@Override
public boolean run(JEXEntry optionalEntry) {
if (imageData == null || !imageData.getTypeName().getType().equals(JEXData.IMAGE)) {
return false;
}
// Run the function
TreeMap<DimensionMap, String> images = ImageReader.readObjectToImagePathTable(imageData);
TreeMap<DimensionMap, String> outputMap = new TreeMap<DimensionMap, String>();
int count = 0;
int total = images.size();
for (DimensionMap dim : images.keySet()) {
if (this.isCanceled()) {
return false;
}
String path = images.get(dim);
// File f = new File(path);
// get the image
ImagePlus im = new ImagePlus(path);
ij.process.ImageProcessor imProc = im.getProcessor();
if (imProc == null) continue;
FloatProcessor imp =
(FloatProcessor) im.getProcessor().convertToFloat(); // should be a float processor
int newWidth = (int) (imp.getWidth() * scale);
imp.setInterpolationMethod(ImageProcessor.BILINEAR);
imp = (FloatProcessor) imp.resize(newWidth);
ImagePlus toSave = FunctionUtility.makeImageToSave(imp, "false", bitDepth);
String finalPath = JEXWriter.saveImage(toSave);
outputMap.put(dim.copy(), finalPath);
Logs.log("Finished processing " + count + " of " + total + ".", 1, this);
count++;
// Status bar
int percentage = (int) (100 * ((double) count / (double) images.size()));
JEXStatics.statusBar.setProgressPercentage(percentage);
}
// Set the outputs
output = ImageWriter.makeImageStackFromPaths("temp", outputMap);
output.setDataObjectInfo("Stack binned using binning function");
// Return status
return true;
}
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));
}
}
}
}
}