Examples with CompositeImage ij.CompositeImage used on opensource projects

Example 16 with CompositeImage

use of ij.CompositeImage in project bioformats by openmicroscopy.

the class ImporterTest method imagePlusLutTest.

// TODO : can I replace all calls to this to colorTests() passing numChannels == 1. Another way: modify lutTest() to
// use a standard ImagePlus rather than a CompImg and have it call getColorTable(). Then pass in just RED ramped
// test values.
private void imagePlusLutTest(ImagePlus imp, boolean indexed, boolean falseColor, Color color) {
    // When numCh < 2 or numCh > 7 the setColorMode() code for Composite and Colorize cannot create a CompositeImage.
    // Therefore it creates a one channel ImagePlus with a LUT that only ramps the red channel. Test this to be
    // the case.
    assertFalse(imp instanceof CompositeImage);
    if (indexed) {
        fail("not yet supporting indexed");
    }
    LUT lut = getColorTable(imp, 0);
    byte[] data = new byte[256];
    if (color.getRed() > 0) {
        lut.getReds(data);
        ascendingValuesTest(data, 256);
    }
    if (color.getGreen() > 0) {
        lut.getGreens(data);
        ascendingValuesTest(data, 256);
    }
    if (color.getBlue() > 0) {
        lut.getBlues(data);
        ascendingValuesTest(data, 256);
    }
}

Example 17 with CompositeImage

use of ij.CompositeImage in project bioformats by openmicroscopy.

the class ImporterTest method colorColorizedTester.

/**
 * tests BF's options.setColorMode(colorized)
 */
private void colorColorizedTester(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("colorColorized", pixType, sizeX, sizeY, sizeZ, channels, sizeT, numSeries, indexed, chanPerPlane, falseColor, -1);
    LOGGER.debug("colorColorizedTester: {}", path);
    ImagePlus[] imps = null;
    try {
        ImporterOptions options = new ImporterOptions();
        options.setAutoscale(false);
        options.setVirtual(virtual);
        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];
    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, 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 18 with CompositeImage

use of ij.CompositeImage in project bioformats by openmicroscopy.

the class Colorizer method applyColors.

// -- Colorizer methods --
public List<ImagePlus> applyColors(List<ImagePlus> imps) {
    final ImporterOptions options = process.getOptions();
    final ImageProcessorReader reader = process.getReader();
    final DimensionSwapper dimSwapper = process.getDimensionSwapper();
    final ChannelFiller channelFiller = process.getChannelFiller();
    final ImageReader imageReader = process.getImageReader();
    for (int i = 0; i < imps.size(); i++) {
        ImagePlus imp = imps.get(i);
        final int series = (Integer) imp.getProperty(ImagePlusReader.PROP_SERIES);
        reader.setSeries(series);
        // get LUT for each channel
        final String stackOrder = dimSwapper.getDimensionOrder();
        final int zSize = imp.getNSlices();
        final int cSize = imp.getNChannels();
        final int tSize = imp.getNFrames();
        final int stackSize = imp.getStackSize();
        final LUT[] channelLUTs = new LUT[cSize];
        boolean hasChannelLUT = false;
        for (int c = 0; c < cSize; c++) {
            final int index = FormatTools.getIndex(stackOrder, zSize, cSize, tSize, stackSize, 0, c, 0);
            channelLUTs[c] = (LUT) imp.getProperty(ImagePlusReader.PROP_LUT + index);
            if (channelLUTs[c] != null)
                hasChannelLUT = true;
        }
        // compute color mode and LUTs to use
        int mode = -1;
        LUT[] luts;
        if (options.isColorModeDefault()) {
            // NB: Default color mode behavior depends on the situation.
            final boolean isRGB = reader.isRGB() || imageReader.isRGB();
            if (isRGB || channelFiller.isFilled()) {
                // NB: The original data had more than one channel per plane
                // (e.g., RGB image planes), so we use the composite display mode.
                mode = CompositeImage.COMPOSITE;
                // preserve original LUTs
                luts = makeLUTs(channelLUTs, true);
            } else if (hasChannelLUT) {
                // NB: The original data had only one channel per plane,
                // but had at least one lookup table defined. We use the color
                // display mode, with missing LUTs as grayscale.
                mode = CompositeImage.COLOR;
                // preserve original LUTs
                luts = makeLUTs(channelLUTs, true);
            } else {
                // NB: The original data had only one channel per plane,
                // and had no lookup tables defined, so we use the grayscale mode.
                mode = CompositeImage.GRAYSCALE;
                luts = null;
            }
        } else if (options.isColorModeComposite()) {
            mode = CompositeImage.COMPOSITE;
            // preserve existing channel LUTs
            luts = makeLUTs(channelLUTs, true);
        } else if (options.isColorModeColorized()) {
            mode = CompositeImage.COLOR;
            // preserve existing channel LUTs
            luts = makeLUTs(channelLUTs, true);
        } else if (options.isColorModeGrayscale()) {
            mode = CompositeImage.GRAYSCALE;
            // use default (grayscale) channel LUTs
            luts = null;
        } else if (options.isColorModeCustom()) {
            mode = CompositeImage.COLOR;
            // override any existing channel LUTs
            luts = makeLUTs(series);
        } else {
            throw new IllegalStateException("Invalid color mode: " + options.getColorMode());
        }
        // apply color mode and LUTs
        final boolean doComposite = !options.isViewStandard() && mode != -1 && cSize > 1 && cSize <= 7;
        if (doComposite) {
            final ImagePlus toClose = imp;
            CompositeImage compImage = new CompositeImage(imp, mode) {

                @Override
                public void close() {
                    super.close();
                    toClose.close();
                }

                @Override
                public void show(String message) {
                    super.show(message);
                    // see ticket #12267
                    if (toClose instanceof VirtualImagePlus) {
                        int channel = getChannel();
                        double min = getDisplayRangeMin();
                        double max = getDisplayRangeMax();
                        for (int c = 0; c < cSize; c++) {
                            setPositionWithoutUpdate(c + 1, getSlice(), getFrame());
                            setDisplayRange(min, max);
                        }
                        reset();
                        setPosition(channel, getSlice(), getFrame());
                    }
                }
            };
            compImage.setProperty(ImagePlusReader.PROP_SERIES, series);
            if (luts != null)
                compImage.setLuts(luts);
            imps.set(i, compImage);
            imp = compImage;
        } else {
            // NB: Cannot use CompositeImage for some reason.
            if (luts != null && luts.length > 0 && luts[0] != null) {
                if (imp instanceof VirtualImagePlus) {
                    ((VirtualImagePlus) imp).setLUTs(luts);
                } else if (cSize == 1)
                    imp.getProcessor().setColorModel(luts[0]);
            }
            if (mode != -1 && cSize > 7) {
                // NB: Cannot use CompositeImage with more than seven channels.
                BF.warn(options.isQuiet(), "Data has too many channels for " + options.getColorMode() + " color mode");
            }
        }
        applyDisplayRanges(imp, series);
    }
    return imps;
}

Example 19 with CompositeImage

use of ij.CompositeImage in project bioformats by openmicroscopy.

the class Slicer method reslice.

// -- Slicer methods --
public ImagePlus[] reslice(ImagePlus imp, boolean sliceC, boolean sliceZ, boolean sliceT, String stackOrder) {
    ImageStack stack = imp.getImageStack();
    boolean hyperstack = imp.isHyperStack();
    Calibration calibration = imp.getCalibration();
    int sizeZ = imp.getNSlices();
    int sizeC = imp.getNChannels();
    int sizeT = imp.getNFrames();
    int slicesPerStack = stack.getSize();
    if (sliceZ)
        slicesPerStack /= sizeZ;
    if (sliceC)
        slicesPerStack /= sizeC;
    if (sliceT)
        slicesPerStack /= sizeT;
    int realSizeZ = sliceZ ? 1 : sizeZ;
    int realSizeC = sliceC ? 1 : sizeC;
    int realSizeT = sliceT ? 1 : sizeT;
    BFVirtualStack virtualStack = null;
    if (stack instanceof BFVirtualStack) {
        virtualStack = (BFVirtualStack) stack;
    }
    ImageStack[] newStacks = new ImageStack[stack.getSize() / slicesPerStack];
    for (int i = 0; i < newStacks.length; i++) {
        newStacks[i] = makeStack(stack);
        if (newStacks[i] == null)
            return null;
    }
    int stackZ = sliceZ ? sizeZ : 1;
    int stackC = sliceC ? sizeC : 1;
    int stackT = sliceT ? sizeT : 1;
    int[][] planeIndexes = new int[newStacks.length][slicesPerStack];
    for (int i = 0; i < sizeZ * sizeC * sizeT; i++) {
        int[] zct = FormatTools.getZCTCoords(stackOrder, sizeZ, sizeC, sizeT, stack.getSize(), i);
        int stackNdx = FormatTools.getIndex(stackOrder, stackZ, stackC, stackT, newStacks.length, sliceZ ? zct[0] : 0, sliceC ? zct[1] : 0, sliceT ? zct[2] : 0);
        String label = stack.getSliceLabel(i + 1);
        if (virtualStack != null) {
            ((BFVirtualStack) newStacks[stackNdx]).addSlice(label);
            int sliceNdx = FormatTools.getIndex(stackOrder, realSizeZ, realSizeC, realSizeT, slicesPerStack, sliceZ ? 0 : zct[0], sliceC ? 0 : zct[1], sliceT ? 0 : zct[2]);
            planeIndexes[stackNdx][sliceNdx] = i;
        } else {
            newStacks[stackNdx].addSlice(label, stack.getProcessor(i + 1));
        }
    }
    ImagePlus[] newImps = new ImagePlus[newStacks.length];
    for (int i = 0; i < newStacks.length; i++) {
        if (virtualStack != null) {
            ((BFVirtualStack) newStacks[i]).setPlaneIndexes(planeIndexes[i]);
        }
        int[] zct = FormatTools.getZCTCoords(stackOrder, stackZ, stackC, stackT, newStacks.length, i);
        if (imp.isComposite()) {
            CompositeImage composite = (CompositeImage) imp;
            if (composite.getMode() == CompositeImage.COLOR) {
                LUT lut = composite.getChannelLut(zct[1] + 1);
                newStacks[i].setColorModel(lut);
            }
        }
        String title = imp.getTitle();
        title += " -";
        if (sliceZ)
            title += " Z=" + zct[0];
        if (sliceT)
            title += " T=" + zct[2];
        if (sliceC)
            title += " C=" + zct[1];
        ImagePlus p = null;
        if (virtualStack != null) {
            p = new VirtualImagePlus(title, newStacks[i]);
            ((VirtualImagePlus) p).setReader(virtualStack.getReader());
        } else {
            p = new ImagePlus(title, newStacks[i]);
        }
        p.setProperty(ImagePlusReader.PROP_SERIES, imp.getProperty(ImagePlusReader.PROP_SERIES));
        p.setProperty("Info", imp.getProperty("Info"));
        p.setDimensions(realSizeC, realSizeZ, realSizeT);
        p.setCalibration(calibration);
        p.setFileInfo(imp.getOriginalFileInfo());
        if (!p.isComposite()) {
            p.setOpenAsHyperStack(hyperstack);
        }
        if (imp.isComposite() && !sliceC) {
            p = reorder(p, stackOrder, "XYCZT");
            int mode = ((CompositeImage) imp).getMode();
            newImps[i] = new CompositeImage(p, mode);
        } else
            newImps[i] = p;
        double max = imp.getDisplayRangeMax();
        double min = imp.getDisplayRangeMin();
        newImps[i].setDisplayRange(min, max);
        if (imp.isComposite() && newImps[i].isComposite()) {
            for (int c = 1; c < newImps[i].getNChannels(); c++) {
                LUT originalLut = ((CompositeImage) imp).getChannelLut(c);
                LUT lut = ((CompositeImage) newImps[i]).getChannelLut(c);
                lut.min = originalLut.min;
                lut.max = originalLut.max;
            }
        }
    }
    return newImps;
}

Example 20 with CompositeImage

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

the class CameraModelManager method runViewCameraModel.

private void runViewCameraModel(CameraModelSettings settings) {
    final GenericDialog gd = new GenericDialog(TITLE);
    final String[] models = listCameraModels(false);
    gd.addChoice("Model", models, pluginSettings.getSelected());
    gd.addHelp(HelpUrls.getUrl("camera-model-manager-view"));
    gd.showDialog();
    if (gd.wasCanceled()) {
        return;
    }
    final String name = gd.getNextChoice();
    pluginSettings.setSelected(name);
    // Try and get the named resource
    final CameraModelResource resource = settings.getCameraModelResourcesMap().get(name);
    if (resource == null) {
        IJ.error(TITLE, "Failed to find camera data for model: " + name);
        return;
    }
    // Try and load the resource.
    // Do not use loadFromFile as that validates the model data. We just want
    // to view the raw image.
    ImagePlus imp = IJ.openImage(resource.getFilename());
    // Remove the status from the ij.io.ImageWriter class
    IJ.showStatus("");
    if (imp == null) {
        IJ.error(TITLE, "Failed to load camera data for model: " + name);
        return;
    }
    final ImageStack stack = imp.getImageStack();
    if (stack.getSize() != 3) {
        IJ.error(TITLE, "Failed to load camera data for model: " + name + ".\nExpecting stack of size 3 but it was " + stack.getSize());
        return;
    }
    ImageJUtils.log("Camera model: %s\n%s", name, resource);
    for (int n = 1; n <= stack.getSize(); n++) {
        logStats(stack.getSliceLabel(n), stack.getProcessor(n));
    }
    // Show normalised variance: var/g^2
    final float[] varG2 = new float[stack.getWidth() * stack.getHeight()];
    try {
        final float[] gain = (float[]) stack.getPixels(2);
        final float[] variance = (float[]) stack.getPixels(3);
        final ExtendedStatistics stats1 = new ExtendedStatistics();
        final ExtendedStatistics stats2 = new ExtendedStatistics();
        for (int i = 0; i < gain.length; i++) {
            final double v1 = variance[i] / MathUtils.pow2(gain[i]);
            varG2[i] = (float) v1;
            stats1.add(Math.sqrt(v1));
            stats2.add(v1);
        }
        logStats("var/g^2", stats2);
        logStats("sqrt(var/g^2)", stats1);
    } catch (final Exception ex) {
        ImageJUtils.log("Failed to load camera model %s from file: %s. %s", name, resource.getFilename(), ex.getMessage());
    }
    stack.addSlice("var/g^2", varG2);
    // Create as a hyper stack
    imp = new ImagePlus(name, stack);
    imp.setDimensions(4, 1, 1);
    imp.setOpenAsHyperStack(true);
    final CompositeImage cimp = new CompositeImage(imp, CompositeImage.GRAYSCALE);
    cimp.resetDisplayRanges();
    for (int n = 1; n <= 4; n++) {
        cimp.setSliceWithoutUpdate(n);
        ImageJUtils.autoAdjust(cimp, true);
    }
    cimp.setSliceWithoutUpdate(1);
    imp = WindowManager.getImage(name);
    if (imp != null) {
        imp.setImage(cimp);
    } else {
        cimp.show();
    }
}