Examples with CompositeImage ij.CompositeImage used on opensource projects

Example 1 with CompositeImage

use of ij.CompositeImage 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 CompositeImage

use of ij.CompositeImage in project bioformats by openmicroscopy.

the class ImporterTest method colorizeSubcaseTester.

private void colorizeSubcaseTester(int pixType, int sizeC, int rgb, boolean indexed, boolean falseColor, int lutLen) {
    if ((pixType != FormatTools.UINT8) && (pixType != FormatTools.UINT16))
        throw new IllegalArgumentException("Invalid pixelType: not UINT8 or UINT16 (" + pixType + ")");
    if (sizeC % rgb != 0)
        throw new IllegalArgumentException("Bad combo of sizeC and rgb: " + sizeC + " " + rgb);
    int channelsPerPlane = rgb;
    if (channelsPerPlane > 7)
        throw new IllegalArgumentException("Bad sizeC; channelsPerPlane > 7 : " + channelsPerPlane);
    int sizeX = 60, sizeY = 30, sizeZ = 1, sizeT = 1, numSeries = 1;
    String path = constructFakeFilename("colorColorized", pixType, sizeX, sizeY, sizeZ, sizeC, sizeT, numSeries, indexed, rgb, falseColor, lutLen);
    LOGGER.debug("colorizeSubcaseTester: {}", path);
    ImagePlus[] imps = null;
    try {
        ImporterOptions options = new ImporterOptions();
        options.setAutoscale(false);
        options.setColorMode(ImporterOptions.COLOR_MODE_COLORIZED);
        options.setId(path);
        imps = BF.openImagePlus(options);
    } catch (IOException e) {
        fail(e.getMessage());
    } catch (FormatException e) {
        fail(e.getMessage());
    }
    impsCountTest(imps, 1);
    ImagePlus imp = imps[0];
    if (lutLen == -1)
        lutLen = 3;
    int expectedSizeC = effectiveC(sizeC, rgb, lutLen, indexed, falseColor);
    xyzctTest(imp, sizeX, sizeY, sizeZ, expectedSizeC, sizeT);
    if (imp.isComposite()) {
        CompositeImage ci = (CompositeImage) imp;
        assertTrue(ci.hasCustomLuts());
        assertEquals(CompositeImage.COLOR, ci.getMode());
        // TODO - falseColor stuff needs to be impl
        if (!falseColor)
            colorTests(ci, expectedSizeC, DEFAULT_COLOR_ORDER);
    } else {
        LOGGER.debug("  Not a composite image");
    }
}

Example 3 with CompositeImage

use of ij.CompositeImage in project bioformats by openmicroscopy.

the class ImporterTest method colorCustomTester.

/**
 * tests BF's options.setColorMode(custom)
 */
private void colorCustomTester(boolean virtual, int pixType, boolean indexed, int channels, int chanPerPlane, boolean falseColor, int numSeries) {
    int sizeX = 55, sizeY = 71, sizeZ = 3, sizeT = 4;
    String path = constructFakeFilename("colorCustom", pixType, sizeX, sizeY, sizeZ, channels, sizeT, numSeries, indexed, chanPerPlane, falseColor, -1);
    LOGGER.debug("colorCustomTester: {}", path);
    ImagePlus[] imps = null;
    try {
        ImporterOptions options = new ImporterOptions();
        options.setAutoscale(false);
        options.setVirtual(virtual);
        options.setColorMode(ImporterOptions.COLOR_MODE_CUSTOM);
        int maxChannels = (channels <= 7) ? channels : 7;
        for (int s = 0; s < numSeries; s++) for (int c = 0; c < maxChannels; c++) options.setCustomColor(s, c, CUSTOM_COLOR_ORDER[c]);
        options.setId(path);
        imps = BF.openImagePlus(options);
    } catch (IOException e) {
        fail(e.getMessage());
    } catch (FormatException e) {
        fail(e.getMessage());
    }
    impsCountTest(imps, 1);
    ImagePlus imp = imps[0];
    int lutLen = 3;
    int expectedSizeC = effectiveC(channels, chanPerPlane, lutLen, indexed, falseColor);
    xyzctTest(imp, sizeX, sizeY, sizeZ, expectedSizeC, sizeT);
    if ((expectedSizeC >= 2) && (expectedSizeC <= 7)) {
        assertTrue(imp.isComposite());
        CompositeImage ci = (CompositeImage) imp;
        assertTrue(ci.hasCustomLuts());
        assertEquals(CompositeImage.COLOR, ci.getMode());
        colorTests(ci, expectedSizeC, CUSTOM_COLOR_ORDER);
    } else // expectedSizeC < 2 or > 7 - we should have gotten back a regular ImagePlus
    {
        assertFalse(imp.isComposite());
        imagePlusLutTest(imp, indexed, falseColor, CUSTOM_COLOR_ORDER[0]);
    }
    stackInCztOrderTest(imp, sizeZ, expectedSizeC, sizeT, indexed, falseColor);
// TODO : i've done no pixel testing
}

Example 4 with CompositeImage

use of ij.CompositeImage in project bioformats by openmicroscopy.

the class ImporterTest method colorGrayscaleTester.

/**
 * tests BF's options.setColorMode(gray)
 */
private void colorGrayscaleTester(boolean virtual, int pixType, boolean indexed, int channels, int chanPerPlane, boolean falseColor, int numSeries) {
    int sizeX = 55, sizeY = 71, sizeZ = 3, sizeT = 4;
    String path = constructFakeFilename("colorGrayscale", pixType, sizeX, sizeY, sizeZ, channels, sizeT, numSeries, indexed, chanPerPlane, falseColor, -1);
    LOGGER.debug("colorGrayscaleTester: {}", path);
    ImagePlus[] imps = null;
    try {
        ImporterOptions options = new ImporterOptions();
        options.setAutoscale(false);
        options.setVirtual(virtual);
        options.setColorMode(ImporterOptions.COLOR_MODE_GRAYSCALE);
        options.setId(path);
        imps = BF.openImagePlus(options);
    } catch (IOException e) {
        fail(e.getMessage());
    } catch (FormatException e) {
        fail(e.getMessage());
    }
    impsCountTest(imps, 1);
    ImagePlus imp = imps[0];
    int lutLen = 3;
    int expectedSizeC = effectiveC(channels, chanPerPlane, lutLen, indexed, falseColor);
    xyzctTest(imp, sizeX, sizeY, sizeZ, expectedSizeC, sizeT);
    if ((expectedSizeC >= 2) && (expectedSizeC <= 7)) {
        assertTrue(imp.isComposite());
        CompositeImage ci = (CompositeImage) imp;
        assertFalse(ci.hasCustomLuts());
        assertEquals(CompositeImage.GRAYSCALE, ci.getMode());
        colorTests(ci, expectedSizeC, DEFAULT_COLOR_ORDER);
    } else // expectedSizeC < 2 or > 7 - we should have gotten back a regular ImagePlus
    {
        assertFalse(imp.isComposite());
        imagePlusLutTest(imp, indexed, falseColor, DEFAULT_COLOR_ORDER[0]);
    }
    stackInCztOrderTest(imp, sizeZ, expectedSizeC, sizeT, indexed, falseColor);
// TODO : i've done no pixel testing
}

Example 5 with CompositeImage

use of ij.CompositeImage in project GDSC-SMLM by aherbert.

the class PulseActivationAnalysis method displayComposite.

private static void displayComposite(ImageProcessor[] images, String name) {
    // We do not yet know the size
    ImageStack stack = null;
    for (int i = 0; i < images.length; i++) {
        final ImageProcessor ip = images[i];
        if (stack == null) {
            stack = new ImageStack(ip.getWidth(), ip.getHeight());
        }
        ip.setColorModel(null);
        stack.addSlice("C" + (i + 1), ip);
    }
    // Create a composite
    ImagePlus imp = new ImagePlus(name, stack);
    imp.setDimensions(images.length, 1, 1);
    final CompositeImage ci = new CompositeImage(imp, IJ.COMPOSITE);
    autoAdjust(ci, ci.getProcessor());
    imp = WindowManager.getImage(name);
    if (imp != null && imp.isComposite()) {
        ci.setMode(imp.getCompositeMode());
        imp.setImage(ci);
        imp.getWindow().toFront();
    } else {
        ci.show();
        imp = ci;
    }
    if (WindowManager.getWindow("Channels") == null) {
        IJ.run("Channels Tool...");
        final Window w = WindowManager.getWindow("Channels");
        if (w == null) {
            return;
        }
        final Window w2 = imp.getWindow();
        if (w2 == null) {
            return;
        }
        final java.awt.Point p = w2.getLocation();
        p.x += w2.getWidth();
        w.setLocation(p);
    }
}