@Override
protected Product doInBackground(com.bc.ceres.core.ProgressMonitor pm) throws Exception {
final TargetProductSelectorModel model = getTargetProductSelector().getModel();
pm.beginTask("Writing...", model.isOpenInAppSelected() ? 100 : 95);
ProgressMonitorList.instance().add(pm); // NESTMOD
saveTime = 0L;
Product product = null;
try {
// free cache // NESTMOD
JAI.getDefaultInstance().getTileCache().flush();
System.gc();
executeStartTime = Calendar.getInstance().getTime();
long t0 = System.currentTimeMillis();
Operator operator = null;
if (targetProduct.getProductReader() instanceof OperatorProductReader) {
final OperatorProductReader opReader =
(OperatorProductReader) targetProduct.getProductReader();
if (opReader.getOperatorContext().getOperator() instanceof Output) {
operator = opReader.getOperatorContext().getOperator();
}
}
if (operator == null) {
WriteOp writeOp =
new WriteOp(targetProduct, model.getProductFile(), model.getFormatName());
writeOp.setDeleteOutputOnFailure(true);
writeOp.setWriteEntireTileRows(true);
writeOp.setClearCacheAfterRowWrite(false);
operator = writeOp;
}
final OperatorExecutor executor = OperatorExecutor.create(operator);
executor.execute(SubProgressMonitor.create(pm, 95));
saveTime = System.currentTimeMillis() - t0;
File targetFile = model.getProductFile();
if (model.isOpenInAppSelected() && targetFile.exists()) {
product = ProductIO.readProduct(targetFile);
if (product == null) {
product = targetProduct; // todo - check - this cannot be ok!!! (nf)
}
pm.worked(5);
}
} finally {
// free cache
JAI.getDefaultInstance().getTileCache().flush();
System.gc();
pm.done();
ProgressMonitorList.instance().remove(pm); // NESTMOD
if (product != targetProduct) {
targetProduct.dispose();
}
}
return product;
}
public void mouseClicked(MouseEvent e) {
int x = e.getX();
int y = e.getY();
int currentTabIndex = -1;
int tabCount = tabPane.getTabCount();
for (int i = 0; i < tabCount; i++) {
if (rects[i].contains(x, y)) {
currentTabIndex = i;
break;
} // if contains
} // for i
if (currentTabIndex >= 0) {
Rectangle tabRect = rects[currentTabIndex];
x = x - tabRect.x;
y = y - tabRect.y;
if ((x >= 5) && (x <= 15) && (y >= 5) && (y <= 15)) {
try {
tabbedPane.remove(currentTabIndex);
} catch (Exception ex) {
ex.printStackTrace();
}
} // if
} // if currentTabIndex >= 0
System.gc();
} // mouseClicked
public static void printImage(final Image image) {
ImageHandler imh = new ImageHandler();
imh.printImage(image, null);
System.gc();
}
public static void printComponent(final java.awt.print.Printable p) {
ImageHandler imh = new ImageHandler();
imh.printComponent(p, null);
System.gc();
}
public static void assertTiming(
String message, long expected, int attempts, @NotNull Runnable actionToMeasure) {
while (true) {
attempts--;
long duration = measure(actionToMeasure);
try {
assertTiming(message, expected, duration);
break;
} catch (AssertionFailedError e) {
if (attempts == 0) throw e;
System.gc();
System.gc();
System.gc();
String s = "Another epic fail (remaining attempts: " + attempts + "): " + e.getMessage();
TeamCityLogger.warning(s, null);
System.err.println(s);
}
}
}
public static void main(String[] args) {
System.gc();
// Schedule a job for the event-dispatching thread:
// creating and showing this application's GUI.
javax.swing.SwingUtilities.invokeLater(
new Runnable() {
public void run() {
createAndShowGUI();
}
});
} // end of main
public void update(GameEvent e) {
this.m_map = e.getMap();
if (e.getState() == Snake.DEAD) {
int respond = JOptionPane.showConfirmDialog(this, "Snake is DEAD!!\nPlay again?");
if (respond == JOptionPane.OK_OPTION) {
this.m_isBegin = true;
this.m_body = new GameBody(this, this.m_map, 125);
System.gc();
} else if (respond == JOptionPane.CANCEL_OPTION || respond == JOptionPane.NO_OPTION) {
System.exit(0);
}
}
this.repaint();
}
// Static main program for executing a test of the class.
public static void main(String args[]) {
// Define int variables.
int width = 0;
int height = 0;
// If arguments are greater than zero.
if (args.length > 0) {
// If arguments are two.
if (args.length >= 2) {
// Use try block to parse for an integer.
try {
// Verify first argument is an integer.
width = Integer.parseInt(args[0]);
height = Integer.parseInt(args[1]);
// Define a default instance of JMessagingFrame.
JMessagingFrame f = new JMessagingFrame(width, height);
} // Catch parsing failure exception.
catch (NumberFormatException e) {
// Print default runtime message.
System.out.println("If you are testing the override constructor,");
System.out.println("then you need to provide two integer values.");
} // End try-catch block on integer parse.
} // End of if two arguments provided.
else // When there are less than or more than two arguments.
{
// Print default runtime message.
System.out.println("If you are testing the override constructor,");
System.out.println("then you need to provide two integer values.");
} // End of else when there are less than or more than two arguments.
} // End of else when there are two arguments.
else // No arguments provided.
{
// Define a default instance of JMessagingFrame.
JMessagingFrame f = new JMessagingFrame();
// Clean-up by signaling the garbage collector.
System.gc();
} // End of else when no arguments are provided.
} // End of static main.
/**
* This method represents the application code that we'd like to run on a separate thread. It
* simulates slowly computing a value, in this case just a string 'All Done'. It updates the
* progress bar every half second to remind the user that we're still busy.
*/
Object doWork() {
try {
if (Thread.interrupted()) {
throw new InterruptedException();
}
while (!this.state.terminator.isTerminated(this.state.optimizer.getPopulation())) {
if (Thread.interrupted()) {
throw new InterruptedException();
}
this.state.optimizer.optimize();
}
System.gc();
} catch (InterruptedException e) {
updateStatus("Interrupted", 0);
return "Interrupted";
}
updateStatus("All Done", 0);
return "All Done";
}
/**
* This method represents the application code that we'd like to run on a separate thread. It
* simulates slowly computing a value, in this case just a string 'All Done'. It updates the
* progress bar every half second to remind the user that we're still busy.
*/
public Object doWork() {
try {
this.optimizationParameters.saveInstance();
if (this.show) {
this.statusField.setText("Optimizing...");
}
RNG.setRandomSeed(optimizationParameters.getRandomSeed());
// opening output file...
if (!this.outputFileName.equalsIgnoreCase("none")) {
String name = "";
SimpleDateFormat formatter = new SimpleDateFormat("E'_'yyyy.MM.dd'_'HH.mm.ss");
String startDate = formatter.format(new Date());
name =
this.outputPath
+ this.outputFileName
+ "_"
+ this.experimentName
+ "_"
+ startDate
+ ".dat";
try {
this.outputFile = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(name)));
} catch (FileNotFoundException e) {
System.out.println("Could not open output file! Filename: " + name);
}
} else {
this.outputFile = null;
}
// initialize problem
this.optimizationParameters.getProblem().initializeProblem();
this.optimizationParameters
.getOptimizer()
.setProblem(this.optimizationParameters.getProblem());
// int optimizer and population
// this.optimizationParameters.getOptimizer().initialize();
// initialize the log data
ArrayList tmpMultiRun = new ArrayList();
this.performedRuns.add(tmpMultiRun);
// something to log file
// if (outputFile != null)
// this.writeToFile(this.optimizationParameters.getOptimizer().getStringRepresentation());
// this.writeToFile("Here i'll write something characterizing the algorithm.");
for (int j = 0; j < this.multiRuns; j++) {
this.optimizationParameters
.getProblem()
.initializeProblem(); // in the loop as well, dynamic probs may need that (MK)
this.tmpData = new ArrayList<>();
this.currentRun = j;
if (this.show) {
this.statusField.setText(
"Optimizing Run " + (j + 1) + " of " + this.multiRuns + " Multi Runs...");
}
if (Thread.interrupted()) {
throw new InterruptedException();
}
// write header to file
this.writeToFile(
" FitnessCalls\t Best\t Mean\t Worst \t"
+ BeanInspector.toString(
this.optimizationParameters.getProblem().getAdditionalDataHeader(),
'\t',
false,
""));
if ((this.continueFlag) && (this.backupPopulation != null)) {
this.recentFunctionCalls += this.backupPopulation.getFunctionCalls();
this.optimizationParameters.getOptimizer().getProblem().initializeProblem();
this.optimizationParameters.getOptimizer().addPopulationChangedEventListener(null);
this.optimizationParameters.getOptimizer().setPopulation(this.backupPopulation);
this.optimizationParameters
.getOptimizer()
.getProblem()
.evaluate(this.optimizationParameters.getOptimizer().getPopulation());
this.optimizationParameters
.getOptimizer()
.getProblem()
.evaluate(this.optimizationParameters.getOptimizer().getPopulation().getArchive());
this.optimizationParameters
.getOptimizer()
.initializeByPopulation(this.backupPopulation, false);
this.optimizationParameters.getOptimizer().getPopulation().setFunctionCalls(0);
this.optimizationParameters.addPopulationChangedEventListener(this);
} else {
this.recentFunctionCalls = 0;
this.optimizationParameters.getOptimizer().initialize();
}
// while (this.optimizationParameters.getOptimizer().getPopulation().getFunctionCalls() <
// this.functionCalls) {
while (!this.optimizationParameters
.getTerminator()
.isTerminated(this.optimizationParameters.getOptimizer().getPopulation())) {
// System.out.println("Simulated Function calls "+
// this.optimizer.getPopulation().getFunctionCalls());
if (Thread.interrupted()) {
throw new InterruptedException();
}
optimizationParameters.getOptimizer().optimize();
}
System.gc();
// @TODO if you want the final report include this
// this.writeToFile(this.optimizationParameters.getProblem().getStringRepresentationForProblem(this.optimizationParameters.getOptimizer()));
tmpMultiRun.add(this.tmpData);
}
if (this.show) {
this.plot.setInfoString(this.currentExperiment, this.experimentName, 0.5f);
}
if (this.show) {
this.draw();
}
this.experimentName =
this.optimizationParameters.getOptimizer().getName() + "-" + this.performedRuns.size();
} catch (InterruptedException e) {
updateStatus(0);
if (this.show) {
this.statusField.setText("Interrupted...");
}
return "Interrupted";
}
if (this.outputFile != null) {
try {
this.outputFile.close();
} catch (IOException e) {
System.out.println("Failed to close output file!");
}
}
if (this.show) {
for (int i = 0; i < this.multiRuns; i++) {
this.plot.clearGraph(1000 + i);
}
}
updateStatus(0);
if (this.show) {
this.statusField.setText("Finished...");
}
return "All Done";
}
private void execute() {
gResult.clear();
String sCmd = null;
if (4096 <= ifHuge.length()) {
sCmd = ifHuge;
} else {
sCmd = txtCommand.getText();
}
if (sCmd.startsWith("-->>>TEST<<<--")) {
testPerformance();
return;
}
String g[] = new String[1];
try {
lTime = System.currentTimeMillis();
sStatement.execute(sCmd);
int r = sStatement.getUpdateCount();
if (r == -1) {
formatResultSet(sStatement.getResultSet());
} else {
g[0] = "update count";
gResult.setHead(g);
g[0] = "" + r;
gResult.addRow(g);
}
lTime = System.currentTimeMillis() - lTime;
addToRecent(txtCommand.getText());
gResult.fireTableChanged(null);
} catch (SQLException e) {
lTime = System.currentTimeMillis() - lTime;
g[0] = "SQL Error";
gResult.setHead(g);
String s = e.getMessage();
s += " / Error Code: " + e.getErrorCode();
s += " / State: " + e.getSQLState();
g[0] = s;
gResult.addRow(g);
gResult.fireTableChanged(null);
}
updateResult();
System.gc();
}
/**
* This method is required if the AlgorithmPerformed interface is implemented. It is called by the
* algorithms when it has completed or failed to to complete, so that the dialog can be display
* the result image and/or clean up.
*
* @param algorithm Algorithm that caused the event.
*/
public void algorithmPerformed(AlgorithmBase algorithm) {
ViewJFrameImage imageFrame = null;
if (algorithm instanceof AlgorithmMosaicToSlices) {
if ((mathAlgo.isCompleted() == true) && (mathAlgo.getResultImage() != null)) {
// The algorithm has completed and produced a new image to be displayed.
if (displayLoc == NEW) {
try {
resultImage = mathAlgo.getResultImage();
new ViewJFrameImage(resultImage, null, new Dimension(610, 200));
} catch (OutOfMemoryError error) {
System.gc();
MipavUtil.displayError("Out of memory: unable to open new frame");
}
} else {
// These next lines set the titles in all frames where the source image is displayed to
// image name so as to indicate that the image is now unlocked!
// The image frames are enabled and then registed to the userinterface.
resultImage = mathAlgo.getResultImage();
Vector<ViewImageUpdateInterface> imageFrames = image.getImageFrameVector();
for (int i = 0; i < imageFrames.size(); i++) {
((Frame) (imageFrames.elementAt(i))).setTitle(titles[i]);
((Frame) (imageFrames.elementAt(i))).setEnabled(true);
if ((((Frame) (imageFrames.elementAt(i))) != parentFrame) && (parentFrame != null)) {
userInterface.registerFrame((Frame) (imageFrames.elementAt(i)));
}
}
Point pt;
if (parentFrame != null) {
pt = ((ViewJFrameBase) parentFrame).getLocation();
} else {
pt =
new Point(
Toolkit.getDefaultToolkit().getScreenSize().width / 2,
Toolkit.getDefaultToolkit().getScreenSize().height / 2);
}
imageFrame = new ViewJFrameImage(resultImage, null, new Dimension(pt.x, pt.y));
if (parentFrame != null) {
((ViewJFrameBase) parentFrame).close();
} else {
((ViewJFrameBase) image.getParentFrame()).close();
}
// Not so sure about this.
if (image.getLightBoxFrame() != null) {
try {
pt = image.getLightBoxFrame().getLocation();
image.getLightBoxFrame().close();
new ViewJFrameLightBox(
imageFrame,
"LightBox",
resultImage,
imageFrame.getComponentImage().getLUTa(),
imageFrame.getComponentImage().getImageB(),
imageFrame.getComponentImage().getLUTb(),
imageFrame.getComponentImage().getResolutionX(),
imageFrame.getComponentImage().getResolutionY(),
new Dimension(pt.x, pt.y),
imageFrame.getControls(),
imageFrame.getVOIManager());
} catch (OutOfMemoryError error) {
MipavUtil.displayError("Out of memory: unable to open new frame");
}
}
}
} else if (resultImage == null) {
// These next lines set the titles in all frames where the source image is displayed to
// image name so as to indicate that the image is now unlocked!
// The image frames are enabled and then registered to the userinterface.
/*Vector imageFrames = imageA.getImageFrameVector();
for (int i = 0; i < imageFrames.size(); i++) {
((Frame) (imageFrames.elementAt(i))).setTitle(titles[i]);
((Frame) (imageFrames.elementAt(i))).setEnabled(true);
if (((Frame) (imageFrames.elementAt(i))) != parentFrame) {
userInterface.registerFrame((Frame) (imageFrames.elementAt(i)));
}
}*/
if (parentFrame != null) {
userInterface.registerFrame(parentFrame);
}
image.notifyImageDisplayListeners(null, true);
} else if (resultImage != null) {
// algorithm failed but result image still has garbage
resultImage.disposeLocal(); // clean up memory
System.gc();
}
}
if (algorithm.isCompleted()) {
insertScriptLine();
}
mathAlgo.finalize();
mathAlgo = null;
dispose();
}
/**
* Use the GUI results to set up the variables needed to run the algorithm.
*
* @return <code>true</code> if parameters set successfully, <code>false</code> otherwise.
*/
private boolean setVariables() {
String tmpStr;
System.gc();
if (replaceImage.isSelected()) {
displayLoc = REPLACE;
} else if (newImage.isSelected()) {
displayLoc = NEW;
}
tmpStr = textSearchWindowSide.getText();
if (testParameter(tmpStr, 5, 101)) {
searchWindowSide = Integer.valueOf(tmpStr).intValue();
} else {
MipavUtil.displayError("Search window side must be between 5 and 101");
textSearchWindowSide.requestFocus();
textSearchWindowSide.selectAll();
return false;
}
if ((searchWindowSide % 2) == 0) {
MipavUtil.displayError("Search window side must be an odd number");
textSearchWindowSide.requestFocus();
textSearchWindowSide.selectAll();
return false;
}
tmpStr = textSimilarityWindowSide.getText();
if (testParameter(tmpStr, 3, 99)) {
similarityWindowSide = Integer.valueOf(tmpStr).intValue();
} else {
MipavUtil.displayError("Similarity window side must be between 3 and 99");
textSimilarityWindowSide.requestFocus();
textSimilarityWindowSide.selectAll();
return false;
}
if ((similarityWindowSide % 2) == 0) {
MipavUtil.displayError("Similarity window side must be an odd number");
textSimilarityWindowSide.requestFocus();
textSimilarityWindowSide.selectAll();
return false;
}
if (similarityWindowSide >= searchWindowSide) {
MipavUtil.displayError("Similarity window side must be less than search window side");
textSimilarityWindowSide.requestFocus();
textSimilarityWindowSide.selectAll();
return false;
}
tmpStr = textNoiseStandardDeviation.getText();
if (testParameter(tmpStr, 0.001, 1000.0)) {
noiseStandardDeviation = Float.valueOf(tmpStr).floatValue();
} else {
MipavUtil.displayError("Radius must be between 0.001 and 1000.0");
textNoiseStandardDeviation.requestFocus();
textNoiseStandardDeviation.selectAll();
return false;
}
doRician = doRicianCheckBox.isSelected();
if (doRician) {
tmpStr = textDegree.getText();
if (testParameter(tmpStr, 1.0, 10.0)) {
degreeOfFiltering = Float.valueOf(tmpStr).floatValue();
} else {
MipavUtil.displayError("Degree of filtering must be between 1.0 and 10.0");
textDegree.requestFocus();
textDegree.selectAll();
}
}
if (image.getNDims() > 2) {
image25D = image25DCheckBox.isSelected();
}
return true;
}
/**
* Initializes the GUI by creating the components, placing them in the dialog, and displaying
* them.
*/
private void init() {
setForeground(Color.black);
setTitle("Nonlocal Means Filter");
JPanel mainPanel;
mainPanel = new JPanel();
mainPanel.setBorder(BorderFactory.createEmptyBorder(3, 3, 3, 3));
mainPanel.setLayout(new GridBagLayout());
GridBagConstraints gbc = new GridBagConstraints();
gbc.gridwidth = 1;
gbc.gridheight = 1;
gbc.anchor = GridBagConstraints.WEST;
gbc.weightx = 1;
gbc.insets = new Insets(3, 3, 3, 3);
gbc.gridx = 0;
gbc.gridy = 0;
gbc.fill = GridBagConstraints.HORIZONTAL;
paramPanel = new JPanel(new GridBagLayout());
paramPanel.setForeground(Color.black);
paramPanel.setBorder(buildTitledBorder("Parameters"));
mainPanel.add(paramPanel, gbc);
GridBagConstraints gbc2 = new GridBagConstraints();
gbc2.gridwidth = 1;
gbc2.gridheight = 1;
gbc2.anchor = GridBagConstraints.WEST;
gbc2.weightx = 1;
gbc2.insets = new Insets(3, 3, 3, 3);
gbc2.gridx = 0;
gbc2.gridy = 0;
gbc2.fill = GridBagConstraints.HORIZONTAL;
labelSearchWindowSide = createLabel("Search window side (odd)");
paramPanel.add(labelSearchWindowSide, gbc2);
gbc2.gridx = 1;
textSearchWindowSide = createTextField("15");
paramPanel.add(textSearchWindowSide, gbc2);
gbc2.gridx = 0;
gbc2.gridy = 1;
labelSimilarityWindowSide = createLabel("Similarity window side (odd) ");
paramPanel.add(labelSimilarityWindowSide, gbc2);
gbc2.gridx = 1;
textSimilarityWindowSide = createTextField("7");
paramPanel.add(textSimilarityWindowSide, gbc2);
gbc2.gridx = 0;
gbc2.gridy = 2;
labelNoiseStandardDeviation = createLabel("Noise standard deviation ");
paramPanel.add(labelNoiseStandardDeviation, gbc2);
gbc2.gridx = 1;
textNoiseStandardDeviation = createTextField("10.0");
paramPanel.add(textNoiseStandardDeviation, gbc2);
gbc2.gridx = 0;
gbc2.gridy = 3;
labelDegree = createLabel("Degree of filtering ");
labelDegree.setEnabled(doRician);
paramPanel.add(labelDegree, gbc2);
gbc2.gridx = 1;
textDegree = createTextField("1.414");
textDegree.setEnabled(doRician);
paramPanel.add(textDegree, gbc2);
gbc2.gridx = 0;
gbc2.gridy = 4;
doRicianCheckBox = new JCheckBox("Deal with Rician noise in MRI");
doRicianCheckBox.setFont(serif12);
doRicianCheckBox.setSelected(false);
doRicianCheckBox.addActionListener(this);
paramPanel.add(doRicianCheckBox, gbc2);
if (image.getNDims() > 2) {
gbc2.gridx = 0;
gbc2.gridy = 5;
gbc2.gridwidth = 2;
image25DCheckBox = new JCheckBox("Process each slice independently (2.5D)");
image25DCheckBox.setFont(serif12);
paramPanel.add(image25DCheckBox, gbc2);
image25DCheckBox.setSelected(false);
} // if (image.getNDims > 2)
JPanel outputOptPanel = new JPanel(new GridLayout(1, 2));
destinationPanel = new JPanel(new BorderLayout());
destinationPanel.setForeground(Color.black);
destinationPanel.setBorder(buildTitledBorder("Destination"));
outputOptPanel.add(destinationPanel);
destinationGroup = new ButtonGroup();
newImage = new JRadioButton("New image", true);
newImage.setBounds(10, 16, 120, 25);
newImage.setFont(serif12);
destinationGroup.add(newImage);
destinationPanel.add(newImage, BorderLayout.NORTH);
replaceImage = new JRadioButton("Replace image", false);
replaceImage.setFont(serif12);
destinationGroup.add(replaceImage);
destinationPanel.add(replaceImage, BorderLayout.CENTER);
// Only if the image is unlocked can it be replaced.
if (image.getLockStatus() == ModelStorageBase.UNLOCKED) {
replaceImage.setEnabled(true);
} else {
replaceImage.setEnabled(false);
}
gbc.gridx = 0;
gbc.gridy = 1;
mainPanel.add(outputOptPanel, gbc);
mainDialogPanel.add(mainPanel, BorderLayout.CENTER);
mainDialogPanel.add(buildButtons(), BorderLayout.SOUTH);
getContentPane().add(mainDialogPanel);
pack();
setResizable(true);
// setVisible(true);
System.gc();
}
/**
* Once all the necessary variables are set, call the Concat algorithm based on what type of image
* this is and whether or not there is a separate destination image.
*/
protected void callAlgorithm() {
int destExtents[] = new int[3];
ModelImage destImage = null;
destExtents[0] = subXDim;
destExtents[1] = subYDim;
destExtents[2] = numberOfImagesInMosaic;
destImage =
new ModelImage(
image.getType(), destExtents, makeImageName(image.getImageName(), "_mosaic_to_slices"));
try {
// Make algorithm
mathAlgo = new AlgorithmMosaicToSlices(image, destImage);
// This is very important. Adding this object as a listener allows the algorithm to
// notify this object when it has completed of failed. See algorithm performed event.
// This is made possible by implementing AlgorithmedPerformed interface
mathAlgo.addListener(this);
createProgressBar(image.getImageName(), mathAlgo);
// Hide dialog
setVisible(false);
if (displayLoc == REPLACE) {
// These next lines set the titles in all frames where the source image is displayed to
// "locked - " image name so as to indicate that the image is now read/write locked!
// The image frames are disabled and then unregisted from the userinterface until the
// algorithm has completed.
Vector<ViewImageUpdateInterface> imageFrames = image.getImageFrameVector();
titles = new String[imageFrames.size()];
for (int i = 0; i < imageFrames.size(); i++) {
titles[i] = ((Frame) (imageFrames.elementAt(i))).getTitle();
((Frame) (imageFrames.elementAt(i))).setTitle("Locked: " + titles[i]);
((Frame) (imageFrames.elementAt(i))).setEnabled(false);
userInterface.unregisterFrame((Frame) (imageFrames.elementAt(i)));
}
}
if (isRunInSeparateThread()) {
// Start the thread as a low priority because we wish to still have user interface work
// fast.
if (mathAlgo.startMethod(Thread.MIN_PRIORITY) == false) {
MipavUtil.displayError("A thread is already running on this object");
}
} else {
mathAlgo.run();
}
} catch (OutOfMemoryError x) {
System.gc();
MipavUtil.displayError("Dialog Concatenation: unable to allocate enough memory");
return;
}
}
protected void process() {
int i, j, len, ch, chunkLength;
long progOff, progLen;
float f1;
// io
AudioFile inF = null;
AudioFile outF = null;
AudioFileDescr inStream;
AudioFileDescr outStream;
FloatFile[] floatF = null;
File tempFile[] = null;
// buffers
float[][] inBuf, outBuf;
float[] win;
float[] convBuf1, convBuf2;
float[] tempFlt;
int inChanNum, inLength, inputStep, outputStep, winSize;
int transLen, skip, inputLen, outputLen, fltLen;
int framesRead, framesWritten;
float warp, a1, b0, b1, x0, x1, y0, y1, b0init;
Param ampRef = new Param(1.0, Param.ABS_AMP); // transform-Referenz
Param peakGain;
float gain = 1.0f; // gain abs amp
float maxAmp = 0.0f;
PathField ggOutput;
topLevel:
try {
// ---- open input, output ----
// input
inF = AudioFile.openAsRead(new File(pr.text[PR_INPUTFILE]));
inStream = inF.getDescr();
inChanNum = inStream.channels;
inLength = (int) inStream.length;
// this helps to prevent errors from empty files!
if ((inLength * inChanNum) < 1) throw new EOFException(ERR_EMPTY);
// .... check running ....
if (!threadRunning) break topLevel;
// output
ggOutput = (PathField) gui.getItemObj(GG_OUTPUTFILE);
if (ggOutput == null) throw new IOException(ERR_MISSINGPROP);
outStream = new AudioFileDescr(inStream);
ggOutput.fillStream(outStream);
outF = AudioFile.openAsWrite(outStream);
// .... check running ....
if (!threadRunning) break topLevel;
// ---- parameter inits ----
warp =
Math.max(-0.98f, Math.min(0.98f, (float) (pr.para[PR_WARP].val / 100))); // DAFx2000 'b'
f1 = (1.0f - warp) / (1.0f + warp); // DAFx2000 (25)
winSize = 32 << pr.intg[PR_FRAMESIZE]; // DAFx2000 'N'
j = winSize >> 1;
transLen = (int) (f1 * winSize + 0.5f); // DAFx2000 'P' (26)
i = pr.intg[PR_OVERLAP] + 1;
while (((float) transLen / (float) i) > j) i++;
inputStep = (int) (((float) transLen / (float) i) + 0.5f); // DAFx2000 'L'
fltLen = Math.max(winSize, transLen);
// System.out.println( "inputStep "+inputStep+"; winSize "+winSize+"; transLen "+transLen+";
// fltLen "+fltLen+"; warp "+warp+"; � "+f1 );
win = Filter.createFullWindow(winSize, Filter.WIN_HANNING); // DAFx2000 (27)
outputStep = inputStep;
b0init = (float) Math.sqrt(1.0f - warp * warp);
progOff = 0;
progLen = (long) inLength * (2 + inChanNum); // + winSize;
tempFlt = new float[fltLen];
inputLen = winSize + inputStep;
inBuf = new float[inChanNum][inputLen];
outputLen = transLen + outputStep;
outBuf = new float[inChanNum][outputLen];
// normalization requires temp files
if (pr.intg[PR_GAINTYPE] == GAIN_UNITY) {
tempFile = new File[inChanNum];
floatF = new FloatFile[inChanNum];
for (ch = 0; ch < inChanNum; ch++) { // first zero them because an exception might be thrown
tempFile[ch] = null;
floatF[ch] = null;
}
for (ch = 0; ch < inChanNum; ch++) {
tempFile[ch] = IOUtil.createTempFile();
floatF[ch] = new FloatFile(tempFile[ch], GenericFile.MODE_OUTPUT);
}
progLen += (long) inLength;
} else {
gain = (float) ((Param.transform(pr.para[PR_GAIN], Param.ABS_AMP, ampRef, null)).val);
}
// .... check running ....
if (!threadRunning) break topLevel;
// ----==================== the real stuff ====================----
framesRead = 0;
framesWritten = 0;
skip = 0;
while (threadRunning && (framesWritten < inLength)) {
chunkLength = Math.min(inputLen, inLength - framesRead + skip);
// ---- read input chunk ----
len = Math.max(0, chunkLength - skip);
inF.readFrames(inBuf, skip, len);
framesRead += len;
progOff += len;
// off += len;
// .... progress ....
setProgression((float) progOff / (float) progLen);
// .... check running ....
if (!threadRunning) break topLevel;
// zero padding
if (chunkLength < inputLen) {
for (ch = 0; ch < inChanNum; ch++) {
convBuf1 = inBuf[ch];
for (i = chunkLength; i < convBuf1.length; i++) {
convBuf1[i] = 0.0f;
}
}
}
for (ch = 0; threadRunning && (ch < inChanNum); ch++) {
convBuf1 = inBuf[ch];
convBuf2 = outBuf[ch];
for (i = 0, j = fltLen; i < winSize; i++) {
tempFlt[--j] = convBuf1[i] * win[i];
}
while (j > 0) {
tempFlt[--j] = 0.0f;
}
a1 = -warp; // inital allpass
b0 = b0init;
b1 = 0.0f;
for (j = 0; j < transLen; j++) {
x1 = 0.0f;
y1 = 0.0f;
// for( i = 0; i < transLen; i++ ) { // DAFx2000 (2 resp. 3)
for (i = 0; i < fltLen; i++) { // DAFx2000 (2 resp. 3)
x0 = tempFlt[i];
y0 = b0 * x0 + b1 * x1 - a1 * y1;
tempFlt[i] = y0; // (work with double precision while computing cascades)
y1 = y0;
x1 = x0;
}
a1 = -warp; // cascaded allpasses
b0 = -warp;
b1 = 1.0f;
convBuf2[j] += (float) y1;
}
// .... progress ....
progOff += chunkLength - skip;
setProgression((float) progOff / (float) progLen);
} // for channels
// .... check running ....
if (!threadRunning) break topLevel;
chunkLength = Math.min(outputStep, inLength - framesWritten);
// ---- write output chunk ----
if (floatF != null) {
for (ch = 0; ch < inChanNum; ch++) {
floatF[ch].writeFloats(outBuf[ch], 0, chunkLength);
}
progOff += chunkLength;
// off += len;
framesWritten += chunkLength;
// .... progress ....
setProgression((float) progOff / (float) progLen);
} else {
for (ch = 0; ch < inChanNum; ch++) {
Util.mult(outBuf[ch], 0, chunkLength, gain);
}
outF.writeFrames(outBuf, 0, chunkLength);
progOff += chunkLength;
// off += len;
framesWritten += chunkLength;
// .... progress ....
setProgression((float) progOff / (float) progLen);
}
// .... check running ....
if (!threadRunning) break topLevel;
// check max amp
for (ch = 0; ch < inChanNum; ch++) {
convBuf1 = outBuf[ch];
for (i = 0; i < chunkLength; i++) {
f1 = Math.abs(convBuf1[i]);
if (f1 > maxAmp) {
maxAmp = f1;
}
}
}
// overlaps
skip = winSize;
for (ch = 0; ch < inChanNum; ch++) {
System.arraycopy(inBuf[ch], inputStep, inBuf[ch], 0, winSize);
convBuf1 = outBuf[ch];
System.arraycopy(convBuf1, outputStep, convBuf1, 0, transLen);
for (i = transLen; i < outputLen; ) {
convBuf1[i++] = 0.0f;
}
}
} // until framesWritten == outLength
// .... check running ....
if (!threadRunning) break topLevel;
// ----==================== normalize output ====================----
if (pr.intg[PR_GAINTYPE] == GAIN_UNITY) {
peakGain = new Param((double) maxAmp, Param.ABS_AMP);
gain =
(float)
(Param.transform(
pr.para[PR_GAIN],
Param.ABS_AMP,
new Param(1.0 / peakGain.val, peakGain.unit),
null))
.val;
normalizeAudioFile(floatF, outF, inBuf, gain, 1.0f);
maxAmp *= gain;
for (ch = 0; ch < inChanNum; ch++) {
floatF[ch].cleanUp();
floatF[ch] = null;
tempFile[ch].delete();
tempFile[ch] = null;
}
}
// .... check running ....
if (!threadRunning) break topLevel;
// ---- Finish ----
outF.close();
outF = null;
outStream = null;
inF.close();
inF = null;
inStream = null;
inBuf = null;
// inform about clipping/ low level
handleClipping(maxAmp);
} catch (IOException e1) {
setError(e1);
} catch (OutOfMemoryError e2) {
inStream = null;
outStream = null;
inBuf = null;
convBuf1 = null;
convBuf2 = null;
System.gc();
setError(new Exception(ERR_MEMORY));
;
}
// ---- cleanup (topLevel) ----
if (inF != null) {
inF.cleanUp();
inF = null;
}
if (outF != null) {
outF.cleanUp();
outF = null;
}
if (floatF != null) {
for (ch = 0; ch < floatF.length; ch++) {
if (floatF[ch] != null) {
floatF[ch].cleanUp();
floatF[ch] = null;
}
if (tempFile[ch] != null) {
tempFile[ch].delete();
tempFile[ch] = null;
}
}
}
} // process()
/** 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()
protected void process() {
int i, j, ch, len, off, chunkLength;
long progOff, progLen;
float f1, f2;
double d1;
boolean extraAudioFile;
// io
AudioFile inF = null;
AudioFile outF = null;
AudioFile envInF = null;
AudioFile envOutF = null;
AudioFileDescr inStream = null;
AudioFileDescr outStream = null;
AudioFileDescr envInStream = null;
AudioFileDescr envOutStream = null;
FloatFile[] outFloatF = null;
FloatFile[] envFloatF = null;
File outTempFile[] = null;
File envTempFile[] = null;
int inChanNum, outChanNum, envInChanNum, envOutChanNum, shapeChanNum;
int[][] shapeChan = null;
int[][] inChan = null;
float[][] shapeChanWeight = null;
float[][] inChanWeight = null;
// buffers
float[][] inBuf = null; // Sound-In
float[][] outBuf = null; // Sound-Out
float[][] inEnvBuf = null; // Envelope of Input
float[][] shapeEnvBuf = null; // Envelope of Shaper
float[][] envInBuf = null; // Direct-In of Shaper-File
float[] convBuf1, convBuf2;
int inLength, outLength, envInLength, envOutLength;
int framesRead, framesWritten; // re sound-files
int framesRead2, framesWritten2; // re env-files
Param ampRef = new Param(1.0, Param.ABS_AMP); // transform-Referenz
Param peakGain;
float gain = 1.0f; // gain abs amp
float envGain = 1.0f; // gain abs amp
float maxAmp = 0.0f;
float envMaxAmp = 0.0f;
float maxChange;
int average, avrOff;
double[] inEnergy, envInEnergy;
PathField ggOutput;
topLevel:
try {
// ---- open input, output; init ----
// input
inF = AudioFile.openAsRead(new File(pr.text[PR_INPUTFILE]));
inStream = inF.getDescr();
inChanNum = inStream.channels;
inLength = (int) inStream.length;
// this helps to prevent errors from empty files!
if ((inLength < 1) || (inChanNum < 1)) throw new EOFException(ERR_EMPTY);
// .... check running ....
if (!threadRunning) break topLevel;
envInLength = 0;
envInChanNum = inChanNum;
shapeChanNum = 0;
// shape input
switch (pr.intg[PR_ENVSOURCE]) {
case SRC_SOUNDFILE:
case SRC_ENVFILE:
envInF = AudioFile.openAsRead(new File(pr.text[PR_ENVINFILE]));
envInStream = envInF.getDescr();
envInChanNum = envInStream.channels;
shapeChanNum = envInChanNum;
envInLength = (int) envInStream.length;
// this helps to prevent errors from empty files!
if ((envInLength < 1) || (envInChanNum < 1)) throw new EOFException(ERR_EMPTY);
i = Math.min(inLength, envInLength);
inLength = i;
envInLength = i;
break;
case SRC_ENV:
if (pr.bool[PR_RIGHTCHAN]) {
shapeChanNum = 2;
envInChanNum = Math.max(envInChanNum, shapeChanNum); // ggf. mono => stereo
} else {
shapeChanNum = 1;
}
break;
case SRC_INPUT:
shapeChanNum = inChanNum;
break;
}
// .... check running ....
if (!threadRunning) break topLevel;
outChanNum = Math.max(inChanNum, envInChanNum);
outLength = inLength;
shapeChan = new int[outChanNum][2];
shapeChanWeight = new float[outChanNum][2];
inChan = new int[outChanNum][2];
inChanWeight = new float[outChanNum][2];
extraAudioFile =
(envInF != null) && (pr.intg[PR_ENVSOURCE] == SRC_SOUNDFILE); // not if SRC_ENVFILE!!!
// calc weights
for (ch = 0; ch < outChanNum; ch++) {
if (shapeChanNum == 1) {
shapeChan[ch][0] = 0;
shapeChan[ch][1] = 0;
shapeChanWeight[ch][0] = 1.0f;
shapeChanWeight[ch][1] = 0.0f;
} else {
f1 = ((float) ch / (float) (outChanNum - 1)) * (float) (shapeChanNum - 1);
shapeChan[ch][0] = (int) f1; // Math.max verhindert ArrayIndex-Fehler
shapeChan[ch][1] = Math.min((int) f1 + 1, shapeChanNum - 1); // (Weight ist dabei eh Null)
f1 %= 1.0f;
shapeChanWeight[ch][0] = 1.0f - f1;
shapeChanWeight[ch][1] = f1;
}
if (inChanNum == 1) {
inChan[ch][0] = 0;
inChan[ch][1] = 0;
inChanWeight[ch][0] = 1.0f;
inChanWeight[ch][1] = 0.0f;
} else {
f1 = ((float) ch / (float) (outChanNum - 1)) * (float) (inChanNum - 1);
inChan[ch][0] = (int) f1;
inChan[ch][1] = Math.min((int) f1 + 1, inChanNum - 1);
f1 %= 1.0f;
inChanWeight[ch][0] = 1.0f - f1;
inChanWeight[ch][1] = f1;
}
/*
for( i = 0; i < 2; i++ ) {
System.out.println( "shapeChan["+ch+"]["+i+"] = "+shapeChan[ch][i] );
System.out.println( "shapeWeig["+ch+"]["+i+"] = "+shapeChanWeight[ch][i] );
System.out.println( "inputChan["+ch+"]["+i+"] = "+inChan[ch][i] );
System.out.println( "inputWeig["+ch+"]["+i+"] = "+inChanWeight[ch][i] );
}
*/
}
// output
ggOutput = (PathField) gui.getItemObj(GG_OUTPUTFILE);
if (ggOutput == null) throw new IOException(ERR_MISSINGPROP);
outStream = new AudioFileDescr(inStream);
ggOutput.fillStream(outStream);
outStream.channels = outChanNum;
outF = AudioFile.openAsWrite(outStream);
// .... check running ....
if (!threadRunning) break topLevel;
envOutLength = 0;
envOutChanNum = 0;
// envelope output
if (pr.bool[PR_ENVOUTPUT]) {
ggOutput = (PathField) gui.getItemObj(GG_ENVOUTFILE);
if (ggOutput == null) throw new IOException(ERR_MISSINGPROP);
envOutStream = new AudioFileDescr(inStream);
ggOutput.fillStream(envOutStream);
envOutStream.file = new File(pr.text[PR_ENVOUTFILE]);
envOutF = AudioFile.openAsWrite(envOutStream);
envOutLength = inLength;
envOutChanNum = inChanNum;
}
// .... check running ....
if (!threadRunning) break topLevel;
// average buffer size
d1 =
Param.transform(
pr.para[PR_AVERAGE],
Param.ABS_MS,
new Param(AudioFileDescr.samplesToMillis(inStream, inLength), Param.ABS_MS),
null)
.val; // average in millis
average = ((int) (AudioFileDescr.millisToSamples(inStream, d1) + 0.5) & ~1) + 1; // always odd
avrOff = (average >> 1) + 1; // first element needed for subtraction (see calcEnv())
progOff = 0;
progLen =
(long) Math.max(average - avrOff, inLength)
+ (long) (extraAudioFile ? Math.max(average - avrOff, envInLength) : envInLength)
+ (long) outLength
+ (long) envOutLength;
// normalization requires temp files
if (pr.intg[PR_GAINTYPE] == GAIN_UNITY) {
outTempFile = new File[outChanNum];
outFloatF = new FloatFile[outChanNum];
for (ch = 0;
ch < outChanNum;
ch++) { // first zero them because an exception might be thrown
outTempFile[ch] = null;
outFloatF[ch] = null;
}
for (ch = 0; ch < outChanNum; ch++) {
outTempFile[ch] = IOUtil.createTempFile();
outFloatF[ch] = new FloatFile(outTempFile[ch], GenericFile.MODE_OUTPUT);
}
progLen += (long) outLength;
} else {
gain = (float) (Param.transform(pr.para[PR_GAIN], Param.ABS_AMP, ampRef, null)).val;
}
// .... check running ....
if (!threadRunning) break topLevel;
// normalization requires temp files
if (pr.intg[PR_ENVGAINTYPE] == GAIN_UNITY) {
envTempFile = new File[envOutChanNum];
envFloatF = new FloatFile[envOutChanNum];
for (ch = 0;
ch < envOutChanNum;
ch++) { // first zero them because an exception might be thrown
envTempFile[ch] = null;
envFloatF[ch] = null;
}
for (ch = 0; ch < envOutChanNum; ch++) {
envTempFile[ch] = IOUtil.createTempFile();
envFloatF[ch] = new FloatFile(envTempFile[ch], GenericFile.MODE_OUTPUT);
}
progLen += (long) envOutLength;
} else {
envGain = (float) (Param.transform(pr.para[PR_ENVGAIN], Param.ABS_AMP, ampRef, null)).val;
}
// .... check running ....
if (!threadRunning) break topLevel;
// ---- further inits ----
maxChange = (float) (Param.transform(pr.para[PR_MAXCHANGE], Param.ABS_AMP, ampRef, null)).val;
inBuf = new float[inChanNum][8192 + average];
Util.clear(inBuf);
outBuf = new float[outChanNum][8192];
Util.clear(outBuf);
if (extraAudioFile) {
envInBuf = new float[envInChanNum][8192 + average];
Util.clear(envInBuf);
}
inEnvBuf = new float[inChanNum][8192]; // = envOutBuf
Util.clear(inEnvBuf);
shapeEnvBuf = new float[envInChanNum][8192];
Util.clear(shapeEnvBuf);
inEnergy = new double[inChanNum];
for (ch = 0; ch < inChanNum; ch++) {
inEnergy[ch] = 0.0;
}
envInEnergy = new double[envInChanNum];
for (ch = 0; ch < envInChanNum; ch++) {
envInEnergy[ch] = 0.0;
}
// System.out.println( "inLength "+inLength+"; envInLength "+envInLength+"; envOutLength
// "+envOutLength+"; outLength "+outLength );
// System.out.println( "average "+average+"; avrOff "+avrOff );
// ----==================== buffer init ====================----
framesRead = 0; // re inF
framesRead2 = 0; // re envInF
// ---- init buffers ----
for (off = avrOff; threadRunning && (off < average); ) {
len = Math.min(inLength - framesRead, Math.min(8192, average - off));
if (len == 0) break;
inF.readFrames(inBuf, off, len);
// calc initial energy per channel (see calcEnv())
for (ch = 0; ch < inChanNum; ch++) {
convBuf1 = inBuf[ch];
d1 = 0.0;
for (i = 0, j = off; i < len; i++) {
f1 = convBuf1[j++];
d1 += f1 * f1;
}
inEnergy[ch] += d1;
}
framesRead += len;
off += len;
progOff += len;
// .... progress ....
setProgression((float) progOff / (float) progLen);
}
// zero padding bereits durch initialisierung mit Util.clear() passiert!
if (extraAudioFile) {
for (off = avrOff; threadRunning && (off < average); ) {
len = Math.min(envInLength - framesRead2, Math.min(8192, average - off));
if (len == 0) break;
envInF.readFrames(envInBuf, off, len);
// calc initial energy per channel (see calcEnv())
for (ch = 0; ch < envInChanNum; ch++) {
convBuf1 = envInBuf[ch];
d1 = 0.0;
for (i = 0, j = off; i < len; i++) {
f1 = convBuf1[j++];
d1 += f1 * f1;
}
envInEnergy[ch] += d1;
}
framesRead2 += len;
off += len;
progOff += len;
// .... progress ....
setProgression((float) progOff / (float) progLen);
}
// zero padding bereits durch initialisierung mit Util.clear() passiert!
}
// .... check running ....
if (!threadRunning) break topLevel;
// ----==================== the real stuff ====================----
framesWritten = 0; // re OutF
framesWritten2 = 0; // re envOutF
while (threadRunning && (framesWritten < outLength)) {
chunkLength = Math.min(8192, outLength - framesWritten);
// ---- read input chunk ----
len = Math.min(inLength - framesRead, chunkLength);
inF.readFrames(inBuf, average, len);
// zero padding
for (ch = 0; ch < inChanNum; ch++) {
convBuf1 = inBuf[ch];
for (i = len, j = len + average; i < chunkLength; i++) {
convBuf1[j++] = 0.0f;
}
}
framesRead += len;
progOff += len;
// .... progress ....
setProgression((float) progOff / (float) progLen);
// .... check running ....
if (!threadRunning) break topLevel;
// ---- read input env chunk ----
if (envInF != null) {
len = Math.min(envInLength - framesRead2, chunkLength);
if (extraAudioFile) { // ........ needs averaging ........
envInF.readFrames(envInBuf, average, len);
// zero padding
for (ch = 0; ch < envInChanNum; ch++) {
convBuf1 = envInBuf[ch];
for (i = len, j = len + average; i < chunkLength; i++) {
convBuf1[j++] = 0.0f;
}
}
} else { // ........ is already env ........
envInF.readFrames(shapeEnvBuf, 0, len);
// zero padding
for (ch = 0; ch < envInChanNum; ch++) {
convBuf1 = shapeEnvBuf[ch];
for (i = len; i < chunkLength; i++) {
convBuf1[i] = 0.0f;
}
}
}
framesRead2 += len;
progOff += len;
// .... progress ....
setProgression((float) progOff / (float) progLen);
}
// .... check running ....
if (!threadRunning) break topLevel;
// ---- calc input envelope ----
for (ch = 0; ch < inChanNum; ch++) {
inEnergy[ch] = calcEnv(inBuf[ch], inEnvBuf[ch], average, chunkLength, inEnergy[ch]);
}
// ---- write output env file ----
if (pr.bool[PR_ENVOUTPUT]) {
if (envFloatF != null) { // i.e. unity gain
for (ch = 0; ch < envOutChanNum; ch++) {
convBuf1 = inEnvBuf[ch];
for (i = 0; i < chunkLength; i++) { // measure max amp
f1 = Math.abs(convBuf1[i]);
if (f1 > envMaxAmp) {
envMaxAmp = f1;
}
}
envFloatF[ch].writeFloats(convBuf1, 0, chunkLength);
}
} else { // i.e. abs gain
for (ch = 0; ch < envOutChanNum; ch++) {
convBuf1 = inEnvBuf[ch];
for (i = 0; i < chunkLength; i++) { // measure max amp + adjust gain
f1 = Math.abs(convBuf1[i]);
convBuf1[i] *= envGain;
if (f1 > envMaxAmp) {
envMaxAmp = f1;
}
}
}
envOutF.writeFrames(inEnvBuf, 0, chunkLength);
}
framesWritten2 += chunkLength;
progOff += chunkLength;
// .... progress ....
setProgression((float) progOff / (float) progLen);
}
// .... check running ....
if (!threadRunning) break topLevel;
// ---- calc shape envelope ----
switch (pr.intg[PR_ENVSOURCE]) {
case SRC_INPUT: // shape env = input env
for (ch = 0; ch < inChanNum; ch++) {
System.arraycopy(inEnvBuf[ch], 0, shapeEnvBuf[ch], 0, chunkLength);
}
break;
case SRC_SOUNDFILE: // calc shape env from envInBuf
for (ch = 0; ch < envInChanNum; ch++) {
envInEnergy[ch] =
calcEnv(envInBuf[ch], shapeEnvBuf[ch], average, chunkLength, envInEnergy[ch]);
}
break;
case SRC_ENVFILE: // nothing to do, we have already loaded the env
break; // in the correct buffer
case SRC_ENV:
throw new IOException("Graphic env not yet supported");
}
// ---- calc output ----
// first generate output envelope
switch (pr.intg[PR_MODE]) {
case MODE_SUPERPOSE:
if (!pr.bool[PR_INVERT]) { // multiply by shape
for (ch = 0; ch < outChanNum; ch++) {
convBuf1 = outBuf[ch];
for (i = 0; i < chunkLength; i++) {
f1 =
shapeEnvBuf[shapeChan[ch][0]][i] * shapeChanWeight[ch][0]
+ shapeEnvBuf[shapeChan[ch][1]][i] * shapeChanWeight[ch][1];
convBuf1[i] = Math.min(maxChange, f1);
}
}
} else { // divide by shape
for (ch = 0; ch < outChanNum; ch++) {
convBuf1 = outBuf[ch];
for (i = 0; i < chunkLength; i++) {
f1 =
shapeEnvBuf[shapeChan[ch][0]][i] * shapeChanWeight[ch][0]
+ shapeEnvBuf[shapeChan[ch][1]][i] * shapeChanWeight[ch][1];
if (f1 > 0.0f) {
convBuf1[i] = Math.min(maxChange, 1.0f / f1);
} else {
convBuf1[i] = maxChange;
}
}
}
}
break;
case MODE_REPLACE:
if (!pr.bool[PR_INVERT]) { // shape / input
for (ch = 0; ch < outChanNum; ch++) {
convBuf1 = outBuf[ch];
for (i = 0; i < chunkLength; i++) {
f1 =
shapeEnvBuf[shapeChan[ch][0]][i] * shapeChanWeight[ch][0]
+ shapeEnvBuf[shapeChan[ch][1]][i] * shapeChanWeight[ch][1];
f2 =
inEnvBuf[inChan[ch][0]][i] * inChanWeight[ch][0]
+ inEnvBuf[inChan[ch][1]][i] * inChanWeight[ch][1];
if (f2 > 0.0f) {
convBuf1[i] = Math.min(maxChange, f1 / f2);
} else {
convBuf1[i] = 0.0f; // input ist eh ueberall null, somit unveraenderlich
}
}
}
} else { // 1 / (shape * input)
for (ch = 0; ch < outChanNum; ch++) {
convBuf1 = outBuf[ch];
for (i = 0; i < chunkLength; i++) {
f1 =
shapeEnvBuf[shapeChan[ch][0]][i] * shapeChanWeight[ch][0]
+ shapeEnvBuf[shapeChan[ch][1]][i] * shapeChanWeight[ch][1];
f1 *=
inEnvBuf[inChan[ch][0]][i] * inChanWeight[ch][0]
+ inEnvBuf[inChan[ch][1]][i] * inChanWeight[ch][1];
if (f1 > 0.0f) {
convBuf1[i] = Math.min(maxChange, 1.0f / f1);
} else {
convBuf1[i] = maxChange;
}
}
}
}
break;
}
// then multiply input bites
if (inChanNum == outChanNum) { // no weighting - use faster routine
for (ch = 0; ch < outChanNum; ch++) {
convBuf1 = outBuf[ch];
convBuf2 = inBuf[ch];
for (i = 0, j = avrOff; i < chunkLength; i++, j++) {
convBuf1[i] *= convBuf2[j];
}
}
} else {
for (ch = 0; ch < outChanNum; ch++) {
convBuf1 = outBuf[ch];
for (i = 0, j = avrOff; i < chunkLength; i++, j++) {
f1 =
inBuf[inChan[ch][0]][j] * inChanWeight[ch][0]
+ inBuf[inChan[ch][1]][j] * inChanWeight[ch][1];
convBuf1[i] *= f1;
}
}
}
// ---- write output sound file ----
if (outFloatF != null) { // i.e. unity gain
for (ch = 0; ch < outChanNum; ch++) {
convBuf1 = outBuf[ch];
for (i = 0; i < chunkLength; i++) { // measure max amp
f1 = Math.abs(convBuf1[i]);
if (f1 > maxAmp) {
maxAmp = f1;
}
}
outFloatF[ch].writeFloats(convBuf1, 0, chunkLength);
}
} else { // i.e. abs gain
for (ch = 0; ch < outChanNum; ch++) {
convBuf1 = outBuf[ch];
for (i = 0; i < chunkLength; i++) { // measure max amp + adjust gain
f1 = Math.abs(convBuf1[i]);
convBuf1[i] *= gain;
if (f1 > maxAmp) {
maxAmp = f1;
}
}
}
outF.writeFrames(outBuf, 0, chunkLength);
}
framesWritten += chunkLength;
progOff += chunkLength;
// .... progress ....
setProgression((float) progOff / (float) progLen);
// ---- shift buffers ----
for (ch = 0;
ch < inChanNum;
ch++) { // zero padding is performed after AudioFile.readFrames()!
System.arraycopy(inBuf[ch], chunkLength, inBuf[ch], 0, average);
}
if (extraAudioFile) {
for (ch = 0;
ch < envInChanNum;
ch++) { // zero padding is performed after AudioFile.readFrames()!
System.arraycopy(envInBuf[ch], chunkLength, envInBuf[ch], 0, average);
}
}
} // until framesWritten == outLength
// .... check running ....
if (!threadRunning) break topLevel;
// ---- normalize output ----
// sound file
if (pr.intg[PR_GAINTYPE] == GAIN_UNITY) {
peakGain = new Param((double) maxAmp, Param.ABS_AMP);
gain =
(float)
(Param.transform(
pr.para[PR_GAIN],
Param.ABS_AMP,
new Param(1.0 / peakGain.val, peakGain.unit),
null))
.val;
f1 = 1.0f;
if ((envOutF != null) && (pr.intg[PR_ENVGAINTYPE] == GAIN_UNITY)) { // leave prog space
f1 = (1.0f + getProgression()) / 2;
}
normalizeAudioFile(outFloatF, outF, outBuf, gain, f1);
for (ch = 0; ch < outChanNum; ch++) {
outFloatF[ch].cleanUp();
outFloatF[ch] = null;
outTempFile[ch].delete();
outTempFile[ch] = null;
}
}
// .... check running ....
if (!threadRunning) break topLevel;
// envelope file
if ((envOutF != null) && (pr.intg[PR_ENVGAINTYPE] == GAIN_UNITY)) {
peakGain = new Param((double) envMaxAmp, Param.ABS_AMP);
envGain =
(float)
(Param.transform(
pr.para[PR_ENVGAIN],
Param.ABS_AMP,
new Param(1.0 / peakGain.val, peakGain.unit),
null))
.val;
normalizeAudioFile(envFloatF, envOutF, inEnvBuf, envGain, 1.0f);
for (ch = 0; ch < envOutChanNum; ch++) {
envFloatF[ch].cleanUp();
envFloatF[ch] = null;
envTempFile[ch].delete();
envTempFile[ch] = null;
}
}
// .... check running ....
if (!threadRunning) break topLevel;
// ---- Finish ----
outF.close();
outF = null;
outStream = null;
if (envOutF != null) {
envOutF.close();
envOutF = null;
envOutStream = null;
}
if (envInF != null) {
envInF.close();
envInF = null;
envInStream = null;
}
inF.close();
inF = null;
inStream = null;
outBuf = null;
inBuf = null;
inEnvBuf = null;
envInBuf = null;
shapeEnvBuf = null;
// inform about clipping/ low level
maxAmp *= gain;
handleClipping(maxAmp);
envMaxAmp *= envGain;
// handleClipping( envMaxAmp ); // ;( routine nicht flexibel genug!
} catch (IOException e1) {
setError(e1);
} catch (OutOfMemoryError e2) {
inStream = null;
outStream = null;
envInStream = null;
envOutStream = null;
inBuf = null;
outBuf = null;
inEnvBuf = null;
envInBuf = null;
shapeEnvBuf = null;
convBuf1 = null;
convBuf2 = null;
System.gc();
setError(new Exception(ERR_MEMORY));
;
}
// ---- cleanup (topLevel) ----
if (inF != null) {
inF.cleanUp();
inF = null;
}
if (outF != null) {
outF.cleanUp();
outF = null;
}
if (envInF != null) {
envInF.cleanUp();
envInF = null;
}
if (envOutF != null) {
envOutF.cleanUp();
envOutF = null;
}
if (outFloatF != null) {
for (ch = 0; ch < outFloatF.length; ch++) {
if (outFloatF[ch] != null) outFloatF[ch].cleanUp();
if (outTempFile[ch] != null) outTempFile[ch].delete();
}
}
if (envFloatF != null) {
for (ch = 0; ch < envFloatF.length; ch++) {
if (envFloatF[ch] != null) envFloatF[ch].cleanUp();
if (envTempFile[ch] != null) envTempFile[ch].delete();
}
}
} // process()
public void assertTiming() {
assert expectedMs != 0 : "Must call .expect() before run test";
if (COVERAGE_ENABLED_BUILD) return;
while (true) {
attempts--;
long start;
try {
if (setup != null) setup.run();
start = System.currentTimeMillis();
test.run();
} catch (Throwable throwable) {
throw new RuntimeException(throwable);
}
long finish = System.currentTimeMillis();
long duration = finish - start;
int expectedOnMyMachine = expectedMs;
if (adjustForCPU) {
expectedOnMyMachine =
adjust(expectedOnMyMachine, Timings.CPU_TIMING, Timings.ETALON_CPU_TIMING);
expectedOnMyMachine =
usesAllCPUCores
? expectedOnMyMachine * 8 / JobSchedulerImpl.CORES_COUNT
: expectedOnMyMachine;
}
if (adjustForIO) {
expectedOnMyMachine =
adjust(expectedOnMyMachine, Timings.IO_TIMING, Timings.ETALON_IO_TIMING);
}
// Allow 10% more in case of test machine is busy.
String logMessage = message;
if (duration > expectedOnMyMachine) {
int percentage = (int) (100.0 * (duration - expectedOnMyMachine) / expectedOnMyMachine);
logMessage += ": " + percentage + "% longer";
}
logMessage +=
". Expected: "
+ formatTime(expectedOnMyMachine)
+ ". Actual: "
+ formatTime(duration)
+ "."
+ Timings.getStatistics();
final double acceptableChangeFactor = 1.1;
if (duration < expectedOnMyMachine) {
int percentage = (int) (100.0 * (expectedOnMyMachine - duration) / expectedOnMyMachine);
logMessage = percentage + "% faster. " + logMessage;
TeamCityLogger.info(logMessage);
System.out.println("SUCCESS: " + logMessage);
} else if (duration < expectedOnMyMachine * acceptableChangeFactor) {
TeamCityLogger.warning(logMessage, null);
System.out.println("WARNING: " + logMessage);
} else {
// try one more time
if (attempts == 0) {
// try {
// Object result =
// Class.forName("com.intellij.util.ProfilingUtil").getMethod("captureCPUSnapshot").invoke(null);
// System.err.println("CPU snapshot captured in '"+result+"'");
// }
// catch (Exception e) {
// }
throw new AssertionFailedError(logMessage);
}
System.gc();
System.gc();
System.gc();
String s = "Another epic fail (remaining attempts: " + attempts + "): " + logMessage;
TeamCityLogger.warning(s, null);
System.err.println(s);
// if (attempts == 1) {
// try {
//
// Class.forName("com.intellij.util.ProfilingUtil").getMethod("startCPUProfiling").invoke(null);
// }
// catch (Exception e) {
// }
// }
continue;
}
break;
}
}
public int print(java.awt.Graphics pg, java.awt.print.PageFormat pageFormat, int pageIndex)
throws java.awt.print.PrinterException {
if (pageIndex >= m_maxNumPage || m_bi == null) {
return NO_SUCH_PAGE;
}
pg.translate((int) pageFormat.getImageableX() + 1, (int) pageFormat.getImageableY() + 1);
int wPage = (int) pageFormat.getImageableWidth() + 1;
int hPage = (int) pageFormat.getImageableHeight() + 1;
double scale = percentSize / 100.0;
wPage = (int) (wPage / scale);
hPage = (int) (hPage / scale);
/*
int wPage = (int)pageFormat.getImageableWidth();
int hPage = (int)pageFormat.getImageableHeight();
int w = m_bi.getWidth(this);
int h = m_bi.getHeight(this);
if (w == 0 || h == 0)
return NO_SUCH_PAGE;
int nCol = Math.max((int)Math.ceil((double)w/wPage), 1);
int nRow = Math.max((int)Math.ceil((double)h/hPage), 1);
m_maxNumPage = nCol*nRow;
int iCol = pageIndex % nCol;
int iRow = pageIndex / nCol;
int x = iCol*wPage;
int y = iRow*hPage;
int wImage = Math.min(wPage, w-x);
int hImage = Math.min(hPage, h-y);
*/
int w = m_bi.getWidth(this);
int h = m_bi.getHeight(this);
// int resizedw = (int)(w*(percentSize/100.0));
// int resizedh = (int)(h*(percentSize/100.0));
java.awt.Graphics2D g2d = (java.awt.Graphics2D) pg;
g2d.scale(percentSize / 100.0, percentSize / 100.0);
if (w == 0 || h == 0) {
return NO_SUCH_PAGE;
}
int nCol = Math.max((int) Math.ceil((double) w / wPage), 1);
int nRow = Math.max((int) Math.ceil((double) h / hPage), 1);
m_maxNumPage = nCol * nRow;
int iCol = pageIndex % nCol;
int iRow = pageIndex / nCol;
int x = iCol * wPage;
int y = iRow * hPage;
int wImage = Math.min(wPage, w - x);
int hImage = Math.min(hPage, h - y);
g2d.drawImage(m_bi, 0, 0, wImage, hImage, x, y, x + wImage, y + hImage, this);
// pg.drawImage(m_bi, 0, 0, 40, 40, x, y, x+wImage, y+hImage, this);
System.gc();
return PAGE_EXISTS;
}
/** Translation durchfuehren */
public void process() {
int i, j, k;
int ch, len;
float f1;
double d1, d2, d3, d4, d5;
long progOff, progLen, lo;
// io
AudioFile reInF = null;
AudioFile imInF = null;
AudioFile reOutF = null;
AudioFile imOutF = null;
AudioFileDescr reInStream = null;
AudioFileDescr imInStream = null;
AudioFileDescr reOutStream = null;
AudioFileDescr imOutStream = null;
FloatFile reFloatF[] = null;
FloatFile imFloatF[] = null;
File reTempFile[] = null;
File imTempFile[] = null;
int outChanNum;
float[][] reInBuf; // [ch][i]
float[][] imInBuf; // [ch][i]
float[][] reOutBuf = null; // [ch][i]
float[][] imOutBuf = null; // [ch][i]
float[] convBuf1, convBuf2;
boolean complex;
PathField ggOutput;
// Synthesize
Param ampRef = new Param(1.0, Param.ABS_AMP); // transform-Referenz
float gain; // gain abs amp
float dryGain, wetGain;
float inGain;
float maxAmp = 0.0f;
Param peakGain;
int inLength, inOff;
int pre;
int post;
int length;
int framesRead, framesWritten, outLength;
boolean polarIn, polarOut;
// phase unwrapping
double[] phi;
int[] wrap;
double[] carry;
Param lenRef;
topLevel:
try {
complex = pr.bool[PR_HASIMINPUT] || pr.bool[PR_HASIMOUTPUT];
polarIn = pr.intg[PR_OPERATOR] == OP_POLAR2RECT;
polarOut = pr.intg[PR_OPERATOR] == OP_RECT2POLAR;
if ((polarIn || polarOut) && !complex) throw new IOException(ERR_NOTCOMPLEX);
// ---- open input ----
reInF = AudioFile.openAsRead(new File(pr.text[PR_REINPUTFILE]));
reInStream = reInF.getDescr();
inLength = (int) reInStream.length;
reInBuf = new float[reInStream.channels][8192];
imInBuf = new float[reInStream.channels][8192];
if (pr.bool[PR_HASIMINPUT]) {
imInF = AudioFile.openAsRead(new File(pr.text[PR_IMINPUTFILE]));
imInStream = imInF.getDescr();
if (imInStream.channels != reInStream.channels) throw new IOException(ERR_COMPLEX);
inLength = (int) Math.min(inLength, imInStream.length);
}
lenRef = new Param(AudioFileDescr.samplesToMillis(reInStream, inLength), Param.ABS_MS);
d1 =
AudioFileDescr.millisToSamples(
reInStream, (Param.transform(pr.para[PR_OFFSET], Param.ABS_MS, lenRef, null).value));
j = (int) (d1 >= 0.0 ? (d1 + 0.5) : (d1 - 0.5)); // correct rounding for negative values!
length =
(int)
(AudioFileDescr.millisToSamples(
reInStream,
(Param.transform(pr.para[PR_LENGTH], Param.ABS_MS, lenRef, null)).value)
+ 0.5);
// System.err.println( "offset = "+j );
if (j >= 0) {
inOff = Math.min(j, inLength);
if (!pr.bool[PR_REVERSE]) {
reInF.seekFrame(inOff);
if (pr.bool[PR_HASIMINPUT]) {
imInF.seekFrame(inOff);
}
}
inLength -= inOff;
pre = 0;
} else {
inOff = 0;
pre = Math.min(-j, length);
}
inLength = Math.min(inLength, length - pre);
post = length - pre - inLength;
if (pr.bool[PR_REVERSE]) {
i = pre;
pre = post;
post = i;
inOff += inLength;
}
// .... check running ....
if (!threadRunning) break topLevel;
// for( op = 0; op < 2; op++ ) {
// System.out.println( op +": pre "+pre[op]+" / len "+inLength[op]+" / post "+post[op] );
// }
// System.out.println( "tot "+length[0]);
outLength = length;
outChanNum = reInStream.channels;
// ---- open output ----
ggOutput = (PathField) gui.getItemObj(GG_REOUTPUTFILE);
if (ggOutput == null) throw new IOException(ERR_MISSINGPROP);
reOutStream = new AudioFileDescr(reInStream);
ggOutput.fillStream(reOutStream);
reOutStream.channels = outChanNum;
// well, more sophisticated code would
// move and truncate the markers...
if ((pre == 0) /* && (post == 0) */) {
reInF.readMarkers();
reOutStream.setProperty(
AudioFileDescr.KEY_MARKERS, reInStream.getProperty(AudioFileDescr.KEY_MARKERS));
}
reOutF = AudioFile.openAsWrite(reOutStream);
reOutBuf = new float[outChanNum][8192];
imOutBuf = new float[outChanNum][8192];
if (pr.bool[PR_HASIMOUTPUT]) {
imOutStream = new AudioFileDescr(reInStream);
ggOutput.fillStream(imOutStream);
imOutStream.channels = outChanNum;
imOutStream.file = new File(pr.text[PR_IMOUTPUTFILE]);
imOutF = AudioFile.openAsWrite(imOutStream);
}
// .... check running ....
if (!threadRunning) break topLevel;
// ---- Further inits ----
phi = new double[outChanNum];
wrap = new int[outChanNum];
carry = new double[outChanNum];
for (ch = 0; ch < outChanNum; ch++) {
phi[ch] = 0.0;
wrap[ch] = 0;
carry[ch] = Double.NEGATIVE_INFINITY;
}
progOff = 0; // read, transform, write
progLen = (long) outLength * 3;
wetGain = (float) (Param.transform(pr.para[PR_WETMIX], Param.ABS_AMP, ampRef, null)).value;
dryGain = (float) (Param.transform(pr.para[PR_DRYMIX], Param.ABS_AMP, ampRef, null)).value;
if (pr.bool[PR_DRYINVERT]) {
dryGain = -dryGain;
}
inGain = (float) (Param.transform(pr.para[PR_INPUTGAIN], Param.ABS_AMP, ampRef, null)).value;
if (pr.bool[PR_INVERT]) {
inGain = -inGain;
}
// normalization requires temp files
if (pr.intg[PR_GAINTYPE] == GAIN_UNITY) {
reTempFile = new File[outChanNum];
reFloatF = new FloatFile[outChanNum];
for (ch = 0;
ch < outChanNum;
ch++) { // first zero them because an exception might be thrown
reTempFile[ch] = null;
reFloatF[ch] = null;
}
for (ch = 0; ch < outChanNum; ch++) {
reTempFile[ch] = IOUtil.createTempFile();
reFloatF[ch] = new FloatFile(reTempFile[ch], GenericFile.MODE_OUTPUT);
}
if (pr.bool[PR_HASIMOUTPUT]) {
imTempFile = new File[outChanNum];
imFloatF = new FloatFile[outChanNum];
for (ch = 0;
ch < outChanNum;
ch++) { // first zero them because an exception might be thrown
imTempFile[ch] = null;
imFloatF[ch] = null;
}
for (ch = 0; ch < outChanNum; ch++) {
imTempFile[ch] = IOUtil.createTempFile();
imFloatF[ch] = new FloatFile(imTempFile[ch], GenericFile.MODE_OUTPUT);
}
}
progLen += outLength;
} else {
gain = (float) (Param.transform(pr.para[PR_GAIN], Param.ABS_AMP, ampRef, null)).value;
wetGain *= gain;
dryGain *= gain;
}
// .... check running ....
if (!threadRunning) break topLevel;
// ----==================== the real stuff ====================----
framesRead = 0;
framesWritten = 0;
while (threadRunning && (framesWritten < outLength)) {
// ---- choose chunk len ----
len = Math.min(8192, outLength - framesWritten);
if (pre > 0) {
len = Math.min(len, pre);
} else if (inLength > 0) {
len = Math.min(len, inLength);
} else {
len = Math.min(len, post);
}
// ---- read input chunks ----
if (pre > 0) {
Util.clear(reInBuf);
if (complex) {
Util.clear(imInBuf);
}
pre -= len;
} else if (inLength > 0) {
if (pr.bool[PR_REVERSE]) { // ---- read reversed ----
reInF.seekFrame(inOff - framesRead - len);
reInF.readFrames(reInBuf, 0, len);
for (ch = 0; ch < reInStream.channels; ch++) {
convBuf1 = reInBuf[ch];
for (i = 0, j = len - 1; i < j; i++, j--) {
f1 = convBuf1[j];
convBuf1[j] = convBuf1[i];
convBuf1[i] = f1;
}
}
if (pr.bool[PR_HASIMINPUT]) {
imInF.seekFrame(inOff - framesRead - len);
imInF.readFrames(imInBuf, 0, len);
for (ch = 0; ch < imInStream.channels; ch++) {
convBuf1 = imInBuf[ch];
for (i = 0, j = len - 1; i < j; i++, j--) {
f1 = convBuf1[j];
convBuf1[j] = convBuf1[i];
convBuf1[i] = f1;
}
}
} else if (complex) {
Util.clear(imInBuf);
}
} else { // ---- read normal ----
reInF.readFrames(reInBuf, 0, len);
if (pr.bool[PR_HASIMINPUT]) {
imInF.readFrames(imInBuf, 0, len);
} else if (complex) {
Util.clear(imInBuf);
}
}
inLength -= len;
framesRead += len;
} else {
Util.clear(reInBuf);
if (complex) {
Util.clear(imInBuf);
}
post -= len;
}
progOff += len;
// .... progress ....
setProgression((float) progOff / (float) progLen);
// .... check running ....
if (!threadRunning) break topLevel;
// ---- save dry signal ----
for (ch = 0; ch < outChanNum; ch++) {
convBuf1 = reInBuf[ch];
convBuf2 = reOutBuf[ch];
for (i = 0; i < len; i++) {
convBuf2[i] = convBuf1[i] * dryGain;
}
if (complex) {
convBuf1 = imInBuf[ch];
convBuf2 = imOutBuf[ch];
for (i = 0; i < len; i++) {
convBuf2[i] = convBuf1[i] * dryGain;
}
}
}
// ---- rectify + apply input gain ----
for (ch = 0; ch < reInStream.channels; ch++) {
convBuf1 = reInBuf[ch];
convBuf2 = imInBuf[ch];
// ---- rectify ----
if (pr.bool[PR_RECTIFY]) {
if (complex) {
if (polarIn) {
for (i = 0; i < len; i++) {
convBuf2[i] = 0.0f;
}
} else {
for (i = 0; i < len; i++) {
d1 = convBuf1[i];
d2 = convBuf2[i];
convBuf1[i] = (float) Math.sqrt(d1 * d1 + d2 * d2);
convBuf2[i] = 0.0f;
}
}
} else {
for (i = 0; i < len; i++) {
convBuf1[i] = Math.abs(convBuf1[i]);
}
}
}
// ---- apply input gain ----
Util.mult(convBuf1, 0, len, inGain);
if (complex & !polarIn) {
Util.mult(convBuf2, 0, len, inGain);
}
}
// ---- heart of the dragon ----
for (ch = 0; ch < outChanNum; ch++) {
convBuf1 = reInBuf[ch];
convBuf2 = imInBuf[ch];
switch (pr.intg[PR_OPERATOR]) {
case OP_NONE: // ================ None ================
for (i = 0; i < len; i++) {
reOutBuf[ch][i] += wetGain * convBuf1[i];
}
if (complex) {
for (i = 0; i < len; i++) {
imOutBuf[ch][i] += wetGain * convBuf2[i];
}
}
break;
case OP_SIN: // ================ Cosinus ================
if (complex) {
for (i = 0; i < len; i++) {
reOutBuf[ch][i] += wetGain * (float) Math.sin(convBuf1[i] * Math.PI);
imOutBuf[ch][i] += wetGain * (float) Math.sin(convBuf2[i] * Math.PI);
}
} else {
for (i = 0; i < len; i++) {
reOutBuf[ch][i] += wetGain * (float) Math.sin(convBuf1[i] * Math.PI);
}
}
break;
case OP_SQR: // ================ Square ================
if (complex) {
for (i = 0; i < len; i++) {
reOutBuf[ch][i] +=
wetGain * (convBuf1[i] * convBuf1[i] - convBuf2[i] * convBuf2[i]);
imOutBuf[ch][i] -= wetGain * (convBuf1[i] * convBuf2[i] * 2);
}
} else {
for (i = 0; i < len; i++) {
reOutBuf[ch][i] += wetGain * (convBuf1[i] * convBuf1[i]);
}
}
break;
case OP_SQRT: // ================ Square root ================
if (complex) {
d3 = phi[ch];
k = wrap[ch];
d4 = k * Constants.PI2;
for (i = 0; i < len; i++) {
d1 =
wetGain
* Math.pow(convBuf1[i] * convBuf1[i] + convBuf2[i] * convBuf2[i], 0.25);
d2 = Math.atan2(convBuf2[i], convBuf1[i]);
if (d2 - d3 > Math.PI) {
k--;
d4 = k * Constants.PI2;
} else if (d3 - d2 > Math.PI) {
k++;
d4 = k * Constants.PI2;
}
d2 += d4;
d3 = d2;
d2 /= 2;
reOutBuf[ch][i] += (float) (d1 * Math.cos(d2));
imOutBuf[ch][i] += (float) (d1 * Math.sin(d2));
}
phi[ch] = d3;
wrap[ch] = k;
} else {
for (i = 0; i < len; i++) {
f1 = convBuf1[i];
if (f1 > 0) {
reOutBuf[ch][i] += wetGain * (float) Math.sqrt(f1);
} // else undefiniert
}
}
break;
case OP_RECT2POLARW: // ================ Rect->Polar (wrapped) ================
for (i = 0; i < len; i++) {
d1 = wetGain * Math.sqrt(convBuf1[i] * convBuf1[i] + convBuf2[i] * convBuf2[i]);
d2 = Math.atan2(convBuf2[i], convBuf1[i]);
reOutBuf[ch][i] += (float) d1;
imOutBuf[ch][i] += (float) d2;
}
break;
case OP_RECT2POLAR: // ================ Rect->Polar ================
d3 = phi[ch];
k = wrap[ch];
d4 = k * Constants.PI2;
for (i = 0; i < len; i++) {
d1 = wetGain * Math.sqrt(convBuf1[i] * convBuf1[i] + convBuf2[i] * convBuf2[i]);
d2 = Math.atan2(convBuf2[i], convBuf1[i]);
if (d2 - d3 > Math.PI) {
k--;
d4 = k * Constants.PI2;
} else if (d3 - d2 > Math.PI) {
k++;
d4 = k * Constants.PI2;
}
d2 += d4;
reOutBuf[ch][i] += (float) d1;
imOutBuf[ch][i] += (float) d2;
d3 = d2;
}
phi[ch] = d3;
wrap[ch] = k;
break;
case OP_POLAR2RECT: // ================ Polar->Rect ================
for (i = 0; i < len; i++) {
f1 = wetGain * convBuf1[i];
reOutBuf[ch][i] += f1 * (float) Math.cos(convBuf2[i]);
imOutBuf[ch][i] += f1 * (float) Math.sin(convBuf2[i]);
}
break;
case OP_LOG: // ================ Log ================
if (complex) {
d3 = phi[ch];
k = wrap[ch];
d4 = k * Constants.PI2;
d5 = carry[ch];
for (i = 0; i < len; i++) {
d1 = Math.sqrt(convBuf1[i] * convBuf1[i] + convBuf2[i] * convBuf2[i]);
d2 = Math.atan2(convBuf2[i], convBuf1[i]);
if (d2 - d3 > Math.PI) {
k--;
d4 = k * Constants.PI2;
} else if (d3 - d2 > Math.PI) {
k++;
d4 = k * Constants.PI2;
}
if (d1 > 0.0) {
d5 = Math.log(d1);
}
d2 += d4;
reOutBuf[ch][i] += (float) d5;
imOutBuf[ch][i] += (float) d2;
d3 = d2;
}
phi[ch] = d3;
wrap[ch] = k;
carry[ch] = d5;
} else {
for (i = 0; i < len; i++) {
f1 = convBuf1[i];
if (f1 > 0) {
reOutBuf[ch][i] += wetGain * (float) Math.log(f1);
} // else undefiniert
}
}
break;
case OP_EXP: // ================ Exp ================
if (complex) {
for (i = 0; i < len; i++) {
d1 = wetGain * Math.exp(convBuf1[i]);
reOutBuf[ch][i] += (float) (d1 * Math.cos(convBuf2[i]));
imOutBuf[ch][i] += (float) (d1 * Math.sin(convBuf2[i]));
}
} else {
for (i = 0; i < len; i++) {
reOutBuf[ch][i] += wetGain * (float) Math.exp(convBuf1[i]);
}
}
break;
case OP_NOT: // ================ NOT ================
for (i = 0; i < len; i++) {
lo = ~((long) (convBuf1[i] * 2147483647.0));
reOutBuf[ch][i] += wetGain * (float) ((lo & 0xFFFFFFFFL) / 2147483647.0);
}
if (complex) {
for (i = 0; i < len; i++) {
lo = ~((long) (convBuf2[i] * 2147483647.0));
imOutBuf[ch][i] += wetGain * (float) ((lo & 0xFFFFFFFFL) / 2147483647.0);
}
}
break;
}
} // for outChan
progOff += len;
// .... progress ....
setProgression((float) progOff / (float) progLen);
// .... check running ....
if (!threadRunning) break topLevel;
// ---- write output chunk ----
if (reFloatF != null) {
for (ch = 0; ch < outChanNum; ch++) {
reFloatF[ch].writeFloats(reOutBuf[ch], 0, len);
if (pr.bool[PR_HASIMOUTPUT]) {
imFloatF[ch].writeFloats(imOutBuf[ch], 0, len);
}
}
} else {
reOutF.writeFrames(reOutBuf, 0, len);
if (pr.bool[PR_HASIMOUTPUT]) {
imOutF.writeFrames(imOutBuf, 0, len);
}
}
// check max amp
for (ch = 0; ch < outChanNum; ch++) {
convBuf1 = reOutBuf[ch];
for (i = 0; i < len; i++) {
f1 = Math.abs(convBuf1[i]);
if (f1 > maxAmp) {
maxAmp = f1;
}
}
if (pr.bool[PR_HASIMOUTPUT]) {
convBuf1 = imOutBuf[ch];
for (i = 0; i < len; i++) {
f1 = Math.abs(convBuf1[i]);
if (f1 > maxAmp) {
maxAmp = f1;
}
}
}
}
progOff += len;
framesWritten += len;
// .... progress ....
setProgression((float) progOff / (float) progLen);
} // while not framesWritten
// ----==================== normalize output ====================----
if (pr.intg[PR_GAINTYPE] == GAIN_UNITY) {
peakGain = new Param(maxAmp, Param.ABS_AMP);
gain =
(float)
(Param.transform(
pr.para[PR_GAIN],
Param.ABS_AMP,
new Param(1.0 / peakGain.value, peakGain.unit),
null))
.value;
f1 = pr.bool[PR_HASIMOUTPUT] ? ((1.0f + getProgression()) / 2) : 1.0f;
normalizeAudioFile(reFloatF, reOutF, reOutBuf, gain, f1);
if (pr.bool[PR_HASIMOUTPUT]) {
normalizeAudioFile(imFloatF, imOutF, imOutBuf, gain, 1.0f);
}
maxAmp *= gain;
for (ch = 0; ch < outChanNum; ch++) {
reFloatF[ch].cleanUp();
reFloatF[ch] = null;
reTempFile[ch].delete();
reTempFile[ch] = null;
if (pr.bool[PR_HASIMOUTPUT]) {
imFloatF[ch].cleanUp();
imFloatF[ch] = null;
imTempFile[ch].delete();
imTempFile[ch] = null;
}
}
}
// .... check running ....
if (!threadRunning) break topLevel;
// ---- Finish ----
reOutF.close();
reOutF = null;
reOutStream = null;
if (imOutF != null) {
imOutF.close();
imOutF = null;
imOutStream = null;
}
reInF.close();
reInF = null;
reInStream = null;
if (pr.bool[PR_HASIMINPUT]) {
imInF.close();
imInF = null;
imInStream = null;
}
reOutBuf = null;
imOutBuf = null;
reInBuf = null;
imInBuf = null;
// inform about clipping/ low level
handleClipping(maxAmp);
} catch (IOException e1) {
setError(e1);
} catch (OutOfMemoryError e2) {
reOutBuf = null;
imOutBuf = null;
reInBuf = null;
imInBuf = null;
convBuf1 = null;
convBuf2 = null;
System.gc();
setError(new Exception(ERR_MEMORY));
}
// ---- cleanup (topLevel) ----
convBuf1 = null;
convBuf2 = null;
if (reInF != null) {
reInF.cleanUp();
reInF = null;
}
if (imInF != null) {
imInF.cleanUp();
imInF = null;
}
if (reOutF != null) {
reOutF.cleanUp();
reOutF = null;
}
if (imOutF != null) {
imOutF.cleanUp();
imOutF = null;
}
if (reFloatF != null) {
for (ch = 0; ch < reFloatF.length; ch++) {
if (reFloatF[ch] != null) {
reFloatF[ch].cleanUp();
reFloatF[ch] = null;
}
if (reTempFile[ch] != null) {
reTempFile[ch].delete();
reTempFile[ch] = null;
}
}
}
if (imFloatF != null) {
for (ch = 0; ch < imFloatF.length; ch++) {
if (imFloatF[ch] != null) {
imFloatF[ch].cleanUp();
imFloatF[ch] = null;
}
if (imTempFile[ch] != null) {
imTempFile[ch].delete();
imTempFile[ch] = null;
}
}
}
} // process()
// create a new profile: read the script and possibly execute the queries,
// save the stats (if 'import' == true, we assume the profile already exists
// and don't run the queries)
public void createWkld(String name, String scriptFile, boolean runQueries) {
System.gc();
Workload wkld = new Workload(name);
if (showCmdsItem.getState()) {
consoleFrame.echoCmd((!runQueries ? "importprof " : "newwkld ") + name + " " + scriptFile);
}
// construct the Workload object from the script;
// first, check if the file exists
try {
FileReader reader = new FileReader(scriptFile);
reader.close();
} catch (FileNotFoundException e) {
System.out.println("couldn't open " + scriptFile);
return;
} catch (IOException e) {
System.out.println("couldn't close " + scriptFile);
}
// now, check if it contains only queries
int scriptId = 0;
try {
scriptId = Libgist.openScript(scriptFile);
} catch (LibgistException e) {
System.out.println("couldn't open (C) " + scriptFile);
return;
}
char[] arg1 = new char[64 * 1024];
StringBuffer arg1Buf = new StringBuffer();
char[] arg2 = new char[64 * 1024];
StringBuffer arg2Buf = new StringBuffer();
// for (;;) {
// int cmd = Libgist.getCommand(scriptId, arg1, arg2);
// if (cmd == Libgist.EOF) break;
// if (cmd != Libgist.FETCH) {
// there should only be queries
// System.out.println("Script file contains non-SELECT command");
// return;
// }
// }
if (runQueries) {
// turn profiling on and execute queries
// Libgist.setProfilingEnabled(true);
Libgist.disableBps(true); // we don't want to stop at breakpoints
// rescan queries
try {
scriptId = Libgist.openScript(scriptFile);
} catch (LibgistException e) {
System.out.println("couldn't open (C) " + scriptFile);
return;
}
int cnt = 1;
// for (;;) {
// int cmd = Libgist.getCommand(scriptId, arg1, arg2);
// if (cmd == Libgist.EOF) break;
// arg1Buf.setLength(0);
// arg1Buf.append(arg1, 0, strlen(arg1));
// arg2Buf.setLength(0);
// arg2Buf.append(arg2, 0, strlen(arg2));
// OpThread.execCmd(LibgistCommand.FETCH, arg1Buf.toString(),
// arg2Buf.toString(), false);
// System.out.print(cnt + " ");
// System.out.println(cnt + ": execute " + arg2Buf.toString() + " "
// + arg1Buf.toString());
// cnt++;
// }
System.out.println();
Libgist.disableBps(false);
// compute optimal clustering and some more statistics
// Libgist.computeMetrics(wkld.filename);
}
// save profile
try {
// we're saving Java and C++ data in separate files (filename and filename.prof)
// the profile object only contains the filename, the queries will be
// read in from the file when the profile is opened (faster that way)
ObjectOutputStream out = new ObjectOutputStream(new FileOutputStream(wkld.filename));
out.writeObject(wkld);
out.close();
System.out.println("copy query file");
Runtime.getRuntime().exec("cp " + scriptFile + " " + wkld.filename + ".queries");
System.out.println("saving tree and profile");
Libgist.saveToFile(wkld.filename + ".idx");
if (runQueries) {
// Libgist.saveProfile(wkld.filename + ".prof");
}
} catch (Exception e) {
System.out.println("Error saving profile: " + e);
return;
}
if (runQueries) {
// turn profiling off (after the metrics were computed and
// the profile saved)
// Libgist.setProfilingEnabled(false);
}
}
@Override
public void run() {
this.cardIndex = 0;
File base = new File(Constants.IO.imageBaseDir);
if (!base.exists()) {
base.mkdir();
}
Connection.ProxyType configProxyType =
Connection.ProxyType.valueByText(
PreferencesDialog.getCachedValue(PreferencesDialog.KEY_PROXY_TYPE, "None"));
Proxy.Type type = Proxy.Type.DIRECT;
switch (configProxyType) {
case HTTP:
type = Proxy.Type.HTTP;
break;
case SOCKS:
type = Proxy.Type.SOCKS;
break;
case NONE:
default:
p = Proxy.NO_PROXY;
break;
}
if (type != Proxy.Type.DIRECT) {
try {
String address = PreferencesDialog.getCachedValue(PreferencesDialog.KEY_PROXY_ADDRESS, "");
Integer port =
Integer.parseInt(
PreferencesDialog.getCachedValue(PreferencesDialog.KEY_PROXY_PORT, "80"));
p = new Proxy(type, new InetSocketAddress(address, port));
} catch (Exception ex) {
throw new RuntimeException("Gui_DownloadPictures : error 1 - " + ex);
}
}
if (p != null) {
HashSet<String> ignoreUrls = SettingsManager.getIntance().getIgnoreUrls();
ArrayList<CardDownloadData> cardsToDownload = this.checkBox.isSelected() ? type2cards : cards;
update(0, cardsToDownload.size());
for (int i = 0; i < cardsToDownload.size() && !cancel; i++) {
try {
CardDownloadData card = cardsToDownload.get(i);
log.info("Downloading card: " + card.getName() + " (" + card.getSet() + ")");
String url;
if (ignoreUrls.contains(card.getSet()) || card.isToken()) {
if (card.getCollectorId() != 0) {
continue;
}
url = cardImageSource.generateTokenUrl(card);
} else {
url = cardImageSource.generateURL(card);
}
if (url != null) {
Logger.getLogger(this.getClass()).info(url);
Runnable task = new DownloadTask(card, new URL(url), cardsToDownload.size());
executor.execute(task);
} else {
synchronized (sync) {
update(cardIndex + 1, cardsToDownload.size());
}
}
} catch (Exception ex) {
log.error(ex, ex);
}
}
executor.shutdown();
while (!executor.isTerminated()) {
try {
Thread.sleep(1000);
} catch (InterruptedException ie) {
}
}
}
try {
TVFS.umount();
} catch (FsSyncException e) {
e.printStackTrace();
JOptionPane.showMessageDialog(
null, "Couldn't unmount zip files", "Error", JOptionPane.ERROR_MESSAGE);
} finally {
System.gc();
}
closeButton.setText("Close");
}
private void closeFile() {
upperTabbedPane.remove(upperTabbedPane.getSelectedComponent());
menuBar.setFileOpen(upperTabbedPane.getComponentCount() > 0);
System.gc();
}
private void refreshTableWithData(ArrayList<PasswordModel> models) {
currentTableSelect = 0; // 重新默认选择第0行
currentListContent = models; // 设置最新的数据
listTable.setModel(new MainTableDataModel(models)); // 模型转换
System.gc();
}