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

Example 11 with ChannelSeparator

use of loci.formats.ChannelSeparator 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 12 with ChannelSeparator

use of loci.formats.ChannelSeparator 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 13 with ChannelSeparator

use of loci.formats.ChannelSeparator 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;
}

Example 14 with ChannelSeparator

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

the class BaseModelReaderTest 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 15 with ChannelSeparator

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

the class NDPISReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    Location parent = new Location(id).getAbsoluteFile().getParentFile();
    String[] lines = DataTools.readFile(currentId).split("\r\n");
    for (String line : lines) {
        int eq = line.indexOf('=');
        if (eq < 0) {
            continue;
        }
        String key = line.substring(0, eq).trim();
        String value = line.substring(eq + 1).trim();
        if (key.equals("NoImages")) {
            ndpiFiles = new String[Integer.parseInt(value)];
            readers = new ChannelSeparator[ndpiFiles.length];
        } else if (key.startsWith("Image")) {
            int index = Integer.parseInt(key.replaceAll("Image", ""));
            ndpiFiles[index] = new Location(parent, value).getAbsolutePath();
            readers[index] = new ChannelSeparator(new NDPIReader());
            readers[index].setFlattenedResolutions(hasFlattenedResolutions());
        }
    }
    MetadataStore store = makeFilterMetadata();
    readers[0].getReader().setMetadataStore(store);
    readers[0].setId(ndpiFiles[0]);
    core = new ArrayList<CoreMetadata>(readers[0].getCoreMetadataList());
    for (int i = 0; i < core.size(); i++) {
        CoreMetadata ms = core.get(i);
        ms.sizeC = readers.length;
        ms.rgb = false;
        ms.imageCount = ms.sizeC * ms.sizeZ * ms.sizeT;
    }
    MetadataTools.populatePixels(store, this);
    bandUsed = new int[ndpiFiles.length];
    IFD ifd;
    for (int c = 0; c < readers.length; c++) {
        // populate channel names based on IFD entry
        try (RandomAccessInputStream in = new RandomAccessInputStream(ndpiFiles[c])) {
            TiffParser tp = new TiffParser(in);
            ifd = tp.getIFDs().get(0);
        }
        String channelName = ifd.getIFDStringValue(TAG_CHANNEL);
        Float wavelength = (Float) ifd.getIFDValue(TAG_EMISSION_WAVELENGTH);
        store.setChannelName(channelName, 0, c);
        store.setChannelEmissionWavelength(new Length(wavelength, UNITS.NANOMETER), 0, c);
        bandUsed[c] = 0;
        if (ifd.getSamplesPerPixel() >= 3) {
            // 580 < wavelength <= 780 Red
            if (380 < wavelength && wavelength <= 490)
                bandUsed[c] = 2;
            else if (490 < wavelength && wavelength <= 580)
                bandUsed[c] = 1;
            else if (580 < wavelength && wavelength <= 780)
                bandUsed[c] = 0;
        }
    }
}