/**
* Computes an alpha trimmed mean upon the current region of the current function. Note that this
* method uses memory to make a copy of the input values. Larger input regions might require a lot
* of memory.
*
* @param alpha A number between 0 and 0.5 specifying the proportion of samples to ignore on each
* end.
* @return The measured value
*/
public double alphaTrimmedMean(double alpha) {
if ((alpha < 0) || (alpha >= 0.5))
throw new IllegalArgumentException("alpha value must be >= 0 and < 0.5");
T tmp = func.createOutput();
values.clear();
iter.reset();
while (iter.hasNext()) {
long[] pos = iter.next();
func.compute(pos, tmp);
values.add(tmp.getRealDouble());
}
values.sortValues();
double tailSize = alpha * values.size();
// can we avoid interpolation?
if (tailSize == Math.floor(tailSize)) {
// yes, trim count is exactly an integer
return calcTrimmedMean(values, (int) tailSize);
}
// no, trim count is a float value
// calc two trimmed means and interpolate to find the value between them
double mean1 = calcTrimmedMean(values, (int) Math.floor(tailSize));
double mean2 = calcTrimmedMean(values, (int) Math.ceil(tailSize));
double fraction = tailSize - Math.floor(tailSize);
double interpolation = ((1 - fraction) * mean1) + (fraction * mean2);
return interpolation;
}
/**
* Computes the minimum value upon the current region of the current function.
*
* @return The measured value
*/
public double min() {
T tmp = func.createOutput();
double min = Double.POSITIVE_INFINITY;
iter.reset();
while (iter.hasNext()) {
long[] pos = iter.next();
func.compute(pos, tmp);
double value = tmp.getRealDouble();
min = Math.min(min, value);
}
return min;
}
/**
* Computes the product of all the values of the current region of the current function.
*
* @return The measured value
*/
public double product() {
T tmp = func.createOutput();
double prod = 1;
iter.reset();
while (iter.hasNext()) {
long[] pos = iter.next();
func.compute(pos, tmp);
double value = tmp.getRealDouble();
prod *= value;
}
return prod;
}
/**
* Computes a trimmed mean upon the current region of the current function. Note that this method
* uses memory to make a copy of the input values. Larger input regions might require a lot of
* memory.
*
* @param halfTrimSize The number of samples to ignore from each end of the data
* @return The measured value
*/
public double trimmedMean(int halfTrimSize) {
T tmp = func.createOutput();
values.clear();
iter.reset();
while (iter.hasNext()) {
long[] pos = iter.next();
func.compute(pos, tmp);
values.add(tmp.getRealDouble());
}
values.sortValues();
return calcTrimmedMean(values, halfTrimSize);
}
/**
* Computes the sum of all the values of the current region of the current function.
*
* @return The measured value
*/
public double sum() {
T tmp = func.createOutput();
double sum = 0;
iter.reset();
while (iter.hasNext()) {
long[] pos = iter.next();
func.compute(pos, tmp);
double value = tmp.getRealDouble();
sum += value;
}
return sum;
}
/**
* Computes the maximum value upon the current region of the current function.
*
* @return The measured value
*/
public double max() {
T tmp = func.createOutput();
double max = Double.NEGATIVE_INFINITY;
iter.reset();
while (iter.hasNext()) {
long[] pos = iter.next();
func.compute(pos, tmp);
double value = tmp.getRealDouble();
max = Math.max(max, value);
}
return max;
}
/**
* Computes the arithmetic mean (or average) upon the current region of the current function.
*
* @return The measured value
*/
public double arithmeticMean() {
T tmp = func.createOutput();
double sum = 0;
long numElements = 0;
iter.reset();
while (iter.hasNext()) {
long[] pos = iter.next();
func.compute(pos, tmp);
sum += tmp.getRealDouble();
numElements++;
}
return sum / numElements;
}
/**
* Computes the sum of squared deviations of the values of the current region of the current
* function.
*
* @return The measured value
*/
public double sumOfSquaredDeviations() {
T tmp = func.createOutput();
final double xbar = arithmeticMean();
double sum = 0;
iter.reset();
while (iter.hasNext()) {
long[] pos = iter.next();
func.compute(pos, tmp);
double value = tmp.getRealDouble();
double term = value - xbar;
sum += (term * term);
}
return sum;
}
/**
* Computes the harmonic mean upon the current region of the current function.
*
* @return The measured value
*/
public double harmonicMean() {
T tmp = func.createOutput();
double sum = 0;
long numElements = 0;
iter.reset();
while (iter.hasNext()) {
long[] pos = iter.next();
func.compute(pos, tmp);
double value = tmp.getRealDouble();
sum += 1 / value;
numElements++;
}
return numElements / sum; // looks weird but it is correct
}
/**
* Computes the contraharmonic mean upon the current region of the current function.
*
* @return The measured value
*/
public double contraharmonicMean(double order) {
T tmp = func.createOutput();
double sum1 = 0;
double sum2 = 0;
iter.reset();
while (iter.hasNext()) {
long[] pos = iter.next();
func.compute(pos, tmp);
double value = tmp.getRealDouble();
sum1 += Math.pow(value, order + 1);
sum2 += Math.pow(value, order);
}
return sum1 / sum2;
}
/**
* Computes the centroid point of the current region and returns it as a pair of Doubles. The
* first element in the pair is the x component and the second element is the y component.
*
* @return The measured point stored in a Tuple2
*/
public Tuple2<Double, Double> centroidXY() {
double sumX = 0;
double sumY = 0;
long numElements = 0;
iter.reset();
while (iter.hasNext()) {
long[] pos = iter.next();
sumX += pos[0];
sumY += pos[1];
numElements++;
}
double cx = (sumX / numElements) + 0.5;
double cy = (sumY / numElements) + 0.5;
return new Tuple2<Double, Double>(cx, cy);
}
/**
* Computes a weighted sum of the current function values over the current region. The weights are
* provided and there must be as many weights as there are points in the current region.
*
* @return The measured value
*/
public double weightedSum(double[] weights) {
long numElements = region.size();
if (numElements != weights.length)
throw new IllegalArgumentException("number of weights does not equal number of samples");
T tmp = func.createOutput();
double sum = 0;
int i = 0;
iter.reset();
while (iter.hasNext()) {
long[] pos = iter.next();
func.compute(pos, tmp);
double value = tmp.getRealDouble();
sum += weights[i++] * value;
}
return sum;
}
/**
* Computes the center of mass point of the current region of the current function. Returns it as
* a pair of Doubles. The first element in the pair is the x component and the second element is
* the y component.
*
* @return The measured point stored in a Tuple2
*/
public Tuple2<Double, Double> centerOfMassXY() {
T tmp = func.createOutput();
double sumV = 0;
double sumX = 0;
double sumY = 0;
iter.reset();
while (iter.hasNext()) {
long[] pos = iter.next();
func.compute(pos, tmp);
double v = tmp.getRealDouble();
sumV += v;
sumX += v * pos[0];
sumY += v * pos[1];
}
double cx = (sumX / sumV) + 0.5;
double cy = (sumY / sumV) + 0.5;
return new Tuple2<Double, Double>(cx, cy);
}
@Override
public void run() {
if (!threshSrv.hasThreshold(input)) {
cancel("This command requires a thresholded image.");
return;
}
ThresholdOverlay thresh = threshSrv.getThreshold(input);
PointSetIterator iter = thresh.getPointsWithin().iterator();
if (!iter.hasNext()) {
cancel("No pixels are within the threshold");
return;
}
Dataset ds = dispSrv.getActiveDataset(input);
final int numDims = ds.numDimensions();
final long[] dimensions = new long[numDims];
final long[] min = new long[numDims];
/*
* First pass - find minima and maxima so we can use a shrunken image in some cases.
*/
for (int i = 0; i < numDims; i++) {
min[i] = (long) Math.floor(thresh.realMin(i));
dimensions[i] = (long) Math.floor(thresh.realMax(i) - thresh.realMin(i) + 1);
}
final ArrayImg<BitType, BitArray> arrayMask =
new ArrayImgFactory<BitType>().createBitInstance(dimensions, 1);
final BitType t = new BitType(arrayMask);
arrayMask.setLinkedType(t);
final Img<BitType> mask =
new ImgTranslationAdapter<BitType, ArrayImg<BitType, BitArray>>(arrayMask, min);
final RandomAccess<BitType> raMask = mask.randomAccess();
iter.reset();
while (iter.hasNext()) {
long[] pos = iter.next();
raMask.setPosition(pos);
raMask.get().set(true);
}
output =
new BinaryMaskOverlay(context, new BinaryMaskRegionOfInterest<BitType, Img<BitType>>(mask));
output.setAlpha(alpha);
output.setFillColor(color);
for (int i = 0; i < numDims; i++) {
output.setAxis(ds.getImgPlus().axis(i), i);
}
}
/**
* Computes the (biased) skew value upon the current region of the current function.
*
* @return The measured value
*/
public double populationSkew() {
T tmp = func.createOutput();
double xbar = arithmeticMean();
double s2 = 0;
double s3 = 0;
long numElements = 0;
iter.reset();
while (iter.hasNext()) {
long[] pos = iter.next();
func.compute(pos, tmp);
double value = tmp.getRealDouble();
numElements++;
double v = value - xbar;
double v2 = v * v;
double v3 = v2 * v;
s2 += v2;
s3 += v3;
}
double n = numElements;
double m2 = s2 / n;
double m3 = s3 / n;
return m3 / Math.pow(m2, 1.5);
}
/**
* Computes the (biased) kurtosis value upon the current region of the current function.
*
* @return The measured value
*/
public double populationKurtosis() {
T tmp = func.createOutput();
double xbar = arithmeticMean();
double s2 = 0;
double s4 = 0;
long numElements = 0;
iter.reset();
while (iter.hasNext()) {
long[] pos = iter.next();
func.compute(pos, tmp);
double value = tmp.getRealDouble();
numElements++;
double v = value - xbar;
double v2 = v * v;
double v4 = v2 * v2;
s2 += v2;
s4 += v4;
}
double n = numElements;
double m2 = s2 / n;
double m4 = s4 / n;
return m4 / (m2 * m2);
}
/**
* Computes the median upon the current region of the current function. Note that this method uses
* memory to make a copy of the input values. Larger input regions might require a lot of memory.
*
* @return The measured value
*/
public double median() {
T tmp = func.createOutput();
values.clear();
iter.reset();
while (iter.hasNext()) {
long[] pos = iter.next();
func.compute(pos, tmp);
values.add(tmp.getRealDouble());
}
final int numElements = values.size();
if (numElements <= 0)
throw new IllegalArgumentException("number of samples must be greater than 0");
values.sortValues();
// odd number of elements
if ((numElements % 2) == 1) return values.get(numElements / 2);
// else an even number of elements
double value1 = values.get((numElements / 2) - 1);
double value2 = values.get((numElements / 2));
return (value1 + value2) / 2;
}