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

Example 1 with ChannelMerger

use of loci.formats.ChannelMerger 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;
}

Example 2 with ChannelMerger

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

the class BFVirtualStack method getProcessor.

// -- VirtualStack API methods --
@Override
public synchronized ImageProcessor getProcessor(int n) {
    reader.setSeries(series);
    // check cache first
    if (currentSlice >= 0 && currentProcessor != null) {
        List<MethodEntry> currentStack = currentProcessor.getMethodStack();
        if (currentStack.size() > 1) {
            methodStacks.get(currentSlice).addAll(currentStack);
        }
    }
    int sliceIndex = planeIndexes == null ? n - 1 : planeIndexes[n - 1];
    int[] pos = reader.getZCTCoords(sliceIndex);
    if (merge)
        pos = new ChannelMerger(reader).getZCTCoords(sliceIndex);
    int[] cachePos = FormatTools.rasterToPosition(len, sliceIndex);
    ImageProcessor ip = null;
    try {
        ip = (ImageProcessor) cache.getObject(cachePos);
        cache.setCurrentPos(cachePos);
    } catch (CacheException exc) {
        exc.printStackTrace();
    }
    // cache missed
    try {
        if (ip == null) {
            ip = reader.openProcessors(reader.getIndex(pos[0], pos[1], pos[2]))[0];
        }
    } catch (FormatException exc) {
        exc.printStackTrace();
    } catch (IOException exc) {
        exc.printStackTrace();
    }
    if (colorize) {
        // apply color table, if necessary
        byte[] lut = new byte[256];
        byte[] blank = new byte[256];
        for (int i = 0; i < lut.length; i++) {
            lut[i] = (byte) i;
            blank[i] = (byte) 0;
        }
        IndexColorModel model = null;
        if (pos[1] < 3) {
            model = new IndexColorModel(8, 256, pos[1] == 0 ? lut : blank, pos[1] == 1 ? lut : blank, pos[1] == 2 ? lut : blank);
        } else
            model = new IndexColorModel(8, 256, lut, lut, lut);
        if (ip != null)
            ip.setColorModel(model);
    } else if (merge) {
        currentSlice = n - 1;
        ImageProcessor[] otherChannels = new ImageProcessor[reader.getSizeC() - 1];
        for (int i = 0; i < otherChannels.length; i++) {
            int channel = i >= pos[1] ? i + 1 : i;
            try {
                cachePos[0] = channel;
                otherChannels[i] = (ImageProcessor) cache.getObject(cachePos);
            } catch (CacheException exc) {
                exc.printStackTrace();
            }
            if (otherChannels[i] == null) {
                try {
                    int index = reader.getIndex(pos[0], channel, pos[2]);
                    otherChannels[i] = reader.openProcessors(index)[0];
                } catch (FormatException exc) {
                    exc.printStackTrace();
                } catch (IOException exc) {
                    exc.printStackTrace();
                }
            }
        }
        currentProcessor = new RecordedImageProcessor(ip, pos[1], otherChannels);
        currentProcessor.setDoRecording(record);
        if (calibrationTable == null) {
            calibrationTable = currentProcessor.getChild().getCalibrationTable();
        } else {
            currentProcessor.setCalibrationTable(calibrationTable);
        }
        return currentProcessor.getChild();
    }
    if (ip != null) {
        currentSlice = n - 1;
        currentProcessor = new RecordedImageProcessor(ip);
        currentProcessor.setDoRecording(record);
        if (calibrationTable == null) {
            calibrationTable = currentProcessor.getChild().getCalibrationTable();
        } else {
            currentProcessor.setCalibrationTable(calibrationTable);
        }
        return currentProcessor.getChild();
    }
    return null;
}

Example 3 with ChannelMerger

use of loci.formats.ChannelMerger 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 ChannelMerger

use of loci.formats.ChannelMerger 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 ChannelMerger

use of loci.formats.ChannelMerger 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;
}