);
index(patientIndex, patientID, studyInstanceUID);
index(studyIndex, studyInstanceUID, seriesInstanceUID);
index(seriesIndex, seriesInstanceUID, sopInstanceUID);
recman.commit();
}
} catch (Exception skip) {
logger.debug("Unable to process " + fileObject.getFile());
}
lastFileOut = new File(fileObject.getFile().getAbsolutePath());
lastTimeOut = System.currentTimeMillis();
return fileObject;
}
/**
* Check a DicomObject and record any failing lookups in the database.
*
* @param fileObject the object to process.
* @return the same FileObject if the result is true; otherwise null.
*/
public FileObject process(FileObject fileObject) {
String cmd;
lastFileIn = new File(fileObject.getFile().getAbsolutePath());
lastTimeIn = System.currentTimeMillis();
if (fileObject instanceof DicomObject) {
DicomObject dob = (DicomObject) fileObject;
if (dcmScriptFile != null) {
DAScript daScript = DAScript.getInstance(dcmScriptFile);
scriptTable = new ScriptTable(daScript);
lutProps = LookupTable.getProperties(lutFile);
synchronized (this) {
Dataset ds = dob.getDataset();
charset = ds.getSpecificCharacterSet();
boolean ok = checkDataset(ds);
if (!ok) {
try {
recman.commit();
} catch (Exception unable) {
}
;
if (quarantine != null) quarantine.insert(fileObject);
return null;
}
}
}
}
lastFileOut = new File(fileObject.getFile().getAbsolutePath());
lastTimeOut = System.currentTimeMillis();
return fileObject;
}
/**
* Get the tag for a DICOM element. This method supports dcm4che names as well as hex strings,
* with or without enclosing parentheses or square brackets and with or without a comma separating
* the group and the element numbers. This method also supports private group names defined in the
* script. This method differs from the DicomObject method of the same name in that it also
* supports names for private group elements in the form 0009[ID]02, where ID is the block owner
* ID. Examples of element specifications containing block owner IDs are:
*
* <ul>
* <li>9,[blockID]02
* <li>(9,[blockID]02)
* <li>[9,[blockID]02]
* <li>0009[blockID]02
* </ul>
*
* @param name the dcm4che element name or coded hex value.
* @return the tag, or zero if the name cannot be parsed as an element specification
*/
public int getElementTag(String name) {
if (name == null) return 0;
name = name.trim();
int k = name.length() - 1;
if (name.startsWith("[") && name.endsWith("]")) name = name.substring(1, k).trim();
else if (name.startsWith("(") && name.endsWith(")")) name = name.substring(1, k).trim();
// Try it as a standard element specification
int tag = DicomObject.getElementTag(name);
if (tag != 0) return tag;
// Try it as a private element name
Integer tagInteger = privateElementNames.get(name);
if (tagInteger != null) return tagInteger.intValue();
// Try to match it as a private group element with a block specification
Matcher matcher = pgPattern.matcher(name);
if (matcher.matches()) {
int group = StringUtil.getHexInt(matcher.group(1));
if ((group & 1) == 1) {
// It's a private group; get the block ID and the element offset
String blockID = matcher.group(2).toUpperCase();
int elem = StringUtil.getHexInt(matcher.group(3));
// Now get the tag of the private group creator
int creatorTag = pgIndex.getTagForID(group, blockID);
if (creatorTag != 0) {
return (group << 16) | ((creatorTag & 0xFF) << 8) | (elem & 0xFF);
}
}
}
// Try to match it as a private creator element with a block specification
matcher = pcPattern.matcher(name);
if (matcher.matches()) {
int group = StringUtil.getHexInt(matcher.group(1));
if ((group & 1) == 1) {
// It's a private group; get the block ID
String blockID = matcher.group(2).toUpperCase();
// Now get the tag of the private group creator
int creatorTag = pgIndex.getTagForID(group, blockID);
if (creatorTag != 0) return creatorTag;
}
}
return 0;
}
private boolean checkDataset(Dataset ds) {
boolean ok = true;
for (Iterator it = ds.iterator(); it.hasNext(); ) {
DcmElement el = (DcmElement) it.next();
int tag = 0;
try {
tag = el.tag();
} catch (Exception useZero) {
}
String command = scriptTable.get(new Integer(tag));
if (command != null) {
if (el.vr() == VRs.SQ) {
Matcher processMatcher = processPattern.matcher(command);
if (processMatcher.find()) {
int i = 0;
Dataset child;
while ((child = el.getItem(i++)) != null) {
ok &= checkDataset(child);
}
}
} else {
Matcher lookupMatcher = lookupPattern.matcher(command);
// logger.info("Parsing: "+command);
while (lookupMatcher.find()) {
int nGroups = lookupMatcher.groupCount();
String element = lookupMatcher.group(1).trim();
String keyType = lookupMatcher.group(2).trim() + "/";
String action = (nGroups > 2) ? lookupMatcher.group(3).trim() : "";
String regex = (nGroups > 3) ? lookupMatcher.group(4).trim() : "";
// logger.info("...nGroups = "+nGroups);
// logger.info("...element: |"+element+"|");
// logger.info("...keyType: |"+keyType+"|");
// logger.info("...action : |"+action+"|");
// logger.info("...regex: |"+regex+"|");
int targetTag = (element.equals("this") ? tag : DicomObject.getElementTag(element));
String targetValue = handleNull(ds.getString(targetTag));
if (!targetValue.equals("")) {
String key = keyType + targetValue;
if (lutProps.getProperty(key) == null) {
boolean there = false;
if (action.equals("keep")
|| action.equals("skip")
|| action.equals("remove")
|| action.equals("empty")
|| action.equals("default")) there = true;
else if (action.equals("ignore")) {
regex = removeQuotes(regex);
there = targetValue.matches(regex);
}
try {
if (!there) {
index.insert(key, keyType, true);
ok = false;
}
} catch (Exception ignore) {
}
}
}
}
}
}
}
return ok;
}