Examples with MetakitService loci.formats.services.MetakitService used on opensource projects

Example 1 with MetakitService

use of loci.formats.services.MetakitService in project bioformats by openmicroscopy.

the class VolocityReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    if (!checkSuffix(id, "mvd2")) {
        Location file = new Location(id).getAbsoluteFile();
        Location parent = file.getParentFile().getParentFile();
        String[] files = parent.list(true);
        for (String f : files) {
            if (checkSuffix(f, "mvd2")) {
                id = new Location(parent, f).getAbsolutePath();
                break;
            }
        }
    }
    super.initFile(id);
    stacks = new ArrayList<Stack>();
    extraFiles = new ArrayList<String>();
    Location file = new Location(id).getAbsoluteFile();
    extraFiles.add(file.getAbsolutePath());
    Location parentDir = file.getParentFile();
    dir = new Location(parentDir, DATA_DIR);
    if (dir.exists()) {
        String[] files = dir.list(true);
        for (String f : files) {
            if (!checkSuffix(f, "aisf") && !checkSuffix(f, "atsf")) {
                extraFiles.add(new Location(dir, f).getAbsolutePath());
            }
        }
    }
    try {
        ServiceFactory factory = new ServiceFactory();
        MetakitService reader = factory.getInstance(MetakitService.class);
        reader.initialize(id);
        sampleTable = reader.getTableData(1);
        stringTable = reader.getTableData(2);
        reader.close();
    } catch (DependencyException e) {
        throw new MissingLibraryException("Could not find Metakit library", e);
    }
    ArrayList<String> stackNames = new ArrayList<String>();
    ArrayList<Integer> parentIDs = new ArrayList<Integer>();
    for (int i = 0; i < sampleTable.length; i++) {
        Integer stringID = (Integer) sampleTable[i][11];
        String name = getString(stringID);
        int channelIndex = getChildIndex((Integer) sampleTable[i][0], "Channels");
        if (i > 0 && (Integer) sampleTable[i][2] == 1 && (channelIndex >= 0 || (sampleTable[i][14] != null && !sampleTable[i][14].equals(0)) || ((byte[]) sampleTable[i][13]).length > 21)) {
            if (channelIndex < 0) {
                RandomAccessInputStream s = getStream(i);
                s.seek(0);
                if (s.read() != 'I') {
                    s.order(false);
                }
                s.seek(22);
                int x = s.readInt();
                int y = s.readInt();
                int z = s.readInt();
                if (x * y * z > 0 && x * y * z < (s.length() * 3)) {
                    stackNames.add(name);
                    parentIDs.add((Integer) sampleTable[i][0]);
                }
                s.close();
            } else {
                stackNames.add(name);
                parentIDs.add((Integer) sampleTable[i][0]);
            }
        }
    }
    for (int i = 0; i < parentIDs.size(); i++) {
        Stack stack = new Stack();
        stack.core = new CoreMetadata();
        Integer parent = parentIDs.get(i);
        int channelIndex = getChildIndex(parent, "Channels");
        if (channelIndex >= 0) {
            Integer[] channels = getAllChildren((Integer) sampleTable[channelIndex][0]);
            stack.core.sizeC = channels.length;
            stack.pixelsFiles = new String[stack.core.sizeC];
            stack.channelNames = new String[channels.length];
            for (int c = 0; c < channels.length; c++) {
                stack.channelNames[c] = getString((Integer) sampleTable[channels[c]][11]);
                RandomAccessInputStream data = getStream(channels[c]);
                if (data.length() > 22) {
                    data.seek(22);
                    int stackID = data.readInt();
                    Location f = new Location(dir, stackID + ".aisf");
                    if (!f.exists()) {
                        f = new Location(dir, DataTools.swap(stackID) + ".aisf");
                    }
                    stack.pixelsFiles[c] = f.getAbsolutePath();
                } else {
                    Integer child = getAllChildren((Integer) sampleTable[channels[c]][0])[0];
                    stack.pixelsFiles[c] = getFile((Integer) sampleTable[child][0], dir);
                }
                data.close();
            }
        } else {
            stack.pixelsFiles = new String[1];
            stack.pixelsFiles[0] = getFile(parent, dir);
            if (stack.pixelsFiles[0] == null || !new Location(stack.pixelsFiles[0]).exists()) {
                int row = -1;
                for (int r = 0; r < sampleTable.length; r++) {
                    if (sampleTable[r][0].equals(parent)) {
                        row = r;
                        break;
                    }
                }
                stack.pixelsFiles[0] = EMBEDDED_STREAM;
                IRandomAccess data = new ByteArrayHandle((byte[]) sampleTable[row][13]);
                Location.mapFile(stack.pixelsFiles[0], data);
            }
        }
        RandomAccessInputStream data = null;
        int timestampIndex = getChildIndex(parent, "Timepoint times stream");
        if (timestampIndex >= 0) {
            data = getStream(timestampIndex);
            data.seek(22);
            int timestampID = data.readInt();
            Location f = new Location(dir, timestampID + ".atsf");
            if (!f.exists()) {
                f = new Location(dir, DataTools.swap(timestampID) + ".atsf");
            }
            stack.timestampFile = f.getAbsolutePath();
            data.close();
        }
        int xIndex = getChildIndex(parent, "um/pixel (X)");
        if (xIndex >= 0) {
            data = getStream(xIndex);
            data.seek(SIGNATURE_SIZE);
            stack.physicalX = data.readDouble();
            data.close();
        }
        int yIndex = getChildIndex(parent, "um/pixel (Y)");
        if (yIndex >= 0) {
            data = getStream(yIndex);
            data.seek(SIGNATURE_SIZE);
            stack.physicalY = data.readDouble();
            data.close();
        }
        int zIndex = getChildIndex(parent, "um/pixel (Z)");
        if (zIndex >= 0) {
            data = getStream(zIndex);
            data.seek(SIGNATURE_SIZE);
            stack.physicalZ = data.readDouble();
            data.close();
        }
        timestampIndex = getChildIndex(parent, "TimepointTimes");
        if (timestampIndex >= 0) {
            data = getStream(timestampIndex);
            data.seek(SIGNATURE_SIZE);
            data.close();
        }
        int objectiveIndex = getChildIndex(parent, "Microscope Objective");
        if (objectiveIndex >= 0) {
            data = getStream(objectiveIndex);
            data.seek(SIGNATURE_SIZE);
            stack.magnification = data.readDouble();
            data.close();
        }
        int detectorIndex = getChildIndex(parent, "Camera/Detector");
        if (detectorIndex >= 0) {
            data = getStream(detectorIndex);
            data.seek(SIGNATURE_SIZE);
            int len = data.readInt();
            stack.detector = data.readString(len);
            data.close();
        }
        int descriptionIndex = getChildIndex(parent, "Experiment Description");
        if (descriptionIndex >= 0) {
            data = getStream(descriptionIndex);
            data.seek(SIGNATURE_SIZE);
            int len = data.readInt();
            stack.description = data.readString(len);
            data.close();
        }
        int xLocationIndex = getChildIndex(parent, "X Location");
        if (xLocationIndex >= 0) {
            data = getStream(xLocationIndex);
            data.seek(SIGNATURE_SIZE);
            stack.xLocation = data.readDouble();
            data.close();
        }
        int yLocationIndex = getChildIndex(parent, "Y Location");
        if (yLocationIndex >= 0) {
            data = getStream(yLocationIndex);
            data.seek(SIGNATURE_SIZE);
            stack.yLocation = data.readDouble();
            data.close();
        }
        int zLocationIndex = getChildIndex(parent, "Z Location");
        if (zLocationIndex >= 0) {
            data = getStream(zLocationIndex);
            data.seek(SIGNATURE_SIZE);
            stack.zLocation = data.readDouble();
            data.close();
        }
        stacks.add(stack);
    }
    for (int i = 0; i < stacks.size(); i++) {
        Stack stack = stacks.get(i);
        if (!new Location(stack.pixelsFiles[0]).exists()) {
            stacks.remove(i);
            i--;
            continue;
        }
        RandomAccessInputStream base = new RandomAccessInputStream(stack.pixelsFiles[0]);
        long baseLength = base.length();
        base.close();
        for (int q = 1; q < stack.pixelsFiles.length; q++) {
            if (!new Location(stack.pixelsFiles[q]).exists()) {
                continue;
            }
            base = new RandomAccessInputStream(stack.pixelsFiles[q]);
            long length = base.length();
            base.close();
            if (length > baseLength) {
                // split the stack
                Stack newStack = new Stack();
                newStack.timestampFile = stack.timestampFile;
                newStack.core = new CoreMetadata();
                newStack.physicalX = stack.physicalX;
                newStack.physicalY = stack.physicalY;
                newStack.physicalZ = stack.physicalZ;
                newStack.magnification = stack.magnification;
                newStack.detector = stack.detector;
                newStack.description = stack.description;
                newStack.xLocation = stack.xLocation;
                newStack.yLocation = stack.yLocation;
                newStack.zLocation = stack.zLocation;
                String[] pixels = stack.pixelsFiles;
                newStack.pixelsFiles = new String[pixels.length - q];
                System.arraycopy(pixels, q, newStack.pixelsFiles, 0, newStack.pixelsFiles.length);
                stack.pixelsFiles = new String[q];
                System.arraycopy(pixels, 0, stack.pixelsFiles, 0, q);
                String[] channels = stack.channelNames;
                newStack.channelNames = new String[channels.length - q];
                System.arraycopy(channels, q, newStack.channelNames, 0, newStack.channelNames.length);
                stack.channelNames = new String[q];
                System.arraycopy(channels, 0, stack.channelNames, 0, q);
                newStack.core.sizeC = newStack.channelNames.length;
                stack.core.sizeC = stack.channelNames.length;
                stacks.add(i + 1, newStack);
                stackNames.add(i + 1, stackNames.get(i));
            }
        }
    }
    int seriesCount = stacks.size();
    core.clear();
    for (int i = 0; i < seriesCount; i++) {
        Stack stack = stacks.get(i);
        CoreMetadata ms = stack.core;
        core.add(ms);
        setSeries(i);
        ms.littleEndian = true;
        if (stack.timestampFile != null) {
            RandomAccessInputStream s = new RandomAccessInputStream(stack.timestampFile);
            s.seek(0);
            if (s.read() != 'I') {
                ms.littleEndian = false;
            }
            s.seek(17);
            s.order(isLittleEndian());
            ms.sizeT = s.readInt();
            Double firstStamp = null;
            Double[] stamps = new Double[ms.sizeT];
            for (int t = 0; t < ms.sizeT; t++) {
                // timestamps are stored in microseconds
                double timestamp = s.readLong() / 1000000.0;
                if (firstStamp == null) {
                    firstStamp = timestamp;
                }
                stamps[t] = timestamp - firstStamp;
            }
            timestamps.add(stamps);
            s.close();
        } else {
            ms.sizeT = 1;
        }
        ms.rgb = false;
        ms.interleaved = true;
        ms.dimensionOrder = "XYCZT";
        RandomAccessInputStream s = new RandomAccessInputStream(stack.pixelsFiles[0]);
        s.order(isLittleEndian());
        if (checkSuffix(stack.pixelsFiles[0], "aisf")) {
            s.seek(18);
            stack.blockSize = s.readShort() * 256;
            s.skipBytes(5);
            int x = s.readInt();
            int y = s.readInt();
            int zStart = s.readInt();
            int w = s.readInt();
            int h = s.readInt();
            if (w - x < 0 || h - y < 0 || (w - x) * (h - y) < 0) {
                ms.littleEndian = !isLittleEndian();
                s.order(isLittleEndian());
                s.seek(s.getFilePointer() - 20);
                x = s.readInt();
                y = s.readInt();
                zStart = s.readInt();
                w = s.readInt();
                h = s.readInt();
            }
            ms.sizeX = w - x;
            ms.sizeY = h - y;
            ms.sizeZ = s.readInt() - zStart;
            ms.imageCount = getSizeZ() * getSizeC() * getSizeT();
            ms.pixelType = FormatTools.INT8;
            int planesPerFile = getSizeZ() * getSizeT();
            int planeSize = FormatTools.getPlaneSize(this);
            int bytesPerPlane = (int) ((s.length() - stack.blockSize) / planesPerFile);
            int bytesPerPixel = 0;
            while (bytesPerPlane >= planeSize) {
                bytesPerPixel++;
                bytesPerPlane -= planeSize;
            }
            if ((bytesPerPixel % 3) == 0) {
                ms.sizeC *= 3;
                ms.rgb = true;
                bytesPerPixel /= 3;
            }
            ms.pixelType = FormatTools.pixelTypeFromBytes(bytesPerPixel, false, bytesPerPixel > 2);
            // full timepoints are padded to have a multiple of 256 bytes
            int timepoint = FormatTools.getPlaneSize(this) * getSizeZ();
            stack.planePadding = stack.blockSize - (timepoint % stack.blockSize);
            if (stack.planePadding == stack.blockSize) {
                stack.planePadding = 0;
            }
        } else {
            boolean embedded = Location.getMappedFile(EMBEDDED_STREAM) != null;
            s.seek(0);
            if (s.read() != 'I') {
                ms.littleEndian = false;
                s.order(false);
            }
            s.seek(22);
            ms.sizeX = s.readInt();
            ms.sizeY = s.readInt();
            ms.sizeZ = s.readInt();
            ms.sizeC = embedded ? 1 : 4;
            ms.imageCount = getSizeZ() * getSizeT();
            ms.rgb = ms.sizeC > 1;
            ms.pixelType = FormatTools.UINT8;
            stack.blockSize = embedded ? (int) s.getFilePointer() : 99;
            stack.planePadding = 0;
            if (s.length() > ms.sizeX * ms.sizeY * ms.sizeZ * 6) {
                ms.pixelType = FormatTools.UINT16;
                ms.sizeC = 3;
                ms.rgb = true;
            }
            if (s.length() < (ms.sizeX * ms.sizeY * ms.sizeZ * ms.sizeC)) {
                ms.rgb = false;
                ms.sizeC = 1;
                long pixels = ms.sizeX * ms.sizeY * ms.sizeZ;
                double approximateBytes = (double) s.length() / pixels;
                int bytes = (int) Math.ceil(approximateBytes);
                if (bytes == 0) {
                    bytes = 1;
                } else if (bytes == 3) {
                    bytes = 2;
                }
                ms.pixelType = FormatTools.pixelTypeFromBytes(bytes, false, false);
                s.seek(70);
                stack.blockSize = s.readInt();
                stack.clippingData = true;
            }
        }
        s.close();
    }
    setSeries(0);
    for (int i = 0; i < getSeriesCount(); i++) {
        setSeries(i);
        Stack stack = stacks.get(i);
        addSeriesMeta("Name", stackNames.get(i));
        addSeriesMeta("Pixel width (in microns)", stack.physicalX);
        addSeriesMeta("Pixel height (in microns)", stack.physicalY);
        addSeriesMeta("Z step (in microns)", stack.physicalZ);
        addSeriesMeta("Objective magnification", stack.magnification);
        addSeriesMeta("Camera/Detector", stack.detector);
        addSeriesMeta("Description", stack.description);
        addSeriesMeta("X Location", stack.xLocation);
        addSeriesMeta("Y Location", stack.yLocation);
        addSeriesMeta("Z Location", stack.zLocation);
        if (stack.channelNames != null) {
            for (int c = 0; c < stack.channelNames.length; c++) {
                addSeriesMetaList("Channel", stack.channelNames[c]);
            }
        }
    }
    setSeries(0);
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, true);
    String instrument = MetadataTools.createLSID("Instrument", 0);
    store.setInstrumentID(instrument, 0);
    for (int i = 0; i < getSeriesCount(); i++) {
        store.setImageInstrumentRef(instrument, i);
        setSeries(i);
        Stack stack = stacks.get(i);
        store.setImageName(stackNames.get(i), i);
        store.setImageDescription(stack.description, i);
        if (stack.channelNames != null) {
            for (int c = 0; c < getEffectiveSizeC(); c++) {
                store.setChannelName(stack.channelNames[c], i, c);
            }
        }
        Length sizeX = FormatTools.getPhysicalSizeX(stack.physicalX);
        Length sizeY = FormatTools.getPhysicalSizeY(stack.physicalY);
        Length sizeZ = FormatTools.getPhysicalSizeZ(stack.physicalZ);
        if (sizeX != null) {
            store.setPixelsPhysicalSizeX(sizeX, i);
        }
        if (sizeY != null) {
            store.setPixelsPhysicalSizeY(sizeY, i);
        }
        if (sizeZ != null) {
            store.setPixelsPhysicalSizeZ(sizeZ, i);
        }
        String objective = MetadataTools.createLSID("Objective", 0, i);
        store.setObjectiveID(objective, 0, i);
        store.setObjectiveNominalMagnification(stack.magnification, 0, i);
        store.setObjectiveCorrection(getCorrection("Other"), 0, i);
        store.setObjectiveImmersion(getImmersion("Other"), 0, i);
        store.setObjectiveSettingsID(objective, i);
        String detectorID = MetadataTools.createLSID("Detector", 0, i);
        store.setDetectorID(detectorID, 0, i);
        store.setDetectorModel(stack.detector, 0, i);
        for (int c = 0; c < getEffectiveSizeC(); c++) {
            store.setDetectorSettingsID(detectorID, i, c);
        }
        for (int img = 0; img < getImageCount(); img++) {
            int[] coords = getZCTCoords(img);
            int z = coords[0];
            final Length xLoc = new Length(stack.xLocation, UNITS.REFERENCEFRAME);
            final Length yLoc = new Length(stack.yLocation, UNITS.REFERENCEFRAME);
            store.setPlanePositionX(xLoc, i, img);
            store.setPlanePositionY(yLoc, i, img);
            if (stack.physicalZ != null) {
                final double zLocNumber = stack.zLocation + z * stack.physicalZ;
                final Length zLoc = new Length(zLocNumber, UNITS.REFERENCEFRAME);
                store.setPlanePositionZ(zLoc, i, img);
            }
            if (i < timestamps.size() && coords[2] < timestamps.get(i).length && timestamps.get(i)[coords[2]] != null) {
                store.setPlaneDeltaT(new Time(timestamps.get(i)[coords[2]], UNITS.SECOND), i, img);
            }
        }
    }
    setSeries(0);
}