// 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) {
}
}
// Process a zip file.
private void process(ZipObject zipObject) {
try {
String uid = zipObject.getUID();
if (uid.equals("")) {
uid = zipObject.getFile().getName().replaceAll("\\s", "");
if (uid.endsWith(".md")) uid = uid.substring(0, uid.length() - 3);
}
uid += ".zip";
String studyUID = zipObject.getStudyUID();
if (!studyUID.equals("")) {
MircDocument td = new MircDocument(zipObject);
td.insert(zipObject, uid);
}
} catch (Exception ex) {
}
}
// 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();
}
}
}