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Example 1 with ChannelSeparator

use of loci.formats.ChannelSeparator 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);
}
Also used : IFormatReader(loci.formats.IFormatReader) FileStitcher(loci.formats.FileStitcher) ImageProcessorReader(loci.plugins.util.ImageProcessorReader) MinMaxCalculator(loci.formats.MinMaxCalculator) DimensionSwapper(loci.formats.DimensionSwapper) TileStitcher(loci.formats.TileStitcher) ChannelFiller(loci.formats.ChannelFiller) VirtualReader(loci.plugins.util.VirtualReader) ChannelSeparator(loci.formats.ChannelSeparator)

Example 2 with ChannelSeparator

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

the class SPWModelReaderTest 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());
}
Also used : MinMaxCalculator(loci.formats.MinMaxCalculator) ChannelFiller(loci.formats.ChannelFiller) ImageReader(loci.formats.ImageReader) ChannelSeparator(loci.formats.ChannelSeparator) OMEXMLMetadataImpl(loci.formats.ome.OMEXMLMetadataImpl) Test(org.testng.annotations.Test)

Example 3 with ChannelSeparator

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

the class SPWModelReaderTest method testSetIdWithNoLightSources.

@Test
public void testSetIdWithNoLightSources() throws Exception {
    readerWithNoLightSources = new MinMaxCalculator(new ChannelSeparator(new ChannelFiller(new ImageReader())));
    metadataWithNoLightSources = new OMEXMLMetadataImpl();
    readerWithNoLightSources.setMetadataStore(metadataWithNoLightSources);
    readerWithNoLightSources.setId(temporaryFileWithNoLightSources.getAbsolutePath());
}
Also used : MinMaxCalculator(loci.formats.MinMaxCalculator) ChannelFiller(loci.formats.ChannelFiller) ImageReader(loci.formats.ImageReader) ChannelSeparator(loci.formats.ChannelSeparator) OMEXMLMetadataImpl(loci.formats.ome.OMEXMLMetadataImpl) Test(org.testng.annotations.Test)

Example 4 with ChannelSeparator

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

the class ImageConverter method testConvert.

// -- Utility methods --
/**
 * A utility method for converting a file from the command line.
 */
public boolean testConvert(IFormatWriter writer, String[] args) throws FormatException, IOException {
    nextOutputIndex.clear();
    options.setValidate(validate);
    writer.setMetadataOptions(options);
    firstTile = true;
    boolean success = parseArgs(args);
    if (!success) {
        return false;
    }
    if (printVersion) {
        CommandLineTools.printVersion();
        return true;
    }
    CommandLineTools.runUpgradeCheck(args);
    if (in == null || out == null) {
        printUsage();
        return false;
    }
    if (new Location(out).exists()) {
        if (overwrite == null) {
            LOGGER.warn("Output file {} exists.", out);
            LOGGER.warn("Do you want to overwrite it? ([y]/n)");
            BufferedReader r = new BufferedReader(new InputStreamReader(System.in, Constants.ENCODING));
            String choice = r.readLine().trim().toLowerCase();
            overwrite = !choice.startsWith("n");
        }
        if (!overwrite) {
            LOGGER.warn("Exiting; next time, please specify an output file that " + "does not exist.");
            return false;
        } else {
            new Location(out).delete();
        }
    }
    if (map != null)
        Location.mapId(in, map);
    long start = System.currentTimeMillis();
    LOGGER.info(in);
    reader = new ImageReader();
    if (stitch) {
        reader = new FileStitcher(reader);
        Location f = new Location(in);
        String pat = null;
        if (!f.exists()) {
            pat = in;
        } else {
            pat = FilePattern.findPattern(f);
        }
        if (pat != null)
            in = pat;
    }
    if (separate)
        reader = new ChannelSeparator(reader);
    if (merge)
        reader = new ChannelMerger(reader);
    if (fill)
        reader = new ChannelFiller(reader);
    minMax = null;
    if (autoscale) {
        reader = new MinMaxCalculator(reader);
        minMax = (MinMaxCalculator) reader;
    }
    reader.setMetadataOptions(options);
    reader.setGroupFiles(group);
    reader.setMetadataFiltered(true);
    reader.setOriginalMetadataPopulated(true);
    OMEXMLService service = null;
    try {
        ServiceFactory factory = new ServiceFactory();
        service = factory.getInstance(OMEXMLService.class);
        reader.setMetadataStore(service.createOMEXMLMetadata());
    } catch (DependencyException de) {
        throw new MissingLibraryException(OMEXMLServiceImpl.NO_OME_XML_MSG, de);
    } catch (ServiceException se) {
        throw new FormatException(se);
    }
    reader.setId(in);
    MetadataStore store = reader.getMetadataStore();
    MetadataTools.populatePixels(store, reader, false, false);
    boolean dimensionsSet = true;
    if (width == 0 || height == 0) {
        // otherwise default to series 0
        if (series >= 0) {
            reader.setSeries(series);
        }
        width = reader.getSizeX();
        height = reader.getSizeY();
        dimensionsSet = false;
    }
    if (channel >= reader.getEffectiveSizeC()) {
        throw new FormatException("Invalid channel '" + channel + "' (" + reader.getEffectiveSizeC() + " channels in source file)");
    }
    if (timepoint >= reader.getSizeT()) {
        throw new FormatException("Invalid timepoint '" + timepoint + "' (" + reader.getSizeT() + " timepoints in source file)");
    }
    if (zSection >= reader.getSizeZ()) {
        throw new FormatException("Invalid Z section '" + zSection + "' (" + reader.getSizeZ() + " Z sections in source file)");
    }
    if (store instanceof MetadataRetrieve) {
        try {
            String xml = service.getOMEXML(service.asRetrieve(store));
            OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) store.getRoot();
            IMetadata meta = service.createOMEXMLMetadata(xml);
            if (series >= 0) {
                Image exportImage = new Image(root.getImage(series));
                Pixels exportPixels = new Pixels(root.getImage(series).getPixels());
                exportImage.setPixels(exportPixels);
                OMEXMLMetadataRoot newRoot = (OMEXMLMetadataRoot) meta.getRoot();
                while (newRoot.sizeOfImageList() > 0) {
                    newRoot.removeImage(newRoot.getImage(0));
                }
                newRoot.addImage(exportImage);
                meta.setRoot(newRoot);
                meta.setPixelsSizeX(new PositiveInteger(width), 0);
                meta.setPixelsSizeY(new PositiveInteger(height), 0);
                if (autoscale) {
                    store.setPixelsType(PixelType.UINT8, 0);
                }
                if (channel >= 0) {
                    meta.setPixelsSizeC(new PositiveInteger(1), 0);
                }
                if (zSection >= 0) {
                    meta.setPixelsSizeZ(new PositiveInteger(1), 0);
                }
                if (timepoint >= 0) {
                    meta.setPixelsSizeT(new PositiveInteger(1), 0);
                }
                writer.setMetadataRetrieve((MetadataRetrieve) meta);
            } else {
                for (int i = 0; i < reader.getSeriesCount(); i++) {
                    meta.setPixelsSizeX(new PositiveInteger(width), 0);
                    meta.setPixelsSizeY(new PositiveInteger(height), 0);
                    if (autoscale) {
                        store.setPixelsType(PixelType.UINT8, i);
                    }
                    if (channel >= 0) {
                        meta.setPixelsSizeC(new PositiveInteger(1), 0);
                    }
                    if (zSection >= 0) {
                        meta.setPixelsSizeZ(new PositiveInteger(1), 0);
                    }
                    if (timepoint >= 0) {
                        meta.setPixelsSizeT(new PositiveInteger(1), 0);
                    }
                }
                writer.setMetadataRetrieve((MetadataRetrieve) meta);
            }
        } catch (ServiceException e) {
            throw new FormatException(e);
        }
    }
    writer.setWriteSequentially(true);
    if (writer instanceof TiffWriter) {
        ((TiffWriter) writer).setBigTiff(bigtiff);
    } else if (writer instanceof ImageWriter) {
        IFormatWriter w = ((ImageWriter) writer).getWriter(out);
        if (w instanceof TiffWriter) {
            ((TiffWriter) w).setBigTiff(bigtiff);
        }
    }
    String format = writer.getFormat();
    LOGGER.info("[{}] -> {} [{}]", new Object[] { reader.getFormat(), out, format });
    long mid = System.currentTimeMillis();
    int total = 0;
    int num = writer.canDoStacks() ? reader.getSeriesCount() : 1;
    long read = 0, write = 0;
    int first = series == -1 ? 0 : series;
    int last = series == -1 ? num : series + 1;
    long timeLastLogged = System.currentTimeMillis();
    for (int q = first; q < last; q++) {
        reader.setSeries(q);
        firstTile = true;
        if (!dimensionsSet) {
            width = reader.getSizeX();
            height = reader.getSizeY();
        }
        int writerSeries = series == -1 ? q : 0;
        writer.setSeries(writerSeries);
        writer.setInterleaved(reader.isInterleaved() && !autoscale);
        writer.setValidBitsPerPixel(reader.getBitsPerPixel());
        int numImages = writer.canDoStacks() ? reader.getImageCount() : 1;
        int startPlane = (int) Math.max(0, firstPlane);
        int endPlane = (int) Math.min(numImages, lastPlane);
        numImages = endPlane - startPlane;
        if (channel >= 0) {
            numImages /= reader.getEffectiveSizeC();
        }
        if (zSection >= 0) {
            numImages /= reader.getSizeZ();
        }
        if (timepoint >= 0) {
            numImages /= reader.getSizeT();
        }
        total += numImages;
        int count = 0;
        for (int i = startPlane; i < endPlane; i++) {
            int[] coords = reader.getZCTCoords(i);
            if ((zSection >= 0 && coords[0] != zSection) || (channel >= 0 && coords[1] != channel) || (timepoint >= 0 && coords[2] != timepoint)) {
                continue;
            }
            String outputName = FormatTools.getFilename(q, i, reader, out, zeroPadding);
            if (outputName.equals(FormatTools.getTileFilename(0, 0, 0, outputName))) {
                writer.setId(outputName);
                if (compression != null)
                    writer.setCompression(compression);
            } else {
                int tileNum = outputName.indexOf(FormatTools.TILE_NUM);
                int tileX = outputName.indexOf(FormatTools.TILE_X);
                int tileY = outputName.indexOf(FormatTools.TILE_Y);
                if (tileNum < 0 && (tileX < 0 || tileY < 0)) {
                    throw new FormatException("Invalid file name pattern; " + FormatTools.TILE_NUM + " or both of " + FormatTools.TILE_X + " and " + FormatTools.TILE_Y + " must be specified.");
                }
            }
            int outputIndex = 0;
            if (nextOutputIndex.containsKey(outputName)) {
                outputIndex = nextOutputIndex.get(outputName);
            }
            long s = System.currentTimeMillis();
            long m = convertPlane(writer, i, outputIndex, outputName);
            long e = System.currentTimeMillis();
            read += m - s;
            write += e - m;
            nextOutputIndex.put(outputName, outputIndex + 1);
            if (i == endPlane - 1) {
                nextOutputIndex.remove(outputName);
            }
            // log number of planes processed every second or so
            if (count == numImages - 1 || (e - timeLastLogged) / 1000 > 0) {
                int current = (count - startPlane) + 1;
                int percent = 100 * current / numImages;
                StringBuilder sb = new StringBuilder();
                sb.append("\t");
                int numSeries = last - first;
                if (numSeries > 1) {
                    sb.append("Series ");
                    sb.append(q);
                    sb.append(": converted ");
                } else
                    sb.append("Converted ");
                LOGGER.info(sb.toString() + "{}/{} planes ({}%)", new Object[] { current, numImages, percent });
                timeLastLogged = e;
            }
            count++;
        }
    }
    writer.close();
    long end = System.currentTimeMillis();
    LOGGER.info("[done]");
    // output timing results
    float sec = (end - start) / 1000f;
    long initial = mid - start;
    float readAvg = (float) read / total;
    float writeAvg = (float) write / total;
    LOGGER.info("{}s elapsed ({}+{}ms per plane, {}ms overhead)", new Object[] { sec, readAvg, writeAvg, initial });
    return true;
}
Also used : ServiceFactory(loci.common.services.ServiceFactory) ChannelMerger(loci.formats.ChannelMerger) ImageWriter(loci.formats.ImageWriter) ChannelFiller(loci.formats.ChannelFiller) Image(ome.xml.model.Image) OMEXMLService(loci.formats.services.OMEXMLService) Pixels(ome.xml.model.Pixels) IMetadata(loci.formats.meta.IMetadata) ImageReader(loci.formats.ImageReader) MetadataRetrieve(loci.formats.meta.MetadataRetrieve) PositiveInteger(ome.xml.model.primitives.PositiveInteger) TiffWriter(loci.formats.out.TiffWriter) InputStreamReader(java.io.InputStreamReader) DependencyException(loci.common.services.DependencyException) ChannelSeparator(loci.formats.ChannelSeparator) FormatException(loci.formats.FormatException) MetadataStore(loci.formats.meta.MetadataStore) IFormatWriter(loci.formats.IFormatWriter) FileStitcher(loci.formats.FileStitcher) ServiceException(loci.common.services.ServiceException) OMEXMLMetadataRoot(ome.xml.meta.OMEXMLMetadataRoot) BufferedReader(java.io.BufferedReader) MinMaxCalculator(loci.formats.MinMaxCalculator) MissingLibraryException(loci.formats.MissingLibraryException) Location(loci.common.Location)

Example 5 with ChannelSeparator

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

the class OpenBytesPerformanceTest method setId.

@Test
public void setId() throws Exception {
    reader = new ImageReader();
    reader = new ChannelFiller(reader);
    reader = new ChannelSeparator(reader);
    reader = new MinMaxCalculator(reader);
    if (memMap && reader.isSingleFile(id)) {
        TestTools.mapFile(id);
    }
    StopWatch stopWatch = new Slf4JStopWatch();
    reader.setId(id);
    stopWatch.stop(String.format("%s.setId.%s", ((ReaderWrapper) reader).unwrap().getClass().getName(), filename));
    seriesCount = reader.getSeriesCount();
}
Also used : Slf4JStopWatch(org.perf4j.slf4j.Slf4JStopWatch) MinMaxCalculator(loci.formats.MinMaxCalculator) ChannelFiller(loci.formats.ChannelFiller) ImageReader(loci.formats.ImageReader) ChannelSeparator(loci.formats.ChannelSeparator) ReaderWrapper(loci.formats.ReaderWrapper) Slf4JStopWatch(org.perf4j.slf4j.Slf4JStopWatch) StopWatch(org.perf4j.StopWatch) Test(org.testng.annotations.Test)

Aggregations

ChannelSeparator (loci.formats.ChannelSeparator)17 ChannelFiller (loci.formats.ChannelFiller)11 MinMaxCalculator (loci.formats.MinMaxCalculator)11 ImageReader (loci.formats.ImageReader)10 FormatException (loci.formats.FormatException)8 IOException (java.io.IOException)6 IFormatReader (loci.formats.IFormatReader)6 ChannelMerger (loci.formats.ChannelMerger)5 DimensionSwapper (loci.formats.DimensionSwapper)5 Test (org.testng.annotations.Test)5 Location (loci.common.Location)4 FileStitcher (loci.formats.FileStitcher)4 OMEXMLMetadataImpl (loci.formats.ome.OMEXMLMetadataImpl)4 MetadataStore (loci.formats.meta.MetadataStore)3 DataProvider (org.testng.annotations.DataProvider)3 RandomAccessInputStream (loci.common.RandomAccessInputStream)2 DependencyException (loci.common.services.DependencyException)2 ServiceException (loci.common.services.ServiceException)2 ServiceFactory (loci.common.services.ServiceFactory)2 CoreMetadata (loci.formats.CoreMetadata)2