private void drawGraph(
final double[] params, final double[] boxSizes, final double[] boxCountSums) {
final int samples = 100;
final float[] px = new float[samples];
final float[] py = new float[samples];
double[] a = Tools.getMinMax(boxSizes);
final double xmin = a[0], xmax = a[1];
a = Tools.getMinMax(boxCountSums);
double ymin = a[0], ymax = a[1];
final double inc = (xmax - xmin) / ((double) samples - 1);
double tmp = xmin;
for (int i = 0; i < samples; i++) {
px[i] = (float) tmp;
tmp += inc;
}
for (int i = 0; i < samples; i++) {
py[i] = (float) CurveFitter.f(CurveFitter.STRAIGHT_LINE, params, px[i]);
}
a = Tools.getMinMax(py);
ymin = Math.min(ymin, a[0]);
ymax = Math.max(ymax, a[1]);
final Plot plot = new Plot("Plot", "-log(box size)", "log(box count)", px, py);
plot.setLimits(xmin, xmax * 0.9, ymin, ymax * 1.1);
plot.draw();
plot.addPoints(boxSizes, boxCountSums, Plot.CIRCLE);
plot.addPoints(px, py, Plot.LINE);
final CurveFitter cf = new CurveFitter(boxSizes, boxCountSums);
cf.doFit(CurveFitter.STRAIGHT_LINE);
plot.addLabel(
0.1, 0.1, "Slope: " + IJ.d2s(params[1], 4) + "\n" + "R²: " + IJ.d2s(cf.getRSquared(), 4));
final ImagePlus plotImage = new ImagePlus("Plot", plot.getProcessor());
plotImage.show();
return;
}
// TODO split run method into more sensible methods
public void run(final String arg) {
if (!ImageCheck.checkEnvironment()) return;
final ImagePlus imp = IJ.getImage();
if (null == imp) {
IJ.noImage();
return;
}
final ImageCheck ic = new ImageCheck();
if (!ImageCheck.isBinary(imp)) {
IJ.showMessage("Fractal Count requires a binary image.");
return;
}
if (noGo) return;
final ImagePlus surfaceImp = findSurfaceVoxels(imp);
try {
// Fetch data
final int width = imp.getWidth();
final int height = imp.getHeight();
final int depth = imp.getStackSize();
if (autoParam) {
maxBox = Math.max(width, Math.max(height, depth)) / autoDiv;
if (verboseOutput) {
IJ.log("Automatic max box size " + maxBox + " selected");
}
}
// Create variables we need and set them
long bestCount; // keep track of best count so far
long count = 0; // current count
final ArrayList<Double> xList = new ArrayList<Double>();
final ArrayList<Double> yList = new ArrayList<Double>();
int xPos, yPos, zPos, yPart;
int xGrid, yGrid, zGrid;
int xStart, yStart, zStart;
int xEnd, yEnd, zEnd;
// Start timer
final long startTime = System.currentTimeMillis();
for (int boxSize = maxBox; boxSize >= minBox; boxSize /= divBox) {
if (verboseOutput) {
IJ.showStatus("Estimating dimension, box size: " + boxSize);
}
bestCount = Long.MAX_VALUE; // init count for this boxSize
final int increment = Math.max(1, boxSize / numOffsets);
for (int gridOffsetX = 0;
(gridOffsetX < boxSize) && (gridOffsetX < width);
gridOffsetX += increment) {
for (int gridOffsetY = 0;
(gridOffsetY < boxSize) && (gridOffsetY < height);
gridOffsetY += increment) {
for (int gridOffsetZ = 0;
(gridOffsetZ < boxSize) && (gridOffsetZ < depth);
gridOffsetZ += increment) {
count = 0;
final int iMax = width + gridOffsetX;
final int jMax = height + gridOffsetY;
final int kMax = depth + gridOffsetZ;
// Iterate over box-grid
for (int i = 0; i <= iMax; i += boxSize) {
xGrid = -gridOffsetX + i;
for (int j = 0; j <= jMax; j += boxSize) {
yGrid = -gridOffsetY + j;
for (int k = 0; k <= kMax; k += boxSize) {
zGrid = -gridOffsetZ + k;
xStart = 0;
if (xGrid < 0) {
xStart = -xGrid;
}
if ((boxSize + xGrid) >= width) {
xEnd = Math.min(width, (width - xGrid));
} else {
xEnd = boxSize;
}
yStart = 0;
if (yGrid < 0) {
yStart = -yGrid;
}
if ((boxSize + yGrid) >= height) {
yEnd = Math.min(height, (height - yGrid));
} else {
yEnd = boxSize;
}
zStart = 0;
if (zGrid < 0) {
zStart = -zGrid;
}
if ((boxSize + zGrid) >= depth) {
zEnd = Math.min(depth, (depth - zGrid));
} else {
zEnd = boxSize;
}
for (int x = xStart; x < xEnd; x++) {
xPos = x + xGrid;
for (int y = yStart; y < yEnd; y++) {
yPos = (y + yGrid);
yPart = yPos * width;
for (int z = zStart; z < zEnd; z++) {
zPos = z + zGrid;
// If pixel inside region,
// count it
if ((0xff
& ((byte[]) surfaceImp.getStack().getPixels(zPos + 1))
[xPos + yPart])
>= threshold) {
count++;
z = x = y = boxSize; // stops
// things
}
}
}
}
}
}
}
if (count < bestCount) {
bestCount = count;
}
}
}
}
xList.add(new Double(boxSize));
yList.add(new Double(bestCount));
}
if (verboseOutput) {
IJ.log("\nDuration: " + (System.currentTimeMillis() - startTime) / 1000.0 + " seconds\n");
}
final double[] boxSizes = new double[xList.size()];
final double[] boxCountSums = new double[yList.size()];
for (int i = 0; i < boxSizes.length; i++) {
boxSizes[i] = -Math.log((xList.get(i)).doubleValue());
boxCountSums[i] = Math.log((yList.get(i)).doubleValue());
}
if (verboseOutput) {
IJ.log(
"Used " + boxSizes.length + " different box sizes, from " + maxBox + " to " + minBox);
IJ.log(
"with a reduction rate of "
+ divBox
+ " and "
+ numOffsets
+ " translations of each box.");
}
if (boxSizes.length == 0) {
IJ.error(
"\nError: No boxes!\n"
+ "Make sure that starting and ending box size and"
+ "reduction rate allow for at least one"
+ " box size to exist!");
return;
}
final CurveFitter cf = new CurveFitter(boxSizes, boxCountSums);
cf.doFit(CurveFitter.STRAIGHT_LINE);
final double[] p = cf.getParams();
final double RSq = cf.getRSquared();
if (verboseOutput) {
IJ.log(
imp.getTitle()
+ ": Dimension estimate: "
+ IJ.d2s(p[1], 4)
+ ": R²: "
+ RSq
+ ": Settings: "
+ maxBox
+ ":"
+ minBox
+ ":"
+ divBox
+ ":"
+ numOffsets);
}
if (verboseOutput) {
IJ.log("Box Size Box Count");
for (int i = 0; i < boxSizes.length; i++) {
IJ.log(IJ.d2s(xList.get(i), 0) + " " + IJ.d2s(yList.get(i), 0));
}
}
final ResultInserter ri = ResultInserter.getInstance();
ri.setResultInRow(imp, "Fractal Dimension", p[1]);
ri.setResultInRow(imp, "R²", RSq);
ri.updateTable();
if (plotGraph && !Interpreter.isBatchMode()) {
drawGraph(p, boxSizes, boxCountSums);
}
} catch (final Exception e) {
e.printStackTrace();
}
UsageReporter.reportEvent(this).send();
}