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

Example 21 with ImageReader

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

the class FileHandleTest method testHandleCount.

@Test
public void testHandleCount() throws FormatException, IOException {
    ArrayList<String> initialHandles = getHandles();
    reader = new ImageReader();
    reader.setId(id);
    ArrayList<String> intermediateHandles = getHandles();
    reader.close();
    ArrayList<String> finalHandles = getHandles();
    int intermediateHandleCount = intermediateHandles.size();
    for (int i = 0; i < initialHandles.size(); i++) {
        String s = initialHandles.get(i);
        initialHandles.remove(s);
        finalHandles.remove(s);
        intermediateHandles.remove(s);
        i--;
    }
    for (int i = 0; i < finalHandles.size(); i++) {
        String s = finalHandles.get(i);
        if (s.endsWith("libnio.so") || s.endsWith("resources.jar") || s.startsWith("/usr/lib") || s.startsWith("/opt/") || s.startsWith("/usr/share/locale") || s.startsWith("/lib") || s.indexOf("turbojpeg") > 0 || s.indexOf("/jre/") > 0 || s.indexOf("nativedata") > 0 || s.indexOf("jhdf") > 0) {
            finalHandles.remove(s);
            i--;
        } else {
            LOGGER.warn(s);
        }
    }
    assertEquals(finalHandles.size(), initialHandles.size());
    assertTrue(intermediateHandles.size() >= initialHandles.size());
    assertTrue(intermediateHandleCount < 1024);
}

Example 22 with ImageReader

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

the class FormatReaderTest method testConsistentReader.

@Test(groups = { "all", "fast", "automated" })
public void testConsistentReader() {
    if (config == null)
        throw new SkipException("No config tree");
    String testName = "testConsistentReader";
    if (!initFile())
        result(testName, false, "initFile");
    String format = config.getReader();
    IFormatReader r = reader;
    if (r instanceof ImageReader) {
        r = ((ImageReader) r).getReader();
    } else if (r instanceof ReaderWrapper) {
        try {
            r = ((ReaderWrapper) r).unwrap();
        } catch (FormatException e) {
        } catch (IOException e) {
        }
    }
    String realFormat = TestTools.shortClassName(r);
    result(testName, realFormat.equals(format), realFormat);
}

Example 23 with ImageReader

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

the class FormatReaderTest method testIsThisType.

@Test(groups = { "all", "fast", "automated" })
public void testIsThisType() {
    String testName = "testIsThisType";
    if (!initFile())
        result(testName, false, "initFile");
    boolean success = true;
    String msg = null;
    try {
        IFormatReader r = reader;
        // unwrap reader
        while (true) {
            if (r instanceof ReaderWrapper) {
                r = ((ReaderWrapper) r).getReader();
            } else if (r instanceof FileStitcher) {
                r = ((FileStitcher) r).getReader();
            } else
                break;
        }
        if (r instanceof ImageReader) {
            ImageReader ir = (ImageReader) r;
            r = ir.getReader();
            IFormatReader[] readers = ir.getReaders();
            String[] used = reader.getUsedFiles();
            for (int i = 0; i < used.length && success; i++) {
                // and only one reader, identifies the dataset as its own
                for (int j = 0; j < readers.length; j++) {
                    boolean result = readers[j].isThisType(used[i]);
                    // TIFF reader is allowed to redundantly green-light files
                    if (result && readers[j] instanceof TiffDelegateReader)
                        continue;
                    // green-light PIC files from NRRD datasets
                    if (result && r instanceof NRRDReader && readers[j] instanceof BioRadReader) {
                        String low = used[i].toLowerCase();
                        boolean isPic = low.endsWith(".pic") || low.endsWith(".pic.gz");
                        if (isPic)
                            continue;
                    }
                    // Analyze reader is allowed to redundantly accept NIfTI files
                    if (result && r instanceof NiftiReader && readers[j] instanceof AnalyzeReader) {
                        continue;
                    }
                    if (result && r instanceof MetamorphReader && readers[j] instanceof MetamorphTiffReader) {
                        continue;
                    }
                    if (result && (readers[j] instanceof L2DReader) || ((r instanceof L2DReader) && (readers[j] instanceof GelReader) || readers[j] instanceof L2DReader)) {
                        continue;
                    }
                    // ND2Reader is allowed to accept JPEG-2000 files
                    if (result && r instanceof JPEG2000Reader && readers[j] instanceof ND2Reader) {
                        continue;
                    }
                    if ((result && r instanceof APLReader && readers[j] instanceof SISReader) || (!result && r instanceof APLReader && readers[j] instanceof APLReader)) {
                        continue;
                    }
                    // reader to pick up TIFFs from a Prairie dataset
                    if (result && r instanceof PrairieReader && readers[j] instanceof OMETiffReader) {
                        continue;
                    }
                    // extra metadata files
                    if (result && r instanceof ColumbusReader && readers[j] instanceof OMETiffReader) {
                        continue;
                    }
                    // with an extra metadata file
                    if (result && r instanceof MicromanagerReader && readers[j] instanceof OMETiffReader) {
                        continue;
                    }
                    if (!result && r instanceof MicromanagerReader && readers[j] instanceof MicromanagerReader && (used[i].toLowerCase().endsWith(".ome.tif") || used[i].toLowerCase().endsWith(".ome.tiff"))) {
                        continue;
                    }
                    if (result && r instanceof TrestleReader && (readers[j] instanceof JPEGReader || readers[j] instanceof PGMReader || readers[j] instanceof TiffDelegateReader)) {
                        continue;
                    }
                    if (result && ((r instanceof HitachiReader) || (readers[j] instanceof HitachiReader && (r instanceof TiffDelegateReader || r instanceof JPEGReader || r instanceof BMPReader)))) {
                        continue;
                    }
                    if (result && r instanceof BDReader && readers[j] instanceof BMPReader) {
                        continue;
                    }
                    if (!result && readers[j] instanceof BDReader && (used[i].endsWith(".bmp") || used[i].endsWith(".adf") || used[i].endsWith(".txt") || used[i].endsWith(".roi"))) {
                        continue;
                    }
                    if (!result && r instanceof VolocityReader && readers[j] instanceof VolocityReader) {
                        continue;
                    }
                    if (!result && r instanceof InCellReader && readers[j] instanceof InCellReader && !used[i].toLowerCase().endsWith(".xdce")) {
                        continue;
                    }
                    if (!result && r instanceof BrukerReader && readers[j] instanceof BrukerReader && !used[i].toLowerCase().equals("acqp") && !used[i].toLowerCase().equals("fid")) {
                        continue;
                    }
                    // Volocity reader is allowed to accept files of other formats
                    if (result && r instanceof VolocityReader) {
                        continue;
                    }
                    if (result && r instanceof NikonReader && readers[j] instanceof DNGReader) {
                        continue;
                    }
                    // DICOM reader is not expected to pick up companion files
                    if (!result && r instanceof DicomReader && readers[j] instanceof DicomReader) {
                        continue;
                    }
                    // AFI reader is not expected to pick up .svs files
                    if (r instanceof AFIReader && (readers[j] instanceof AFIReader || readers[j] instanceof SVSReader)) {
                        continue;
                    }
                    if (!result && readers[j] instanceof MIASReader) {
                        continue;
                    }
                    if ((readers[j] instanceof NDPISReader || r instanceof NDPISReader) && used[i].toLowerCase().endsWith(".ndpi")) {
                        continue;
                    }
                    // Hamamatsu VMS dataset
                    if (readers[j] instanceof JPEGReader && r instanceof HamamatsuVMSReader && used[i].toLowerCase().endsWith(".jpg")) {
                        continue;
                    }
                    // the Hamamatsu VMS reader only picks up its .vms file
                    if (!result && !used[i].toLowerCase().endsWith(".vms") && r instanceof HamamatsuVMSReader) {
                        continue;
                    }
                    // QuickTime reader doesn't pick up resource forks
                    if (!result && i > 0 && r instanceof QTReader) {
                        continue;
                    }
                    if (r instanceof CellVoyagerReader && (!result || readers[j] instanceof OMEXMLReader) && used[i].toLowerCase().endsWith(".ome.xml")) {
                        continue;
                    }
                    // the pattern reader only picks up pattern files
                    if (!used[i].toLowerCase().endsWith(".pattern") && r instanceof FilePatternReader) {
                        continue;
                    }
                    // ignore companion files for Leica LIF
                    if (!used[i].toLowerCase().endsWith(".lif") && r instanceof LIFReader) {
                        continue;
                    }
                    boolean expected = r == readers[j];
                    if (result != expected) {
                        success = false;
                        if (result) {
                            msg = TestTools.shortClassName(readers[j]) + " flagged \"" + used[i] + "\" but so did " + TestTools.shortClassName(r);
                        } else {
                            msg = TestTools.shortClassName(readers[j]) + " skipped \"" + used[i] + "\"";
                        }
                        break;
                    }
                }
            }
        } else {
            success = false;
            msg = "Reader " + r.getClass().getName() + " is not an ImageReader";
        }
    } catch (Throwable t) {
        LOGGER.info("", t);
        success = false;
    }
    result(testName, success, msg);
}

Example 24 with ImageReader

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

the class FileConvert method initialize.

/**
 * Set up the file reader and writer, ensuring that the input file is
 * associated with the reader and the output file is associated with the
 * writer.
 *
 * @return true if the reader and writer were successfully set up, or false
 *   if an error occurred
 */
private boolean initialize() {
    Exception exception = null;
    try {
        // construct the object that stores OME-XML metadata
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        IMetadata omexml = service.createOMEXMLMetadata();
        // set up the reader and associate it with the input file
        reader = new ImageReader();
        reader.setMetadataStore(omexml);
        reader.setId(inputFile);
        // set up the writer and associate it with the output file
        writer = new ImageWriter();
        writer.setMetadataRetrieve(omexml);
        writer.setInterleaved(reader.isInterleaved());
        writer.setId(outputFile);
    } catch (FormatException e) {
        exception = e;
    } catch (IOException e) {
        exception = e;
    } catch (DependencyException e) {
        exception = e;
    } catch (ServiceException e) {
        exception = e;
    }
    if (exception != null) {
        System.err.println("Failed to initialize files.");
        exception.printStackTrace();
    }
    return exception == null;
}

Example 25 with ImageReader

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

the class OverlappedTiledWriter method initialize.

/**
 * Set up the file reader and writer, ensuring that the input file is
 * associated with the reader and the output file is associated with the
 * writer.
 *
 * @return true if the reader and writer were successfully set up, or false
 *   if an error occurred
 * @throws DependencyException thrown if failed to create an OMEXMLService
 * @throws IOException thrown if unable to setup input or output stream for reader or writer
 * @throws FormatException thrown if invalid ID set for reader or writer or invalid tile size set
 * @throws ServiceException thrown if unable to create OME-XML meta data
 */
private void initialize() throws DependencyException, FormatException, IOException, ServiceException {
    // construct the object that stores OME-XML metadata
    ServiceFactory factory = new ServiceFactory();
    OMEXMLService service = factory.getInstance(OMEXMLService.class);
    IMetadata omexml = service.createOMEXMLMetadata();
    // set up the reader and associate it with the input file
    reader = new ImageReader();
    reader.setMetadataStore(omexml);
    reader.setId(inputFile);
    // set up the writer and associate it with the output file
    writer = new OMETiffWriter();
    writer.setMetadataRetrieve(omexml);
    writer.setInterleaved(reader.isInterleaved());
    // set the tile size height and width for writing
    this.tileSizeX = writer.setTileSizeX(tileSizeX);
    this.tileSizeY = writer.setTileSizeY(tileSizeY);
    writer.setId(outputFile);
}