public void scrollToAttribute(Attribute a) {
if (!a.getDescriptor().getConfig().equals(getConfig())) {
logger.fine("Cannot scroll to attribute that isn't attached to this type of descriptor");
return;
}
int rowIndex = getCurrentModel().getRowForDescriptor(a.getDescriptor());
int colIndex = getCurrentModel().getColumnForAttribute(a);
JScrollPane scrollPane = (JScrollPane) this.getComponent(0);
JViewport viewport = (JViewport) scrollPane.getViewport();
EnhancedTable table = (EnhancedTable) viewport.getView();
// This rectangle is relative to the table where the
// northwest corner of cell (0,0) is always (0,0).
Rectangle rect = table.getCellRect(rowIndex, colIndex, true);
// The location of the viewport relative to the table
Point pt = viewport.getViewPosition();
// Translate the cell location so that it is relative
// to the view, assuming the northwest corner of the
// view is (0,0)
rect.setLocation(rect.x - pt.x, rect.y - pt.y);
// Scroll the area into view
viewport.scrollRectToVisible(rect);
}
/**
* Gets the selected node in the tags tree and applies all attributes fro the attributes list to
* it. Do nothing if no node is selected.
*/
public void apply() {
JTree tree = (JTree) document.getTagById("tagsTree").getComponent();
if (tree.getSelectionPath() != null) {
DefaultMutableTreeNode node =
(DefaultMutableTreeNode) tree.getSelectionPath().getLastPathComponent();
Tag tag = (Tag) node.getUserObject();
for (Attribute attr : attributes) {
tag.setAttribute(attr.getName(), attr.getValue());
}
tag.applyAttributes(tag.getComponent());
}
}
/**
* Updates attributes list on node selection change in the tags tree. Loads attributes of the
* selected node into the attributes list. Just clears attributes if no node is selected.
*
* @param e
*/
public void onTagChange(TreeSelectionEvent e) {
if (e.getNewLeadSelectionPath() != null) {
TreePath path = e.getNewLeadSelectionPath();
attributes.clear();
if (path.getPathCount() >= 1) {
DefaultMutableTreeNode node = (DefaultMutableTreeNode) path.getLastPathComponent();
Tag tag = (Tag) node.getUserObject();
for (String name : tag.getAttributes().keySet()) {
Attribute attr = new Attribute();
attr.setName(name);
attr.setValue(tag.getAttribute(name));
attributes.add(attr);
}
}
}
}
public String getValue() {
Array value = att.getValues();
try {
return NCdumpW.printArray(value, null, null);
} catch (IOException e) {
return e.getMessage();
}
}
/**
* @param list
* @return array of two String values, row then column orientation, else array of two nulls if
* cannot be obtained
*/
private static String[] getPatientOrientation(AttributeList list) {
String[] vPatientOrientation = null;
Attribute aPatientOrientation = list.get(TagFromName.PatientOrientation);
if (aPatientOrientation != null && aPatientOrientation.getVM() == 2) {
try {
vPatientOrientation = aPatientOrientation.getStringValues();
if (vPatientOrientation != null && vPatientOrientation.length != 2) {
vPatientOrientation = null;
}
} catch (DicomException e) {
vPatientOrientation = null;
}
}
if (vPatientOrientation == null) {
vPatientOrientation = new String[2];
}
return vPatientOrientation;
}
public void show(Component invoker, int x, int y) {
ViperViewMediator mediator = getMediator();
Point pnt = new Point(x, y);
EnhancedTable tab = getTable();
int row = tab.rowAtPoint(pnt);
desc = getCurrentModel().getDescriptorAtRow(row);
int col = tab.columnAtPoint(pnt);
Object cellValue = tab.getValueAt(row, col);
if (cellValue instanceof Attribute) {
attr = (Attribute) cellValue;
// hide the "Occlusions..." option when we're not dealing with a Textline object
boolean isTextline = attr.getAttrConfig().getAttrType().endsWith("textline");
occlusions.setVisible(isTextline);
occSeparator.setVisible(isTextline);
Instant now = mediator.getCurrentFrame();
if (now == null) {
mediator.getDisplayWRTManager().setAttribute(null, null);
wrt.setEnabled(false);
wrt.setSelected(false);
} else {
boolean isDwrt = attr == mediator.getDisplayWRTManager().getAttribute();
boolean dwrtable =
(attr.getAttrValueAtInstant(now) instanceof HasCentroid
&& attr.getDescriptor().getValidRange().contains(now));
wrt.setEnabled(dwrtable);
wrt.setSelected(isDwrt);
}
} else {
attr = null;
wrt.setEnabled(false);
wrt.setSelected(false);
}
if (null != desc) {
PropagateInterpolateModule proper = getMediator().getPropagator();
p.setSelected(proper.isPropagatingThis(desc));
v.setSelected(mediator.isThisValidNow(desc));
resetMarks();
super.show(invoker, x, y);
}
}
/**
* This looks through a list of object classes in an attribute until it finds a unique editor
* corresponding to a particular value. If no editor is found 'null' is returned. Note that If
* multiple unique editors exist, which one is returned is undefined.
*
* <p>
*
* @param oc the objectClass attribute; a list of object classes
* @return the unique pluggable editor corresponding to one particular object class value, or null
* if none is found.
*/
public PluggableEditor getUniqueEditor(Attribute oc) {
try {
Enumeration values = oc.getAll();
while (values.hasMoreElements()) {
String objectClassName = (String) values.nextElement();
PluggableEditor editor = getEditor(objectClassName);
if (editor != null) {
if (editor.isUnique()) return editor;
}
}
return null;
} catch (Exception e) {
log.log(Level.FINE, "Unable to find unique pluggable editor: ", e);
return null;
}
}
// create from a dataset
public ObsBean(Structure obs, StructureData sdata) {
// first choice
for (Variable v : obs.getVariables()) {
Attribute att = v.findAttribute("BUFR:TableB_descriptor");
if (att == null) continue;
String val = att.getStringValue();
if (val.equals("0-5-1") && Double.isNaN(lat)) {
lat = sdata.convertScalarDouble(v.getShortName());
} else if (val.equals("0-6-1") && Double.isNaN(lon)) {
lon = sdata.convertScalarDouble(v.getShortName());
} else if (val.equals("0-7-30") && Double.isNaN(alt)) {
alt = sdata.convertScalarDouble(v.getShortName());
} else if (val.equals("0-4-1") && (year < 0)) {
year = sdata.convertScalarInt(v.getShortName());
} else if (val.equals("0-4-2") && (month < 0)) {
month = sdata.convertScalarInt(v.getShortName());
} else if (val.equals("0-4-3") && (day < 0)) {
day = sdata.convertScalarInt(v.getShortName());
} else if (val.equals("0-4-4") && (hour < 0)) {
hour = sdata.convertScalarInt(v.getShortName());
} else if (val.equals("0-4-5") && (minute < 0)) {
minute = sdata.convertScalarInt(v.getShortName());
} else if (val.equals("0-4-6") && (sec < 0)) {
sec = sdata.convertScalarInt(v.getShortName());
} else if (val.equals("0-1-1") && (wmo_block < 0)) {
wmo_block = sdata.convertScalarInt(v.getShortName());
} else if (val.equals("0-1-2") && (wmo_id < 0)) {
wmo_id = sdata.convertScalarInt(v.getShortName());
} else if ((stn == null)
&& (val.equals("0-1-7")
|| val.equals("0-1-194")
|| val.equals("0-1-11")
|| val.equals("0-1-18"))) {
if (v.getDataType().isString()) stn = sdata.getScalarString(v.getShortName());
else stn = Integer.toString(sdata.convertScalarInt(v.getShortName()));
}
}
// second choice
for (Variable v : obs.getVariables()) {
Attribute att = v.findAttribute("BUFR:TableB_descriptor");
if (att == null) continue;
String val = att.getStringValue();
if (val.equals("0-5-2") && Double.isNaN(lat)) {
lat = sdata.convertScalarDouble(v.getShortName());
} else if (val.equals("0-6-2") && Double.isNaN(lon)) {
lon = sdata.convertScalarDouble(v.getShortName());
} else if (val.equals("0-7-1") && Double.isNaN(alt)) {
alt = sdata.convertScalarDouble(v.getShortName());
} else if ((val.equals("0-4-7")) && (sec < 0)) {
sec = sdata.convertScalarInt(v.getShortName());
}
}
// third choice
for (Variable v : obs.getVariables()) {
Attribute att = v.findAttribute("BUFR:TableB_descriptor");
if (att == null) continue;
String val = att.getStringValue();
if (val.equals("0-7-10") && Double.isNaN(alt)) {
alt = sdata.convertScalarDouble(v.getShortName());
} else if (val.equals("0-7-2") && Double.isNaN(alt)) {
alt = sdata.convertScalarDouble(v.getShortName());
}
}
}
public String getValue() {
Array value = att.getValues();
return NCdumpW.toString(value, null, null);
}
public String getName() {
return att.getShortName();
}
public String getAbbrev() {
Attribute att = ve.findAttributeIgnoreCase(CDM.ABBREV);
return (att == null) ? null : att.getStringValue();
}
private String getCalendarAttribute(VariableEnhanced vds) {
Attribute cal = vds.findAttribute("calendar");
return (cal == null) ? null : cal.getStringValue();
}
/**
* @param list
* @return a single String value, null if cannot be obtained
*/
private static String getDate(AttributeList list) {
return Attribute.getSingleStringValueOrNull(list, TagFromName.StudyDate);
}
/**
* @param list
* @return a single String value, null if cannot be obtained
*/
private static String getLaterality(AttributeList list) {
return Attribute.getSingleStringValueOrNull(list, TagFromName.ImageLaterality);
}
/**
* @param filenames
* @exception Exception if internal error
*/
public void loadMultiPanelFromSpecifiedFiles(String filenames[]) throws Exception {
int nFiles = filenames.length;
SingleImagePanel imagePanels[] = new SingleImagePanel[nFiles];
String orientations[][] = new String[nFiles][];
String views[] = new String[nFiles];
String lateralityViewAndModifiers[] = new String[nFiles];
String lateralities[] = new String[nFiles];
int widths[] = new int[nFiles];
int heights[] = new int[nFiles];
PixelSpacing spacing[] = new PixelSpacing[nFiles];
String rowOrientations[] = new String[nFiles];
String columnOrientations[] = new String[nFiles];
HashMap eventContexts = new HashMap();
double maximumHorizontalExtentInMm = 0;
double maximumVerticalExtentInMm = 0;
StructuredReport sr[] = new StructuredReport[nFiles];
int nImages = 0;
int nCAD = 0;
ClassLoader classLoader = Thread.currentThread().getContextClassLoader();
for (int f = 0; f < nFiles; ++f) {
try {
String filename = filenames[f];
DicomInputStream distream = null;
InputStream in = classLoader.getResourceAsStream(filename);
if (in != null) {
distream = new DicomInputStream(in);
} else {
distream = new DicomInputStream(new File(filename));
}
AttributeList list = new AttributeList();
list.read(distream);
if (list.isImage()) {
int i = nImages++;
System.err.println("IMAGE [" + i + "] is file " + f + " (" + filenames[f] + ")");
orientations[i] = getPatientOrientation(list);
// System.err.println("IMAGE ["+i+"] orientation="+(orientations[i] == null &&
// orientations[i].length == 2 ? "" : (orientations[i][0] + " " + orientations[i][1])));
views[i] = getView(list);
// System.err.println("IMAGE ["+i+"] view="+views[i]);
lateralityViewAndModifiers[i] = getImageLateralityViewModifierAndViewModifier(list);
// System.err.println("IMAGE ["+i+"]
// lateralityViewAndModifiers="+lateralityViewAndModifiers[i]);
// System.err.println("File "+filenames[f]+": "+lateralityViewAndModifiers[i]);
lateralities[i] = getLaterality(list);
// System.err.println("IMAGE ["+i+"] laterality="+lateralities[i]);
spacing[i] = new PixelSpacing(list);
// System.err.println("IMAGE ["+i+"] spacing="+spacing[i]);
SourceImage sImg = new SourceImage(list);
BufferedImage img = sImg.getBufferedImage();
widths[i] = sImg.getWidth();
heights[i] = sImg.getHeight();
boolean shareVOIEventsInStudy =
false; // does not seem to work anyway, since adding VOITransform to panel constructor
// :(
EventContext eventContext = new EventContext(Integer.toString(i));
SingleImagePanel imagePanel = makeNewImagePanel(sImg, eventContext);
imagePanel.setDemographicAndTechniqueAnnotations(
new DemographicAndTechniqueAnnotations(list),
"SansSerif",
Font.PLAIN,
10,
Color.pink);
imagePanel.setOrientationAnnotations(
new OrientationAnnotations(rowOrientations[i], columnOrientations[i]),
"SansSerif",
Font.PLAIN,
20,
Color.pink);
imagePanel.setPixelSpacingInSourceImage(
spacing[i].getSpacing(), spacing[i].getDescription());
if (Attribute.getSingleStringValueOrEmptyString(list, TagFromName.VOILUTFunction)
.equals("SIGMOID")) {
imagePanel.setVOIFunctionToLogistic();
}
imagePanels[i] = imagePanel;
} else {
throw new DicomException("Unsupported SOP Class in file " + filenames[f]);
}
} catch (Exception e) { // FileNotFoundException,IOException,DicomException
e.printStackTrace(System.err);
}
}
// int imagesPerRow = nImages; // i.e., 1 -> 1, 2 -> 1, 4 -> 4, 5 -> 4, 8 -> 4
// int imagesPerCol = 1;
int imagesPerRow = nImages >= 8 ? 8 : nImages; // i.e., 1 -> 1, 2 -> 1, 4 -> 4, 5 -> 4, 8 -> 4
int imagesPerCol =
(nImages - 1) / imagesPerRow + 1; // i.e., 1 -> 1, 2 -> 2, 4 -> 1, 5 -> 2, 8 -> 2
int singleWidth = frameWidth / imagesPerRow;
int singleHeight = frameHeight / imagesPerCol;
if (nImages == 1 && singleWidth > singleHeight) {
singleWidth =
singleWidth / 2; // use only half the screen for a single view and a landscape monitor
}
for (int i = 0; i < nImages; ++i) {
DisplayedAreaSelection displayedAreaSelection = null;
displayedAreaSelection =
new DisplayedAreaSelection(
widths[i],
heights[i],
0,
0,
widths[i],
heights[i],
true, // in case spacing was not supplied
0,
0,
0,
0,
0,
false /*crop*/);
imagePanels[i].setDisplayedAreaSelection(displayedAreaSelection);
imagePanels[i].setPreTransformImageRelativeCoordinates(null);
}
SingleImagePanel.deconstructAllSingleImagePanelsInContainer(multiPanel);
multiPanel.removeAll();
multiPanel.setLayout(new GridLayout(imagesPerCol, imagesPerRow));
multiPanel.setBackground(Color.black);
for (int x = 0; x < imagesPerCol; ++x) {
for (int y = 0; y < imagesPerRow; ++y) {
int i = x * imagesPerRow + y;
if (i < nImages) {
imagePanels[i].setPreferredSize(new Dimension(singleWidth, singleHeight));
multiPanel.add(imagePanels[i]);
}
}
}
frame.getContentPane().validate();
frame.getContentPane().repaint();
}
/**
* Clear out all the old editors, and get new editors corresponding to the new object classes.
*
* @param entry the entry to be displayed by all the editors
* @param ds the datasource the editors may use for more info
* @param ocs the object classes (in order) to find editors for.
*/
protected void setEditors(DXEntry entry, DataBrokerQueryInterface ds, Vector ocs) {
try {
clearPluggableEditors(); // clear all extra editors
// search for unique structural editors...
if ("false".equalsIgnoreCase(JXConfig.getProperty("plugins.ignoreUniqueness"))) {
if (ocs == null) // TE: may happen if virtual entry.
return;
int size = ocs.size();
for (int i = 0; i < size; i++) {
Object objectClass = ocs.get(i);
if (objectClass != null) {
PluggableEditor ed = getEditor(objectClass.toString());
if (ed != null && ed.isUnique() == true) // found a unique editor
{ // so clear old ones,
addUniqueEditor(ed); // and use the unique one
refreshEditors(entry, ds); // to display the data
setCurrentEditor(ed);
return; // ... and exit.
}
}
}
} else log.warning("skipping uniqueness test for pluggable editors");
boolean newEdSet = false;
// search for non-unique structural editors
for (int i = 0; i < ocs.size(); i++) {
Object objectClass = ocs.get(i);
if (objectClass != null) {
PluggableEditor ed = getEditor(objectClass.toString());
if (ed != null) {
addEditor(ed);
// Force the displayed editor to be the first pluggable one...
if (newEdSet == false) {
setCurrentEditor(ed);
newEdSet = true;
}
}
}
}
// search for non-structural editors
try {
Attribute allOCs = entry.getAllObjectClasses();
if (allOCs != null) {
Enumeration vals = allOCs.getAll();
while (vals.hasMoreElements()) {
Object oc = vals.nextElement();
if (oc != null) {
String ocName = oc.toString();
if (ocs.contains(ocName)
== false) // don't bother with struct objectclasses dealt with above
{
PluggableEditor ed = getEditor(ocName);
if (ed != null) {
addEditor(ed);
if (ed.isUnique()) // a special service to users...
log.warning(
"WARNING: Illegal unique editor defined for oc: "
+ ocName
+ " not allowed - (oc not in primary structural inheritance chain)");
}
}
}
}
}
} catch (NamingException e) {
log.log(
Level.WARNING,
"WARNING: non-fatal exception getting object classes for plugin editors. ",
e);
}
addEditor(templateDisplay); // and always add old faithfulls...
// XXX
if (entry.getStatus() != DXEntry.NEW) // well, almost always...
addEditor(tableDisplay);
} catch (Exception e) {
log.warning("Unexpected Exception in AttributeDisplay\n" + e);
e.printStackTrace();
}
}