Examples with ImageStatistics ij.process.ImageStatistics used on opensource projects

Example 6 with ImageStatistics

use of ij.process.ImageStatistics in project bioformats by openmicroscopy.

the class VirtualImagePlus method getStatistics.

@Override
public ImageStatistics getStatistics(int mOptions, int nBins, double histMin, double histMax) {
    if (this.ip instanceof RecordedImageProcessor) {
        RecordedImageProcessor currentProc = (RecordedImageProcessor) this.ip;
        this.ip = currentProc.getChild();
        setProcessor(getTitle(), this.ip);
        ImageStatistics s = super.getStatistics(mOptions, nBins, histMin, histMax);
        this.ip = currentProc;
        return s;
    }
    return super.getStatistics(mOptions, nBins, histMin, histMax);
}

Example 7 with ImageStatistics

use of ij.process.ImageStatistics in project GDSC-SMLM by aherbert.

the class GaussianFit method getLimits.

/**
 * Calculate the min/max limits for the image. The max is set at the 99th percentile of the data.
 *
 * @param ip the ip
 * @return The limits
 */
private static double[] getLimits(ImageProcessor ip) {
    final ImageStatistics stats = ImageStatistics.getStatistics(ip, Measurements.MIN_MAX, null);
    final double[] limits = new double[] { stats.min, stats.max };
    // Use histogram to cover x% of the data
    final int[] data = ip.getHistogram();
    if (data == null) {
        return limits;
    }
    // 8/16 bit greyscale image. Set upper limit to the height of the 99% percentile.
    final int limit = (int) (99.0 * ip.getPixelCount() / 100.0);
    int count = 0;
    int index = 0;
    while (index < data.length) {
        count += data[index];
        if (count > limit) {
            break;
        }
        index++;
    }
    limits[1] = index;
    return limits;
}

Example 8 with ImageStatistics

use of ij.process.ImageStatistics in project GDSC-SMLM by aherbert.

the class PulseActivationAnalysis method autoAdjust.

/**
 * Auto adjust. Copied from {@link ij.plugin.frame.ContrastAdjuster}.
 *
 * <p>Although the ContrastAdjuster records its actions as 'run("Enhance Contrast",
 * "saturated=0.35");' it actually does something else which makes the image easier to see than
 * the afore mentioned command.
 *
 * @param imp the image
 * @param ip the image
 */
private static void autoAdjust(ImagePlus imp, ImageProcessor ip) {
    final ij.measure.Calibration cal = imp.getCalibration();
    imp.setCalibration(null);
    // get uncalibrated stats
    final ImageStatistics stats = imp.getStatistics();
    imp.setCalibration(cal);
    final int limit = stats.pixelCount / 10;
    final int[] histogram = stats.histogram;
    int autoThreshold = 0;
    if (autoThreshold < 10) {
        autoThreshold = 5000;
    } else {
        autoThreshold /= 2;
    }
    final int threshold = stats.pixelCount / autoThreshold;
    int index = -1;
    boolean found = false;
    int count;
    do {
        index++;
        count = histogram[index];
        if (count > limit) {
            count = 0;
        }
        found = count > threshold;
    } while (!found && index < 255);
    final int hmin = index;
    index = 256;
    do {
        index--;
        count = histogram[index];
        if (count > limit) {
            count = 0;
        }
        found = count > threshold;
    } while (!found && index > 0);
    final int hmax = index;
    if (hmax >= hmin) {
        double min = stats.histMin + hmin * stats.binSize;
        double max = stats.histMin + hmax * stats.binSize;
        if (Double.compare(min, max) == 0) {
            min = stats.min;
            max = stats.max;
        }
        imp.setDisplayRange(min, max);
    } else {
        reset(imp);
    }
}