/** Loads the default settings from Preferences to set up the dialog. */
public void legacyLoadDefaults() {
String defaultsString = Preferences.getDialogDefaults(getDialogName());
if ((defaultsString != null) && (newImage != null)) {
try {
StringTokenizer st = new StringTokenizer(defaultsString, ",");
textSearchWindowSide.setText("" + MipavUtil.getInt(st));
textSimilarityWindowSide.setText("" + MipavUtil.getInt(st));
textNoiseStandardDeviation.setText("" + MipavUtil.getFloat(st));
textDegree.setText("" + MipavUtil.getFloat(st));
doRician = MipavUtil.getBoolean(st);
doRicianCheckBox.setSelected(doRician);
textDegree.setEnabled(doRician);
labelDegree.setEnabled(doRician);
image25DCheckBox.setSelected(MipavUtil.getBoolean(st));
if (MipavUtil.getBoolean(st)) {
newImage.setSelected(true);
} else {
replaceImage.setSelected(true);
}
} catch (Exception ex) {
// since there was a problem parsing the defaults string, start over with the original
// defaults
Preferences.debug("Resetting defaults for dialog: " + getDialogName());
Preferences.removeProperty(getDialogName());
}
}
}
/**
* Returns the name of an image output by this algorithm, the image returned depends on the
* parameter label given (which can be used to retrieve the image object from the image registry).
*
* @param imageParamName The output image parameter label for which to get the image name.
* @return The image name of the requested output image parameter label.
*/
public String getOutputImageName(final String imageParamName) {
if (imageParamName.equals(AlgorithmParameters.RESULT_IMAGE)) {
return getResultImage().getImageName();
}
Preferences.debug(
"Unrecognized output image parameter: " + imageParamName + "\n",
Preferences.DEBUG_SCRIPTING);
return null;
}
/**
* Returns the name of an image output by this algorithm, the image returned depends on the
* parameter label given (which can be used to retrieve the image object from the image registry).
*
* @param imageParamName The output image parameter label for which to get the image name.
* @return The image name of the requested output image parameter label.
*/
public String getOutputImageName(final String imageParamName) {
if (imageParamName.equals(AlgorithmParameters.RESULT_IMAGE)) {
if (getResultImage() != null) {
// algo produced a new result image
return getResultImage().getImageName();
} else {
// algo was done in place
return image.getImageName();
}
}
Preferences.debug(
"Unrecognized output image parameter: " + imageParamName + "\n",
Preferences.DEBUG_SCRIPTING);
return null;
}
/**
* The top level rendering call. This function calls beforeResampleAll, resampleAll, and
* mapIntermediateToFinal, all virtual functions that are implemented in derived classes.
*
* @param iDS The number of slices to increment during the resampling phase. The value should be
* one or larger. If one, all slices of the volume data are resampled. If two, only every
* other slice is resampled. An input larger than one is used to allow fast rendering during
* rotation of the volume data. Once the rotation terminates, a composite with input of one
* should be called.
*/
public synchronized void composite(int iDS) {
long startTime = 0, now = 0;
double elapsedTime = 0d;
// compute maximum component of the box direction vector
float fMax = 0.0f;
int i, iMax = -1;
for (i = 0; i < 3; i++) {
float fAbs = Math.abs(m_aafBox[2][i]);
if (fAbs > fMax) {
fMax = fAbs;
iMax = i;
}
}
startTime = System.currentTimeMillis();
traceInit();
// composite in the appropriate direction
if (iMax == 0) {
beforeResampleAll(1, 2, 0);
} else if (iMax == 1) {
beforeResampleAll(2, 0, 1);
} else {
beforeResampleAll(0, 1, 2);
}
resampleAll(iDS);
mapIntermediateToFinal();
now = System.currentTimeMillis();
elapsedTime = (double) (now - startTime);
if (elapsedTime <= 0) {
elapsedTime = (double) 0.0;
}
Preferences.debug(
"Shear elapse time = " + (double) (elapsedTime / 1000.0) + "\n"); // in seconds
}
/** 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);
}