/**
* 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;
}
/**
* 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;
}
/**
* The servlet method that responds to an HTTP GET. This method returns a summary page containing
* information on the pipeline or stage specified by the p and s query parameters.
*
* @param req The HttpServletRequest provided by the servlet container.
* @param res The HttpServletResponse provided by the servlet container.
*/
public void doGet(HttpRequest req, HttpResponse res) {
super.loadParameters(req);
// Get the parameters.
int x = StringUtil.getInt(req.getParameter("plugin"), -1);
// Return the page
res.write(getPage(p, s, x));
res.setContentType("html");
res.disableCaching();
res.send();
}
/**
* Construct a Query from an XML document in the form described on the RSNA MIRC wiki.
*
* @param queryDoc the MIRCquery XML DOM object.
*/
public Query(Document queryDoc) {
super();
Element root = queryDoc.getDocumentElement();
unknown = root.getAttribute("unknown").trim().equals("yes");
bgcolor = root.getAttribute("bgcolor").trim();
display = root.getAttribute("display").trim();
icons = root.getAttribute("icons").trim();
orderby = root.getAttribute("orderby").trim();
firstresult = StringUtil.getInt(root.getAttribute("firstresult"));
if (firstresult <= 0) firstresult = 1;
maxresults = StringUtil.getInt(root.getAttribute("maxresults"));
if (maxresults <= 0) maxresults = 1;
StringBuffer sb = new StringBuffer();
Node child = root.getFirstChild();
while (child != null) {
if (child.getNodeType() == Node.ELEMENT_NODE) {
String dbname = child.getNodeName();
String text = getTextContent(child);
if (!text.equals("")) {
this.put(dbname, text);
containsNonFreetextQueries = true;
}
if (dbname.equals("temp")) isTempQuery = true;
} else if (child.getNodeType() == Node.TEXT_NODE) {
sb.append(" " + child.getTextContent());
}
child = child.getNextSibling();
}
String freetext = sb.toString().replaceAll("\\s+", " ").trim();
isBlankQuery = freetext.equals("");
isSpecialQuery = root.getAttribute("special").trim().equals("yes");
this.put("freetext", freetext);
setAgeRange(root);
// log();
}
// Create an HTML page containing the form for configuring the file.
private String getScriptPage(int pipe, int stage, File file) {
String template = "/DAEditor.html";
String page = FileUtil.getText(Cache.getInstance().getFile(template));
String table = makeList();
Properties props = new Properties();
props.setProperty("closebox", "/icons/home.png");
props.setProperty("home", home);
props.setProperty("context", "/" + context);
props.setProperty("profilespath", "/profiles");
props.setProperty("profilepath", "/profile");
props.setProperty("scriptpath", "/script");
props.setProperty("scriptfile", file.getAbsolutePath().replaceAll("\\\\", "/"));
props.setProperty("pipe", "" + pipe);
props.setProperty("stage", "" + stage);
page = StringUtil.replace(page, props);
return page;
}
// Create an HTML page containing the list of script files.
private String getListPage() {
String template = "/DAList.html";
String page = FileUtil.getText(Cache.getInstance().getFile(template));
String table = makeList();
Properties props = new Properties();
props.setProperty("home", home);
props.setProperty("table", table);
props.setProperty("homeicon", "");
if (!home.equals("")) {
props.setProperty(
"homeicon",
"<img src=\"/icons/home.png\" onclick=\"window.open('"
+ home
+ "','_self');\" title=\"Return to the home page\" style=\"margin:2\"/>");
}
page = StringUtil.replace(page, props);
return page;
}
public ScriptTable(DAScript script) {
super();
Document scriptXML = script.toXML();
Element scriptRoot = scriptXML.getDocumentElement();
Node child = scriptRoot.getFirstChild();
while (child != null) {
if ((child instanceof Element) && child.getNodeName().equals("e")) {
Element eChild = (Element) child;
if (eChild.getAttribute("en").equals("T")) {
int tag = StringUtil.getHexInt(eChild.getAttribute("t"));
String command = eChild.getTextContent();
Matcher processMatcher = processPattern.matcher(command);
Matcher lookupMatcher = lookupPattern.matcher(command);
Integer tagInteger = new Integer(tag);
if (processMatcher.find() || lookupMatcher.find()) {
this.put(tagInteger, command);
}
}
}
child = child.getNextSibling();
}
}