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

Example 6 with ImageProcessorReader

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

the class ImagePlusReader method createVirtualStack.

private ImageStack createVirtualStack(ImportProcess process, int s, List<LUT> luts) throws FormatException, IOException {
    final ImporterOptions options = process.getOptions();
    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();
    final int imageCount = reader.getImageCount();
    // CTR FIXME: Make virtual stack work with different color modes?
    final BFVirtualStack virtualStack = new BFVirtualStack(options.getId(), reader, false, false, false);
    for (int i = 0; i < imageCount; i++) {
        String label = constructSliceLabel(i, reader, meta, s, zCount, cCount, tCount);
        virtualStack.addSlice(label);
    }
    if (luts != null) {
        for (int c = 0; c < cCount; c++) {
            int index = reader.getIndex(0, c, 0);
            ImageProcessor ip = reader.openProcessors(index)[0];
            final ColorModel cm = ip.getColorModel();
            final LUT lut = cm instanceof LUT ? (LUT) cm : null;
            luts.add(lut);
        }
    }
    return virtualStack;
}

Example 7 with ImageProcessorReader

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

the class ColorDialog method constructDialog.

@Override
protected GenericDialog constructDialog() {
    GenericDialog gd = new GenericDialog("Bio-Formats Custom Colorization");
    // CTR FIXME - avoid problem with MAX_SLIDERS in GenericDialog
    final ImageProcessorReader reader = process.getReader();
    final List<Panel> swatches = new ArrayList<Panel>();
    for (int s = 0; s < process.getSeriesCount(); s++) {
        if (!options.isSeriesOn(s))
            continue;
        reader.setSeries(s);
        for (int c = 0; c < reader.getSizeC(); c++) {
            Color color = options.getCustomColor(s, c);
            if (color == null)
                color = options.getDefaultCustomColor(c);
            gd.addSlider(makeLabel("Red:", s, c), 0, 255, color.getRed());
            gd.addSlider(makeLabel("Green:", s, c), 0, 255, color.getGreen());
            gd.addSlider(makeLabel("Blue:", s, c), 0, 255, color.getBlue());
            Panel swatch = createSwatch(color);
            gd.addPanel(swatch, GridBagConstraints.CENTER, new Insets(5, 0, 5, 0));
            swatches.add(swatch);
        }
    }
    // change swatch colors when sliders move
    List<TextField> colorFields = getNumericFields(gd);
    attachListeners(colorFields, swatches);
    WindowTools.addScrollBars(gd);
    return gd;
}

Example 8 with ImageProcessorReader

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

the class ColorDialog method harvestResults.

@Override
protected boolean harvestResults(GenericDialog gd) {
    final ImageProcessorReader reader = process.getReader();
    for (int s = 0; s < process.getSeriesCount(); s++) {
        if (!options.isSeriesOn(s))
            continue;
        reader.setSeries(s);
        for (int c = 0; c < reader.getSizeC(); c++) {
            int red = (int) gd.getNextNumber();
            int green = (int) gd.getNextNumber();
            int blue = (int) gd.getNextNumber();
            Color color = new Color(red, green, blue);
            options.setCustomColor(s, c, color);
        }
    }
    return true;
}

Example 9 with ImageProcessorReader

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

the class ImportProcess method initializeStack.

/**
 * Performed following ImportStep.STACK notification.
 */
private void initializeStack() throws FormatException, IOException {
    IFormatReader r = baseReader;
    if (options.isGroupFiles()) {
        r = fileStitcher = new FileStitcher(baseReader);
        // overwrite base filename with file pattern
        String id = options.getId();
        fileStitcher.setId(id);
        fileStitcher.setUsingPatternIds(true);
        fileStitcher.setCanChangePattern(false);
    }
    r.setId(options.getId());
    if (options.isGroupFiles()) {
        options.setId(fileStitcher.getFilePattern().getPattern());
    }
    final byte[][] lut8 = r.get8BitLookupTable();
    final int sizeC = r.getSizeC();
    r = channelFiller = new ChannelFiller(r);
    if (channelFiller.isFilled()) {
        BF.warn(options.isQuiet(), getIdName() + ": index values will be lost");
    }
    r = channelSeparator = new ChannelSeparator(r);
    r = dimensionSwapper = new DimensionSwapper(r);
    if (options.isAutoscale() || FormatTools.isFloatingPoint(r)) {
        r = minMaxCalculator = new MinMaxCalculator(r);
    }
    if (options.doStitchTiles()) {
        r = tileStitcher = new TileStitcher(r);
    }
    r = virtualReader = new VirtualReader(r);
    reader = new ImageProcessorReader(r);
    if (options != null && !options.showROIs()) {
        baseReader.getMetadataOptions().setMetadataLevel(MetadataLevel.NO_OVERLAYS);
    }
    setId();
    computeSeriesLabels(reader);
}

Example 10 with ImageProcessorReader

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

the class SwapDialog method constructDialog.

@Override
protected GenericDialog constructDialog() {
    ImageProcessorReader reader = process.getReader();
    int seriesCount = process.getSeriesCount();
    GenericDialog gd = new GenericDialog("Dimension swapping options");
    String[] labels = { "Z", "C", "T" };
    for (int s = 0; s < seriesCount; s++) {
        if (!options.isSeriesOn(s))
            continue;
        reader.setSeries(s);
        String[] sizes = new String[] { String.valueOf(reader.getSizeZ()), String.valueOf(reader.getSizeC()), String.valueOf(reader.getSizeT()) };
        gd.addMessage("Series " + (s + 1) + ":\n");
        for (int i = 0; i < labels.length; i++) {
            gd.addChoice(labels[i] + "_" + (s + 1), sizes, sizes[i]);
        }
    }
    List<Choice> choices = WindowTools.getChoices(gd);
    zChoice = choices.get(0);
    cChoice = choices.get(1);
    tChoice = choices.get(2);
    zChoice.addItemListener(this);
    cChoice.addItemListener(this);
    tChoice.addItemListener(this);
    WindowTools.addScrollBars(gd);
    return gd;
}