/** Sets up the GUI (panels, buttons, etc) and displays it on the screen. */
  private void init() {
    DecimalFormat df;
    int xUnits;
    String unitStr;
    String distStr;
    setForeground(Color.black);
    setTitle("Center Distances version 2  07/14/08");

    df = new DecimalFormat("0.000E0");

    GridBagConstraints gbc = new GridBagConstraints();
    int yPos = 0;
    gbc.gridwidth = 1;
    gbc.gridheight = 1;
    gbc.anchor = GridBagConstraints.WEST;
    gbc.weightx = 1;
    gbc.insets = new Insets(3, 3, 3, 3);
    gbc.fill = GridBagConstraints.HORIZONTAL;
    gbc.gridx = 0;
    gbc.gridy = yPos++;

    JPanel mainPanel = new JPanel(new GridBagLayout());
    mainPanel.setForeground(Color.black);
    mainPanel.setBorder(buildTitledBorder("Input parameters"));

    blueMinLabel = new JLabel("Minimum number of blue pixels per nucleus");
    blueMinLabel.setForeground(Color.black);
    blueMinLabel.setFont(serif12);
    gbc.gridx = 0;
    gbc.gridy = yPos;
    mainPanel.add(blueMinLabel, gbc);

    blueMinText = new JTextField(5);
    if (image.getNDims() == 2) {
      blueMinText.setText("1000");
    } else {
      blueMinText.setText("20000");
    }
    blueMinText.setFont(serif12);
    gbc.gridx = 1;
    gbc.gridy = yPos++;
    mainPanel.add(blueMinText, gbc);

    redMinLabel = new JLabel("Minimum red pixel count");
    redMinLabel.setForeground(Color.black);
    redMinLabel.setFont(serif12);
    gbc.gridx = 0;
    gbc.gridy = yPos;
    mainPanel.add(redMinLabel, gbc);

    redMinText = new JTextField(5);
    redMinText.setText("50");
    redMinText.setFont(serif12);
    gbc.gridx = 1;
    gbc.gridy = yPos++;
    mainPanel.add(redMinText, gbc);

    redFractionLabel = new JLabel("Fraction of red pixels to consider");
    redFractionLabel.setForeground(Color.black);
    redFractionLabel.setFont(serif12);
    gbc.gridx = 0;
    gbc.gridy = yPos;
    mainPanel.add(redFractionLabel, gbc);

    redFractionText = new JTextField(5);
    redFractionText.setText("0.15");
    redFractionText.setFont(serif12);
    gbc.gridx = 1;
    gbc.gridy = yPos++;
    mainPanel.add(redFractionText, gbc);

    xUnits = image.getFileInfo(0).getUnitsOfMeasure()[0];
    if (xUnits != Unit.UNKNOWN_MEASURE.getLegacyNum()) {
      unitStr = (Unit.getUnitFromLegacyNum(xUnits)).toString();
      greenMergingLabel = new JLabel("Green merging radius around peak (" + unitStr + ")");
    } else {
      greenMergingLabel = new JLabel("Green merging radius around peak");
    }
    greenMergingLabel.setForeground(Color.black);
    greenMergingLabel.setFont(serif12);
    gbc.gridx = 0;
    gbc.gridy = yPos;
    mainPanel.add(greenMergingLabel, gbc);

    if (image.getNDims() == 2) {
      // mergingDistance = 8.0f * image.getFileInfo(0).getResolutions()[0];
      mergingDistance = 0.0f;
    } else {
      // mergingDistance = 4.0f * image.getFileInfo(0).getResolutions()[0];
      mergingDistance = 0.0f;
    }
    distStr = df.format(mergingDistance);
    greenMergingText = new JTextField(10);
    greenMergingText.setText(distStr);
    greenMergingText.setFont(serif12);
    gbc.gridx = 1;
    gbc.gridy = yPos++;
    mainPanel.add(greenMergingText, gbc);

    greenMinLabel = new JLabel("Minimum green pixel count");
    greenMinLabel.setForeground(Color.black);
    greenMinLabel.setFont(serif12);
    gbc.gridx = 0;
    gbc.gridy = yPos;
    mainPanel.add(greenMinLabel, gbc);

    greenMinText = new JTextField(5);
    greenMinText.setText("10");
    greenMinText.setFont(serif12);
    gbc.gridx = 1;
    gbc.gridy = yPos++;
    mainPanel.add(greenMinText, gbc);

    greenFractionLabel = new JLabel("Fraction of green pixels to consider");
    greenFractionLabel.setForeground(Color.black);
    greenFractionLabel.setFont(serif12);
    gbc.gridx = 0;
    gbc.gridy = yPos;
    mainPanel.add(greenFractionLabel, gbc);

    greenFractionText = new JTextField(5);
    greenFractionText.setText("0.01");
    greenFractionText.setFont(serif12);
    gbc.gridx = 1;
    gbc.gridy = yPos++;
    mainPanel.add(greenFractionText, gbc);

    greenRegionsLabel = new JLabel("Green regions per cell");
    greenRegionsLabel.setForeground(Color.black);
    greenRegionsLabel.setFont(serif12);
    gbc.gridx = 0;
    gbc.gridy = yPos;
    mainPanel.add(greenRegionsLabel, gbc);

    JPanel buttonPanel = new JPanel(new GridBagLayout());

    greenGroup = new ButtonGroup();

    oneButton = new JRadioButton("1", false);
    oneButton.setForeground(Color.black);
    oneButton.setFont(serif12);
    greenGroup.add(oneButton);
    gbc.gridx = 0;
    gbc.gridy = 0;
    buttonPanel.add(oneButton, gbc);

    twoButton = new JRadioButton("2", true);
    twoButton.setForeground(Color.black);
    twoButton.setFont(serif12);
    greenGroup.add(twoButton);
    gbc.gridx = 1;
    gbc.gridy = 0;
    buttonPanel.add(twoButton, gbc);

    threeButton = new JRadioButton("3", false);
    threeButton.setForeground(Color.black);
    threeButton.setFont(serif12);
    greenGroup.add(threeButton);
    gbc.gridx = 2;
    gbc.gridy = 0;
    buttonPanel.add(threeButton, gbc);

    fourButton = new JRadioButton("4", false);
    fourButton.setForeground(Color.black);
    fourButton.setFont(serif12);
    greenGroup.add(fourButton);
    gbc.gridx = 3;
    gbc.gridy = 0;
    buttonPanel.add(fourButton, gbc);

    gbc.gridx = 1;
    gbc.gridy = yPos++;
    mainPanel.add(buttonPanel, gbc);

    twoBox = new JCheckBox("Use 2 top gray levels in green segmentation", true);
    twoBox.setForeground(Color.black);
    twoBox.setFont(serif12);
    gbc.gridx = 0;
    gbc.gridy = yPos++;
    mainPanel.add(twoBox, gbc);

    blueValueLabel =
        new JLabel("Fraction of blue transition from image min to max at nucleus boundary");
    blueValueLabel.setForeground(Color.black);
    blueValueLabel.setFont(serif12);
    gbc.gridx = 0;
    gbc.gridy = yPos;
    mainPanel.add(blueValueLabel, gbc);

    blueValueText = new JTextField(5);
    blueValueText.setText("0.15");
    blueValueText.setFont(serif12);
    gbc.gridx = 1;
    gbc.gridy = yPos++;
    mainPanel.add(blueValueText, gbc);

    blueSmoothBox = new JCheckBox("Smooth blue VOI contours with AlgorithmBSmooth", true);
    blueSmoothBox.setForeground(Color.black);
    blueSmoothBox.setFont(serif12);
    blueSmoothBox.addActionListener(this);
    gbc.gridx = 0;
    gbc.gridy = yPos++;
    mainPanel.add(blueSmoothBox, gbc);

    interpolationLabel = new JLabel("Number of interpolation points determined by divisor (> 1.0)");
    interpolationLabel.setForeground(Color.black);
    interpolationLabel.setFont(serif12);
    gbc.gridx = 0;
    gbc.gridy = yPos;
    mainPanel.add(interpolationLabel, gbc);

    interpolationText = new JTextField(5);
    interpolationText.setText("24.0");
    interpolationText.setFont(serif12);
    gbc.gridx = 1;
    gbc.gridy = yPos++;
    mainPanel.add(interpolationText, gbc);

    getContentPane().add(mainPanel, BorderLayout.CENTER);
    getContentPane().add(buildButtons(), BorderLayout.SOUTH);

    pack();
    setVisible(true);
    setResizable(false);
    System.gc();
  } // end init()
Пример #2
0
  /**
   * This function produces a new image that has been concatenated. Two 2D-images become one 3D
   * image.
   */
  private void cat2D_2D_3D() {

    int length;
    int xDim, yDim;
    int i;
    float[] buffer;
    int cFactor = 1;
    float[] resols = new float[3];
    FileInfoBase[] fileInfo = null;
    FileInfoDicom[] fileInfoDicom = null;

    try {
      resols = new float[3];
      xDim = srcImage1.getExtents()[0];
      yDim = srcImage1.getExtents()[1];

      if (srcImage1.isColorImage()) {
        cFactor = 4;
      }

      length = cFactor * xDim * yDim;
      buffer = new float[length];
      srcImage1.exportData(0, length, buffer);
      destImage.importData(0, buffer, false);
      srcImage2.exportData(0, length, buffer);
      destImage.importData(buffer.length, buffer, true);
    } catch (IOException error) {
      buffer = null;
      destImage.disposeLocal(); // Clean up memory of result image
      destImage = null;
      errorCleanUp("Algorithm Concat. Images: Image(s) locked", true);

      return;
    } catch (OutOfMemoryError e) {
      buffer = null;
      destImage.disposeLocal(); // Clean up memory of result image
      destImage = null;
      errorCleanUp("Algorithm Concat. Images: Out of memory", true);

      return;
    }

    resols[0] = srcImage1.getFileInfo()[0].getResolutions()[0];
    resols[1] = srcImage1.getFileInfo()[0].getResolutions()[1];
    resols[2] = 1;

    if ((srcImage1.getFileInfo()[0] instanceof FileInfoDicom)
        && (srcImage2.getFileInfo()[0] instanceof FileInfoDicom)) {
      fileInfoDicom = new FileInfoDicom[destImage.getExtents()[2]];
      fileInfoDicom[0] = (FileInfoDicom) (((FileInfoDicom) srcImage1.getFileInfo()[0]).clone());
      fileInfoDicom[1] = (FileInfoDicom) (((FileInfoDicom) srcImage2.getFileInfo()[0]).clone());
      destImage.setFileInfo(fileInfoDicom);
    } else {
      fileInfo = destImage.getFileInfo();

      for (i = 0; (i < destImage.getExtents()[2]) && !threadStopped; i++) {
        fileInfo[i].setModality(srcImage1.getFileInfo()[0].getModality());
        fileInfo[i].setFileDirectory(srcImage1.getFileInfo()[0].getFileDirectory());
        fileInfo[i].setEndianess(srcImage1.getFileInfo()[0].getEndianess());
        fileInfo[i].setUnitsOfMeasure(srcImage1.getFileInfo()[0].getUnitsOfMeasure());
        fileInfo[i].setResolutions(resols);
        fileInfo[i].setExtents(destImage.getExtents());
        fileInfo[i].setMax(destImage.getMax());
        fileInfo[i].setMin(destImage.getMin());
        fileInfo[i].setImageOrientation(srcImage1.getImageOrientation());
        fileInfo[i].setPixelPadValue(srcImage1.getFileInfo()[0].getPixelPadValue());
        fileInfo[i].setPhotometric(srcImage1.getFileInfo()[0].getPhotometric());
        fileInfo[i].setAxisOrientation(srcImage1.getAxisOrientation());
      }

      if (srcImage1.getFileInfo()[0] instanceof FileInfoImageXML) {

        if (((FileInfoImageXML) srcImage1.getFileInfo()[0]).getPSetHashtable() != null) {
          ((FileInfoImageXML) fileInfo[0])
              .setPSetHashtable(((FileInfoImageXML) srcImage1.getFileInfo()[0]).getPSetHashtable());
        }
      }

      if (srcImage2.getFileInfo()[0] instanceof FileInfoImageXML) {

        if (((FileInfoImageXML) srcImage2.getFileInfo()[0]).getPSetHashtable() != null) {
          ((FileInfoImageXML) fileInfo[1])
              .setPSetHashtable(((FileInfoImageXML) srcImage2.getFileInfo()[0]).getPSetHashtable());
        }
      }
    }

    if (threadStopped) {
      buffer = null;
      finalize();

      return;
    }

    setCompleted(true);

    fileInfo = null;
    fileInfoDicom = null;
  }
Пример #3
0
  /** cat. */
  private void cat3D_4D_4D() {

    int length;
    int xDim, yDim;
    float[] buffer;
    int cFactor = 1;
    int i, j;
    float[] resols = new float[3];
    float[] origins = new float[3];
    FileInfoBase[] fileInfo = null;
    FileInfoDicom[] fileInfoDicom = null;
    int srcALength, srcBLength;

    try {
      fireProgressStateChanged(srcImage1.getImageName(), "Concatenating images ...");
      resols = new float[4];
      origins = new float[4];
      xDim = srcImage1.getExtents()[0];
      yDim = srcImage1.getExtents()[1];

      if (srcImage1.isColorImage()) {
        cFactor = 4;
      }

      length = cFactor * xDim * yDim;
      buffer = new float[length];

      int nImages;

      if (srcImage1.getNDims() > srcImage2.getNDims()) {
        nImages =
            (srcImage1.getExtents()[2] * srcImage1.getExtents()[3]) + srcImage2.getExtents()[2];

        for (i = 0;
            (i < (srcImage1.getExtents()[2] * srcImage1.getExtents()[3])) && !threadStopped;
            i++) {
          fireProgressStateChanged(Math.round((float) (i) / (nImages - 1) * 100));

          srcImage1.exportData(i * length, length, buffer);
          destImage.importData(i * length, buffer, false);
        }

        if (threadStopped) {
          buffer = null;
          finalize();

          return;
        }

        for (j = 0; (j < srcImage2.getExtents()[2]) && !threadStopped; j++) {
          fireProgressStateChanged(Math.round((float) (i + j) / (nImages - 1) * 100));

          srcImage2.exportData(j * length, length, buffer);
          destImage.importData((i + j) * length, buffer, false);
        }

        if (threadStopped) {
          buffer = null;
          finalize();

          return;
        }

        destImage.calcMinMax();
      } else {
        nImages =
            (srcImage2.getExtents()[2] * srcImage2.getExtents()[3]) + srcImage1.getExtents()[2];

        for (j = 0; (j < srcImage1.getExtents()[2]) && !threadStopped; j++) {
          fireProgressStateChanged(Math.round((float) (j) / (nImages - 1) * 100));

          srcImage1.exportData(j * length, length, buffer);
          destImage.importData(j * length, buffer, false);
        }

        if (threadStopped) {
          buffer = null;
          finalize();

          return;
        }

        for (i = 0;
            (i < (srcImage2.getExtents()[2] * srcImage2.getExtents()[3])) && !threadStopped;
            i++) {
          fireProgressStateChanged(Math.round((float) (i + j) / (nImages - 1) * 100));

          srcImage2.exportData(i * buffer.length, length, buffer);
          destImage.importData((i + j) * buffer.length, buffer, false);
        }

        if (threadStopped) {
          buffer = null;
          finalize();

          return;
        }

        destImage.calcMinMax();
      }
    } catch (IOException error) {
      buffer = null;
      destImage.disposeLocal(); // Clean up memory of result image
      destImage = null;
      errorCleanUp("Algorithm Concat. Images: Image(s) locked", true);

      return;
    } catch (OutOfMemoryError e) {
      buffer = null;
      destImage.disposeLocal(); // Clean up memory of result image
      destImage = null;
      errorCleanUp("Algorithm Concat. Images: Out of memory", true);

      return;
    }

    resols[0] = srcImage1.getFileInfo()[0].getResolutions()[0];
    resols[1] = srcImage1.getFileInfo()[0].getResolutions()[1];
    resols[2] = srcImage1.getFileInfo()[0].getResolutions()[2];
    resols[3] = srcImage1.getFileInfo()[0].getResolutions()[3];
    origins[0] = srcImage1.getFileInfo()[0].getOrigin()[0];
    origins[1] = srcImage1.getFileInfo()[0].getOrigin()[1];
    origins[2] = srcImage1.getFileInfo()[0].getOrigin()[2];
    origins[3] = srcImage1.getFileInfo()[0].getOrigin()[3];

    if ((srcImage1.getFileInfo()[0] instanceof FileInfoDicom)
        && (srcImage2.getFileInfo()[0] instanceof FileInfoDicom)) {
      fileInfoDicom = new FileInfoDicom[destImage.getExtents()[2] * destImage.getExtents()[3]];

      if (srcImage1.getNDims() > srcImage2.getNDims()) {
        srcALength = srcImage1.getExtents()[2] * srcImage1.getExtents()[3];

        for (i = 0; (i < srcALength) && !threadStopped; i++) {
          fileInfoDicom[i] = (FileInfoDicom) (((FileInfoDicom) srcImage1.getFileInfo()[i]).clone());
          fileInfoDicom[i].setOrigin(origins);
        }

        for (i = 0; (i < srcImage2.getExtents()[2]) && !threadStopped; i++) {
          fileInfoDicom[srcALength + i] =
              (FileInfoDicom) (((FileInfoDicom) srcImage2.getFileInfo()[i]).clone());
          fileInfoDicom[srcALength + i].setOrigin(origins);
        }
      } else {
        srcBLength = srcImage2.getExtents()[2] * srcImage2.getExtents()[3];

        for (i = 0; (i < srcImage1.getExtents()[2]) && !threadStopped; i++) {
          fileInfoDicom[i] = (FileInfoDicom) (((FileInfoDicom) srcImage1.getFileInfo()[i]).clone());
          fileInfoDicom[i].setOrigin(origins);
        }

        for (i = 0; (i < srcBLength) && !threadStopped; i++) {
          fileInfoDicom[srcImage1.getExtents()[2] + i] =
              (FileInfoDicom) (((FileInfoDicom) srcImage2.getFileInfo()[i]).clone());
          fileInfoDicom[srcImage1.getExtents()[2] + i].setOrigin(origins);
        }
      }

      destImage.setFileInfo(fileInfoDicom);
    } else {
      fileInfo = destImage.getFileInfo();

      for (i = 0;
          (i < (destImage.getExtents()[2] * destImage.getExtents()[3])) && !threadStopped;
          i++) {
        fileInfo[i].setModality(srcImage1.getFileInfo()[0].getModality());
        fileInfo[i].setFileDirectory(srcImage1.getFileInfo()[0].getFileDirectory());
        fileInfo[i].setEndianess(srcImage1.getFileInfo()[0].getEndianess());
        fileInfo[i].setUnitsOfMeasure(srcImage1.getFileInfo()[0].getUnitsOfMeasure());
        fileInfo[i].setResolutions(resols);
        fileInfo[i].setExtents(destImage.getExtents());
        fileInfo[i].setMax(destImage.getMax());
        fileInfo[i].setMin(destImage.getMin());
        fileInfo[i].setImageOrientation(srcImage1.getImageOrientation());
        fileInfo[i].setPixelPadValue(srcImage1.getFileInfo()[0].getPixelPadValue());
        fileInfo[i].setPhotometric(srcImage1.getFileInfo()[0].getPhotometric());
        fileInfo[i].setAxisOrientation(srcImage1.getAxisOrientation());
      }

      if (srcImage1.getFileInfo()[0] instanceof FileInfoImageXML) {

        if (srcImage1.getNDims() > srcImage2.getNDims()) {
          srcALength = srcImage1.getExtents()[2] * srcImage1.getExtents()[3];

          for (i = 0; (i < srcALength) && !threadStopped; i++) {

            if (((FileInfoImageXML) srcImage1.getFileInfo()[i]).getPSetHashtable() != null) {
              ((FileInfoImageXML) fileInfo[i])
                  .setPSetHashtable(
                      ((FileInfoImageXML) srcImage1.getFileInfo()[i]).getPSetHashtable());
            }
          }
        } else {

          for (i = 0; (i < srcImage1.getExtents()[2]) && !threadStopped; i++) {

            if (((FileInfoImageXML) srcImage1.getFileInfo()[i]).getPSetHashtable() != null) {
              ((FileInfoImageXML) fileInfo[i])
                  .setPSetHashtable(
                      ((FileInfoImageXML) srcImage1.getFileInfo()[i]).getPSetHashtable());
            }
          }
        }
      }

      if (srcImage2.getFileInfo()[0] instanceof FileInfoImageXML) {

        if (srcImage1.getNDims() > srcImage2.getNDims()) {
          srcALength = srcImage1.getExtents()[2] * srcImage1.getExtents()[3];

          for (i = 0; (i < srcImage2.getExtents()[2]) && !threadStopped; i++) {

            if (((FileInfoImageXML) srcImage2.getFileInfo()[i]).getPSetHashtable() != null) {
              ((FileInfoImageXML) fileInfo[srcALength + i])
                  .setPSetHashtable(
                      ((FileInfoImageXML) srcImage2.getFileInfo()[i]).getPSetHashtable());
            }
          }

        } else {
          srcBLength = srcImage2.getExtents()[2] * srcImage2.getExtents()[3];

          for (i = 0; (i < srcBLength) && !threadStopped; i++) {

            if (((FileInfoImageXML) srcImage2.getFileInfo()[i]).getPSetHashtable() != null) {
              ((FileInfoImageXML) fileInfo[srcImage1.getExtents()[2] + i])
                  .setPSetHashtable(
                      ((FileInfoImageXML) srcImage2.getFileInfo()[i]).getPSetHashtable());
            }
          }
        }
      }
    }

    if (threadStopped) {
      buffer = null;
      finalize();

      return;
    }

    setCompleted(true);
    fileInfo = null;
    fileInfoDicom = null;
  }
Пример #4
0
  /** Sets up the GUI (panels, buttons, etc) and displays it on the screen. */
  private void init() {
    if (image.getFileInfo(0).getFileFormat() == FileUtility.DICOM) {
      FileInfoDicom dicomInfo = (FileInfoDicom) image.getFileInfo(0);
      FileDicomTagTable tagTable = dicomInfo.getTagTable();
      if (tagTable.getValue("0018,1310") != null) {
        // Acquisition matrix
        FileDicomTag tag = tagTable.get(new FileDicomKey("0018,1310"));
        Object[] values = tag.getValueList();
        int valNumber = values.length;
        if ((valNumber == 4) && (values instanceof Short[])) {
          int frequencyRows = ((Short) values[0]).intValue();
          Preferences.debug("frequencyRows = " + frequencyRows + "\n");
          int frequencyColumns = ((Short) values[1]).intValue();
          Preferences.debug("frequencyColumns = " + frequencyColumns + "\n");
          int phaseRows = ((Short) values[2]).intValue();
          Preferences.debug("phaseRows = " + phaseRows + "\n");
          int phaseColumns = ((Short) values[3]).intValue();
          Preferences.debug("phaseColumns = " + phaseColumns + "\n");
          if ((frequencyRows > 0) && (phaseRows == 0)) {
            subYDim = frequencyRows;
          } else if ((frequencyRows == 0) && (phaseRows > 0)) {
            subYDim = phaseRows;
          }
          if ((frequencyColumns > 0) && (phaseColumns == 0)) {
            subXDim = frequencyColumns;
          } else if ((frequencyColumns == 0) && (phaseColumns > 0)) {
            subXDim = phaseColumns;
          }
        }
      } // if (tagTable.getValue("0018,1310") != null)
      if (tagTable.getValue("0019,100A") != null) {
        FileDicomTag tag = tagTable.get(new FileDicomKey("0019,100A"));
        Object value = tag.getValue(false);
        if (value instanceof Short) {
          numberOfImagesInMosaic = ((Short) value).intValue();
          Preferences.debug("Number of images in mosaic = " + numberOfImagesInMosaic + "\n");
        }
      } // if (tagTable.getValue("0019,100A") != null)
    } // if (image.getFileInfo(0).getFileFormat() == FileUtility.DICOM)*/
    setForeground(Color.black);
    setTitle("Mosaic To 3D Volume");

    JPanel inputPanel = new JPanel(new GridBagLayout());
    inputPanel.setForeground(Color.black);

    inputPanel.setBorder(buildTitledBorder("Image"));

    JLabel labelUse = new JLabel("Image:");
    labelUse.setForeground(Color.black);
    labelUse.setFont(serif12);

    JLabel labelImage = new JLabel(image.getImageName());
    labelImage.setForeground(Color.black);
    labelImage.setFont(serif12);

    GridBagConstraints gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = 0;
    gbc.gridheight = 1;
    gbc.gridwidth = 1;
    gbc.anchor = GridBagConstraints.WEST;
    gbc.weightx = 1;
    gbc.insets = new Insets(5, 5, 5, 5);
    inputPanel.add(labelUse, gbc);
    gbc.gridx = 1;
    gbc.fill = GridBagConstraints.HORIZONTAL;
    inputPanel.add(labelImage, gbc);

    JPanel dimensionPanel = new JPanel(new GridBagLayout());
    dimensionPanel.setForeground(Color.black);
    dimensionPanel.setBorder(buildTitledBorder("X and Y Dimensions of Result"));

    JLabel labelXDim = new JLabel("X dimension of slices");
    labelXDim.setForeground(Color.black);
    labelXDim.setFont(serif12);

    textXDim = new JTextField(10);
    if (subXDim != 0) {
      textXDim.setText(String.valueOf(subXDim));
    }
    textXDim.setFont(serif12);
    textXDim.setForeground(Color.black);

    JLabel labelYDim = new JLabel("Y dimension of slices");
    labelYDim.setForeground(Color.black);
    labelYDim.setFont(serif12);

    textYDim = new JTextField(10);
    if (subYDim != 0) {
      textYDim.setText(String.valueOf(subYDim));
    }
    textYDim.setFont(serif12);
    textYDim.setForeground(Color.black);

    JLabel labelNumberImages = new JLabel("Number of images in mosaic");
    labelNumberImages.setForeground(Color.black);
    labelNumberImages.setFont(serif12);

    textNumberImages = new JTextField(10);
    if (numberOfImagesInMosaic != 0) {
      textNumberImages.setText(String.valueOf(numberOfImagesInMosaic));
    }
    textNumberImages.setFont(serif12);
    textNumberImages.setForeground(Color.black);

    gbc.gridx = 0;
    gbc.gridy = 0;
    dimensionPanel.add(labelXDim, gbc);
    gbc.gridx = 1;
    dimensionPanel.add(textXDim, gbc);
    gbc.gridx = 0;
    gbc.gridy = 1;
    dimensionPanel.add(labelYDim, gbc);
    gbc.gridx = 1;
    dimensionPanel.add(textYDim, gbc);
    gbc.gridx = 0;
    gbc.gridy = 2;
    dimensionPanel.add(labelNumberImages, gbc);
    gbc.gridx = 1;
    dimensionPanel.add(textNumberImages, gbc);

    JPanel mainPanel = new JPanel(new BorderLayout());
    mainPanel.add(inputPanel, BorderLayout.NORTH);
    mainPanel.add(dimensionPanel, BorderLayout.CENTER);
    mainPanel.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));

    JPanel buttonPanel = new JPanel();
    buttonPanel.add(buildButtons());

    getContentPane().add(mainPanel);
    getContentPane().add(buttonPanel, BorderLayout.SOUTH);
    pack();
    setVisible(true);
  }