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

Example 11 with ImageProcessorReader

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

the class SwapDialog method harvestResults.

@Override
protected boolean harvestResults(GenericDialog gd) {
    ImageProcessorReader reader = process.getReader();
    int seriesCount = process.getSeriesCount();
    for (int s = 0; s < seriesCount; s++) {
        if (!options.isSeriesOn(s))
            continue;
        reader.setSeries(s);
        int z = Integer.parseInt(gd.getNextChoice());
        int c = Integer.parseInt(gd.getNextChoice());
        int t = Integer.parseInt(gd.getNextChoice());
        int originalZ = reader.getSizeZ();
        int originalC = reader.getSizeC();
        int originalT = reader.getSizeT();
        String originalOrder = reader.getDimensionOrder();
        StringBuffer sb = new StringBuffer();
        sb.append("XY");
        for (int i = 2; i < originalOrder.length(); i++) {
            int originalValue = 0;
            switch(originalOrder.charAt(i)) {
                case 'Z':
                    originalValue = originalZ;
                    break;
                case 'C':
                    originalValue = originalC;
                    break;
                case 'T':
                    originalValue = originalT;
                    break;
            }
            if (originalValue == z && sb.indexOf("Z") < 0) {
                sb.append("Z");
            } else if (originalValue == c && sb.indexOf("C") < 0) {
                sb.append("C");
            } else if (originalValue == t && sb.indexOf("T") < 0) {
                sb.append("T");
            }
        }
        options.setInputOrder(s, sb.toString());
    }
    return true;
}

Example 12 with ImageProcessorReader

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

the class Slicer method makeStack.

/**
 * Returns a new ImageStack using the given ImageStack as a template.
 */
private ImageStack makeStack(ImageStack stack) {
    if (!(stack instanceof BFVirtualStack)) {
        return new ImageStack(stack.getWidth(), stack.getHeight());
    }
    BFVirtualStack virtualStack = (BFVirtualStack) stack;
    String path = virtualStack.getPath();
    ImageProcessorReader reader = virtualStack.getReader();
    try {
        return new BFVirtualStack(path, reader, false, false, false);
    } catch (FormatException e) {
        WindowTools.reportException(e);
    } catch (IOException e) {
        WindowTools.reportException(e);
    }
    return null;
}

Example 13 with ImageProcessorReader

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

the class Read_Image method run.

public void run(String arg) {
    OpenDialog od = new OpenDialog("Open Image File...", arg);
    String dir = od.getDirectory();
    String name = od.getFileName();
    String id = dir + name;
    ImageProcessorReader r = new ImageProcessorReader(new ChannelSeparator(LociPrefs.makeImageReader()));
    try {
        IJ.showStatus("Examining file " + name);
        r.setId(id);
        int num = r.getImageCount();
        int width = r.getSizeX();
        int height = r.getSizeY();
        ImageStack stack = new ImageStack(width, height);
        byte[][][] lookupTable = new byte[r.getSizeC()][][];
        for (int i = 0; i < num; i++) {
            IJ.showStatus("Reading image plane #" + (i + 1) + "/" + num);
            ImageProcessor ip = r.openProcessors(i)[0];
            stack.addSlice("" + (i + 1), ip);
            int channel = r.getZCTCoords(i)[1];
            lookupTable[channel] = r.get8BitLookupTable();
        }
        IJ.showStatus("Constructing image");
        ImagePlus imp = new ImagePlus(name, stack);
        ImagePlus colorizedImage = applyLookupTables(r, imp, lookupTable);
        r.close();
        colorizedImage.show();
        IJ.showStatus("");
    } catch (FormatException exc) {
        IJ.error("Sorry, an error occurred: " + exc.getMessage());
    } catch (IOException exc) {
        IJ.error("Sorry, an error occurred: " + exc.getMessage());
    }
}

Example 14 with ImageProcessorReader

use of loci.plugins.util.ImageProcessorReader 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 15 with ImageProcessorReader

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

the class Colorizer method makeLUTs.

private LUT[] makeLUTs(int series) {
    final ImageProcessorReader reader = process.getReader();
    reader.setSeries(series);
    LUT[] luts = new LUT[reader.getSizeC()];
    for (int c = 0; c < luts.length; c++) luts[c] = makeLUT(series, c);
    return luts;
}