Examples with Region loci.common.Region used on opensource projects

Example 1 with Region

use of loci.common.Region in project bioformats by openmicroscopy.

the class CropDialog method constructDialog.

@Override
protected GenericDialog constructDialog() {
    final int seriesCount = process.getSeriesCount();
    final IFormatReader r = process.getReader();
    // construct dialog
    final GenericDialog gd = new GenericDialog("Bio-Formats Crop Options");
    for (int s = 0; s < seriesCount; s++) {
        if (!options.isSeriesOn(s))
            continue;
        r.setSeries(s);
        Region region = process.getCropRegion(s);
        gd.addMessage(process.getSeriesLabel(s).replaceAll("_", " "));
        gd.addNumericField("X_Coordinate_" + (s + 1), region.x, 0);
        gd.addNumericField("Y_Coordinate_" + (s + 1), region.y, 0);
        gd.addNumericField("Width_" + (s + 1), region.width, 0);
        gd.addNumericField("Height_" + (s + 1), region.height, 0);
    }
    WindowTools.addScrollBars(gd);
    return gd;
}

Example 2 with Region

use of loci.common.Region in project bioformats by openmicroscopy.

the class ImagePlusReader method readPlanes.

private ImageStack readPlanes(ImportProcess process, int s, List<LUT> luts, boolean thumbnail) throws FormatException, IOException {
    final ImageProcessorReader reader = process.getReader();
    reader.setSeries(s);
    final int zCount = process.getZCount(s);
    final int cCount = process.getCCount(s);
    final int tCount = process.getTCount(s);
    final IMetadata meta = process.getOMEMetadata();
    // get list of planes to load
    final boolean[] load = getPlanesToLoad(s);
    int current = 0, total = 0;
    for (int j = 0; j < load.length; j++) if (load[j])
        total++;
    final List<ImageProcessor> procs = new ArrayList<ImageProcessor>();
    final List<String> labels = new ArrayList<String>();
    // read applicable image planes
    final Region region = process.getCropRegion(s);
    for (int i = 0; i < load.length; i++) {
        if (!load[i])
            continue;
        // limit message update rate
        updateTiming(s, current, current++, total);
        // get image processor for ith plane
        final ImageProcessor[] p = readProcessors(process, i, region, thumbnail);
        if (p == null || p.length == 0) {
            throw new FormatException("Cannot read plane #" + i);
        }
        // generate a label for ith plane
        String label = constructSliceLabel(i, reader, meta, s, zCount, cCount, tCount);
        for (ImageProcessor ip : p) {
            procs.add(ip);
            labels.add(label);
        }
    }
    return createStack(procs, labels, luts);
}

Example 3 with Region

use of loci.common.Region in project bioformats by openmicroscopy.

the class MIASReader method openBytes.

/**
 * @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
 */
@Override
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, IOException {
    FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
    if (tileRows == 1 && tileCols == 1) {
        readers[getSeries()][no].setId(tiffs[getSeries()][no]);
        readers[getSeries()][no].openBytes(0, buf, x, y, w, h);
        readers[getSeries()][no].close();
        return buf;
    }
    int outputRowLen = w * bpp[getSeries()];
    Region image = new Region(x, y, w, h);
    int outputRow = 0, outputCol = 0;
    Region intersection = null;
    byte[] tileBuf = null;
    for (int row = 0; row < tileRows; row++) {
        for (int col = 0; col < tileCols; col++) {
            Region tile = new Region(col * tileWidth, row * tileHeight, tileWidth, tileHeight);
            if (!tile.intersects(image))
                continue;
            intersection = tile.intersection(image);
            int tileIndex = (no * tileRows + row) * tileCols + col;
            tileBuf = getTile(getSeries(), no, row, col, intersection);
            int rowLen = tileBuf.length / intersection.height;
            // copy tile into output image
            int outputOffset = outputRow * outputRowLen + outputCol;
            for (int trow = 0; trow < intersection.height; trow++) {
                System.arraycopy(tileBuf, trow * rowLen, buf, outputOffset, rowLen);
                outputOffset += outputRowLen;
            }
            outputCol += rowLen;
        }
        if (intersection != null) {
            outputRow += intersection.height;
            outputCol = 0;
        }
    }
    return buf;
}

Example 4 with Region

use of loci.common.Region in project bioformats by openmicroscopy.

the class HamamatsuVMSReader method openBytes.

/**
 * @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
 */
@Override
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, IOException {
    FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
    int startCol = x / MAX_JPEG_SIZE;
    int startRow = y / MAX_JPEG_SIZE;
    String file = null;
    switch(getCoreIndex()) {
        case 0:
            file = tileFiles[no][startRow][startCol];
            break;
        case 1:
            file = macroFile;
            break;
        case 2:
            file = mapFile;
            break;
    }
    if (getSizeX() <= MAX_SIZE || getSizeY() <= MAX_SIZE) {
        JPEGReader reader = new JPEGReader();
        reader.setId(file);
        reader.openBytes(0, buf, x, y, w, h);
        reader.close();
        return buf;
    }
    if (service == null) {
        service = new JPEGTurboServiceImpl();
    }
    try {
        Region image = new Region(x, y, w, h);
        for (int row = startRow; row < nRows; row++) {
            for (int col = startCol; col < nCols; col++) {
                Region tile = new Region(col * MAX_JPEG_SIZE, row * MAX_JPEG_SIZE, col == nCols - 1 ? getSizeX() % MAX_JPEG_SIZE : MAX_JPEG_SIZE, row == nRows - 1 ? getSizeY() % MAX_JPEG_SIZE : MAX_JPEG_SIZE);
                if (!tile.intersects(image)) {
                    continue;
                }
                file = tileFiles[no][row][col];
                if (initializedSeries != getCoreIndex() || initializedPlane != no || !file.equals(initializedFile)) {
                    service.close();
                    if (restartMarkers.containsKey(file)) {
                        service.setRestartMarkers(restartMarkers.get(file));
                    } else {
                        service.setRestartMarkers(null);
                    }
                    // closing the service will close this file
                    RandomAccessInputStream s = new RandomAccessInputStream(file);
                    service.initialize(s, tile.width, tile.height);
                    restartMarkers.put(file, service.getRestartMarkers());
                    initializedSeries = getCoreIndex();
                    initializedPlane = no;
                    initializedFile = file;
                }
                Region intersection = tile.intersection(image);
                int tileX = intersection.x % MAX_JPEG_SIZE;
                int tileY = intersection.y % MAX_JPEG_SIZE;
                int rowLen = intersection.width * getRGBChannelCount();
                byte[] b = new byte[rowLen * intersection.height];
                service.getTile(b, tileX, tileY, intersection.width, intersection.height);
                for (int tileRow = 0; tileRow < intersection.height; tileRow++) {
                    int src = tileRow * rowLen;
                    int dest = (((intersection.y + tileRow - y) * w) + (intersection.x - x)) * getRGBChannelCount();
                    System.arraycopy(b, src, buf, dest, rowLen);
                }
            }
        }
    } catch (ServiceException e) {
        throw new FormatException(e);
    }
    return buf;
}

Example 5 with Region

use of loci.common.Region in project bioformats by openmicroscopy.

the class ZeissLSMReader method openBytes.

/**
 * @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
 */
@Override
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, IOException {
    FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
    if (getSeriesCount() > 1) {
        in.close();
        in = new RandomAccessInputStream(getLSMFileFromSeries(getSeries()));
        in.order(!isLittleEndian());
        tiffParser = new TiffParser(in);
    } else if (tiffParser == null) {
        tiffParser = new TiffParser(in);
    }
    IFDList ifds = ifdsList.get(getSeries());
    if (splitPlanes && getSizeC() > 1 && ifds.size() == getSizeZ() * getSizeT()) {
        int bpp = FormatTools.getBytesPerPixel(getPixelType());
        int plane = no / getSizeC();
        int c = no % getSizeC();
        Region region = new Region(x, y, w, h);
        if (prevPlane != plane || prevBuf == null || prevBuf.length < w * h * bpp * getSizeC() || !region.equals(prevRegion)) {
            prevBuf = new byte[w * h * bpp * getSizeC()];
            tiffParser.getSamples(ifds.get(plane), prevBuf, x, y, w, h);
            prevPlane = plane;
            prevRegion = region;
        }
        ImageTools.splitChannels(prevBuf, buf, c, getSizeC(), bpp, false, false, w * h * bpp);
        prevChannel = c;
    } else {
        tiffParser.getSamples(ifds.get(no), buf, x, y, w, h);
        prevChannel = getZCTCoords(no)[1];
    }
    if (getSeriesCount() > 1)
        in.close();
    return buf;
}