int[] smooth(int[] a, int n) {
FloatProcessor fp = new FloatProcessor(n, 1);
for (int i = 0; i < n; i++) fp.putPixelValue(i, 0, a[i]);
GaussianBlur gb = new GaussianBlur();
gb.blur1Direction(fp, 2.0, 0.01, true, 0);
for (int i = 0; i < n; i++) a[i] = (int) Math.round(fp.getPixelValue(i, 0));
return a;
}
public static double[] getPixels(ImagePlus imp, int[] slices, int[] frames, int[] channels) {
ImagePlus subImp = AccessImage.getSubHyperStack(imp, slices, frames, channels);
ImageStack imageStack = subImp.getImageStack();
double[] pixels = new double[subImp.getWidth() * subImp.getHeight() * imageStack.getSize()];
for (int i = 0; i < imageStack.getSize(); i++) {
switch (subImp.getType()) {
case ImagePlus.GRAY8:
ByteProcessor byteProcessor = (ByteProcessor) imageStack.getProcessor(i + 1);
for (int iX = 0; iX < subImp.getWidth(); iX++) {
for (int iY = 0; iY < subImp.getHeight(); iY++) {
pixels[i * subImp.getWidth() * subImp.getHeight() + iY * subImp.getWidth() + iX] =
(double) byteProcessor.getPixelValue(iX, iY);
}
}
break;
case ImagePlus.GRAY16:
ShortProcessor shortProcessor = (ShortProcessor) imageStack.getProcessor(i + 1);
for (int iX = 0; iX < subImp.getWidth(); iX++) {
for (int iY = 0; iY < subImp.getHeight(); iY++) {
pixels[i * subImp.getWidth() * subImp.getHeight() + iY * subImp.getWidth() + iX] =
(double) shortProcessor.getPixelValue(iX, iY);
}
}
break;
case ImagePlus.GRAY32:
FloatProcessor floatProcessor = (FloatProcessor) imageStack.getProcessor(i + 1);
for (int iX = 0; iX < subImp.getWidth(); iX++) {
for (int iY = 0; iY < subImp.getHeight(); iY++) {
pixels[i * subImp.getWidth() * subImp.getHeight() + iY * subImp.getWidth() + iX] =
(double) floatProcessor.getPixelValue(iX, iY);
}
}
break;
case ImagePlus.COLOR_RGB:
ColorProcessor colorProcessor = (ColorProcessor) imageStack.getProcessor(i + 1);
int nX = subImp.getWidth();
int nY = subImp.getHeight();
byte[] red = new byte[nX * nY];
byte[] green = new byte[nX * nY];
byte[] blue = new byte[nX * nY];
colorProcessor.getRGB(red, green, blue);
int r, g, b;
for (int j = 0; j < nX * nY; j++) {
r = red[j] << 16;
g = green[j] << 8;
b = blue[j] << 0;
pixels[i * nX * nY + j] = (double) (r + g + b);
}
break;
}
}
return (pixels);
}
public void runStuff(
DimensionMap map,
TreeMap<DimensionMap, ROIPlus> maximaMap,
TreeMap<DimensionMap, String> segMap,
TreeMap<DimensionMap, String> maskMap,
TreeMap<DimensionMap, String> imageMap,
TreeMap<DimensionMap, Double> results,
Canceler canceler) {
// Get the Maxima
ROIPlus maxima = maximaMap.get(map);
// Make the mask image impMask
// ByteProcessor impMask = (ByteProcessor) (new
// ImagePlus(maskMap.get(map)).getProcessor().convertToByte(false));
// ByteProcessor impSeg = (ByteProcessor) (new
// ImagePlus(segMap.get(map)).getProcessor().convertToByte(false));
ByteProcessor impSeg = (ByteProcessor) (new ImagePlus(segMap.get(map))).getProcessor();
ByteProcessor impMask = (ByteProcessor) (new ImagePlus(maskMap.get(map))).getProcessor();
ByteBlitter blit = new ByteBlitter(impSeg);
blit.copyBits(impMask, 0, 0, Blitter.AND);
FloatProcessor impImage =
(FloatProcessor) (new ImagePlus(imageMap.get(map))).getProcessor().convertToFloat();
Wand wand = new Wand(impSeg);
Wand wand2 = new Wand(impMask);
Vector<Double> measurements;
for (IdPoint p : maxima.getPointList()) {
if (canceler.isCanceled()) {
return;
}
if (impSeg.getPixel(p.x, p.y)
== 255) // if we land on a cell that made it through thresholding
{
wand.autoOutline(p.x, p.y); // outline it
wand2.autoOutline(p.x, p.y);
boolean partOfCellClump =
!this.selectionsAreEqual(
wand,
wand2); // If the segmented and unsegmented masks do not agree on the roi, then this
// cell is part of a clump.
if (wand.npoints > 0) {
Roi roi =
new PolygonRoi(
wand.xpoints,
wand.ypoints,
wand.npoints,
Roi.POLYGON); // The roi helps for using getLength() (DON'T USE Roi.TRACED_ROI.,
// IT SCREWS UP THE Polygon OBJECTS!!!! Bug emailed to ImageJ
// folks)
Polygon poly =
new Polygon(
wand.xpoints,
wand.ypoints,
wand.npoints); // The polygon helps for using contains()
Rectangle r = roi.getBounds();
measurements = new Vector<Double>();
for (int i = r.x; i < r.x + r.width; i++) {
for (int j = r.y; j < r.y + r.height; j++) {
// innerBoundary
if (poly.contains(i, j) && impSeg.getPixelValue(i, j) == 255) {
measurements.add((double) impImage.getPixelValue(i, j));
// Logs.log("In - " + innerT, this);
}
}
}
impMask.setRoi(roi);
ImageStatistics stats =
ImageStatistics.getStatistics(
impMask,
ImageStatistics.AREA
& ImageStatistics.PERIMETER
& ImageStatistics.CIRCULARITY
& ImageStatistics.ELLIPSE,
null);
if (measurements.size() > 0) {
DimensionMap resultsMap = map.copy();
resultsMap.put("Id", "" + p.id);
resultsMap.put("Measurement", "X");
results.put(resultsMap.copy(), (double) p.x);
resultsMap.put("Measurement", "Y");
results.put(resultsMap.copy(), (double) p.y);
resultsMap.put("Measurement", "AREA");
results.put(resultsMap.copy(), stats.area);
resultsMap.put("Measurement", "PERIMETER");
results.put(resultsMap.copy(), roi.getLength());
resultsMap.put("Measurement", "CIRCULARITY");
results.put(
resultsMap.copy(), 4.0 * Math.PI * (stats.area / (Math.pow(roi.getLength(), 2))));
resultsMap.put("Measurement", "ELLIPSE MAJOR");
results.put(resultsMap.copy(), stats.major);
resultsMap.put("Measurement", "ELLIPSE MINOR");
results.put(resultsMap.copy(), stats.minor);
resultsMap.put("Measurement", "MEAN");
results.put(resultsMap.copy(), StatisticsUtility.mean(measurements));
resultsMap.put("Measurement", "MEDIAN");
results.put(resultsMap.copy(), StatisticsUtility.median(measurements));
resultsMap.put("Measurement", "SUM");
results.put(resultsMap.copy(), StatisticsUtility.sum(measurements));
resultsMap.put("Measurement", "MIN");
results.put(resultsMap.copy(), StatisticsUtility.min(measurements));
resultsMap.put("Measurement", "MAX");
results.put(resultsMap.copy(), StatisticsUtility.max(measurements));
resultsMap.put("Measurement", "STDDEV");
results.put(resultsMap.copy(), StatisticsUtility.stdDev(measurements));
resultsMap.put("Measurement", "VARIANCE");
results.put(resultsMap.copy(), StatisticsUtility.variance(measurements));
resultsMap.put("Measurement", "CLUMP");
results.put(resultsMap.copy(), (double) (partOfCellClump ? 1 : 0));
}
}
}
}
}
