// Process a DICOM file.
private void process(DicomObject dicomObject) {
try {
dicomObject.setExtension(".dcm");
// get the document for this study or create it if necessary
MircDocument td = new MircDocument(dicomObject);
// Put in the object and store the updated document.
// Note that since all http imports should have been
// anonymized before transmission over the internet,
// we assume that is the case. There is no way to tell.
td.insert(dicomObject, TrialConfig.allowOverwrite(), true, null, null);
// export the image via DICOM if in auto mode
dicomExportDirectories = TrialConfig.getDicomExportDirectories();
dicomExportDirectoryFiles = TrialConfig.getDicomExportDirectoryFiles();
if (TrialConfig.getDicomExportMode().equals("auto") && (dicomExportDirectoryFiles != null)) {
for (int i = 0; i < dicomExportDirectoryFiles.length; i++) {
try {
ExportQueueElement eqe = ExportQueueElement.createEQE(dicomObject);
eqe.queue(dicomExportDirectoryFiles[i]);
} catch (Exception e) {
String name = dicomObject.getFile().getName();
Log.message(
processorServiceName
+ ": "
+ dicomExportDirectories[i]
+ " DICOM export failed:"
+ name);
logger.warn(dicomExportDirectories[i] + " DICOM export failed:" + name);
}
}
}
// log the object if logging is enabled
makeTrialLogEntry("http-import", dicomObject);
} catch (Exception notDicom) {
}
}
// Initialize and start the SCP
private static void startSCP(ObjectProcessor op) {
if (scp != null) {
// There is already a storage SCP; stop it.
// This throws an exception, but ignore it.
try {
scp.stop();
} catch (Exception ignore) {
}
scp = null;
}
// Now get a new SCP with the new params.
scp = getDicomStore();
// Start listening.
scp.addDicomEventListener(op);
// And start the scp.
try {
scp.start();
Log.message(
dicomImportServiceName
+ ": "
+ TrialConfig.getDicomStoreAETitle()
+ " Storage SCP started on port "
+ TrialConfig.getDicomStorePort());
} catch (Exception e) {
Log.message(dicomImportServiceName + ": SCP failed to start<br>" + e.getMessage());
}
}
// Get and initialize the DICOM Storage SCP
private static DicomStorageScp getDicomStore() {
String aetitle, port;
Properties p = new Properties();
aetitle = TrialConfig.getDicomStoreAETitle();
port = TrialConfig.getDicomStorePort();
p.setProperty("storage-scp-aet", aetitle);
p.setProperty("port", port);
p.setProperty("dest", TrialConfig.basepath + TrialConfig.dicomStoreDir);
Dicom.initialize(p);
return Dicom.getStorageScp();
}
// Queue a file for the DatabaseExportService.
private boolean queueForDatabase(FileObject fileObject) {
if (TrialConfig.getDatabaseExportMode().equals("auto")) {
File databaseExportDirectoryFile = TrialConfig.getDatabaseExportDirectoryFile();
try {
ExportQueueElement eqe = ExportQueueElement.createEQE(fileObject);
eqe.queue(databaseExportDirectoryFile);
} catch (Exception e) {
Log.message(
processorServiceName
+ ": Unable to queue "
+ fileObject.getFile().getName()
+ " for database export");
logger.warn("Unable to queue " + fileObject.getFile().getName() + " for database export");
}
}
return true;
}
// Preprocess a FileObject.
private boolean preprocess(FileObject fileObject) {
if (TrialConfig.getPreprocessorEnabled().equals("yes")) {
// Load the preprocessor class specified in the TrialConfig.
// Reload each time in case the class changes behind our back.
PreprocessorAdapter ppa = null;
String className = TrialConfig.getPreprocessorClassName();
try {
Class theClass = Class.forName(className);
ppa = (PreprocessorAdapter) theClass.newInstance();
if (fileObject instanceof DicomObject) return ppa.process((DicomObject) fileObject);
if (fileObject instanceof XmlObject) return ppa.process((XmlObject) fileObject);
if (fileObject instanceof ZipObject) return ppa.process((ZipObject) fileObject);
return ppa.process(fileObject);
} catch (Exception ex) {
Log.message("Exception while loading or running the preprocessor: " + className);
logger.warn("Exception while loading or running the preprocessor: " + className);
return false;
}
}
return true;
}
/**
* The DicomEventListener implementation. Listen for an event from the SCP, log the file, and move
* it to the dicom-import directory for anonymization and export.
*
* @param event the event identifying the file that was received.
*/
public void dicomEventOccurred(DicomEvent event) {
if ((event.getStatus() == 0)
&& event.serviceAsString(event.getService()).equals("C_STORE_RQ")) {
File inFile = new File(event.getFilename());
Log.message(dicomImportServiceName + ": Image received: " + inFile.getName());
// Make the output directory in case it doesn't exist.
File outDir = new File(TrialConfig.basepath + TrialConfig.dicomImportDir);
outDir.mkdirs();
// Put the new file in it, using the overwrite attribute of the trial to determine
// whether duplicate SOPInstanceUIDs are to be renamed so as not to lose them.
FileObject fileObject = new FileObject(inFile);
fileObject.moveToDirectory(outDir, TrialConfig.allowOverwrite());
} else if (event.getStatus() != 0xff00)
Log.message(dicomImportServiceName + ": unexpected status: " + event.toStringNoPath());
}
// Load the anonymizer.properties file.
// This function is called whenever the Clinical Trial Service is restarted,
// allowing new anonymization scripts to be loaded.
private void initialize() {
reinitialize = false;
try {
File propFile = new File(TrialConfig.basepath + TrialConfig.dicomAnonymizerFilename);
dicomAnonymizerProperties = new Properties();
dicomAnonymizerProperties.load(new FileInputStream(propFile));
File lkupFile = new File(TrialConfig.basepath + TrialConfig.lookupTableFilename);
lookupTableProperties = new Properties();
try {
lookupTableProperties.load(new FileInputStream(lkupFile));
} catch (Exception ex) {
lookupTableProperties = null;
}
if (TrialConfig.dicomImportAnonymizerEnabled())
Log.message(processorServiceName + ": DicomAnonymizer initialized");
else Log.message(processorServiceName + ": DicomAnonymizer not enabled");
} catch (Exception e) {
Log.message(processorServiceName + ": Unable to configure the DicomAnonymizer");
}
}
// Create a Log4J log file with a monthly rolling appender and populate
// it with information from the dataset in a csv format so the log file
// can be opened and processed with a spreadsheet.
private void makeTrialLogEntry(String service, DicomObject dicomObject) {
if (!TrialConfig.log()) return;
if (processorLog == null) {
try {
processorLog = Logger.getLogger("trial");
processorLog.setAdditivity(false);
PatternLayout layout = new PatternLayout("%d{yyyy-MM-dd},%d{HH:mm:ss},%m%n");
File logs = new File(TrialConfig.basepath + TrialConfig.logDirectory);
logs.mkdirs();
DailyRollingFileAppender appender =
new DailyRollingFileAppender(
layout,
TrialConfig.basepath
+ TrialConfig.logDirectory
+ File.separator
+ TrialConfig.serviceName
+ ".csv",
"'.'yyyy-MM");
processorLog.addAppender(appender);
processorLog.setLevel((Level) Level.ALL);
} catch (Exception e) {
logger.warn("Unable to instantiate a trial logger");
processorLog = null;
return;
}
}
processorLog.info(
service
+ ","
+ dicomObject.getPatientName()
+ ","
+ dicomObject.getPatientID()
+ ","
+ dicomObject.getModality()
+ ","
+ dicomObject.getSeriesNumber()
+ ","
+ dicomObject.getAcquisitionNumber()
+ ","
+ dicomObject.getInstanceNumber());
}
// Look through the dicom-import directory and process
// all the files there. Note that these are actual files,
// not queue elements.
private void processDicomImportFiles() {
File importDirFile = new File(TrialConfig.basepath + TrialConfig.dicomImportDir);
if (!importDirFile.exists()) return;
File[] files = importDirFile.listFiles();
for (int k = 0; k < files.length; k++) {
File next = files[k];
if (files[k].canRead() && files[k].canWrite()) {
try {
boolean forceQuarantine = false;
httpExportDirectories = TrialConfig.getHttpExportDirectories();
httpExportDirectoryFiles = TrialConfig.getHttpExportDirectoryFiles();
// If enabled, anonymize.
// Note: in normal clinical trials, the anonymizer is enabled and de-identified
// images are transmitted by the HttpExportProcessor.
// For normal research applications, images are not anonymized and the document
// creates directories of identified and de-identified images. In this situation,
// the anonymizer is disabled and the document takes care of de-identifying the
// images.
// Note: in research applications, the document takes its elements from the
// identified (e.g., containing PHI) image, so such documents contain PHI.
if (TrialConfig.dicomImportAnonymizerEnabled()) {
String exceptions =
DicomAnonymizer.anonymize(
next,
next,
dicomAnonymizerProperties,
lookupTableProperties,
new LocalRemapper(),
false,
false);
if (!exceptions.equals("")) {
if (exceptions.indexOf("!quarantine!") != -1) {
Log.message(
"<font color=\"red\">DicomAnonymizer quarantine call:<br>"
+ next.getName()
+ "</font>");
forceQuarantine = true;
} else if (exceptions.indexOf("!error!") != -1) {
Log.message(
"<font color=\"red\">DicomAnonymizer error call: "
+ exceptions
+ "<br>"
+ next.getName()
+ "</font>");
forceQuarantine = true;
} else {
// Note: the anonymizer logs the exception list to Log4J,
// so we just have to log it to the displayed log.
Log.message("Anonymization exceptions: " + exceptions + "<br>" + next.getName());
}
} else {
Log.message(
"<font color=\"blue\">Anonymization complete"
+ "<br>"
+ next.getName()
+ "</font>");
}
}
if (!forceQuarantine) {
// get the document for this study or create it if necessary
DicomObject nextObject = new DicomObject(next);
MircDocument td = new MircDocument(nextObject);
// put in the object and store the updated document
td.insert(
nextObject,
TrialConfig.allowOverwrite(),
TrialConfig.dicomImportAnonymizerEnabled(),
dicomAnonymizerProperties,
lookupTableProperties);
// export the object
if (httpExportDirectoryFiles != null) {
for (int i = 0; i < httpExportDirectoryFiles.length; i++) {
try {
ExportQueueElement eqe = ExportQueueElement.createEQE(nextObject);
eqe.queue(httpExportDirectoryFiles[i]);
} catch (Exception e) {
Log.message(
processorServiceName
+ ": "
+ httpExportDirectories[i]
+ " export failed:"
+ next.getName());
logger.warn(httpExportDirectories[i] + " export failed:" + next.getName());
}
}
}
if (!queueForDatabase(nextObject))
Log.message(Quarantine.file(next, processorServiceName));
else Log.message(processorServiceName + ": Processing complete: " + next.getName());
// log the event if logging is enabled
makeTrialLogEntry("dicom-import", nextObject);
}
// if the file still exists, then either the object was
// set for quarantining or there is a bug somewhere;
// log it and quarantine the file so we don't
// fall into an infinite loop.
if (next.exists()) {
logger.warn("Forced quarantine: " + next);
Log.message(Quarantine.file(next, processorServiceName));
}
} catch (Exception e) {
Log.message(
processorServiceName
+ ": Error during processing: "
+ next.getName()
+ " - "
+ e.getMessage());
logger.warn("Error during processing: object quarantined: " + next.getName(), e);
Log.message(Quarantine.file(next, processorServiceName));
}
yield();
}
}
}