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

Example 6 with ChannelSeparator

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

the class BaseModelNoBinDataReaderTest method testSetId.

@Test
public void testSetId() throws Exception {
    reader = new MinMaxCalculator(new ChannelSeparator(new ChannelFiller(new ImageReader())));
    metadata = new OMEXMLMetadataImpl();
    reader.setMetadataStore(metadata);
    reader.setId(temporaryFile.getAbsolutePath());
}

Example 7 with ChannelSeparator

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

the class ImageInfo method configureReaderPreInit.

public void configureReaderPreInit() throws FormatException, IOException {
    if (omexml) {
        reader.setOriginalMetadataPopulated(originalMetadata);
        try {
            ServiceFactory factory = new ServiceFactory();
            OMEXMLService service = factory.getInstance(OMEXMLService.class);
            reader.setMetadataStore(service.createOMEXMLMetadata(null, omexmlVersion));
        } catch (DependencyException de) {
            throw new MissingLibraryException(OMEXMLServiceImpl.NO_OME_XML_MSG, de);
        } catch (ServiceException se) {
            throw new FormatException(se);
        }
    }
    // check file format
    if (reader instanceof ImageReader) {
        // determine format
        ImageReader ir = (ImageReader) reader;
        if (new Location(id).exists()) {
            LOGGER.info("Checking file format [{}]", ir.getFormat(id));
        }
    } else {
        // verify format
        LOGGER.info("Checking {} format [{}]", reader.getFormat(), reader.isThisType(id) ? "yes" : "no");
    }
    LOGGER.info("Initializing reader");
    if (stitch) {
        reader = new FileStitcher(reader, true);
        Location f = new Location(id);
        String pat = null;
        if (!f.exists()) {
            ((FileStitcher) reader).setUsingPatternIds(true);
            pat = id;
        } else {
            pat = FilePattern.findPattern(f);
        }
        if (pat != null)
            id = pat;
    }
    if (expand)
        reader = new ChannelFiller(reader);
    if (separate)
        reader = new ChannelSeparator(reader);
    if (merge)
        reader = new ChannelMerger(reader);
    if (cache) {
        if (cachedir != null) {
            reader = new Memoizer(reader, 0, new File(cachedir));
        } else {
            reader = new Memoizer(reader, 0);
        }
    }
    minMaxCalc = null;
    if (minmax || autoscale)
        reader = minMaxCalc = new MinMaxCalculator(reader);
    dimSwapper = null;
    if (swapOrder != null || shuffleOrder != null) {
        reader = dimSwapper = new DimensionSwapper(reader);
    }
    reader = biReader = new BufferedImageReader(reader);
    reader.close();
    reader.setNormalized(normalize);
    reader.setMetadataFiltered(filter);
    reader.setGroupFiles(group);
    options.setMetadataLevel(doMeta ? MetadataLevel.ALL : MetadataLevel.MINIMUM);
    options.setValidate(validate);
    reader.setMetadataOptions(options);
    reader.setFlattenedResolutions(flat);
}

Example 8 with ChannelSeparator

use of loci.formats.ChannelSeparator 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 9 with ChannelSeparator

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

the class AFIReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    // The AFI file is just simple XML that lists the .svs files from
    // which to read pixel data.  Each .svs corresponds to a single channel;
    // we assemble the channels in the order in which they are stored in
    // the XML.
    // 
    // Note that the last two series are identical across the .svs files,
    // so we just use the ones from the first listed file.
    String xml = DataTools.readFile(id);
    XMLTools.parseXML(xml, new AFIHandler());
    String parent = new Location(id).getAbsoluteFile().getParent();
    String[] channelNames = new String[pixels.size()];
    reader = new ChannelSeparator[pixels.size()];
    for (int i = 0; i < pixels.size(); i++) {
        String file = pixels.get(i);
        int underscore = file.indexOf('_');
        int fullStop = file.indexOf('.');
        if (underscore >= 0 && fullStop > underscore) {
            channelNames[i] = file.substring(underscore + 1, fullStop);
        }
        pixels.set(i, new Location(parent, file).getAbsolutePath());
        reader[i] = new ChannelSeparator(new SVSReader());
        reader[i].setFlattenedResolutions(hasFlattenedResolutions());
        reader[i].setId(pixels.get(i));
    }
    core = reader[0].getCoreMetadataList();
    for (int i = 0; i < core.size() - EXTRA_IMAGES; i++) {
        CoreMetadata c = core.get(i);
        c.sizeC = pixels.size();
        c.imageCount = c.sizeC * c.sizeZ * c.sizeT;
        c.rgb = false;
        if (i == 0) {
            c.resolutionCount = core.size() - EXTRA_IMAGES;
        }
    }
    MetadataStore store = makeFilterMetadata();
    boolean minimalMetadata = getMetadataOptions().getMetadataLevel() == MetadataLevel.MINIMUM;
    MetadataTools.populatePixels(store, this, !minimalMetadata);
    String fileID = currentId.substring(currentId.lastIndexOf(File.separator) + 1, currentId.lastIndexOf("."));
    for (int i = 0; i < getSeriesCount(); i++) {
        store.setImageName(fileID + " - image #" + (i + 1), i);
    }
    if (!minimalMetadata) {
        Length[] emission = new Length[pixels.size()];
        Length[] excitation = new Length[pixels.size()];
        Double[] exposure = new Double[pixels.size()];
        Timestamp[] datestamp = new Timestamp[pixels.size()];
        Length[] physicalSizes = null;
        double magnification = Double.NaN;
        for (int c = 0; c < pixels.size(); c++) {
            SVSReader baseReader = (SVSReader) reader[c].getReader();
            emission[c] = baseReader.getEmission();
            excitation[c] = baseReader.getExcitation();
            exposure[c] = baseReader.getExposureTime();
            datestamp[c] = baseReader.getDatestamp();
            physicalSizes = baseReader.getPhysicalSizes();
            if (c == 0) {
                magnification = baseReader.getMagnification();
            }
        }
        String instrument = MetadataTools.createLSID("Instrument", 0);
        String objective = MetadataTools.createLSID("Objective", 0, 0);
        store.setInstrumentID(instrument, 0);
        store.setObjectiveID(objective, 0, 0);
        store.setObjectiveNominalMagnification(magnification, 0, 0);
        for (int i = 0; i < getSeriesCount() - EXTRA_IMAGES; i++) {
            if (datestamp[0] != null) {
                store.setImageAcquisitionDate(datestamp[0], i);
            }
            store.setImageInstrumentRef(instrument, i);
            store.setObjectiveSettingsID(objective, i);
            if (i < physicalSizes.length && physicalSizes[i] != null && physicalSizes[i].value(UNITS.MICROMETER).doubleValue() - Constants.EPSILON > 0) {
                Length size = physicalSizes[i];
                store.setPixelsPhysicalSizeX(size, i);
                store.setPixelsPhysicalSizeY(size, i);
            }
            for (int c = 0; c < channelNames.length; c++) {
                store.setChannelName(channelNames[c], i, c);
                if (emission[c] != null) {
                    store.setChannelEmissionWavelength(emission[c], i, c);
                }
                if (excitation[c] != null) {
                    store.setChannelExcitationWavelength(excitation[c], i, c);
                }
                store.setPlaneExposureTime(FormatTools.createTime(exposure[c], UNITS.SECOND), i, c);
            }
        }
    }
}

Example 10 with ChannelSeparator

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

the class AFIReader method close.

/* @see loci.formats.IFormatReader#close(boolean) */
@Override
public void close(boolean fileOnly) throws IOException {
    super.close(fileOnly);
    if (!fileOnly) {
        if (reader != null) {
            for (ChannelSeparator r : reader) {
                if (r != null) {
                    r.close();
                }
            }
        }
        reader = null;
        pixels.clear();
    }
}