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);
        }
      }
    }
  }
Example #4
0
 public String getValue() {
   Array value = att.getValues();
   try {
     return NCdumpW.printArray(value, null, null);
   } catch (IOException e) {
     return e.getMessage();
   }
 }
Example #5
0
 /**
  * @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);
 }
Example #10
0
 public String getName() {
   return att.getShortName();
 }
Example #11
0
 public String getAbbrev() {
   Attribute att = ve.findAttributeIgnoreCase(CDM.ABBREV);
   return (att == null) ? null : att.getStringValue();
 }
Example #12
0
 private String getCalendarAttribute(VariableEnhanced vds) {
   Attribute cal = vds.findAttribute("calendar");
   return (cal == null) ? null : cal.getStringValue();
 }
Example #13
0
 /**
  * @param list
  * @return a single String value, null if cannot be obtained
  */
 private static String getDate(AttributeList list) {
   return Attribute.getSingleStringValueOrNull(list, TagFromName.StudyDate);
 }
Example #14
0
 /**
  * @param list
  * @return a single String value, null if cannot be obtained
  */
 private static String getLaterality(AttributeList list) {
   return Attribute.getSingleStringValueOrNull(list, TagFromName.ImageLaterality);
 }
Example #15
0
  /**
   * @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();
    }
  }