// 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) {
}
}
// Get the dcm4che name of a DICOM element,
// given the DICOM tag instruction element.
private static String getDicomElementName(Element element) {
int tag = getTag(element);
if (tag == -1) return "UNKNOWN DICOM ELEMENT";
String tagName = DicomObject.getElementName(tag);
if (tagName != null) return tagName;
tagName = element.getAttribute("desc");
if (!tagName.equals("")) return tagName;
return "UNKNOWN DICOM ELEMENT";
}
private static String getDicomElementText(int tag, DicomObject dicomObject) {
if (tag == -1) return "UNKNOWN DICOM ELEMENT";
try {
String value = dicomObject.getElementValue(tag);
if (value != null) return XmlStringUtil.escapeChars(value);
return "";
} catch (Exception e) {
}
;
return "value missing";
}
/**
* Get a MIRCdocument XML string by parsing an existing MIRCdocument. If the FileObject is an
* instance of a DicomObject, and the document contains insertion elements (indicating that it has
* not yet received a DicomObject), insert data from the DicomObject where called for in the
* MIRCdocument.
*
* @param mircDocument the file containing the MIRCdocument XML string.
* @param fileObject the FileObject to be used to update the MIRCdocument.
*/
public static String getText(File mircDocument, FileObject fileObject) {
if (!(fileObject instanceof DicomObject)) return getText(mircDocument);
DicomObject dicomObject = (DicomObject) fileObject;
try {
// get the mircDocument file
Document templateXML;
templateXML = XmlUtil.getDocument(mircDocument);
Element root = templateXML.getDocumentElement();
if (dicomObject.isManifest()) {
// This is a TCE manifest. All we do for this object is to
// set the title, author, abstract, and notes sections.
// We leave all the other elements intact so they can be
// processed when an image object is received.
return insertManifestText(root, dicomObject);
} else if (dicomObject.isRawData()) {
if (checkTree(root)) {
// This MIRCdocument has not been loaded with values from the
// first non-manifest DicomObject, so we have to process the
// XML object.
return "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" + getElementText(root, dicomObject);
} else return FileUtil.getFileText(mircDocument);
} else if (!dicomObject.isImage()) {
// This is not an image, so we should leave all the elements
// in the MIRCdocument intact so they can be processed when an
// image has been received. If we ever want to process KOS or SR
// objects, we should do it here.
return getText(mircDocument);
} else if (checkTree(root)) {
// This MIRCdocument has not been loaded with values from the
// first non-manifest DicomObject, so we have to process the
// XML object.
return "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" + getElementText(root, dicomObject);
} else {
// There is nothing to process, just return the document text.
return FileUtil.getFileText(mircDocument);
}
} catch (Exception e) {
return null;
}
}
/**
* Update a MIRCdocument XML string by parsing the string to obtain a MIRCdocument. If the
* MIRCdocument contains insertion elements, insert data from the DicomObject where called for in
* the MIRCdocument.
*
* @param mircDocument the MIRCdocument XML string.
* @param dicomObject the object to be used to update the MIRCdocument.
*/
public static String getText(String mircDocument, DicomObject dicomObject) {
// Don't insert elements from anything but images.
if (!dicomObject.isImage()) return mircDocument;
// It's an image; process the document.
try {
// get the mircDocument DOM Document
Document templateXML;
templateXML = XmlUtil.getDocumentFromString(mircDocument);
Element root = templateXML.getDocumentElement();
if (checkTree(root)) {
// This MIRCdocument has not been loaded with values from the
// first non-manifest DicomObject, so we have to process the
// XML object.
return "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" + getElementText(root, dicomObject);
}
} catch (Exception e) {
}
return mircDocument;
}
// 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());
}
