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

Example 71 with FormatException

use of loci.formats.FormatException 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);
    }
}

Example 72 with FormatException

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

the class AmiraReader method getLookupTable.

// -- Helper methods --
byte[][] getLookupTable(Map materials) throws FormatException {
    byte[][] result = new byte[3][256];
    int i = -1;
    for (Object label : materials.keySet()) {
        i++;
        Object object = materials.get(label);
        if (!(object instanceof Map)) {
            throw new FormatException("Invalid material: " + label);
        }
        Map material = (Map) object;
        object = material.get("Color");
        // black
        if (object == null)
            continue;
        if (!(object instanceof Number[])) {
            throw new FormatException("Invalid material: " + label);
        }
        Number[] color = (Number[]) object;
        if (color.length != 3) {
            throw new FormatException("Invalid color: " + color.length + " channels");
        }
        for (int j = 0; j < 3; j++) {
            result[j][i] = (byte) (int) (255 * color[j].floatValue());
        }
    }
    return result;
}

Example 73 with FormatException

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

the class BDReader method isThisType.

// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(String, boolean) */
@Override
public boolean isThisType(String name, boolean open) {
    Location location = new Location(name);
    String id = location.getAbsolutePath();
    boolean dirCheck = location.isDirectory();
    if (dirCheck)
        return false;
    if (name.endsWith(EXPERIMENT_FILE))
        return true;
    if (!open)
        return false;
    try {
        id = locateExperimentFile(id);
    } catch (FormatException f) {
        return false;
    } catch (IOException f) {
        return false;
    } catch (NullPointerException e) {
        return false;
    }
    if (id.endsWith(EXPERIMENT_FILE)) {
        return true;
    }
    return super.isThisType(name, open);
}

Example 74 with FormatException

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

the class BDReader method locateExperimentFile.

// -- Helper methods --
/* Locate the experiment file given any file in set */
private String locateExperimentFile(String id) throws FormatException, IOException {
    if (!checkSuffix(id, "exp")) {
        Location parent = new Location(id).getAbsoluteFile().getParentFile();
        if (checkSuffix(id, "tif"))
            parent = parent.getParentFile();
        Location expFile = new Location(parent, EXPERIMENT_FILE);
        if (expFile.exists()) {
            return expFile.getAbsolutePath();
        }
        throw new FormatException("Could not find " + EXPERIMENT_FILE + " in " + parent.getAbsolutePath());
    }
    return id;
}

Example 75 with FormatException

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

the class WriterUtilities method createMetadata.

public static IMetadata createMetadata(String pixelType, int rgbChannels, int seriesCount, boolean littleEndian, int sizeT) throws Exception {
    IMetadata metadata;
    try {
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        metadata = service.createOMEXMLMetadata();
    } catch (DependencyException exc) {
        throw new FormatException("Could not create OME-XML store.", exc);
    } catch (ServiceException exc) {
        throw new FormatException("Could not create OME-XML store.", exc);
    }
    for (int i = 0; i < seriesCount; i++) {
        MetadataTools.populateMetadata(metadata, i, "image #" + i, littleEndian, "XYCZT", pixelType, 160, 160, 1, rgbChannels, sizeT, rgbChannels);
    }
    return metadata;
}