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

Example 91 with FormatException

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

the class LociFunctions method openImagePlus.

public void openImagePlus(String path) {
    ImagePlus[] imps = null;
    try {
        ImporterOptions options = new ImporterOptions();
        options.setId(path);
        options.setSeriesOn(series, true);
        imps = BF.openImagePlus(options);
        for (ImagePlus imp : imps) imp.show();
    } catch (IOException exc) {
        IJ.handleException(exc);
    } catch (FormatException exc) {
        IJ.handleException(exc);
    }
}

Example 92 with FormatException

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

the class LociFunctions method openThumbImagePlus.

public void openThumbImagePlus(String path) {
    ImagePlus[] imps = null;
    try {
        ImporterOptions options = new ImporterOptions();
        options.setId(path);
        options.setSeriesOn(series, true);
        imps = BF.openThumbImagePlus(options);
        for (ImagePlus imp : imps) imp.show();
    } catch (IOException exc) {
        IJ.handleException(exc);
    } catch (FormatException exc) {
        IJ.handleException(exc);
    }
}

Example 93 with FormatException

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

the class MetadataConfigurableTest method testSetId.

@Test
public void testSetId() throws FormatException, IOException {
    long t0 = System.currentTimeMillis();
    pixelsOnly.setId(id);
    assertEquals(MetadataLevel.MINIMUM, pixelsOnly.getMetadataOptions().getMetadataLevel());
    long t1 = System.currentTimeMillis();
    all.setId(id);
    assertEquals(MetadataLevel.ALL, all.getMetadataOptions().getMetadataLevel());
    assertFalse(0 == all.getSeriesMetadata().size() + all.getGlobalMetadata().size());
    long t2 = System.currentTimeMillis();
    System.err.println(String.format("Pixels only: %d -- All: %d", t1 - t0, t2 - t1));
    IMetadata metadata = null;
    try {
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        metadata = service.createOMEXMLMetadata();
        noOverlays.setMetadataStore(metadata);
    } catch (Exception e) {
        throw new FormatException("Cannot initialize OMEXML metadata store");
    }
    noOverlays.setId(id);
    assertEquals(MetadataLevel.NO_OVERLAYS, noOverlays.getMetadataOptions().getMetadataLevel());
    assertEquals(metadata.getROICount(), 0);
}

Example 94 with FormatException

use of loci.formats.FormatException 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 95 with FormatException

use of loci.formats.FormatException 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;
}