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

Example 6 with ChannelFiller

use of loci.formats.ChannelFiller 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 7 with ChannelFiller

use of loci.formats.ChannelFiller 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 8 with ChannelFiller

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

the class ReaderEqualityTest method createEqualWrappers.

@DataProvider(name = "equalWrappers")
public Object[][] createEqualWrappers() {
    Location.mapId(TEST_FILE_A, TEST_FILE_A);
    Location.mapId(TEST_FILE_B, TEST_FILE_B);
    Object[][] wrappers = new Object[][] { { new ImageReader(), new ImageReader() }, { new ImageReader(), new ImageReader() }, { new MinMaxCalculator(new ChannelSeparator(new ChannelFiller())), new MinMaxCalculator(new ChannelSeparator(new ChannelFiller())) }, { new DimensionSwapper(new ChannelMerger()), new DimensionSwapper(new ChannelMerger()) } };
    for (int i = 1; i < wrappers.length; i++) {
        IFormatReader readerA = (IFormatReader) wrappers[i][0];
        IFormatReader readerB = (IFormatReader) wrappers[i][1];
        try {
            readerA.setId(TEST_FILE_A);
            readerB.setId(TEST_FILE_B);
        } catch (FormatException e) {
            e.printStackTrace();
        } catch (IOException e) {
            e.printStackTrace();
        }
    }
    return wrappers;
}

Example 9 with ChannelFiller

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

the class ReaderEqualityTest method createUnequalWrappers.

@DataProvider(name = "unequalWrappers")
public Object[][] createUnequalWrappers() {
    Object[][] wrappers = new Object[][] { { new ImageReader(), new ImageReader() }, { new ImageReader(), new ImageReader() }, { new MinMaxCalculator(new ChannelSeparator(new ChannelFiller())), new MinMaxCalculator(new ChannelSeparator()) }, { new DimensionSwapper(new ChannelMerger()), new DimensionSwapper(new ChannelMerger()) } };
    for (int i = 0; i < wrappers.length; i++) {
        IFormatReader readerA = (IFormatReader) wrappers[i][0];
        IFormatReader readerB = (IFormatReader) wrappers[i][1];
        try {
            if (i != 1) {
                readerA.setId(TEST_FILE_A);
            } else {
                readerA.setId(TEST_FILE_B);
            }
            if (i > 1) {
                readerB.setId(TEST_FILE_B);
            } else if (i == 1) {
                readerB.setId(TEST_FILE_A);
            }
        } catch (FormatException e) {
            e.printStackTrace();
        } catch (IOException e) {
            e.printStackTrace();
        }
    }
    return wrappers;
}

Example 10 with ChannelFiller

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

the class WrapperTest method createWrappers.

@DataProvider(name = "wrappers")
public Object[][] createWrappers() {
    Location.mapId(TEST_FILE, TEST_FILE);
    Object[][] wrappers = new Object[][] { { new ChannelFiller() }, { new ChannelMerger() }, { new ChannelSeparator() }, { new DimensionSwapper() }, { new FileStitcher() }, { new ImageReader() }, { new MinMaxCalculator() }, { new Memoizer() } };
    for (int i = 0; i < wrappers.length; i++) {
        IFormatReader reader = (IFormatReader) wrappers[i][0];
        try {
            reader.setId(TEST_FILE);
        } catch (FormatException e) {
            e.printStackTrace();
        } catch (IOException e) {
            e.printStackTrace();
        }
    }
    return wrappers;
}