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

Example 1 with DimensionSwapper

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

the class ImportProcess method initializeStack.

/**
 * Performed following ImportStep.STACK notification.
 */
private void initializeStack() throws FormatException, IOException {
    IFormatReader r = baseReader;
    if (options.isGroupFiles()) {
        r = fileStitcher = new FileStitcher(baseReader);
        // overwrite base filename with file pattern
        String id = options.getId();
        fileStitcher.setId(id);
        fileStitcher.setUsingPatternIds(true);
        fileStitcher.setCanChangePattern(false);
    }
    r.setId(options.getId());
    if (options.isGroupFiles()) {
        options.setId(fileStitcher.getFilePattern().getPattern());
    }
    final byte[][] lut8 = r.get8BitLookupTable();
    final int sizeC = r.getSizeC();
    r = channelFiller = new ChannelFiller(r);
    if (channelFiller.isFilled()) {
        BF.warn(options.isQuiet(), getIdName() + ": index values will be lost");
    }
    r = channelSeparator = new ChannelSeparator(r);
    r = dimensionSwapper = new DimensionSwapper(r);
    if (options.isAutoscale() || FormatTools.isFloatingPoint(r)) {
        r = minMaxCalculator = new MinMaxCalculator(r);
    }
    if (options.doStitchTiles()) {
        r = tileStitcher = new TileStitcher(r);
    }
    r = virtualReader = new VirtualReader(r);
    reader = new ImageProcessorReader(r);
    if (options != null && !options.showROIs()) {
        baseReader.getMetadataOptions().setMetadataLevel(MetadataLevel.NO_OVERLAYS);
    }
    setId();
    computeSeriesLabels(reader);
}

Example 2 with DimensionSwapper

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

the class DimensionSwapperTest method createDimSwapper.

@DataProvider(name = "swapper")
public Object[][] createDimSwapper() {
    Location.mapId(TEST_FILE, TEST_FILE);
    DimensionSwapper swapper = new DimensionSwapper();
    try {
        swapper.setId(TEST_FILE);
    } catch (FormatException e) {
        e.printStackTrace();
    } catch (IOException e) {
        e.printStackTrace();
    }
    swapper.setOutputOrder(OUTPUT_ORDER);
    return new Object[][] { { swapper } };
}

Example 3 with DimensionSwapper

use of loci.formats.DimensionSwapper 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 4 with DimensionSwapper

use of loci.formats.DimensionSwapper 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 5 with DimensionSwapper

use of loci.formats.DimensionSwapper 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;
}