Examples with MetadataStore loci.formats.meta.MetadataStore used on opensource projects

Example 61 with MetadataStore

use of loci.formats.meta.MetadataStore in project bioformats by openmicroscopy.

the class BurleighReader 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);
    CoreMetadata m = core.get(0);
    m.littleEndian = true;
    in.order(isLittleEndian());
    int version = (int) in.readFloat() - 1;
    m.sizeX = in.readShort();
    m.sizeY = in.readShort();
    double xSize = 0d, ySize = 0d, zSize = 0d;
    pixelsOffset = version == 1 ? 8 : 260;
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        double timePerPixel = 0d;
        int mode = 0, gain = 0, mag = 0;
        double sampleVolts = 0d, tunnelCurrent = 0d;
        if (version == 1) {
            in.seek(in.length() - 40);
            in.skipBytes(12);
            xSize = in.readInt();
            ySize = in.readInt();
            zSize = in.readInt();
            timePerPixel = in.readShort() * 50;
            mag = in.readShort();
            switch(mag) {
                case 3:
                    mag = 10;
                    break;
                case 4:
                    mag = 50;
                    break;
                case 5:
                    mag = 250;
                    break;
            }
            xSize /= mag;
            ySize /= mag;
            zSize /= mag;
            mode = in.readShort();
            gain = in.readShort();
            sampleVolts = in.readFloat() / 1000;
            tunnelCurrent = in.readFloat();
        } else if (version == 2) {
            in.skipBytes(14);
            xSize = in.readInt();
            ySize = in.readInt();
            zSize = in.readInt();
            mode = in.readShort();
            in.skipBytes(4);
            gain = in.readShort();
            timePerPixel = in.readShort() * 50;
            in.skipBytes(12);
            sampleVolts = in.readFloat();
            tunnelCurrent = in.readFloat();
            addGlobalMeta("Force", in.readFloat());
        }
        addGlobalMeta("Version", version);
        addGlobalMeta("Image mode", mode);
        addGlobalMeta("Z gain", gain);
        addGlobalMeta("Time per pixel (s)", timePerPixel);
        addGlobalMeta("Sample volts", sampleVolts);
        addGlobalMeta("Tunnel current", tunnelCurrent);
        addGlobalMeta("Magnification", mag);
    }
    m.pixelType = FormatTools.UINT16;
    m.sizeZ = 1;
    m.sizeC = 1;
    m.sizeT = 1;
    m.imageCount = 1;
    m.dimensionOrder = "XYZCT";
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        Length sizeX = FormatTools.getPhysicalSizeX(xSize / getSizeX());
        Length sizeY = FormatTools.getPhysicalSizeY(ySize / getSizeY());
        Length sizeZ = FormatTools.getPhysicalSizeZ(zSize / getSizeZ());
        if (sizeX != null) {
            store.setPixelsPhysicalSizeX(sizeX, 0);
        }
        if (sizeY != null) {
            store.setPixelsPhysicalSizeY(sizeY, 0);
        }
        if (sizeZ != null) {
            store.setPixelsPhysicalSizeZ(sizeZ, 0);
        }
    }
}

Example 62 with MetadataStore

use of loci.formats.meta.MetadataStore in project bioformats by openmicroscopy.

the class AIMReader 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);
    CoreMetadata m = core.get(0);
    m.littleEndian = true;
    in.order(isLittleEndian());
    // check for newer version of AIM format with wider offsets
    String version = in.readString(16);
    boolean widerOffsets = version.startsWith("AIMDATA_V030");
    if (widerOffsets) {
        in.seek(96);
        m.sizeX = (int) in.readLong();
        m.sizeY = (int) in.readLong();
        m.sizeZ = (int) in.readLong();
        in.seek(280);
    } else {
        in.seek(56);
        m.sizeX = in.readInt();
        m.sizeY = in.readInt();
        m.sizeZ = in.readInt();
        in.seek(160);
    }
    m.sizeC = 1;
    m.sizeT = 1;
    m.imageCount = getSizeZ();
    m.pixelType = FormatTools.INT16;
    m.dimensionOrder = "XYZCT";
    String processingLog = in.readCString();
    pixelOffset = in.getFilePointer();
    String date = null;
    Double xSize = null, xLength = null;
    Double ySize = null, yLength = null;
    Double zSize = null, zLength = null;
    String[] lines = processingLog.split("\n");
    for (String line : lines) {
        line = line.trim();
        int split = line.indexOf("  ");
        if (split > 0) {
            String key = line.substring(0, split).trim();
            String value = line.substring(split).trim();
            addGlobalMeta(key, value);
            if (key.equals("Original Creation-Date")) {
                date = DateTools.formatDate(value, "dd-MMM-yyyy HH:mm:ss", ".");
            } else if (key.equals("Orig-ISQ-Dim-p")) {
                String[] tokens = value.split(" ");
                for (String token : tokens) {
                    token = token.trim();
                    if (token.length() > 0) {
                        if (xSize == null) {
                            xSize = new Double(token);
                        } else if (ySize == null) {
                            ySize = new Double(token);
                        } else if (zSize == null) {
                            zSize = new Double(token);
                        }
                    }
                }
            } else if (key.equals("Orig-ISQ-Dim-um")) {
                String[] tokens = value.split(" ");
                for (String token : tokens) {
                    token = token.trim();
                    if (token.length() > 0) {
                        if (xLength == null) {
                            xLength = new Double(token);
                        } else if (yLength == null) {
                            yLength = new Double(token);
                        } else if (zLength == null) {
                            zLength = new Double(token);
                        }
                    }
                }
            }
        }
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    if (date != null) {
        store.setImageAcquisitionDate(new Timestamp(date), 0);
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        if (xSize != null && xLength != null) {
            Double size = xLength / xSize;
            Length physicalSize = FormatTools.getPhysicalSizeX(size);
            if (physicalSize != null) {
                store.setPixelsPhysicalSizeX(physicalSize, 0);
            }
        }
        if (ySize != null && yLength != null) {
            Double size = yLength / ySize;
            Length physicalSize = FormatTools.getPhysicalSizeY(size);
            if (physicalSize != null) {
                store.setPixelsPhysicalSizeY(physicalSize, 0);
            }
        }
        if (zSize != null && zLength != null) {
            Double size = zLength / zSize;
            Length physicalSize = FormatTools.getPhysicalSizeZ(size);
            if (physicalSize != null) {
                store.setPixelsPhysicalSizeZ(physicalSize, 0);
            }
        }
    }
}

Example 63 with MetadataStore

use of loci.formats.meta.MetadataStore in project bioformats by openmicroscopy.

the class ARFReader 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);
    // parse file header
    LOGGER.info("Reading file header");
    byte endian1 = in.readByte();
    byte endian2 = in.readByte();
    boolean little;
    if (endian1 == 1 && endian2 == 0)
        little = true;
    else if (endian1 == 0 && endian2 == 1)
        little = false;
    else
        throw new FormatException("Undefined endianness");
    in.order(little);
    // 'AR' signature
    in.skipBytes(2);
    int version = in.readUnsignedShort();
    int width = in.readUnsignedShort();
    int height = in.readUnsignedShort();
    int bitsPerPixel = in.readUnsignedShort();
    int numImages = version == 2 ? in.readUnsignedShort() : 1;
    // NB: The next 510 bytes are unused 'application dependent' data,
    // followed by raw image data with no padding.
    // populate core metadata
    CoreMetadata m = core.get(0);
    m.sizeX = width;
    m.sizeY = height;
    m.sizeZ = 1;
    m.sizeC = 1;
    m.sizeT = numImages;
    int bpp = bitsPerPixel / 8;
    if ((bitsPerPixel % 8) != 0)
        bpp++;
    m.pixelType = FormatTools.pixelTypeFromBytes(bpp, false, false);
    m.bitsPerPixel = bitsPerPixel;
    m.imageCount = numImages;
    m.dimensionOrder = "XYCZT";
    m.orderCertain = true;
    m.littleEndian = little;
    m.rgb = false;
    m.interleaved = false;
    m.indexed = false;
    m.metadataComplete = true;
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        // populate original metadata
        addGlobalMeta("Endianness", little ? "little" : "big");
        addGlobalMeta("Version", version);
        addGlobalMeta("Width", width);
        addGlobalMeta("Height", height);
        addGlobalMeta("Bits per pixel", bitsPerPixel);
        addGlobalMeta("Image count", numImages);
    }
    // populate OME metadata
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
}

Example 64 with MetadataStore

use of loci.formats.meta.MetadataStore in project bioformats by openmicroscopy.

the class AliconaReader 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);
    CoreMetadata m = core.get(0);
    // check that this is a valid AL3D file
    LOGGER.info("Verifying Alicona format");
    String magicString = in.readString(17);
    if (!magicString.trim().equals("AliconaImaging")) {
        throw new FormatException("Invalid magic string : " + "expected 'AliconaImaging', got " + magicString);
    }
    // now we read a series of tags
    // each one is 52 bytes - 20 byte key + 30 byte value + 2 byte CRLF
    LOGGER.info("Reading tags");
    int count = 2;
    boolean hasC = false;
    String voltage = null, magnification = null, workingDistance = null;
    String pntX = null, pntY = null;
    int depthOffset = 0;
    for (int i = 0; i < count; i++) {
        String key = in.readString(20).trim();
        String value = in.readString(30).trim();
        addGlobalMeta(key, value);
        in.skipBytes(2);
        if (key.equals("TagCount"))
            count += Integer.parseInt(value);
        else if (key.equals("Rows"))
            m.sizeY = Integer.parseInt(value);
        else if (key.equals("Cols"))
            m.sizeX = Integer.parseInt(value);
        else if (key.equals("NumberOfPlanes")) {
            m.imageCount = Integer.parseInt(value);
        } else if (key.equals("TextureImageOffset")) {
            textureOffset = Integer.parseInt(value);
        } else if (key.equals("TexturePtr") && !value.equals("7"))
            hasC = true;
        else if (key.equals("Voltage"))
            voltage = value;
        else if (key.equals("Magnification"))
            magnification = value;
        else if (key.equals("PixelSizeXMeter"))
            pntX = value;
        else if (key.equals("PixelSizeYMeter"))
            pntY = value;
        else if (key.equals("WorkingDistance"))
            workingDistance = value;
        else if (key.equals("DepthImageOffset")) {
            depthOffset = Integer.parseInt(value);
        }
    }
    LOGGER.info("Populating metadata");
    if (textureOffset != 0) {
        numBytes = (int) (in.length() - textureOffset) / (getSizeX() * getSizeY() * getImageCount());
        m.sizeC = hasC ? 3 : 1;
        m.sizeZ = 1;
        m.sizeT = getImageCount() / getSizeC();
        m.pixelType = FormatTools.pixelTypeFromBytes(numBytes, false, false);
    } else {
        textureOffset = depthOffset;
        m.pixelType = FormatTools.FLOAT;
        m.sizeC = 1;
        m.sizeZ = 1;
        m.sizeT = 1;
        m.imageCount = 1;
    }
    m.rgb = false;
    m.interleaved = false;
    m.littleEndian = true;
    m.dimensionOrder = "XYCTZ";
    m.metadataComplete = true;
    m.indexed = false;
    m.falseColor = false;
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        // link Image and Instrument
        String instrumentID = MetadataTools.createLSID("Instrument", 0);
        store.setInstrumentID(instrumentID, 0);
        store.setImageInstrumentRef(instrumentID, 0);
        // used when the dataset was acquired, i.e. detector settings.
        if (voltage != null) {
            store.setDetectorSettingsVoltage(new ElectricPotential(new Double(voltage), UNITS.VOLT), 0, 0);
            // link DetectorSettings to an actual Detector
            String detectorID = MetadataTools.createLSID("Detector", 0, 0);
            store.setDetectorID(detectorID, 0, 0);
            store.setDetectorSettingsID(detectorID, 0, 0);
            // set required Detector type
            store.setDetectorType(getDetectorType("Other"), 0, 0);
        }
        if (magnification != null) {
            store.setObjectiveCalibratedMagnification(new Double(magnification), 0, 0);
        }
        if (workingDistance != null) {
            store.setObjectiveWorkingDistance(new Length(new Double(workingDistance), UNITS.MICROMETER), 0, 0);
        }
        store.setObjectiveCorrection(getCorrection("Other"), 0, 0);
        store.setObjectiveImmersion(getImmersion("Other"), 0, 0);
        // link Objective to an Image using ObjectiveSettings
        String objectiveID = MetadataTools.createLSID("Objective", 0, 0);
        store.setObjectiveID(objectiveID, 0, 0);
        store.setObjectiveSettingsID(objectiveID, 0);
        if (pntX != null && pntY != null) {
            double pixelSizeX = Double.parseDouble(pntX);
            double pixelSizeY = Double.parseDouble(pntY);
            Length sizeX = FormatTools.getPhysicalSizeX(pixelSizeX, UNITS.METER);
            Length sizeY = FormatTools.getPhysicalSizeY(pixelSizeY, UNITS.METER);
            if (sizeX != null) {
                store.setPixelsPhysicalSizeX(sizeX, 0);
            }
            if (sizeY != null) {
                store.setPixelsPhysicalSizeY(sizeY, 0);
            }
        }
    }
}

Example 65 with MetadataStore

use of loci.formats.meta.MetadataStore in project bioformats by openmicroscopy.

the class AnalyzeReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    // the dataset has two files - we want the one ending in '.hdr'
    if (id.endsWith(".img")) {
        LOGGER.info("Looking for header file");
        String header = id.substring(0, id.lastIndexOf(".")) + ".hdr";
        if (new Location(header).exists()) {
            setId(header);
            return;
        } else
            throw new FormatException("Header file not found.");
    }
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    pixelsFilename = id.substring(0, id.lastIndexOf(".")) + ".img";
    pixelFile = new RandomAccessInputStream(pixelsFilename);
    LOGGER.info("Reading header");
    int fileSize = in.readInt();
    boolean little = fileSize != in.length();
    in.order(little);
    pixelFile.order(little);
    in.skipBytes(10);
    String imageName = in.readString(18);
    in.skipBytes(8);
    int ndims = in.readShort();
    int x = in.readShort();
    int y = in.readShort();
    int z = in.readShort();
    int t = in.readShort();
    in.skipBytes(20);
    int dataType = in.readShort();
    int nBitsPerPixel = in.readShort();
    String description = null;
    double voxelWidth = 0d, voxelHeight = 0d, sliceThickness = 0d, deltaT = 0d;
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        in.skipBytes(6);
        voxelWidth = in.readFloat();
        voxelHeight = in.readFloat();
        sliceThickness = in.readFloat();
        deltaT = in.readFloat();
        in.skipBytes(12);
        pixelOffset = (int) in.readFloat();
        in.skipBytes(12);
        float calibratedMax = in.readFloat();
        float calibratedMin = in.readFloat();
        float compressed = in.readFloat();
        float verified = in.readFloat();
        float pixelMax = in.readFloat();
        float pixelMin = in.readFloat();
        description = in.readString(80);
        String auxFile = in.readString(24);
        char orient = (char) in.readByte();
        String originator = in.readString(10);
        String generated = in.readString(10);
        String scannum = in.readString(10);
        String patientID = in.readString(10);
        String expDate = in.readString(10);
        String expTime = in.readString(10);
        in.skipBytes(3);
        int views = in.readInt();
        int volsAdded = in.readInt();
        int startField = in.readInt();
        int fieldSkip = in.readInt();
        int omax = in.readInt();
        int omin = in.readInt();
        int smax = in.readInt();
        int smin = in.readInt();
        addGlobalMeta("Database name", imageName);
        addGlobalMeta("Number of dimensions", ndims);
        addGlobalMeta("Data type", dataType);
        addGlobalMeta("Number of bits per pixel", nBitsPerPixel);
        addGlobalMeta("Voxel width", voxelWidth);
        addGlobalMeta("Voxel height", voxelHeight);
        addGlobalMeta("Slice thickness", sliceThickness);
        addGlobalMeta("Exposure time", deltaT);
        addGlobalMeta("Pixel offset", pixelOffset);
        addGlobalMeta("Calibrated maximum", calibratedMax);
        addGlobalMeta("Calibrated minimum", calibratedMin);
        addGlobalMeta("Compressed", compressed);
        addGlobalMeta("Verified", verified);
        addGlobalMeta("Pixel maximum", pixelMax);
        addGlobalMeta("Pixel minimum", pixelMin);
        addGlobalMeta("Description", description);
        addGlobalMeta("Auxiliary file", auxFile);
        addGlobalMeta("Orientation", orient);
        addGlobalMeta("Originator", originator);
        addGlobalMeta("Generated", generated);
        addGlobalMeta("Scan Number", scannum);
        addGlobalMeta("Patient ID", patientID);
        addGlobalMeta("Acquisition Date", expDate);
        addGlobalMeta("Acquisition Time", expTime);
    } else {
        in.skipBytes(34);
        pixelOffset = (int) in.readFloat();
    }
    LOGGER.info("Populating core metadata");
    CoreMetadata m = core.get(0);
    m.littleEndian = little;
    m.sizeX = x;
    m.sizeY = y;
    m.sizeZ = z;
    m.sizeT = t;
    m.sizeC = 1;
    if (getSizeZ() == 0)
        m.sizeZ = 1;
    if (getSizeT() == 0)
        m.sizeT = 1;
    m.imageCount = getSizeZ() * getSizeT();
    m.rgb = false;
    m.interleaved = false;
    m.indexed = false;
    m.dimensionOrder = "XYZTC";
    switch(dataType) {
        case 1:
        case 2:
            m.pixelType = FormatTools.UINT8;
            break;
        case 4:
            m.pixelType = FormatTools.INT16;
            break;
        case 8:
            m.pixelType = FormatTools.INT32;
            break;
        case 16:
            m.pixelType = FormatTools.FLOAT;
            break;
        case 64:
            m.pixelType = FormatTools.DOUBLE;
            break;
        case 128:
            m.pixelType = FormatTools.UINT8;
            m.sizeC = 3;
            m.rgb = true;
            m.interleaved = true;
            m.dimensionOrder = "XYCZT";
        default:
            throw new FormatException("Unsupported data type: " + dataType);
    }
    LOGGER.info("Populating MetadataStore");
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    store.setImageName(imageName, 0);
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        store.setImageDescription(description, 0);
        Length sizeX = FormatTools.getPhysicalSizeX(voxelWidth, UNITS.MILLIMETER);
        Length sizeY = FormatTools.getPhysicalSizeY(voxelHeight, UNITS.MILLIMETER);
        Length sizeZ = FormatTools.getPhysicalSizeZ(sliceThickness, UNITS.MILLIMETER);
        if (sizeX != null) {
            store.setPixelsPhysicalSizeX(sizeX, 0);
        }
        if (sizeY != null) {
            store.setPixelsPhysicalSizeY(sizeY, 0);
        }
        if (sizeZ != null) {
            store.setPixelsPhysicalSizeZ(sizeZ, 0);
        }
        store.setPixelsTimeIncrement(new Time(deltaT, UNITS.MILLISECOND), 0);
    }
}