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

Example 36 with ImageReader

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

the class PrintFormatTable method printSupportedFormats.

public static void printSupportedFormats(String[] args) {
    PrintStyles printStyle = PrintStyles.TXT;
    boolean usage = false;
    if (args != null) {
        for (int i = 0; i < args.length; i++) {
            if (args[i].equals("-help"))
                usage = true;
            else if (args[i].equals("-xml"))
                printStyle = PrintStyles.XML;
            else if (args[i].equals("-html"))
                printStyle = PrintStyles.HTML;
            else if (args[i].equals("-txt"))
                printStyle = PrintStyles.TXT;
            else {
                LOGGER.warn("unknown flag: {}; try -help for options", args[i]);
            }
        }
    }
    if (usage) {
        LOGGER.info("Usage: formatlist [-html] [-txt] [-xml]");
        LOGGER.info("  -html: show formats in an HTML table");
        LOGGER.info("   -txt: show formats in plaintext (default)");
        LOGGER.info("   -xml: show formats as XML data");
        return;
    }
    LOGGER.info(getHeader(printStyle));
    // retrieve all of the file format readers and writers
    ImageReader baseReader = new ImageReader();
    IFormatReader[] readers = baseReader.getReaders();
    ImageWriter baseWriter = new ImageWriter();
    IFormatWriter[] writers = baseWriter.getWriters();
    for (int i = 0; i < readers.length; i++) {
        String readerFormatName = readers[i].getFormat();
        boolean read = true;
        boolean write = false;
        boolean wmp = false;
        // check if there is a corresponding writer
        IFormatWriter writer = null;
        for (int j = 0; j < writers.length; j++) {
            if (writers[j].getFormat().equals(readerFormatName)) {
                writer = writers[j];
            }
        }
        if (writer != null) {
            write = true;
            // written to a single file
            if (writer.canDoStacks())
                wmp = true;
        }
        String[] extensions = readers[i].getSuffixes();
        StringBuilder ext = new StringBuilder();
        for (int j = 0; j < extensions.length; j++) {
            ext.append(extensions[j]);
            if (j < extensions.length - 1) {
                ext.append(", ");
            }
        }
        // display information about the format
        LOGGER.info(getFormatLine(printStyle, readerFormatName, read, write, wmp, ext.toString()));
    }
    LOGGER.info(getFooter(printStyle));
}

Example 37 with ImageReader

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

the class ImageConverterTest method checkImage.

public void checkImage() throws FormatException, IOException {
    IFormatReader r = new ImageReader();
    r.setId(outFile.getAbsolutePath());
    assertEquals(r.getSizeX(), 512);
    r.close();
}

Example 38 with ImageReader

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

the class GUITools method buildFileFilters.

// -- File chooser --
/**
 * Constructs a list of file filters for the given file format handler.
 */
public static FileFilter[] buildFileFilters(IFormatHandler handler) {
    FileFilter[] filters = null;
    // unwrap reader
    while (true) {
        if (handler instanceof ReaderWrapper) {
            handler = ((ReaderWrapper) handler).getReader();
        } else if (handler instanceof FileStitcher) {
            handler = ((FileStitcher) handler).getReader();
        } else if (handler instanceof WriterWrapper) {
            handler = ((WriterWrapper) handler).getWriter();
        } else
            break;
    }
    // handle special cases of ImageReader and ImageWriter
    if (handler instanceof ImageReader) {
        ImageReader imageReader = (ImageReader) handler;
        IFormatReader[] readers = imageReader.getReaders();
        Vector filterList = new Vector();
        Vector comboList = new Vector();
        for (int i = 0; i < readers.length; i++) {
            filterList.add(new FormatFileFilter(readers[i]));
            // NB: Some readers need to open a file to determine if it is the
            // proper type, when the extension alone is insufficient to
            // distinguish. This behavior is fine for individual filters, but not
            // for ImageReader's combination filter, because it makes the combo
            // filter too slow. So rather than composing the combo filter from
            // FormatFileFilters, we use faster but less accurate
            // ExtensionFileFilters instead.
            String[] suffixes = readers[i].getSuffixes();
            String format = readers[i].getFormat();
            comboList.add(new ExtensionFileFilter(suffixes, format));
        }
        comboList.add(new NoExtensionFileFilter());
        FileFilter combo = makeComboFilter(sortFilters(comboList));
        if (combo != null)
            filterList.add(combo);
        filters = sortFilters(filterList);
    } else if (handler instanceof ImageWriter) {
        IFormatWriter[] writers = ((ImageWriter) handler).getWriters();
        Vector filterList = new Vector();
        for (int i = 0; i < writers.length; i++) {
            String[] suffixes = writers[i].getSuffixes();
            String format = writers[i].getFormat();
            filterList.add(new ExtensionFileFilter(suffixes, format));
        }
        filters = sortFilters(filterList);
    } else // handle default reader and writer cases
    if (handler instanceof IFormatReader) {
        IFormatReader reader = (IFormatReader) handler;
        filters = new FileFilter[] { new FormatFileFilter(reader) };
    } else {
        String[] suffixes = handler.getSuffixes();
        String format = handler.getFormat();
        filters = new FileFilter[] { new ExtensionFileFilter(suffixes, format) };
    }
    return filters;
}

Example 39 with ImageReader

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

the class Schema_Transform_Test method setUp.

/**
 * Overridden to initialize the list.
 *
 * @see AbstractServerTest#setUp()
 */
@Override
@BeforeClass
protected void setUp() throws Exception {
    super.setUp();
    upgrades = new HashMap<String, List<String>>();
    downgrades = currentSchema();
    windowsOS = (System.getProperty("os.name").toLowerCase().indexOf("windows") > -1);
    factory = new ServiceFactory();
    service = factory.getInstance(OMEXMLService.class);
    metadata = service.createOMEXMLMetadata();
    reader = new ImageReader();
    reader.setMetadataStore(metadata);
}

Example 40 with ImageReader

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

the class SixteenBitLosslessJPEG2000Test method testLosslessPixels.

@Test
public void testLosslessPixels() throws Exception {
    int failureCount = 0;
    for (int v = Short.MIN_VALUE; v < Short.MAX_VALUE; v += increment) {
        int index = v + Short.MAX_VALUE + 1;
        byte[] pixels = DataTools.shortToBytes((short) v, false);
        String file = index + ".jp2";
        ByteArrayHandle tmpFile = new ByteArrayHandle(1);
        Location.mapFile(file, tmpFile);
        IMetadata metadata16;
        try {
            ServiceFactory factory = new ServiceFactory();
            OMEXMLService service = factory.getInstance(OMEXMLService.class);
            metadata16 = service.createOMEXMLMetadata();
        } catch (DependencyException exc) {
            throw new FormatException("Could not create OME-XML store.", exc);
        } catch (ServiceException exc) {
            throw new FormatException("Could not create OME-XML store.", exc);
        }
        MetadataTools.populateMetadata(metadata16, 0, "foo", false, "XYCZT", "uint16", 1, 1, 1, 1, 1, 1);
        IFormatWriter writer16 = new JPEG2000Writer();
        writer16.setMetadataRetrieve(metadata16);
        writer16.setId(file);
        writer16.saveBytes(0, pixels);
        writer16.close();
        byte[] buf = tmpFile.getBytes();
        byte[] realData = new byte[(int) tmpFile.length()];
        System.arraycopy(buf, 0, realData, 0, realData.length);
        tmpFile.close();
        tmpFile = new ByteArrayHandle(realData);
        Location.mapFile(file, tmpFile);
        ImageReader reader = new ImageReader();
        reader.setId(file);
        byte[] plane = reader.openBytes(0);
        for (int q = 0; q < plane.length; q++) {
            if (plane[q] != pixels[q]) {
                LOGGER.debug("FAILED on {}", DataTools.bytesToShort(pixels, false));
                failureCount++;
                break;
            }
        }
        reader.close();
        tmpFile.close();
        Location.mapFile(file, null);
    }
    assertEquals(failureCount, 0);
}