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

Example 36 with CoreMetadata

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

the class FujiReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    if (checkSuffix(id, "inf")) {
        infFile = new Location(id).getAbsolutePath();
        pixelsFile = infFile.substring(0, infFile.lastIndexOf(".")) + ".img";
    } else {
        pixelsFile = new Location(id).getAbsolutePath();
        infFile = pixelsFile.substring(0, pixelsFile.lastIndexOf(".")) + ".inf";
    }
    String[] lines = DataTools.readFile(infFile).split("\r{0,1}\n");
    int bits = Integer.parseInt(lines[5]);
    CoreMetadata m = core.get(0);
    m.pixelType = FormatTools.pixelTypeFromBytes(bits / 8, false, false);
    m.sizeX = Integer.parseInt(lines[6]);
    m.sizeY = Integer.parseInt(lines[7]);
    m.sizeC = 1;
    m.sizeT = 1;
    m.sizeZ = 1;
    m.imageCount = getSizeZ() * getSizeC() * getSizeT();
    m.dimensionOrder = "XYCZT";
    for (String line : lines) {
        addGlobalMetaList("Line", line);
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    String imageName = lines[1];
    String timestamp = lines[10];
    timestamp = DateTools.formatDate(timestamp, DATE_FORMAT);
    store.setImageName(imageName, 0);
    if (timestamp != null) {
        store.setImageAcquisitionDate(new Timestamp(timestamp), 0);
    }
    double physicalWidth = Double.parseDouble(lines[3]);
    double physicalHeight = Double.parseDouble(lines[4]);
    Length sizeX = FormatTools.getPhysicalSizeX(physicalWidth);
    Length sizeY = FormatTools.getPhysicalSizeY(physicalHeight);
    if (sizeX != null) {
        store.setPixelsPhysicalSizeX(sizeX, 0);
    }
    if (sizeY != null) {
        store.setPixelsPhysicalSizeY(sizeY, 0);
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        String instrument = lines[13];
        String instrumentID = MetadataTools.createLSID("Instrument", 0);
        store.setInstrumentID(instrumentID, 0);
        store.setMicroscopeModel(instrument, 0);
    }
}

Example 37 with CoreMetadata

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

the class GatanReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    pixelOffset = 0;
    CoreMetadata m = core.get(0);
    LOGGER.info("Verifying Gatan format");
    m.littleEndian = false;
    pixelSizes = new ArrayList<Double>();
    units = new ArrayList<String>();
    shapes = new ArrayList<ROIShape>();
    in.order(isLittleEndian());
    // only support version 3
    version = in.readInt();
    if (version != 3 && version != 4) {
        throw new FormatException("invalid header");
    }
    LOGGER.info("Reading tags");
    in.skipBytes(4);
    skipPadding();
    m.littleEndian = in.readInt() != 1;
    in.order(isLittleEndian());
    // TagGroup instance
    in.skipBytes(2);
    skipPadding();
    int numTags = in.readInt();
    if (numTags > in.length()) {
        m.littleEndian = !isLittleEndian();
        in.order(isLittleEndian());
        adjustEndianness = false;
    }
    LOGGER.debug("tags ({}) {", numTags);
    try {
        parseTags(numTags, null, "  ");
    } catch (Exception e) {
        throw new FormatException("Unable to parse metadata tag", e);
    }
    LOGGER.debug("}");
    LOGGER.info("Populating metadata");
    m.littleEndian = true;
    if (getSizeX() == 0 || getSizeY() == 0) {
        throw new FormatException("Dimensions information not found");
    }
    if (m.sizeZ == 0) {
        m.sizeZ = 1;
    }
    m.sizeC = 1;
    m.sizeT = 1;
    m.dimensionOrder = "XYZTC";
    m.imageCount = getSizeZ() * getSizeC() * getSizeT();
    int bytes = (int) (numPixelBytes / (getSizeX() * getSizeY() * (long) getImageCount()));
    if (bytes != FormatTools.getBytesPerPixel(getPixelType())) {
        m.pixelType = FormatTools.pixelTypeFromBytes(bytes, signed, false);
    }
    m.rgb = false;
    m.interleaved = false;
    m.metadataComplete = true;
    m.indexed = false;
    m.falseColor = false;
    // The metadata store we're working with.
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, true);
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        int index = 0;
        if (pixelSizes.size() > 4) {
            index = pixelSizes.size() - 3;
        } else if (pixelSizes.size() == 4) {
            if (Math.abs(pixelSizes.get(0) - 1.0) < Constants.EPSILON) {
                index = pixelSizes.size() - 2;
            }
        }
        if (index + 2 < pixelSizes.size() && Math.abs(pixelSizes.get(index + 1) - pixelSizes.get(index + 2)) < Constants.EPSILON) {
            if (Math.abs(pixelSizes.get(index) - pixelSizes.get(index + 1)) > Constants.EPSILON && getSizeY() > 1) {
                index++;
            }
        }
        if (index < pixelSizes.size() - 1) {
            Double x = pixelSizes.get(index);
            Double y = pixelSizes.get(index + 1);
            String xUnits = index < units.size() ? units.get(index) : "";
            String yUnits = index + 1 < units.size() ? units.get(index + 1) : "";
            Length sizeX = FormatTools.getPhysicalSizeX(x, convertUnits(xUnits));
            Length sizeY = FormatTools.getPhysicalSizeY(y, convertUnits(yUnits));
            if (sizeX != null) {
                store.setPixelsPhysicalSizeX(sizeX, 0);
            }
            if (sizeY != null) {
                store.setPixelsPhysicalSizeY(sizeY, 0);
            }
            if (index < pixelSizes.size() - 2) {
                Double z = pixelSizes.get(index + 2);
                String zUnits = index + 2 < units.size() ? units.get(index + 2) : "";
                Length sizeZ = FormatTools.getPhysicalSizeZ(z, convertUnits(zUnits));
                if (sizeZ != null) {
                    store.setPixelsPhysicalSizeZ(sizeZ, 0);
                }
            }
        }
        String instrument = MetadataTools.createLSID("Instrument", 0);
        store.setInstrumentID(instrument, 0);
        store.setImageInstrumentRef(instrument, 0);
        String objective = MetadataTools.createLSID("Objective", 0, 0);
        store.setObjectiveID(objective, 0, 0);
        store.setObjectiveCorrection(getCorrection("Unknown"), 0, 0);
        store.setObjectiveImmersion(getImmersion("Unknown"), 0, 0);
        store.setObjectiveNominalMagnification(mag, 0, 0);
        store.setObjectiveSettingsID(objective, 0);
        String detector = MetadataTools.createLSID("Detector", 0, 0);
        store.setDetectorID(detector, 0, 0);
        store.setDetectorSettingsID(detector, 0, 0);
        store.setDetectorSettingsVoltage(new ElectricPotential(voltage, UNITS.VOLT), 0, 0);
        if (info == null)
            info = "";
        String[] scopeInfo = info.split("\\(");
        for (String token : scopeInfo) {
            token = token.trim();
            if (token.startsWith("Mode")) {
                token = token.substring(token.indexOf(' ')).trim();
                String mode = token.substring(0, token.indexOf(' ')).trim();
                if (mode.equals("TEM"))
                    mode = "Other";
                store.setChannelAcquisitionMode(getAcquisitionMode(mode), 0, 0);
            }
        }
        store.setPlanePositionX(posX, 0, 0);
        store.setPlanePositionY(posY, 0, 0);
        store.setPlanePositionZ(posZ, 0, 0);
        for (int i = 0; i < getImageCount(); i++) {
            store.setPlaneExposureTime(new Time(sampleTime, UNITS.SECOND), 0, i);
        }
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.NO_OVERLAYS && shapes.size() > 0) {
        for (int i = 0; i < shapes.size(); i++) {
            String roi = MetadataTools.createLSID("ROI", i);
            store.setROIID(roi, i);
            store.setImageROIRef(roi, 0, i);
            String shapeID = MetadataTools.createLSID("Shape", i, 0);
            ROIShape shape = shapes.get(i);
            switch(shape.type) {
                case LINE:
                    store.setLineID(shapeID, i, 0);
                    store.setLineX1(shape.x1, i, 0);
                    store.setLineY1(shape.y1, i, 0);
                    store.setLineX2(shape.x2, i, 0);
                    store.setLineY2(shape.y2, i, 0);
                    store.setLineText(shape.text, i, 0);
                    store.setLineFontSize(shape.fontSize, i, 0);
                    store.setLineStrokeColor(shape.strokeColor, i, 0);
                    break;
                case TEXT:
                    store.setLabelID(shapeID, i, 0);
                    store.setLabelX(shape.x1, i, 0);
                    store.setLabelY(shape.y1, i, 0);
                    store.setLabelText(shape.text, i, 0);
                    store.setLabelFontSize(shape.fontSize, i, 0);
                    store.setLabelStrokeColor(shape.strokeColor, i, 0);
                    break;
                case ELLIPSE:
                    store.setEllipseID(shapeID, i, 0);
                    double radiusX = (shape.x2 - shape.x1) / 2;
                    double radiusY = (shape.y2 - shape.y1) / 2;
                    store.setEllipseX(shape.x1 + radiusX, i, 0);
                    store.setEllipseY(shape.y1 + radiusY, i, 0);
                    store.setEllipseRadiusX(radiusX, i, 0);
                    store.setEllipseRadiusY(radiusY, i, 0);
                    store.setEllipseText(shape.text, i, 0);
                    store.setEllipseFontSize(shape.fontSize, i, 0);
                    store.setEllipseStrokeColor(shape.strokeColor, i, 0);
                    break;
                case RECTANGLE:
                    store.setRectangleID(shapeID, i, 0);
                    store.setRectangleX(shape.x1, i, 0);
                    store.setRectangleY(shape.y1, i, 0);
                    store.setRectangleWidth(shape.x2 - shape.x1, i, 0);
                    store.setRectangleHeight(shape.y2 - shape.y1, i, 0);
                    store.setRectangleText(shape.text, i, 0);
                    store.setRectangleFontSize(shape.fontSize, i, 0);
                    store.setRectangleStrokeColor(shape.strokeColor, i, 0);
                    break;
                default:
                    LOGGER.warn("Unknown ROI type: {}", shape.type);
            }
        }
    }
}

Example 38 with CoreMetadata

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

the class HISReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    in.order(true);
    in.skipBytes(14);
    int nSeries = in.readShort();
    pixelOffset = new long[nSeries];
    String[] date = new String[nSeries];
    String[] binning = new String[nSeries];
    double[] offset = new double[nSeries];
    double[] exposureTime = new double[nSeries];
    boolean adjustedBitDepth = false;
    in.seek(0);
    core.clear();
    for (int i = 0; i < nSeries; i++) {
        CoreMetadata ms = new CoreMetadata();
        core.add(ms);
        String checkString = in.readString(2);
        if (!checkString.equals("IM") && i > 0) {
            if (getBitsPerPixel() == 12) {
                core.get(i - 1).bitsPerPixel = 16;
                int prevSkip = (getSizeX() * getSizeY() * getSizeC() * 12) / 8;
                int totalBytes = FormatTools.getPlaneSize(this);
                in.skipBytes(totalBytes - prevSkip);
                adjustedBitDepth = true;
            }
        }
        setSeries(i);
        int commentBytes = in.readShort();
        ms.sizeX = in.readShort();
        ms.sizeY = in.readShort();
        in.skipBytes(4);
        int dataType = in.readShort();
        switch(dataType) {
            case 1:
                ms.pixelType = FormatTools.UINT8;
                break;
            case 2:
                ms.pixelType = FormatTools.UINT16;
                break;
            case 6:
                ms.pixelType = FormatTools.UINT16;
                ms.bitsPerPixel = adjustedBitDepth ? 16 : 12;
                break;
            case 11:
                ms.pixelType = FormatTools.UINT8;
                ms.sizeC = 3;
                break;
            case 12:
                ms.pixelType = FormatTools.UINT16;
                ms.sizeC = 3;
                break;
            case 14:
                ms.pixelType = FormatTools.UINT16;
                ms.sizeC = 3;
                ms.bitsPerPixel = adjustedBitDepth ? 16 : 12;
                break;
        }
        in.skipBytes(50);
        String comment = in.readString(commentBytes);
        if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
            String[] data = comment.split(";");
            for (String token : data) {
                int eq = token.indexOf('=');
                if (eq != -1) {
                    String key = token.substring(0, eq);
                    String value = token.substring(eq + 1);
                    addSeriesMeta(key, value);
                    if (key.equals("vDate")) {
                        date[i] = value;
                    } else if (key.equals("vTime")) {
                        date[i] += " " + value;
                        date[i] = DateTools.formatDate(date[i], "yyyy/MM/dd HH:mm:ss");
                    } else if (key.equals("vOffset")) {
                        offset[i] = Double.parseDouble(value);
                    } else if (key.equals("vBinX")) {
                        binning[i] = value;
                    } else if (key.equals("vBinY")) {
                        binning[i] += "x" + value;
                    } else if (key.equals("vExpTim1")) {
                        exposureTime[i] = Double.parseDouble(value) * 100;
                    }
                }
            }
        }
        pixelOffset[i] = in.getFilePointer();
        ms.littleEndian = true;
        if (ms.sizeC == 0)
            ms.sizeC = 1;
        ms.sizeT = 1;
        ms.sizeZ = 1;
        ms.imageCount = 1;
        ms.rgb = ms.sizeC > 1;
        ms.interleaved = isRGB();
        ms.dimensionOrder = "XYCZT";
        in.skipBytes((getSizeX() * getSizeY() * getSizeC() * getBitsPerPixel()) / 8);
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, true);
    String instrumentID = MetadataTools.createLSID("Instrument", 0);
    store.setInstrumentID(instrumentID, 0);
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        for (int i = 0; i < nSeries; i++) {
            store.setImageInstrumentRef(instrumentID, i);
            if (date[i] != null) {
                store.setImageAcquisitionDate(new Timestamp(date[i]), i);
            }
            store.setPlaneExposureTime(new Time(exposureTime[i], UNITS.SECOND), i, 0);
            String detectorID = MetadataTools.createLSID("Detector", 0, i);
            store.setDetectorID(detectorID, 0, i);
            store.setDetectorOffset(offset[i], 0, i);
            store.setDetectorType(getDetectorType("Other"), 0, i);
            store.setDetectorSettingsID(detectorID, i, 0);
            store.setDetectorSettingsBinning(getBinning(binning[i]), i, 0);
        }
    }
}

Example 39 with CoreMetadata

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

the class HamamatsuVMSReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    IniParser parser = new IniParser();
    IniList layout = parser.parseINI(new BufferedReader(new InputStreamReader(in, Constants.ENCODING)));
    IniTable slideInfo = layout.getTable("Virtual Microscope Specimen");
    int nLayers = Integer.parseInt(slideInfo.get("NoLayers"));
    nRows = Integer.parseInt(slideInfo.get("NoJpegRows"));
    nCols = Integer.parseInt(slideInfo.get("NoJpegColumns"));
    String imageFile = slideInfo.get("ImageFile");
    mapFile = slideInfo.get("MapFile");
    String optimisationFile = slideInfo.get("OptimisationFile");
    macroFile = slideInfo.get("MacroImage");
    Double physicalWidth = new Double(slideInfo.get("PhysicalWidth"));
    Double physicalHeight = new Double(slideInfo.get("PhysicalHeight"));
    Double magnification = new Double(slideInfo.get("SourceLens"));
    Double macroWidth = new Double(slideInfo.get("PhysicalMacroWidth"));
    Double macroHeight = new Double(slideInfo.get("PhysicalMacroHeight"));
    for (String key : slideInfo.keySet()) {
        addGlobalMeta(key, slideInfo.get(key));
    }
    Location dir = new Location(id).getAbsoluteFile().getParentFile();
    if (imageFile != null) {
        imageFile = new Location(dir, imageFile).getAbsolutePath();
        files.add(imageFile);
    }
    tileFiles = new String[nLayers][nRows][nCols];
    tileFiles[0][0][0] = imageFile;
    for (int layer = 0; layer < nLayers; layer++) {
        for (int row = 0; row < nRows; row++) {
            for (int col = 0; col < nCols; col++) {
                String f = slideInfo.get("ImageFile(" + col + "," + row + ")");
                if (f != null) {
                    f = new Location(dir, f).getAbsolutePath();
                    tileFiles[layer][row][col] = f;
                    files.add(f);
                }
            }
        }
    }
    if (mapFile != null) {
        mapFile = new Location(dir, mapFile).getAbsolutePath();
        files.add(mapFile);
    }
    if (optimisationFile != null) {
        optimisationFile = new Location(dir, optimisationFile).getAbsolutePath();
        files.add(optimisationFile);
    }
    if (macroFile != null) {
        macroFile = new Location(dir, macroFile).getAbsolutePath();
        files.add(macroFile);
    }
    int seriesCount = 3;
    core.clear();
    for (int i = 0; i < seriesCount; i++) {
        String file = null;
        switch(i) {
            case 0:
                file = tileFiles[0][nRows - 1][nCols - 1];
                break;
            case 1:
                file = macroFile;
                break;
            case 2:
                file = mapFile;
                break;
        }
        int[] dims;
        try (RandomAccessInputStream s = new RandomAccessInputStream(file);
            JPEGTileDecoder decoder = new JPEGTileDecoder()) {
            dims = decoder.preprocess(s);
        }
        CoreMetadata m = new CoreMetadata();
        if (i == 0) {
            m.sizeX = (MAX_JPEG_SIZE * (nCols - 1)) + dims[0];
            m.sizeY = (MAX_JPEG_SIZE * (nRows - 1)) + dims[1];
        } else {
            m.sizeX = dims[0];
            m.sizeY = dims[1];
        }
        m.sizeZ = 1;
        m.sizeC = 3;
        m.sizeT = 1;
        m.rgb = true;
        m.imageCount = 1;
        m.dimensionOrder = "XYCZT";
        m.pixelType = FormatTools.UINT8;
        m.interleaved = m.sizeX > MAX_SIZE && m.sizeY > MAX_SIZE;
        m.thumbnail = i > 0;
        core.add(m);
    }
    CoreMetadata ms0 = core.get(0);
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    String path = new Location(currentId).getAbsoluteFile().getName();
    store.setImageName(path + " full resolution", 0);
    store.setImageName(path + " macro", 1);
    store.setImageName(path + " map", 2);
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        Length sizeX = FormatTools.getPhysicalSizeX(physicalWidth / ms0.sizeX);
        Length sizeY = FormatTools.getPhysicalSizeY(physicalHeight / ms0.sizeY);
        Length macroSizeX = FormatTools.getPhysicalSizeX(macroWidth / core.get(1).sizeX);
        Length macroSizeY = FormatTools.getPhysicalSizeY(macroHeight / core.get(1).sizeY);
        if (sizeX != null) {
            store.setPixelsPhysicalSizeX(sizeX, 0);
        }
        if (sizeY != null) {
            store.setPixelsPhysicalSizeY(sizeY, 0);
        }
        if (macroSizeX != null) {
            store.setPixelsPhysicalSizeX(macroSizeX, 1);
        }
        if (macroSizeY != null) {
            store.setPixelsPhysicalSizeY(macroSizeY, 1);
        }
        String instrumentID = MetadataTools.createLSID("Instrument", 0);
        store.setInstrumentID(instrumentID, 0);
        store.setImageInstrumentRef(instrumentID, 0);
        String objectiveID = MetadataTools.createLSID("Objective", 0, 0);
        store.setObjectiveID(objectiveID, 0, 0);
        store.setObjectiveNominalMagnification(magnification, 0, 0);
        store.setObjectiveSettingsID(objectiveID, 0);
    }
}

Example 40 with CoreMetadata

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

the class I2IReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
public void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    CoreMetadata m = core.get(0);
    char pixelType = (char) in.readByte();
    switch(pixelType) {
        case 'I':
            m.pixelType = FormatTools.INT16;
            break;
        case 'R':
            m.pixelType = FormatTools.FLOAT;
            break;
        case 'C':
            throw new FormatException("Complex pixel data not yet supported");
        default:
            throw new FormatException("Invalid pixel type: " + pixelType);
    }
    if ((char) in.readByte() != ' ') {
        throw new FormatException("Expected space after pixel type character");
    }
    m.sizeX = getDimension(in);
    m.sizeY = getDimension(in);
    m.sizeZ = getDimension(in);
    m.littleEndian = (char) in.readByte() != 'B';
    in.order(isLittleEndian());
    short minPixelValue = in.readShort();
    short maxPixelValue = in.readShort();
    short xCoordinate = in.readShort();
    short yCoordinate = in.readShort();
    int n = in.readShort();
    // reserved for future use
    in.skipBytes(33);
    for (int i = 0; i < 15; i++) {
        String history = in.readString(64);
        addGlobalMetaList("Image history", history.trim());
    }
    addGlobalMeta("Minimum intensity value", minPixelValue);
    addGlobalMeta("Maximum intensity value", maxPixelValue);
    addGlobalMeta("Image position X", xCoordinate);
    addGlobalMeta("Image position Y", yCoordinate);
    // needs to be adjusted to reflect the true Z count
    if (n > 0) {
        m.sizeZ /= n;
    }
    // the user defines what the N dimension means
    // in practice, it could be timepoints, channels, etc. but we have no
    // way of knowing based on the file metadata
    m.sizeT = n;
    m.imageCount = getSizeZ() * getSizeT();
    m.sizeC = 1;
    m.rgb = false;
    m.dimensionOrder = "XYZTC";
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
}