Examples with ImageProcessorReader loci.plugins.util.ImageProcessorReader used on opensource projects

Example 1 with ImageProcessorReader

use of loci.plugins.util.ImageProcessorReader in project bioformats by openmicroscopy.

the class Colorizer method applyDisplayRanges.

// -- Helper methods --
private void applyDisplayRanges(ImagePlus imp, int series) {
    if (imp instanceof VirtualImagePlus) {
        // virtual stacks handle their own display ranges
        return;
    }
    final ImporterOptions options = process.getOptions();
    final ImageProcessorReader reader = process.getReader();
    final int pixelType = reader.getPixelType();
    final boolean autoscale = options.isAutoscale() || // always autoscale float data
    FormatTools.isFloatingPoint(pixelType);
    final int cSize = imp.getNChannels();
    final double[] cMin = new double[cSize];
    final double[] cMax = new double[cSize];
    Arrays.fill(cMin, Double.NaN);
    Arrays.fill(cMax, Double.NaN);
    if (autoscale) {
        // extract display ranges for autoscaling
        final MinMaxCalculator minMaxCalc = process.getMinMaxCalculator();
        final int cBegin = process.getCBegin(series);
        final int cStep = process.getCStep(series);
        for (int c = 0; c < cSize; c++) {
            final int cIndex = cBegin + c * cStep;
            Double cMinVal = null, cMaxVal = null;
            try {
                cMinVal = minMaxCalc.getChannelGlobalMinimum(cIndex);
                cMaxVal = minMaxCalc.getChannelGlobalMaximum(cIndex);
                if (cMinVal == null) {
                    cMinVal = minMaxCalc.getChannelKnownMinimum(cIndex);
                }
                if (cMaxVal == null) {
                    cMaxVal = minMaxCalc.getChannelKnownMaximum(cIndex);
                }
            } catch (FormatException exc) {
            } catch (IOException exc) {
            }
            if (cMinVal != null)
                cMin[c] = cMinVal;
            if (cMaxVal != null)
                cMax[c] = cMaxVal;
        }
    }
    // for calibrated data, the offset from zero
    final double zeroOffset = getZeroOffset(imp);
    // fill in default display ranges as appropriate
    final double min, max;
    if (FormatTools.isFloatingPoint(pixelType)) {
        // no defined min and max values for floating point data
        min = max = Double.NaN;
    } else {
        final int bitDepth = reader.getBitsPerPixel();
        final double halfPow = Math.pow(2, bitDepth - 1);
        final double fullPow = 2 * halfPow;
        final boolean signed = FormatTools.isSigned(pixelType);
        if (signed) {
            // signed data is centered at 0
            min = -halfPow;
            max = halfPow - 1;
        } else {
            // unsigned data begins at 0
            min = 0;
            max = fullPow - 1;
        }
        for (int c = 0; c < cSize; c++) {
            if (Double.isNaN(cMin[c]))
                cMin[c] = min;
            if (Double.isNaN(cMax[c]))
                cMax[c] = max;
        }
    }
    // apply display ranges
    if (imp instanceof CompositeImage) {
        // apply channel display ranges
        final CompositeImage compImage = (CompositeImage) imp;
        for (int c = 0; c < cSize; c++) {
            LUT lut = compImage.getChannelLut(c + 1);
            // NB: Uncalibrate values before assigning to LUT min/max.
            lut.min = cMin[c] - zeroOffset;
            lut.max = cMax[c] - zeroOffset;
        }
    } else {
        // compute global display range from channel display ranges
        double globalMin = Double.POSITIVE_INFINITY;
        double globalMax = Double.NEGATIVE_INFINITY;
        for (int c = 0; c < cSize; c++) {
            if (cMin[c] < globalMin)
                globalMin = cMin[c];
            if (cMax[c] > globalMax)
                globalMax = cMax[c];
        }
        // NB: Uncalibrate values before assigning to display range min/max.
        globalMin -= zeroOffset;
        globalMax -= zeroOffset;
        // apply global display range
        ImageProcessor proc = imp.getProcessor();
        if (proc instanceof ColorProcessor) {
            // NB: Should never occur. ;-)
            final ColorProcessor colorProc = (ColorProcessor) proc;
            colorProc.setMinAndMax(globalMin, globalMax, 3);
        } else {
            ColorModel model = proc.getColorModel();
            proc.setMinAndMax(globalMin, globalMax);
            proc.setColorModel(model);
            imp.setDisplayRange(globalMin, globalMax);
        }
    }
}

Example 2 with ImageProcessorReader

use of loci.plugins.util.ImageProcessorReader in project bioformats by openmicroscopy.

the class ImagePlusReader method finishTiming.

private void finishTiming() {
    final ImageProcessorReader reader = process.getReader();
    long endTime = System.currentTimeMillis();
    double elapsed = (endTime - startTime) / 1000.0;
    if (reader.getImageCount() == 1) {
        notifyListeners(new StatusEvent("Bio-Formats: " + elapsed + " seconds"));
    } else {
        long average = (endTime - startTime) / reader.getImageCount();
        notifyListeners(new StatusEvent("Bio-Formats: " + elapsed + " seconds (" + average + " ms per plane)"));
    }
}

Example 3 with ImageProcessorReader

use of loci.plugins.util.ImageProcessorReader in project bioformats by openmicroscopy.

the class ImagePlusReader method readPlanes.

private ImageStack readPlanes(ImportProcess process, int s, List<LUT> luts, boolean thumbnail) throws FormatException, IOException {
    final ImageProcessorReader reader = process.getReader();
    reader.setSeries(s);
    final int zCount = process.getZCount(s);
    final int cCount = process.getCCount(s);
    final int tCount = process.getTCount(s);
    final IMetadata meta = process.getOMEMetadata();
    // get list of planes to load
    final boolean[] load = getPlanesToLoad(s);
    int current = 0, total = 0;
    for (int j = 0; j < load.length; j++) if (load[j])
        total++;
    final List<ImageProcessor> procs = new ArrayList<ImageProcessor>();
    final List<String> labels = new ArrayList<String>();
    // read applicable image planes
    final Region region = process.getCropRegion(s);
    for (int i = 0; i < load.length; i++) {
        if (!load[i])
            continue;
        // limit message update rate
        updateTiming(s, current, current++, total);
        // get image processor for ith plane
        final ImageProcessor[] p = readProcessors(process, i, region, thumbnail);
        if (p == null || p.length == 0) {
            throw new FormatException("Cannot read plane #" + i);
        }
        // generate a label for ith plane
        String label = constructSliceLabel(i, reader, meta, s, zCount, cCount, tCount);
        for (ImageProcessor ip : p) {
            procs.add(ip);
            labels.add(label);
        }
    }
    return createStack(procs, labels, luts);
}

Example 4 with ImageProcessorReader

use of loci.plugins.util.ImageProcessorReader in project bioformats by openmicroscopy.

the class ImagePlusReader method getPlanesToLoad.

private boolean[] getPlanesToLoad(int s) {
    final ImageProcessorReader reader = process.getReader();
    final boolean[] load = new boolean[reader.getImageCount()];
    final int cBegin = process.getCBegin(s);
    final int cEnd = process.getCEnd(s);
    final int cStep = process.getCStep(s);
    final int zBegin = process.getZBegin(s);
    final int zEnd = process.getZEnd(s);
    final int zStep = process.getZStep(s);
    final int tBegin = process.getTBegin(s);
    final int tEnd = process.getTEnd(s);
    final int tStep = process.getTStep(s);
    for (int c = cBegin; c <= cEnd; c += cStep) {
        for (int z = zBegin; z <= zEnd; z += zStep) {
            for (int t = tBegin; t <= tEnd; t += tStep) {
                int index = reader.getIndex(z, c, t);
                load[index] = true;
            }
        }
    }
    return load;
}

Example 5 with ImageProcessorReader

use of loci.plugins.util.ImageProcessorReader in project bioformats by openmicroscopy.

the class ImagePlusReader method updateTiming.

private void updateTiming(int s, int i, int current, int total) {
    final ImageProcessorReader reader = process.getReader();
    long clock = System.currentTimeMillis();
    if (clock - time >= 100) {
        String sLabel = reader.getSeriesCount() > 1 ? ("series " + (s + 1) + ", ") : "";
        String pLabel = "plane " + (i + 1) + "/" + total;
        notifyListeners(new StatusEvent("Reading " + sLabel + pLabel));
        time = clock;
    }
    notifyListeners(new StatusEvent(current, total, null));
}