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

Example 31 with ImageReader

use of loci.formats.ImageReader 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 32 with ImageReader

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

the class EightBitLosslessJPEG2000Test method testLosslessPixels.

@Test
public void testLosslessPixels() throws Exception {
    int failureCount = 0;
    for (int i = 0; i < files.size(); i++) {
        ImageReader reader = new ImageReader();
        reader.setId(files.get(i));
        byte[] plane = reader.openBytes(0);
        if (plane[0] != pixels[i][0]) {
            LOGGER.debug("FAILED on {}", pixels[i][0]);
            failureCount++;
        }
        reader.close();
    }
    assertEquals(failureCount, 0);
}

Example 33 with ImageReader

use of loci.formats.ImageReader in project digilib by robcast.

the class BioFormatsDocuImage method identify.

/*
     * (non-Javadoc)
     * 
     * @see digilib.image.DocuImageImpl#identify(digilib.io.ImageInput)
     */
@Override
public ImageInput identify(ImageInput ii) throws IOException {
    ImageReader reader = new ImageReader();
    try {
        reader.setId(ii.getFile().getAbsolutePath());
    } catch (FormatException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    int width = reader.getSizeX();
    int height = reader.getSizeY();
    String fmt = reader.getFormat();
    String mt = "";
    if (fmt.equalsIgnoreCase("Tagged Image File Format")) {
        mt = "image/tiff";
    } else if (fmt.equalsIgnoreCase("JPEG")) {
        mt = "image/jpeg";
    }
    logger.debug("BioFormats identify: width=" + width + " height=" + height + " format=" + fmt + " mimetype=" + mt);
    ii.setSize(new ImageSize(width, height));
    ii.setMimetype(mt);
    return ii;
}

Example 34 with ImageReader

use of loci.formats.ImageReader 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 35 with ImageReader

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

the class ImageInfo method testRead.

/**
 * A utility method for reading a file from the command line,
 * and displaying the results in a simple display.
 */
public boolean testRead(String[] args) throws FormatException, ServiceException, IOException {
    for (final String arg : args) {
        if (HELP_ARGUMENTS.contains(arg)) {
            if (reader == null) {
                reader = new ImageReader();
            }
            printUsage();
            return false;
        }
    }
    boolean validArgs = parseArgs(args);
    if (!validArgs)
        return false;
    if (printVersion) {
        CommandLineTools.printVersion();
        return true;
    }
    CommandLineTools.runUpgradeCheck(args);
    createReader();
    if (id == null) {
        printUsage();
        return false;
    }
    mapLocation();
    configureReaderPreInit();
    // initialize reader
    long s = System.currentTimeMillis();
    try {
        reader.setId(id);
    } catch (FormatException exc) {
        reader.close();
        LOGGER.error("Failure during the reader initialization");
        LOGGER.debug("", exc);
        return false;
    }
    long e = System.currentTimeMillis();
    float sec = (e - s) / 1000f;
    LOGGER.info("Initialization took {}s", sec);
    configureReaderPostInit();
    checkWarnings();
    readCoreMetadata();
    reader.setSeries(series);
    if (flat == false)
        reader.setResolution(resolution);
    initPreMinMaxValues();
    // read pixels
    if (pixels)
        readPixels();
    // read format-specific metadata table
    if (doMeta) {
        printGlobalMetadata();
        printOriginalMetadata();
    }
    // output OME-XML
    if (omexml)
        printOMEXML();
    if (!pixels) {
        reader.close();
    }
    return true;
}