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

Example 51 with ImageReader

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

the class TrestleReader method parseROIs.

// -- Helper methods --
private void parseROIs(MetadataStore store) throws FormatException, IOException {
    String roiID = MetadataTools.createLSID("ROI", 0, 0);
    String maskID = MetadataTools.createLSID("Shape", 0, 0);
    store.setROIID(roiID, 0);
    store.setMaskID(maskID, 0, 0);
    String positionData = DataTools.readFile(roiDrawFile);
    String[] coordinates = positionData.split("[ ,]");
    double x1 = Double.parseDouble(coordinates[1]);
    double y1 = Double.parseDouble(coordinates[2]);
    double x2 = Double.parseDouble(coordinates[3]);
    double y2 = Double.parseDouble(coordinates[5]);
    store.setMaskX(x1, 0, 0);
    store.setMaskY(y1, 0, 0);
    store.setMaskWidth(x2 - x1, 0, 0);
    store.setMaskHeight(y2 - y1, 0, 0);
    store.setImageROIRef(roiID, 0, 0);
    ImageReader roiReader = new ImageReader();
    roiReader.setId(roiFile);
    byte[] roiPixels = roiReader.openBytes(0);
    roiReader.close();
    BitWriter bits = new BitWriter(roiPixels.length / 8);
    for (int i = 0; i < roiPixels.length; i++) {
        bits.write(roiPixels[i] == 0 ? 0 : 1, 1);
    }
    store.setMaskBinData(bits.toByteArray(), 0, 0);
}

Example 52 with ImageReader

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

the class ConvertToOmeTiff method main.

public static void main(String[] args) throws Exception {
    if (args.length == 0) {
        System.out.println("Usage: java ConvertToOmeTiff file1 file2 ...");
        return;
    }
    ImageReader reader = new ImageReader();
    OMETiffWriter writer = new OMETiffWriter();
    for (int i = 0; i < args.length; i++) {
        String id = args[i];
        int dot = id.lastIndexOf(".");
        String outId = (dot >= 0 ? id.substring(0, dot) : id) + ".ome.tif";
        System.out.print("Converting " + id + " to " + outId + " ");
        // record metadata to OME-XML format
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        IMetadata omexmlMeta = service.createOMEXMLMetadata();
        reader.setMetadataStore(omexmlMeta);
        reader.setId(id);
        // configure OME-TIFF writer
        writer.setMetadataRetrieve(omexmlMeta);
        writer.setId(outId);
        // writer.setCompression("J2K");
        // write out image planes
        int seriesCount = reader.getSeriesCount();
        for (int s = 0; s < seriesCount; s++) {
            reader.setSeries(s);
            writer.setSeries(s);
            int planeCount = reader.getImageCount();
            for (int p = 0; p < planeCount; p++) {
                byte[] plane = reader.openBytes(p);
                // write plane to output file
                writer.saveBytes(p, plane);
                System.out.print(".");
            }
        }
        writer.close();
        reader.close();
        System.out.println(" [done]");
    }
}

Example 53 with ImageReader

use of loci.formats.ImageReader 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 54 with ImageReader

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

the class Colorizer method makeLUTs.

private LUT[] makeLUTs(ColorModel[] cm, boolean colorize) {
    // lookup tables can come from one of three places (in order of precedence):
    // 1) Color attribute defined in the MetadataStore
    // 2) lookup table returned by the reader's get8BitLookupTable or
    // get16BitLookupTable methods
    // 3) EmissionWavelength attribute defined in the MetadataStore
    final ImporterOptions options = process.getOptions();
    final LUT[] luts = new LUT[cm.length];
    for (int c = 0; c < luts.length; c++) {
        if (cm[c] instanceof LUT)
            luts[c] = (LUT) cm[c];
        else if (cm[c] instanceof IndexColorModel) {
            luts[c] = new LUT((IndexColorModel) cm[c], 0, 255);
        }
        Color color = null;
        if (colorize) {
            // rather than always assuming that the first channel is red, the
            // second green, etc. we will take into account the channel color
            // metadata and the acquisition wavelength
            ImageReader reader = process.getImageReader();
            MetadataStore store = reader.getMetadataStore();
            if (store instanceof MetadataRetrieve) {
                MetadataRetrieve retrieve = (MetadataRetrieve) store;
                if (c < retrieve.getChannelCount(reader.getSeries())) {
                    ome.xml.model.primitives.Color metaColor = retrieve.getChannelColor(reader.getSeries(), c);
                    if (metaColor != null) {
                        int r = metaColor.getRed();
                        int g = metaColor.getGreen();
                        int b = metaColor.getBlue();
                        int a = metaColor.getAlpha();
                        color = new Color(r, g, b, a);
                    } else if (luts[c] == null) {
                        Length wavelength = retrieve.getChannelEmissionWavelength(reader.getSeries(), c);
                        if (wavelength != null) {
                            double wave = wavelength.value(UNITS.NANOMETER).doubleValue();
                            if (wave >= BLUE_MIN && wave < BLUE_TO_GREEN_MIN) {
                                color = Color.BLUE;
                            } else if (wave >= BLUE_TO_GREEN_MIN && wave < GREEN_TO_RED_MIN) {
                                color = Color.GREEN;
                            } else if (wave >= GREEN_TO_RED_MIN && wave <= RED_MAX) {
                                color = Color.RED;
                            }
                        }
                    }
                }
            }
        }
        if (color == null && luts[c] == null) {
            color = options.getDefaultCustomColor(c);
        }
        if (color != null) {
            luts[c] = makeLUT(color);
        }
    }
    return luts;
}

Example 55 with ImageReader

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

the class ImportProcess method createBaseReader.

/**
 * Initializes an {@link loci.formats.IFormatReader}
 * according to the current configuration.
 */
private void createBaseReader() throws FormatException, IOException {
    if (options.isLocal() || options.isHTTP()) {
        BF.status(options.isQuiet(), "Identifying " + idName);
        imageReader = LociPrefs.makeImageReader();
        baseReader = imageReader.getReader(options.isUsingPatternIds() ? new FilePattern(options.getId()).getFiles()[0] : options.getId());
    } else if (options.isOMERO()) {
        BF.status(options.isQuiet(), "Establishing server connection");
        try {
            ReflectedUniverse r = new ReflectedUniverse();
            r.exec("import loci.ome.io.OmeroReader");
            r.exec("baseReader = new OmeroReader()");
            ClassList<IFormatReader> classes = new ClassList<IFormatReader>(IFormatReader.class);
            r.setVar("classes", classes);
            r.exec("class = baseReader.getClass()");
            r.exec("classes.addClass(class)");
            imageReader = new ImageReader(classes);
            baseReader = imageReader.getReader(options.getId());
        } catch (Exception exc) {
            WindowTools.reportException(exc, options.isQuiet(), "Sorry, there was a problem communicating with the server.");
            cancel();
            return;
        }
    } else {
        WindowTools.reportException(null, options.isQuiet(), "Sorry, there has been an internal error: unknown data source");
        cancel();
        return;
    }
    // attach OME-XML metadata store
    Exception exc = null;
    try {
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        meta = service.createOMEXMLMetadata();
        omeXML = null;
    } catch (DependencyException de) {
        exc = de;
    } catch (ServiceException se) {
        exc = se;
    }
    if (exc != null) {
        WindowTools.reportException(exc, options.isQuiet(), "Sorry, there was a problem constructing the OME-XML metadata store");
        throw new FormatException(exc);
    }
    baseReader.setMetadataStore(meta);
    BF.status(options.isQuiet(), "");
    DebugTools.enableIJLogging(IJ.debugMode);
}