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

Example 16 with IFormatReader

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

the class GUITools method buildFileFilters.

// -- File chooser --
/**
 * Constructs a list of file filters for the given file format handler.
 */
public static FileFilter[] buildFileFilters(IFormatHandler handler) {
    FileFilter[] filters = null;
    // unwrap reader
    while (true) {
        if (handler instanceof ReaderWrapper) {
            handler = ((ReaderWrapper) handler).getReader();
        } else if (handler instanceof FileStitcher) {
            handler = ((FileStitcher) handler).getReader();
        } else if (handler instanceof WriterWrapper) {
            handler = ((WriterWrapper) handler).getWriter();
        } else
            break;
    }
    // handle special cases of ImageReader and ImageWriter
    if (handler instanceof ImageReader) {
        ImageReader imageReader = (ImageReader) handler;
        IFormatReader[] readers = imageReader.getReaders();
        Vector filterList = new Vector();
        Vector comboList = new Vector();
        for (int i = 0; i < readers.length; i++) {
            filterList.add(new FormatFileFilter(readers[i]));
            // NB: Some readers need to open a file to determine if it is the
            // proper type, when the extension alone is insufficient to
            // distinguish. This behavior is fine for individual filters, but not
            // for ImageReader's combination filter, because it makes the combo
            // filter too slow. So rather than composing the combo filter from
            // FormatFileFilters, we use faster but less accurate
            // ExtensionFileFilters instead.
            String[] suffixes = readers[i].getSuffixes();
            String format = readers[i].getFormat();
            comboList.add(new ExtensionFileFilter(suffixes, format));
        }
        comboList.add(new NoExtensionFileFilter());
        FileFilter combo = makeComboFilter(sortFilters(comboList));
        if (combo != null)
            filterList.add(combo);
        filters = sortFilters(filterList);
    } else if (handler instanceof ImageWriter) {
        IFormatWriter[] writers = ((ImageWriter) handler).getWriters();
        Vector filterList = new Vector();
        for (int i = 0; i < writers.length; i++) {
            String[] suffixes = writers[i].getSuffixes();
            String format = writers[i].getFormat();
            filterList.add(new ExtensionFileFilter(suffixes, format));
        }
        filters = sortFilters(filterList);
    } else // handle default reader and writer cases
    if (handler instanceof IFormatReader) {
        IFormatReader reader = (IFormatReader) handler;
        filters = new FileFilter[] { new FormatFileFilter(reader) };
    } else {
        String[] suffixes = handler.getSuffixes();
        String format = handler.getFormat();
        filters = new FileFilter[] { new ExtensionFileFilter(suffixes, format) };
    }
    return filters;
}

Example 17 with IFormatReader

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

the class CellWorxReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    if (!checkSuffix(id, "htd")) {
        LOGGER.info("Searching for .htd file");
        String base = new Location(id).getAbsolutePath();
        base = base.substring(0, base.lastIndexOf("_"));
        id = base + ".HTD";
        if (!new Location(id).exists()) {
            Location parent = new Location(id).getAbsoluteFile().getParentFile();
            directoryList = parent.list(true);
            for (String f : directoryList) {
                if (checkSuffix(f, "htd")) {
                    id = new Location(parent, f).getAbsolutePath();
                    LOGGER.info("Found .htd file {}", f);
                    break;
                }
            }
        }
    }
    super.initFile(id);
    try {
        ServiceFactory factory = new ServiceFactory();
        service = factory.getInstance(OMEXMLService.class);
    } catch (DependencyException exc) {
        throw new FormatException("Could not create OME-XML store.", exc);
    }
    String plateData = DataTools.readFile(id);
    String[] lines = plateData.split("\n");
    int xWells = 0, yWells = 0;
    int xFields = 0, yFields = 0;
    String[] wavelengths = null;
    int nTimepoints = 1;
    // determine dataset dimensions
    for (String line : lines) {
        int split = line.indexOf("\",");
        if (split < 1)
            continue;
        String key = line.substring(1, split).trim();
        String value = line.substring(split + 2).trim();
        if (key.equals("XWells")) {
            xWells = Integer.parseInt(value);
        } else if (key.equals("YWells")) {
            yWells = Integer.parseInt(value);
            wellFiles = new String[yWells][xWells][];
            logFiles = new String[yWells][xWells];
        } else if (key.startsWith("WellsSelection")) {
            int row = Integer.parseInt(key.substring(14)) - 1;
            String[] mapping = value.split(",");
            for (int col = 0; col < xWells; col++) {
                if (new Boolean(mapping[col].trim()).booleanValue()) {
                    wellFiles[row][col] = new String[1];
                }
            }
        } else if (key.equals("XSites")) {
            xFields = Integer.parseInt(value);
        } else if (key.equals("YSites")) {
            yFields = Integer.parseInt(value);
            fieldMap = new boolean[yFields][xFields];
        } else if (key.equals("TimePoints")) {
            nTimepoints = Integer.parseInt(value);
        } else if (key.startsWith("SiteSelection")) {
            int row = Integer.parseInt(key.substring(13)) - 1;
            String[] mapping = value.split(",");
            for (int col = 0; col < xFields; col++) {
                fieldMap[row][col] = new Boolean(mapping[col].trim()).booleanValue();
            }
        } else if (key.equals("Waves")) {
            doChannels = new Boolean(value.toLowerCase());
        } else if (key.equals("NWavelengths")) {
            wavelengths = new String[Integer.parseInt(value)];
        } else if (key.startsWith("WaveName")) {
            int index = Integer.parseInt(key.substring(8)) - 1;
            wavelengths[index] = value.replaceAll("\"", "");
        }
    }
    for (int row = 0; row < fieldMap.length; row++) {
        for (int col = 0; col < fieldMap[row].length; col++) {
            if (fieldMap[row][col])
                fieldCount++;
        }
    }
    // find pixels files
    String plateName = new Location(id).getAbsolutePath();
    plateName = plateName.substring(0, plateName.lastIndexOf(".")) + "_";
    int wellCount = 0;
    for (int row = 0; row < wellFiles.length; row++) {
        for (int col = 0; col < wellFiles[row].length; col++) {
            if (wellFiles[row][col] != null) {
                wellCount++;
                char rowLetter = (char) (row + 'A');
                String base = plateName + rowLetter + String.format("%02d", col + 1);
                wellFiles[row][col][0] = base + ".pnl";
                logFiles[row][col] = base + "_scan.log";
                if (!new Location(wellFiles[row][col][0]).exists()) {
                    // using TIFF files instead
                    wellFiles[row][col] = getTiffFiles(plateName, rowLetter, col, wavelengths.length, nTimepoints);
                }
            }
        }
    }
    plateLogFile = plateName + "scan.log";
    String serialNumber = null;
    if (new Location(plateLogFile).exists()) {
        String[] f = DataTools.readFile(plateLogFile).split("\n");
        for (String line : f) {
            if (line.trim().startsWith("Z Map File")) {
                String file = line.substring(line.indexOf(':') + 1);
                file = file.substring(file.lastIndexOf("/") + 1).trim();
                String parent = new Location(id).getAbsoluteFile().getParent();
                zMapFile = new Location(parent, file).getAbsolutePath();
            } else if (line.trim().startsWith("Scanner SN")) {
                serialNumber = line.substring(line.indexOf(':') + 1).trim();
            }
        }
    }
    int seriesCount = fieldCount * wellCount;
    int planeIndex = 0;
    int seriesIndex = 0;
    String file = getFile(seriesIndex, planeIndex);
    while (!new Location(file).exists()) {
        if (planeIndex < nTimepoints * wavelengths.length) {
            planeIndex++;
        } else if (seriesIndex < seriesCount - 1) {
            planeIndex = 0;
            seriesIndex++;
        } else {
            break;
        }
        file = getFile(seriesIndex, planeIndex);
    }
    IFormatReader pnl = getReader(file, true);
    core.clear();
    for (int i = 0; i < seriesCount; i++) {
        CoreMetadata ms = new CoreMetadata();
        core.add(ms);
        setSeries(i);
        ms.littleEndian = pnl.isLittleEndian();
        ms.sizeX = pnl.getSizeX();
        ms.sizeY = pnl.getSizeY();
        ms.pixelType = pnl.getPixelType();
        ms.sizeZ = 1;
        ms.sizeT = nTimepoints;
        ms.sizeC = wavelengths.length;
        ms.imageCount = getSizeZ() * getSizeC() * getSizeT();
        ms.dimensionOrder = "XYCZT";
        ms.rgb = false;
        ms.interleaved = pnl.isInterleaved();
    }
    OMEXMLMetadata readerMetadata = (OMEXMLMetadata) pnl.getMetadataStore();
    OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) readerMetadata.getRoot();
    Instrument instrument = root.getInstrument(0);
    List<Image> images = root.copyImageList();
    OMEXMLMetadataRoot convertRoot = new OMEXMLMetadataRoot();
    convertRoot.addInstrument(instrument);
    for (int i = 0; i < core.size() / images.size(); i++) {
        for (Image img : images) {
            convertRoot.addImage(img);
        }
    }
    OMEXMLMetadata convertMetadata;
    try {
        convertMetadata = service.createOMEXMLMetadata();
    } catch (ServiceException exc) {
        throw new FormatException("Could not create OME-XML store.", exc);
    }
    convertMetadata.setRoot(convertRoot);
    pnl.close();
    MetadataStore store = makeFilterMetadata();
    MetadataConverter.convertMetadata(convertMetadata, store);
    MetadataTools.populatePixels(store, this);
    String plateID = MetadataTools.createLSID("Plate", 0);
    Location plate = new Location(id).getAbsoluteFile();
    store.setPlateID(plateID, 0);
    plateName = plate.getName();
    if (plateName.indexOf('.') > 0) {
        plateName = plateName.substring(0, plateName.lastIndexOf('.'));
    }
    store.setPlateName(plateName, 0);
    store.setPlateRows(new PositiveInteger(wellFiles.length), 0);
    store.setPlateColumns(new PositiveInteger(wellFiles[0].length), 0);
    for (int i = 0; i < core.size(); i++) {
        store.setImageID(MetadataTools.createLSID("Image", i), i);
    }
    String plateAcqID = MetadataTools.createLSID("PlateAcquisition", 0, 0);
    store.setPlateAcquisitionID(plateAcqID, 0, 0);
    PositiveInteger fieldCount = FormatTools.getMaxFieldCount(fieldMap.length * fieldMap[0].length);
    if (fieldCount != null) {
        store.setPlateAcquisitionMaximumFieldCount(fieldCount, 0, 0);
    }
    int nextImage = 0;
    for (int row = 0; row < wellFiles.length; row++) {
        for (int col = 0; col < wellFiles[row].length; col++) {
            int wellIndex = row * wellFiles[row].length + col;
            String wellID = MetadataTools.createLSID("Well", 0, wellIndex);
            store.setWellID(wellID, 0, wellIndex);
            store.setWellColumn(new NonNegativeInteger(col), 0, wellIndex);
            store.setWellRow(new NonNegativeInteger(row), 0, wellIndex);
            int fieldIndex = 0;
            for (int fieldRow = 0; fieldRow < fieldMap.length; fieldRow++) {
                for (int fieldCol = 0; fieldCol < fieldMap[fieldRow].length; fieldCol++) {
                    if (fieldMap[fieldRow][fieldCol] && wellFiles[row][col] != null) {
                        String wellSampleID = MetadataTools.createLSID("WellSample", 0, wellIndex, fieldIndex);
                        store.setWellSampleID(wellSampleID, 0, wellIndex, fieldIndex);
                        String imageID = MetadataTools.createLSID("Image", nextImage);
                        store.setWellSampleImageRef(imageID, 0, wellIndex, fieldIndex);
                        store.setWellSampleIndex(new NonNegativeInteger(nextImage), 0, wellIndex, fieldIndex);
                        store.setPlateAcquisitionWellSampleRef(wellSampleID, 0, 0, nextImage);
                        String well = (char) (row + 'A') + String.format("%02d", col + 1);
                        store.setImageName("Well " + well + " Field #" + (fieldIndex + 1), nextImage);
                        nextImage++;
                        fieldIndex++;
                    }
                }
            }
        }
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        if (serialNumber != null) {
            store.setMicroscopeSerialNumber(serialNumber, 0);
        }
        for (int well = 0; well < wellCount; well++) {
            parseWellLogFile(well, store);
        }
        if (timestamps.size() > 0) {
            store.setPlateAcquisitionStartTime(timestamps.get(0), 0, 0);
            store.setPlateAcquisitionEndTime(timestamps.get(timestamps.size() - 1), 0, 0);
        }
        for (int i = 0; i < core.size(); i++) {
            for (int c = 0; c < getSizeC(); c++) {
                if (c < wavelengths.length && wavelengths[c] != null) {
                    store.setChannelName(wavelengths[c], i, c);
                }
            }
        }
    }
}

Example 18 with IFormatReader

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

the class CellSensReader method decodeTile.

private byte[] decodeTile(int no, int row, int col) throws FormatException, IOException {
    if (tileMap.get(getCoreIndex()) == null) {
        return new byte[getTileSize()];
    }
    int[] zct = getZCTCoords(no);
    TileCoordinate t = new TileCoordinate(nDimensions.get(getCoreIndex()));
    t.coordinate[0] = col;
    t.coordinate[1] = row;
    int resIndex = getResolution();
    int pyramidIndex = getSeries();
    if (hasFlattenedResolutions()) {
        int index = 0;
        pyramidIndex = 0;
        for (int i = 0; i < core.size(); ) {
            if (index + core.get(i).resolutionCount <= getSeries()) {
                index += core.get(i).resolutionCount;
                i += core.get(i).resolutionCount;
                pyramidIndex++;
            } else {
                resIndex = getSeries() - index;
                break;
            }
        }
    }
    Pyramid pyramid = pyramids.get(pyramidIndex);
    for (String dim : pyramid.dimensionOrdering.keySet()) {
        int index = pyramid.dimensionOrdering.get(dim) + 2;
        if (dim.equals("Z")) {
            t.coordinate[index] = zct[0];
        } else if (dim.equals("C")) {
            t.coordinate[index] = zct[1];
        } else if (dim.equals("T")) {
            t.coordinate[index] = zct[2];
        }
    }
    if (resIndex > 0) {
        t.coordinate[t.coordinate.length - 1] = resIndex;
    }
    ArrayList<TileCoordinate> map = tileMap.get(getCoreIndex());
    Integer index = map.indexOf(t);
    if (index == null || index < 0) {
        // fill in the tile with the stored background color
        // usually this is either black or white
        byte[] tile = new byte[getTileSize()];
        byte[] color = backgroundColor.get(getCoreIndex());
        if (color != null) {
            for (int q = 0; q < getTileSize(); q += color.length) {
                for (int i = 0; i < color.length; i++) {
                    tile[q + i] = color[i];
                }
            }
        }
        return tile;
    }
    Long offset = tileOffsets.get(getCoreIndex())[index];
    RandomAccessInputStream ets = new RandomAccessInputStream(fileMap.get(getCoreIndex()));
    ets.seek(offset);
    CodecOptions options = new CodecOptions();
    options.interleaved = isInterleaved();
    options.littleEndian = isLittleEndian();
    int tileSize = getTileSize();
    if (tileSize == 0) {
        tileSize = tileX.get(getCoreIndex()) * tileY.get(getCoreIndex()) * 10;
    }
    options.maxBytes = (int) (offset + tileSize);
    byte[] buf = null;
    long end = index < tileOffsets.get(getCoreIndex()).length - 1 ? tileOffsets.get(getCoreIndex())[index + 1] : ets.length();
    IFormatReader reader = null;
    String file = null;
    switch(compressionType.get(getCoreIndex())) {
        case RAW:
            buf = new byte[tileSize];
            ets.read(buf);
            break;
        case JPEG:
            Codec codec = new JPEGCodec();
            buf = codec.decompress(ets, options);
            break;
        case JPEG_2000:
            codec = new JPEG2000Codec();
            buf = codec.decompress(ets, options);
            break;
        case JPEG_LOSSLESS:
            codec = new LosslessJPEGCodec();
            buf = codec.decompress(ets, options);
            break;
        case PNG:
            file = "tile.png";
            reader = new APNGReader();
        case BMP:
            if (reader == null) {
                file = "tile.bmp";
                reader = new BMPReader();
            }
            byte[] b = new byte[(int) (end - offset)];
            ets.read(b);
            Location.mapFile(file, new ByteArrayHandle(b));
            reader.setId(file);
            buf = reader.openBytes(0);
            Location.mapFile(file, null);
            break;
    }
    if (reader != null) {
        reader.close();
    }
    ets.close();
    return buf;
}

Example 19 with IFormatReader

use of loci.formats.IFormatReader 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 20 with IFormatReader

use of loci.formats.IFormatReader 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;
}