public IntensityPaint(ROI2D roi, Sequence seq, IcyCanvas canv) {
canvas = canv;
sequence = seq;
guideRoi = roi;
displayRectangle =
new ROI2DRectangle(
lastPoint.getX(),
lastPoint.getY(),
lastPoint.getX() + Math.min(800, sequence.getWidth() / 4),
lastPoint.getY() + Math.min(800, sequence.getHeight() / 4));
displayRectangle.setName("(" + guideRoi.getName() + ")");
displayRectangle.setColor(guideRoi.getColor());
displayRectangle.setOpacity((float) 0.2);
cursor1 = new Line2D.Double();
cursor2 = new Line2D.Double();
if (guideRoi.getClass().equals(ROI2DLine.class)) paintMode = PaintMode.line;
else if (guideRoi.getClass().equals(ROI2DPoint.class)) paintMode = PaintMode.point;
else paintMode = PaintMode.area;
(new Thread(new computeRunnable())).start();
sequence.addListener(this);
guideRoi.addListener(this);
if (paintMode == PaintMode.line) canvas.getViewer().addListener(this);
}
/**
* Save the specified sequence in the specified file.<br>
* If sequence contains severals images then file is used as a directory<br>
* to store all single images.
*
* @param sequence sequence to save
* @param file file where we want to save sequence
*/
public static void save(Sequence sequence, File file) {
save(
sequence,
file,
0,
sequence.getSizeZ() - 1,
0,
sequence.getSizeT() - 1,
15,
(sequence.getSizeZ() * sequence.getSizeT()) > 1,
true);
}
/**
* Save the specified sequence in the specified file.<br>
* When the sequence contains severals image the multiFile flag is used to indicate<br>
* if images are saved in severals files (file then specify a directory) or in a single file.
*
* @param sequence sequence to save
* @param file file where we want to save sequence
* @param multipleFiles flag to indicate if images are saved in separate file
* @param showProgress show progress bar
*/
public static void save(
Sequence sequence, File file, boolean multipleFiles, boolean showProgress) {
save(
sequence,
file,
0,
sequence.getSizeZ() - 1,
0,
sequence.getSizeT() - 1,
15,
multipleFiles,
showProgress);
}
/** @deprecated Use {@link #save(Sequence, File, boolean, boolean)} instead. */
@Deprecated
public static void save(Sequence sequence, File file, boolean multipleFiles) {
save(
sequence,
file,
0,
sequence.getSizeZ() - 1,
0,
sequence.getSizeT() - 1,
15,
multipleFiles,
true);
}
public void dispose() {
try {
sequence.removeListener(this);
guideRoi.removeListener(this);
canvas.getViewer().removeListener(this);
} catch (Exception e) {
}
}
@Override
public void sequenceChanged(SequenceEvent sequenceEvent) {
if (sequenceEvent.getSource() == SequenceEvent.SequenceEventSourceType.SEQUENCE_DATA) {
cancelCompute = true;
while (computing)
try {
Thread.sleep(1);
} catch (InterruptedException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
(new Thread(new computeRunnable())).start();
}
if (sequenceEvent.getSourceType() == SequenceEventSourceType.SEQUENCE_OVERLAY
&& sequenceEvent.getSource() == this
&& sequenceEvent.getType() == SequenceEventType.REMOVED)
sequence.removeROI(displayRectangle);
}
void drawHisto(ROI2D roi, Graphics2D g, Sequence sequence, final IcyCanvas canvas) {
if (!roiPairDict.containsKey(roi)) return;
IntensityPaint ip = roiPairDict.get(roi);
String currentValueX = "";
String currentValueV = "";
String maxValue = "";
String minValue = "";
for (int component = 0; component < sequence.getSizeC(); component++) {
AffineTransform originalTransform = g.getTransform();
g.setColor(new Color(236, 10, 170));
if (sequence.getSizeC() != 1) {
if (component == 0) g.setColor(Color.red);
if (component == 1) g.setColor(Color.green);
if (component == 2) g.setColor(Color.blue);
}
Rectangle2D rectBox = ((ROI2DRectangle) ip.displayRectangle).getRectangle();
Rectangle2D polyBox = ip.drawPolygon[component].getBounds2D();
try {
if (ip.paintMode == PaintMode.line) {
Line2D line = ((ROI2DLine) roi).getLine();
Point2D Lp;
Point2D Rp;
if (line.getX2() > line.getX1()) {
Lp = line.getP1();
Rp = line.getP2();
} else {
Lp = line.getP2();
Rp = line.getP1();
}
int pos;
if (Math.min(line.getX1(), line.getX2()) >= cursorPos.x) pos = 0;
else if (Math.max(line.getX1(), line.getX2()) <= cursorPos.x) pos = ip.dataCount;
else {
pos = (int) ((cursorPos.x - Lp.getX()) / (Rp.getX() - Lp.getX()) * ip.dataCount);
try {
currentValueX = String.format("X:%.1f", cursorPos.x);
currentValueV += String.format("%.1f ", ip.dataArr.get(component)[pos]);
} catch (Exception e2) {
}
}
ip.cursor1.setLine(pos, 0, pos, polyBox.getHeight());
} else {
int pos = (int) cursorPos.z;
ip.cursor1.setLine(pos, 0, pos, polyBox.getHeight());
try {
currentValueX = String.format("Z:%.1f", cursorPos.z);
currentValueV += String.format("%.1f ", ip.dataArr.get(component)[pos]);
} catch (Exception e2) {
}
}
double sx = rectBox.getWidth() / polyBox.getWidth();
double sy = rectBox.getHeight() / polyBox.getHeight();
if (sx < 100 && sy < 100) {
g.translate(rectBox.getMinX(), rectBox.getMaxY());
g.scale(sx, -sy);
g.draw(ip.drawPolygon[component]);
g.setColor(new Color(100, 100, 170));
g.draw(ip.cursor1);
g.setColor(new Color(236, 10, 170));
} else {
char[] c = "Exceeding display limit!".toCharArray();
g.drawChars(c, 0, c.length, (int) rectBox.getCenterX() - 10, (int) rectBox.getCenterY());
}
} finally {
g.setTransform(originalTransform);
// min,max
double xStart, xEnd;
if (ip.paintMode == PaintMode.line) {
Line2D line = ((ROI2DLine) roi).getLine();
Point2D Lp;
Point2D Rp;
if (line.getX2() > line.getX1()) {
Lp = line.getP1();
Rp = line.getP2();
} else {
Lp = line.getP2();
Rp = line.getP1();
}
xStart = Lp.getX();
xEnd = Rp.getX();
int pos;
double yp;
if (Math.min(line.getX1(), line.getX2()) >= cursorPos.x) {
pos = (int) Lp.getX();
yp = Lp.getY();
} else if (Math.max(line.getX1(), line.getX2()) <= cursorPos.x) {
pos = (int) Rp.getX();
yp = Rp.getY();
} else {
pos = (int) cursorPos.x;
yp =
(cursorPos.x - Lp.getX())
/ (line.getX2() - line.getX1())
* (line.getY2() - line.getY1())
+ Lp.getY();
}
ip.cursor2.setLine(pos, yp + 10, pos, yp - 10);
g.draw(ip.cursor2);
} else {
xStart = 0;
xEnd = ip.dataCount;
}
maxValue += String.format("%.1f ", ip.maxData[component]);
minValue += String.format("%.1f ", ip.minData[component]);
if (component == sequence.getSizeC() - 1) {
char[] c = String.format("%.1f", xStart).toCharArray();
// x1
g.drawChars(c, 0, c.length, (int) rectBox.getMinX(), (int) rectBox.getMaxY() + 30);
c = String.format("%.1f", xEnd).toCharArray();
// x2
g.drawChars(c, 0, c.length, (int) rectBox.getMaxX(), (int) rectBox.getMaxY() + 30);
c = maxValue.toCharArray();
g.drawChars(c, 0, c.length, (int) rectBox.getMaxX() + 10, (int) rectBox.getMinY() + 10);
c = minValue.toCharArray();
g.drawChars(c, 0, c.length, (int) rectBox.getMaxX() + 10, (int) rectBox.getMaxY() - 5);
c = currentValueX.toCharArray();
g.drawChars(
c,
0,
c.length,
(int) (rectBox.getMinX() + (ip.cursor1.x1 / ip.dataCount) * rectBox.getWidth()) - 20,
(int) rectBox.getMaxY() + 15);
c = currentValueV.toCharArray();
g.drawChars(
c,
0,
c.length,
(int) (rectBox.getMinX() + (ip.cursor1.x1 / ip.dataCount) * rectBox.getWidth()) - 20,
(int) rectBox.getMinY() - 5);
}
}
}
}
@Override
public void paint(Graphics2D g, Sequence sequence, IcyCanvas canv) {
if (canv != canvas) {
canvas = canv;
canvas.getViewer().addListener(this);
canvas.getViewer().addKeyListener(this);
}
if (lastPoint == null) lastPoint = new Point(0, 0);
// create a graphics object so that we can then dispose it at the end of the paint to clean
// all change performed in the paint,
// like transform, color change, stroke (...).
HashMap<ROI2D, IntensityPaint> roiPairTemp = new HashMap<ROI2D, IntensityPaint>();
Graphics2D g2 = (Graphics2D) g.create();
for (ROI2D roi : sequence.getROI2Ds()) {
if (roi.getName().startsWith("(") && roi.getName().endsWith(")")) continue;
{
IntensityPaint ip;
if (roiPairDict.containsKey(roi)) {
ip = roiPairDict.get(roi);
// rect.displayRectangle.setName("["+roi.getName()+"]");
// Rectangle2D box2 = rect.displayRectangle.getBounds2D();
// // if(!sequence.getROI2Ds().contains(ip.displayRectangle)){//
// sequence.removeROI(rect.displayRectangle);//
// rect.displayRectangle.remove();// rect.displayRectangle new
// ROI2DRectangle(lastPoint.getX(),lastPoint.getY(),Math.min(800,sequence.getWidth()),0);;;// rect.displayRectangle.setColor(roi.getColor());// sequence.addROI(rect.displayRectangle);// }
if (ip != null) {
if (!sequence.getROI2Ds().contains(ip.displayRectangle)) {
ip.dispose();
} else roiPairTemp.put(roi, ip);
}
} else {
ip = null;
if (enableAddRoi) {
roi.setName("" + Integer.toString(nameIndex) + "#");
nameIndex += 1;
roi.setColor(getRandomColor());
// roi.setSelectedColor(getRandomColor());
ip = new IntensityPaint(roi, sequence, canvas);
lastPoint.setLocation(lastPoint.getX() + 10, lastPoint.getY() + 10);
if (lastPoint.getX() > sequence.getHeight() || lastPoint.getY() > sequence.getWidth())
lastPoint.setLocation(0, 0);
sequence.addROI(ip.displayRectangle);
}
roiPairTemp.put(roi, ip);
}
if (ip != null && !skipSelect && roi instanceof ROI2DShape) {
if (roi.isSelected()) ip.displayRectangle.setSelected(roi.isSelected());
else if (ip.displayRectangle.isSelected())
roi.setSelected(ip.displayRectangle.isSelected());
}
try {
if (ip != null) drawHisto(roi, g2, sequence, canvas);
} catch (Exception e2) {
}
}
}
for (ROI2D roi : roiPairDict.keySet()) {
if (!roiPairTemp.containsKey(roi)) {
if (roiPairDict.get(roi) != null) {
roiPairDict.get(roi).dispose();
sequence.removeROI(roiPairDict.get(roi).displayRectangle);
}
}
}
roiPairDict.clear();
roiPairDict = roiPairTemp;
g2.dispose();
}
@Override
public void sequenceClosed(Sequence sequence) {
sequence.removeROI(displayRectangle);
}
public void computeData() {
computing = true;
cancelCompute = false;
try {
maxData = new double[sequence.getSizeC()];
minData = new double[sequence.getSizeC()];
drawPolygon = new Polygon[sequence.getSizeC()];
if (paintMode == PaintMode.line) {
Line2D line = ((ROI2DLine) guideRoi).getLine();
dataCount = (int) line.getP1().distance(line.getP2());
} else {
dataCount = sequence.getSizeZ();
}
dataArr = new ArrayList<double[]>();
for (int component = 0; component < sequence.getSizeC(); component++) {
double[] data = new double[dataCount];
dataArr.add(data);
}
if (paintMode == PaintMode.line) {
Line2D line = ((ROI2DLine) guideRoi).getLine();
dataCount = (int) line.getP1().distance(line.getP2());
ShapeUtil.consumeShapeFromPath(
((ROI2DShape) guideRoi).getPathIterator(null),
new ShapeConsumer() {
@Override
public boolean consume(Shape shape) {
if (shape instanceof Line2D) {
Line2D line = (Line2D) shape;
Point2D Lp;
Point2D Rp;
if (line.getX2() > line.getX1()) {
Lp = line.getP1();
Rp = line.getP2();
} else {
Lp = line.getP2();
Rp = line.getP1();
}
for (int component = 0; component < sequence.getSizeC(); component++) {
// create histo data
int distance = dataCount;
double vx = (Rp.getX() - Lp.getX()) / distance;
double vy = (Rp.getY() - Lp.getY()) / distance;
double[] data = dataArr.get(component);
double x = Lp.getX();
double y = Lp.getY();
IcyBufferedImage image = canvas.getCurrentImage();
if (image.isInside((int) x, (int) y)) {
maxData[component] =
Array1DUtil.getValue(
image.getDataXY(component),
image.getOffset((int) x, (int) y),
image.isSignedDataType());
} else {
maxData[component] = 0;
}
minData[component] = maxData[component];
for (int i = 0; i < dataCount; i++) {
if (cancelCompute) break;
if (image.isInside((int) x, (int) y)) {
data[i] =
Array1DUtil.getValue(
image.getDataXY(component),
image.getOffset((int) x, (int) y),
image.isSignedDataType());
} else {
data[i] = 0;
}
if (data[i] > maxData[component]) maxData[component] = data[i];
if (data[i] < minData[component]) minData[component] = data[i];
x += vx;
y += vy;
}
Polygon polygon = new Polygon();
polygon.addPoint(0, 0);
for (int i = 0; i < dataCount; i++) {
polygon.addPoint(i, (int) (data[i] - minData[component]));
}
polygon.addPoint(dataCount, 0);
drawPolygon[component] = polygon;
}
}
return true; // continue
}
});
} else {
for (int component = 0; component < sequence.getSizeC(); component++) {
double[] data = dataArr.get(component);
if (paintMode == PaintMode.point) {
Point p = guideRoi.getPosition();
if (p.x < sequence.getSizeX() && p.y < sequence.getSizeY()) {
maxData[component] = sequence.getData(0, 0, component, p.y, p.x);
minData[component] = maxData[component];
for (int i = 0; i < dataCount; i++) {
if (cancelCompute) break;
data[i] = sequence.getData(0, i, component, p.y, p.x);
if (data[i] > maxData[component]) maxData[component] = data[i];
if (data[i] < minData[component]) minData[component] = data[i];
}
}
} else {
maxData[component] = ROIUtil.getMeanIntensity(sequence, guideRoi, 0, -1, component);
;
minData[component] = maxData[component];
for (int i = 0; i < dataCount; i++) {
if (cancelCompute) break;
data[i] = ROIUtil.getMeanIntensity(sequence, guideRoi, i, -1, component);
if (data[i] > maxData[component]) maxData[component] = data[i];
if (data[i] < minData[component]) minData[component] = data[i];
}
}
Polygon polygon = new Polygon();
polygon.addPoint(0, 0);
for (int i = 0; i < dataCount; i++)
// pity polygon does not support this with double...
polygon.addPoint(i, (int) (data[i] - minData[component]));
polygon.addPoint(dataCount, 0);
drawPolygon[component] = polygon;
}
}
} catch (Exception e) {
System.out.print(e);
}
computing = false;
}
/**
* Save the specified sequence in the specified file.<br>
* When the sequence contains severals image the multipleFile flag is used to indicate<br>
* if images are saved as separate files (file then specify a directory) or not.<br>
* zMin - zMax and tMin - tMax define the Z and T images range to save.<br>
*
* @param formatWriter writer used to save sequence (define the image format)
* @param sequence sequence to save
* @param filePath file name where we want to save sequence
* @param zMin start Z position to save
* @param zMax end Z position to save
* @param tMin start T position to save
* @param tMax end T position to save
* @param fps frame rate for AVI sequence save
* @param saveFrame progress frame for save operation (can be null)
* @throws ServiceException
* @throws IOException
* @throws FormatException
*/
private static void save(
IFormatWriter formatWriter,
Sequence sequence,
String filePath,
int zMin,
int zMax,
int tMin,
int tMax,
int fps,
FileFrame saveFrame)
throws ServiceException, FormatException, IOException {
final File file = new File(filePath);
final IFormatWriter writer;
if (formatWriter == null) writer = getWriter(file, ImageFileFormat.TIFF);
else writer = formatWriter;
// TODO: temporary fix for the "incorrect close operation" bug in Bio-Formats
// with OME TIF writer, remove it when fixed.
// {
// try
// {
// writer = formatWriter.getClass().newInstance();
// }
// catch (Exception e)
// {
// throw new ServiceException("Can't create new writer instance: " + e);
// }
// }
if (writer == null)
throw new UnknownFormatException(
"Can't find a valid image writer for the specified file: " + filePath);
// first delete the file else LOCI won't save it correctly
if (file.exists()) file.delete();
// ensure parent directory exist
FileUtil.ensureParentDirExist(file);
final int sizeC = sequence.getSizeC();
final boolean separateChannel = getSeparateChannelFlag(writer, sequence.getColorModel());
// set settings
writer.setFramesPerSecond(fps);
// generate metadata
writer.setMetadataRetrieve(
MetaDataUtil.generateMetaData(
sequence, (zMax - zMin) + 1, (tMax - tMin) + 1, separateChannel));
// no interleave (XP default viewer want interleaved channel to correctly read image)
writer.setInterleaved(false);
// set id
writer.setId(filePath);
// init
writer.setSeries(0);
// usually give better save performance
writer.setWriteSequentially(true);
// get endianess
final boolean littleEndian =
!writer.getMetadataRetrieve().getPixelsBinDataBigEndian(0, 0).booleanValue();
byte[] data = null;
try {
int imageIndex = 0;
// XYCZT order is important here (see metadata)
for (int t = tMin; t <= tMax; t++) {
for (int z = zMin; z <= zMax; z++) {
if ((saveFrame != null) && saveFrame.isCancelRequested()) return;
final IcyBufferedImage image = sequence.getImage(t, z);
// separated channel data
if (separateChannel) {
for (int c = 0; c < sizeC; c++) {
if (image != null) {
// avoid multiple allocation
data = image.getRawData(c, data, 0, littleEndian);
writer.saveBytes(imageIndex, data);
}
imageIndex++;
}
} else {
if (image != null) {
// avoid multiple allocation
data = image.getRawData(data, 0, littleEndian);
writer.saveBytes(imageIndex, data);
}
imageIndex++;
}
if (saveFrame != null) saveFrame.incPosition();
}
}
} finally {
// always close writer after a file has been saved
writer.close();
}
}
/**
* Save the specified sequence in the specified file.<br>
* When the sequence contains severals image the multipleFile flag is used to indicate if images
* are saved as separate files (file then specify a directory) or not.<br>
* <code>zMin</code> - <code>zMax</code> and <code>tMin</code> - <code>tMax</code> define the Z
* and T images range to save.<br>
*
* @param formatWriter writer used to save sequence (define the image format).<br>
* If set to <code>null</code> then writer is determined from the file extension.<br>
* If destination file does not have a valid extension (for folder for instance) then you have
* to specify a valid Writer to write the image file (see {@link #getWriter(ImageFileFormat)})
* @param sequence sequence to save
* @param file file where we want to save sequence.<br>
* Depending the <code>formatWriter</code> the file extension may be modified.<br>
* That is preferred as saving an image with a wrong extension may result in error on future
* read (wrong reader detection).
* @param zMin start Z position to save
* @param zMax end Z position to save
* @param tMin start T position to save
* @param tMax end T position to save
* @param fps frame rate for AVI sequence save
* @param multipleFile flag to indicate if images are saved in separate file
* @param showProgress show progress bar
* @param addToRecent add the saved sequence to recent opened sequence list
*/
public static void save(
IFormatWriter formatWriter,
Sequence sequence,
File file,
int zMin,
int zMax,
int tMin,
int tMax,
int fps,
boolean multipleFile,
boolean showProgress,
boolean addToRecent) {
final String filePath = FileUtil.cleanPath(FileUtil.getGenericPath(file.getAbsolutePath()));
final int sizeT = (tMax - tMin) + 1;
final int sizeZ = (zMax - zMin) + 1;
final int numImages = sizeT * sizeZ;
final FileFrame saveFrame;
final ApplicationMenu mainMenu;
if (addToRecent) mainMenu = Icy.getMainInterface().getApplicationMenu();
else mainMenu = null;
if (showProgress && !Icy.getMainInterface().isHeadLess())
saveFrame = new FileFrame("Saving", filePath);
else saveFrame = null;
try {
if (saveFrame != null) {
saveFrame.setLength(numImages);
saveFrame.setPosition(0);
}
// need multiple files ?
if ((numImages > 1) && multipleFile) {
final IFormatWriter writer;
// so we won't create it for each image
if (formatWriter == null) writer = getWriter(file, ImageFileFormat.TIFF);
else writer = formatWriter;
if (writer == null)
throw new UnknownFormatException(
"Can't find a valid image writer for the specified file: " + file);
// save as severals images
final DecimalFormat decimalFormat = new DecimalFormat("0000");
final String fileName = FileUtil.getFileName(filePath, false);
String fileExt = FileUtil.getFileExtension(filePath, true);
String fileBaseDirectory = FileUtil.getDirectory(filePath);
if (fileBaseDirectory.endsWith("/"))
fileBaseDirectory = fileBaseDirectory.substring(0, fileBaseDirectory.length() - 1);
// no extension (directory) ?
if (StringUtil.isEmpty(fileExt)) {
// filename is part of directory
fileBaseDirectory += FileUtil.separator + fileName;
// use the default file extension for the specified writer
fileExt = "." + getImageFileFormat(writer, ImageFileFormat.TIFF).getExtensions()[0];
}
final String filePathWithoutExt = fileBaseDirectory + FileUtil.separator + fileName;
// create output directory
FileUtil.createDir(fileBaseDirectory);
// default name used --> use filename
if (sequence.isDefaultName()) sequence.setName(fileName);
sequence.setFilename(fileBaseDirectory);
for (int t = tMin; t <= tMax; t++) {
for (int z = zMin; z <= zMax; z++) {
String filename = filePathWithoutExt;
if ((tMax - tMin) > 0) filename += "_t" + decimalFormat.format(t);
if ((zMax - zMin) > 0) filename += "_z" + decimalFormat.format(z);
filename += fileExt;
// save as single image file
save(writer, sequence, filename, z, z, t, t, fps, saveFrame);
}
}
// add as one item to recent file list
if (mainMenu != null) mainMenu.addRecentFile(fileBaseDirectory);
} else {
final String fileExt = FileUtil.getFileExtension(filePath, false);
final ImageFileFormat iff;
if (formatWriter != null) iff = getImageFileFormat(formatWriter, ImageFileFormat.TIFF);
else iff = ImageFileFormat.getWriteFormat(fileExt, ImageFileFormat.TIFF);
// force to set correct file extension
final String fixedFilePath;
if (iff.matches(fileExt)) fixedFilePath = filePath;
else fixedFilePath = filePath + "." + iff.getExtensions()[0];
// default name used --> use filename
if (sequence.isDefaultName()) sequence.setName(FileUtil.getFileName(fixedFilePath, false));
sequence.setFilename(fixedFilePath);
// save into a single file
save(formatWriter, sequence, fixedFilePath, zMin, zMax, tMin, tMax, fps, saveFrame);
// add as one item to recent file list
if (mainMenu != null) mainMenu.addRecentFile(fixedFilePath);
}
// Sequence persistence enabled --> save XML
if (GeneralPreferences.getSequencePersistence()) sequence.saveXMLData();
} catch (Exception e) {
IcyExceptionHandler.showErrorMessage(e, true);
if (showProgress && !Icy.getMainInterface().isHeadLess())
new FailedAnnounceFrame("Failed to save image(s) (see output console for details)", 15);
return;
} finally {
if (saveFrame != null) saveFrame.close();
}
}
public void removeSequence(final Sequence sequence) {
sequence.close();
}
