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

Example 1 with Memoizer

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

the class MemoizerTest method testConstructorReaderTimeElapsed.

@Test
public void testConstructorReaderTimeElapsed() throws Exception {
    Memoizer memoizer = new Memoizer(reader, 0);
    checkMemoFile(memoizer.getMemoFile(id));
    checkMemo(memoizer, id);
}

Example 2 with Memoizer

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

the class MemoizerTest method testDefaultConstructor.

public void testDefaultConstructor() throws Exception {
    Memoizer memoizer = new Memoizer();
    checkMemoFile(memoizer.getMemoFile(id));
}

Example 3 with Memoizer

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

the class FormatReaderTest method setupReader.

// -- Helper methods --
/**
 * Sets up the current IFormatReader.
 */
private void setupReader() {
    // Remove external SlideBook6Reader class for testing purposes
    ImageReader ir = new ImageReader();
    reader = new BufferedImageReader(new FileStitcher(new Memoizer(ir, Memoizer.DEFAULT_MINIMUM_ELAPSED, new File(""))));
    reader.setMetadataOptions(new DefaultMetadataOptions(MetadataLevel.NO_OVERLAYS));
    reader.setNormalized(true);
    reader.setOriginalMetadataPopulated(false);
    reader.setMetadataFiltered(true);
    MetadataStore store = null;
    try {
        store = omexmlService.createOMEXMLMetadata();
    } catch (ServiceException e) {
        LOGGER.warn("Could not parse OME-XML", e);
    }
    reader.setMetadataStore(store);
}

Example 4 with Memoizer

use of loci.formats.Memoizer 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 5 with Memoizer

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

the class MemoizerTest method testWrappedReader.

@Test
public void testWrappedReader() throws Exception {
    Memoizer memoizer = new Memoizer(reader, 0);
    File memoFile = memoizer.getMemoFile(id);
    assertFalse(memoFile.exists());
    reader.setId(id);
    assertFalse(memoFile.exists());
    reader.close();
    checkMemo(memoizer, id);
}