/**
* 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 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;
}