Examples with DimensionSwapper loci.formats.DimensionSwapper used on opensource projects

Example 6 with DimensionSwapper

use of loci.formats.DimensionSwapper in project bioformats by openmicroscopy.

the class WrapperTest method createWrappers.

@DataProvider(name = "wrappers")
public Object[][] createWrappers() {
    Location.mapId(TEST_FILE, TEST_FILE);
    Object[][] wrappers = new Object[][] { { new ChannelFiller() }, { new ChannelMerger() }, { new ChannelSeparator() }, { new DimensionSwapper() }, { new FileStitcher() }, { new ImageReader() }, { new MinMaxCalculator() }, { new Memoizer() } };
    for (int i = 0; i < wrappers.length; i++) {
        IFormatReader reader = (IFormatReader) wrappers[i][0];
        try {
            reader.setId(TEST_FILE);
        } catch (FormatException e) {
            e.printStackTrace();
        } catch (IOException e) {
            e.printStackTrace();
        }
    }
    return wrappers;
}

Example 7 with DimensionSwapper

use of loci.formats.DimensionSwapper 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;
}