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

Example 31 with MetadataStore

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

the class PSDReader 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 = false;
    if (!in.readString(4).equals("8BPS")) {
        throw new FormatException("Not a valid Photoshop file.");
    }
    addGlobalMeta("Version", in.readShort());
    // reserved, set to 0
    in.skipBytes(6);
    m.sizeC = in.readShort();
    m.sizeY = in.readInt();
    m.sizeX = in.readInt();
    int bits = in.readShort();
    addGlobalMeta("Bits per pixel", bits);
    m.pixelType = FormatTools.pixelTypeFromBytes(bits / 8, false, false);
    int colorMode = in.readShort();
    String modeString = null;
    switch(colorMode) {
        case 0:
            modeString = "monochrome";
            break;
        case 1:
            modeString = "gray-scale";
            break;
        case 2:
            modeString = "palette color";
            break;
        case 3:
            modeString = "RGB";
            break;
        case 4:
            modeString = "CMYK";
            break;
        case 6:
            modeString = "Duotone";
            break;
        case 7:
            modeString = "Multichannel color";
            break;
        case 8:
            modeString = "Duotone";
            break;
        case 9:
            modeString = "LAB color";
            break;
    }
    addGlobalMeta("Color mode", modeString);
    // read color mode block, if present
    int modeDataLength = in.readInt();
    long fp = in.getFilePointer();
    if (modeDataLength != 0) {
        if (colorMode == 2) {
            lut = new byte[3][256];
            for (int i = 0; i < lut.length; i++) {
                in.read(lut[i]);
            }
        }
        in.seek(fp + modeDataLength);
    }
    // read image resources block
    in.skipBytes(4);
    while (in.readString(4).equals("8BIM")) {
        int tag = in.readShort();
        int read = 1;
        while (in.read() != 0) read++;
        if (read % 2 == 1)
            in.skipBytes(1);
        int size = in.readInt();
        if (size % 2 == 1)
            size++;
        in.skipBytes(size);
    }
    in.seek(in.getFilePointer() - 4);
    int blockLen = in.readInt();
    if (blockLen == 0) {
        offset = in.getFilePointer();
    } else {
        int layerLen = in.readInt();
        int layerCount = in.readShort();
        if (layerCount < 0) {
            throw new FormatException("Vector data is not supported.");
        }
        if (layerLen == 0 && layerCount == 0) {
            in.skipBytes(2);
            int check = in.readShort();
            in.seek(in.getFilePointer() - (check == 0 ? 4 : 2));
        }
        int[] w = new int[layerCount];
        int[] h = new int[layerCount];
        int[] c = new int[layerCount];
        for (int i = 0; i < layerCount; i++) {
            int top = in.readInt();
            int left = in.readInt();
            int bottom = in.readInt();
            int right = in.readInt();
            w[i] = right - left;
            h[i] = bottom - top;
            c[i] = in.readShort();
            in.skipBytes(c[i] * 6 + 12);
            int len = in.readInt();
            if (len % 2 == 1)
                len++;
            in.skipBytes(len);
        }
        // skip over pixel data for each layer
        for (int i = 0; i < layerCount; i++) {
            if (h[i] < 0) {
                continue;
            }
            int[] lens = new int[h[i]];
            for (int cc = 0; cc < c[i]; cc++) {
                boolean compressed = in.readShort() == 1;
                if (!compressed)
                    in.skipBytes(w[i] * h[i]);
                else {
                    for (int y = 0; y < h[i]; y++) {
                        lens[y] = in.readShort();
                    }
                    for (int y = 0; y < h[i]; y++) {
                        in.skipBytes(lens[y]);
                    }
                }
            }
        }
        long start = in.getFilePointer();
        while (in.read() != '8') ;
        in.skipBytes(7);
        if (in.getFilePointer() - start > 1024) {
            in.seek(start);
        }
        int len = in.readInt();
        if ((len % 4) != 0)
            len += 4 - (len % 4);
        if (len > in.length() - in.getFilePointer() || (len & 0xff0000) >> 16 == 1) {
            in.seek(start);
            len = 0;
        }
        in.skipBytes(len);
        String s = in.readString(4);
        while (s.equals("8BIM")) {
            in.skipBytes(4);
            len = in.readInt();
            if ((len % 4) != 0)
                len += 4 - (len % 4);
            in.skipBytes(len);
            s = in.readString(4);
        }
        offset = in.getFilePointer() - 4;
    }
    m.sizeZ = 1;
    m.sizeT = 1;
    m.rgb = modeString.equals("RGB") || modeString.equals("CMYK");
    m.imageCount = getSizeC() / (isRGB() ? 3 : 1);
    m.indexed = modeString.equals("palette color");
    m.falseColor = false;
    m.dimensionOrder = "XYCZT";
    m.interleaved = false;
    m.metadataComplete = true;
    in.seek(offset);
    compressed = in.readShort() == 1;
    lens = new int[getSizeC()][getSizeY()];
    if (compressed) {
        for (int c = 0; c < getSizeC(); c++) {
            for (int row = 0; row < getSizeY(); row++) {
                lens[c][row] = in.readShort();
            }
        }
    }
    offset = in.getFilePointer();
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
}

Example 32 with MetadataStore

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

the class PerkinElmerReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    if (currentId != null && (id.equals(currentId) || isUsedFile(id)))
        return;
    LOGGER.info("Finding HTML companion file");
    if (!checkSuffix(id, HTM_SUFFIX)) {
        Location parent = new Location(id).getAbsoluteFile().getParentFile();
        String[] ls = parent.list();
        for (String file : ls) {
            if (checkSuffix(file, HTM_SUFFIX) && !file.startsWith(".")) {
                id = new Location(parent.getAbsolutePath(), file).getAbsolutePath();
                break;
            }
        }
    }
    super.initFile(id);
    allFiles = new ArrayList<String>();
    // get the working directory
    Location tmpFile = new Location(id).getAbsoluteFile();
    Location workingDir = tmpFile.getParentFile();
    if (workingDir == null)
        workingDir = new Location(".");
    String workingDirPath = workingDir.getPath();
    if (!workingDirPath.equals(""))
        workingDirPath += File.separator;
    String[] ls = workingDir.list(true);
    if (!new Location(id).exists()) {
        ls = Location.getIdMap().keySet().toArray(new String[0]);
        workingDirPath = "";
    }
    LOGGER.info("Searching for all metadata companion files");
    // check if we have any of the required header file types
    String cfgFile = null, anoFile = null, recFile = null;
    String timFile = null, csvFile = null, zpoFile = null;
    String htmFile = null;
    final List<PixelsFile> tempFiles = new ArrayList<PixelsFile>();
    int dot = id.lastIndexOf(".");
    String check = dot < 0 ? id : id.substring(0, dot);
    check = check.substring(check.lastIndexOf(File.separator) + 1);
    // locate appropriate .tim, .csv, .zpo, .htm and .tif files
    String prefix = null;
    Arrays.sort(ls);
    for (int i = 0; i < ls.length; i++) {
        // make sure that the file has a name similar to the name of the
        // specified file
        int d = ls[i].lastIndexOf(".");
        while (d == -1 && i < ls.length - 1) {
            i++;
            d = ls[i].lastIndexOf(".");
        }
        String s = d < 0 ? ls[i] : ls[i].substring(0, d);
        if (s.startsWith(check) || check.startsWith(s) || ((prefix != null) && (s.startsWith(prefix)))) {
            prefix = ls[i].substring(0, d);
            if (cfgFile == null && checkSuffix(ls[i], CFG_SUFFIX))
                cfgFile = ls[i];
            if (anoFile == null && checkSuffix(ls[i], ANO_SUFFIX))
                anoFile = ls[i];
            if (recFile == null && checkSuffix(ls[i], REC_SUFFIX))
                recFile = ls[i];
            if (timFile == null && checkSuffix(ls[i], TIM_SUFFIX))
                timFile = ls[i];
            if (csvFile == null && checkSuffix(ls[i], CSV_SUFFIX))
                csvFile = ls[i];
            if (zpoFile == null && checkSuffix(ls[i], ZPO_SUFFIX))
                zpoFile = ls[i];
            if (htmFile == null && checkSuffix(ls[i], HTM_SUFFIX))
                htmFile = ls[i];
            dot = ls[i].lastIndexOf(".");
            PixelsFile f = new PixelsFile();
            f.path = workingDirPath + ls[i];
            if (checkSuffix(ls[i], TiffReader.TIFF_SUFFIXES)) {
                if (dot - 4 >= 0 && dot - 4 < ls[i].length() && ls[i].charAt(dot - 4) == '_') {
                    f.firstIndex = Integer.parseInt(ls[i].substring(dot - 3, dot));
                } else {
                    f.firstIndex = -1;
                }
                if (dot - 9 >= 0 && dot - 9 < ls[i].length() && ls[i].charAt(dot - 9) == '_') {
                    f.extIndex = Integer.parseInt(ls[i].substring(dot - 8, dot - 4));
                } else {
                    f.firstIndex = i;
                    f.extIndex = 0;
                }
                tempFiles.add(f);
            } else {
                try {
                    if (dot - 4 >= 0 && dot - 4 < ls[i].length() && ls[i].charAt(dot - 4) == '_') {
                        f.firstIndex = Integer.parseInt(ls[i].substring(dot - 3, dot));
                    } else {
                        f.firstIndex = -1;
                    }
                    String ext = dot + 1 < ls[i].length() ? ls[i].substring(dot + 1) : "";
                    f.extIndex = Integer.parseInt(ext, 16);
                    isTiff = false;
                    tempFiles.add(f);
                } catch (NumberFormatException exc) {
                    LOGGER.debug("Failed to parse file extension", exc);
                }
            }
        }
    }
    files = tempFiles.toArray(new PixelsFile[tempFiles.size()]);
    // determine the number of different extensions we have
    LOGGER.info("Finding image files");
    List<Integer> foundExts = new ArrayList<Integer>();
    for (PixelsFile f : files) {
        if (!foundExts.contains(f.extIndex)) {
            foundExts.add(f.extIndex);
        }
    }
    extCount = foundExts.size();
    foundExts = null;
    CoreMetadata ms0 = core.get(0);
    ms0.imageCount = 0;
    for (PixelsFile f : files) {
        allFiles.add(f.path);
        ms0.imageCount++;
        if (f.firstIndex < 0 && files.length > extCount) {
            ms0.imageCount += ((files.length - 1) / (extCount - 1)) - 1;
        }
    }
    tiff = new MinimalTiffReader();
    // we always parse the .tim and .htm files if they exist, along with
    // either the .csv file or the .zpo file
    LOGGER.info("Parsing metadata values");
    addUsedFile(workingDirPath, cfgFile);
    addUsedFile(workingDirPath, anoFile);
    addUsedFile(workingDirPath, recFile);
    addUsedFile(workingDirPath, timFile);
    if (timFile != null)
        timFile = allFiles.get(allFiles.size() - 1);
    addUsedFile(workingDirPath, csvFile);
    if (csvFile != null)
        csvFile = allFiles.get(allFiles.size() - 1);
    addUsedFile(workingDirPath, zpoFile);
    if (zpoFile != null)
        zpoFile = allFiles.get(allFiles.size() - 1);
    addUsedFile(workingDirPath, htmFile);
    if (htmFile != null)
        htmFile = allFiles.get(allFiles.size() - 1);
    if (timFile != null)
        parseTimFile(timFile);
    if (csvFile != null)
        parseCSVFile(csvFile);
    if (zpoFile != null && csvFile == null)
        parseZpoFile(zpoFile);
    // be aggressive about parsing the HTML file, since it's the only one that
    // explicitly defines the number of wavelengths and timepoints
    final List<Double> exposureTimes = new ArrayList<Double>();
    final List<Double> zPositions = new ArrayList<Double>();
    final List<Double> emWaves = new ArrayList<Double>();
    final List<Double> exWaves = new ArrayList<Double>();
    if (htmFile != null) {
        String[] tokens = DataTools.readFile(htmFile).split(HTML_REGEX);
        for (int j = 0; j < tokens.length; j++) {
            if (tokens[j].indexOf('<') != -1)
                tokens[j] = "";
        }
        for (int j = 0; j < tokens.length - 1; j += 2) {
            if (tokens[j].indexOf("Exposure") != -1) {
                addGlobalMeta("Camera Data " + tokens[j].charAt(13), tokens[j]);
                int ndx = tokens[j].indexOf("Exposure") + 9;
                String exposure = tokens[j].substring(ndx, tokens[j].indexOf(" ", ndx)).trim();
                if (exposure.endsWith(",")) {
                    exposure = exposure.substring(0, exposure.length() - 1);
                }
                exposureTimes.add(new Double(Double.parseDouble(exposure) / 1000));
                if (tokens[j].indexOf("nm") != -1) {
                    int nmIndex = tokens[j].indexOf("nm");
                    int paren = tokens[j].lastIndexOf("(", nmIndex);
                    int slash = tokens[j].lastIndexOf("/", nmIndex);
                    if (slash == -1)
                        slash = nmIndex;
                    emWaves.add(new Double(tokens[j].substring(paren + 1, slash).trim()));
                    if (tokens[j].indexOf("nm", nmIndex + 3) != -1) {
                        nmIndex = tokens[j].indexOf("nm", nmIndex + 3);
                        paren = tokens[j].lastIndexOf(" ", nmIndex);
                        slash = tokens[j].lastIndexOf("/", nmIndex);
                        if (slash == -1)
                            slash = nmIndex + 2;
                        exWaves.add(new Double(tokens[j].substring(paren + 1, slash).trim()));
                    }
                }
                j--;
            } else if (tokens[j + 1].trim().equals("Slice Z positions")) {
                for (int q = j + 2; q < tokens.length; q++) {
                    if (!tokens[q].trim().equals("")) {
                        try {
                            zPositions.add(new Double(tokens[q].trim()));
                        } catch (NumberFormatException e) {
                        }
                    }
                }
            } else if (!tokens[j].trim().equals("")) {
                tokens[j] = tokens[j].trim();
                tokens[j + 1] = tokens[j + 1].trim();
                parseKeyValue(tokens[j], tokens[j + 1]);
            }
        }
    } else {
        throw new FormatException("Valid header files not found.");
    }
    if (details != null) {
        String[] tokens = details.split("\\s");
        int n = 0;
        for (String token : tokens) {
            if (token.equals("Wavelengths"))
                ms0.sizeC = n;
            else if (token.equals("Frames"))
                ms0.sizeT = n;
            else if (token.equals("Slices"))
                ms0.sizeZ = n;
            try {
                n = Integer.parseInt(token);
            } catch (NumberFormatException e) {
                n = 0;
            }
        }
    }
    LOGGER.info("Populating metadata");
    if (files.length == 0) {
        throw new FormatException("TIFF files not found.");
    }
    if (isTiff) {
        tiff.setId(getFile(0));
        ms0.pixelType = tiff.getPixelType();
    } else {
        RandomAccessInputStream tmp = new RandomAccessInputStream(getFile(0));
        int bpp = (int) (tmp.length() - 6) / (getSizeX() * getSizeY());
        tmp.close();
        if (bpp % 3 == 0)
            bpp /= 3;
        ms0.pixelType = FormatTools.pixelTypeFromBytes(bpp, false, false);
    }
    if (getSizeZ() <= 0)
        ms0.sizeZ = 1;
    if (getSizeC() <= 0)
        ms0.sizeC = 1;
    if (getSizeT() <= 0 || getImageCount() % (getSizeZ() * getSizeC()) == 0) {
        ms0.sizeT = getImageCount() / (getSizeZ() * getSizeC());
    } else {
        ms0.imageCount = getSizeZ() * getSizeC() * getSizeT();
        if (getImageCount() > files.length) {
            ms0.imageCount = files.length;
            ms0.sizeT = getImageCount() / (getSizeZ() * getSizeC());
        }
    }
    ms0.dimensionOrder = "XYCTZ";
    ms0.rgb = isTiff ? tiff.isRGB() : false;
    ms0.interleaved = false;
    ms0.littleEndian = isTiff ? tiff.isLittleEndian() : true;
    ms0.metadataComplete = true;
    ms0.indexed = isTiff ? tiff.isIndexed() : false;
    ms0.falseColor = false;
    if (getImageCount() != getSizeZ() * getSizeC() * getSizeT()) {
        ms0.imageCount = getSizeZ() * getSizeC() * getSizeT();
    }
    if (!isTiff && extCount > getSizeT()) {
        extCount = getSizeT() * getSizeC();
    }
    // Populate metadata store
    // The metadata store we're working with.
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, true);
    // populate Image element
    if (finishTime != null) {
        Timestamp timestamp = Timestamp.valueOf(DateTools.formatDate(finishTime, DATE_FORMAT));
        if (timestamp != null)
            store.setImageAcquisitionDate(timestamp, 0);
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        // populate Dimensions element
        Length sizeX = FormatTools.getPhysicalSizeX(pixelSizeX);
        Length sizeY = FormatTools.getPhysicalSizeY(pixelSizeY);
        if (sizeX != null) {
            store.setPixelsPhysicalSizeX(sizeX, 0);
        }
        if (sizeY != null) {
            store.setPixelsPhysicalSizeY(sizeY, 0);
        }
        // link Instrument and Image
        String instrumentID = MetadataTools.createLSID("Instrument", 0);
        store.setInstrumentID(instrumentID, 0);
        store.setImageInstrumentRef(instrumentID, 0);
        // populate LogicalChannel element
        for (int i = 0; i < getEffectiveSizeC(); i++) {
            if (i < emWaves.size()) {
                Length em = FormatTools.getEmissionWavelength(emWaves.get(i));
                if (em != null) {
                    store.setChannelEmissionWavelength(em, 0, i);
                }
            }
            if (i < exWaves.size()) {
                Length ex = FormatTools.getExcitationWavelength(exWaves.get(i));
                if (ex != null) {
                    store.setChannelExcitationWavelength(ex, 0, i);
                }
            }
        }
        // populate PlaneTiming and StagePosition
        long start = 0, end = 0;
        if (startTime != null) {
            start = DateTools.getTime(startTime, DATE_FORMAT);
        }
        if (finishTime != null) {
            end = DateTools.getTime(finishTime, DateTools.ISO8601_FORMAT);
        }
        double secondsPerPlane = (double) (end - start) / getImageCount() / 1000;
        for (int i = 0; i < getImageCount(); i++) {
            int[] zct = getZCTCoords(i);
            store.setPlaneDeltaT(new Time(i * secondsPerPlane, UNITS.SECOND), 0, i);
            if (zct[1] < exposureTimes.size() && exposureTimes.get(zct[1]) != null) {
                store.setPlaneExposureTime(new Time(exposureTimes.get(zct[1]), UNITS.SECOND), 0, i);
            }
            if (zct[0] < zPositions.size()) {
                final Double zPosition = zPositions.get(zct[0]);
                final Length xl = new Length(0d, UNITS.REFERENCEFRAME);
                final Length yl = new Length(0d, UNITS.REFERENCEFRAME);
                final Length zl;
                if (zPosition == null) {
                    zl = null;
                } else {
                    zl = new Length(zPosition, UNITS.REFERENCEFRAME);
                }
                store.setPlanePositionX(xl, 0, i);
                store.setPlanePositionY(yl, 0, i);
                store.setPlanePositionZ(zl, 0, i);
            }
        }
    }
}

Example 33 with MetadataStore

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

the class ImagicReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    if (!checkSuffix(id, "hed")) {
        id = id.substring(0, id.lastIndexOf(".")) + ".hed";
    }
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    pixels = id.substring(0, id.lastIndexOf(".")) + ".img";
    pixelsFile = new RandomAccessInputStream(pixels);
    CoreMetadata m = core.get(0);
    m.littleEndian = true;
    in.order(isLittleEndian());
    pixelsFile.order(isLittleEndian());
    int nImages = (int) (in.length() / 1024);
    String imageName = null;
    double physicalXSize = 0d;
    double physicalYSize = 0d;
    double physicalZSize = 0d;
    for (int i = 0; i < nImages; i++) {
        in.seek(i * 1024);
        in.skipBytes(16);
        int month = in.readInt();
        int day = in.readInt();
        int year = in.readInt();
        int hour = in.readInt();
        int minute = in.readInt();
        int seconds = in.readInt();
        in.skipBytes(8);
        m.sizeY = in.readInt();
        m.sizeX = in.readInt();
        String type = in.readString(4);
        if (type.equals("REAL")) {
            m.pixelType = FormatTools.FLOAT;
        } else if (type.equals("INTG")) {
            m.pixelType = FormatTools.UINT16;
        } else if (type.equals("PACK")) {
            m.pixelType = FormatTools.UINT8;
        } else if (type.equals("COMP")) {
            throw new FormatException("Unsupported pixel type 'COMP'");
        } else if (type.equals("RECO")) {
            throw new FormatException("Unsupported pixel type 'RECO'");
        }
        int ixold = in.readInt();
        int iyold = in.readInt();
        float averageDensity = in.readFloat();
        float sigma = in.readFloat();
        in.skipBytes(8);
        float maxDensity = in.readFloat();
        float minDensity = in.readFloat();
        in.skipBytes(4);
        float defocus1 = in.readFloat();
        float defocus2 = in.readFloat();
        float defocusAngle = in.readFloat();
        float startAngle = in.readFloat();
        float endAngle = in.readFloat();
        imageName = in.readString(80);
        float ccc3d = in.readFloat();
        int ref3d = in.readInt();
        int micrographID = in.readInt();
        int zShift = in.readInt();
        float alpha = in.readFloat();
        float beta = in.readFloat();
        float gamma = in.readFloat();
        in.skipBytes(8);
        int nAliSum = in.readInt();
        int pointGroup = in.readInt();
        in.skipBytes(28);
        int version = in.readInt();
        int stamp = in.readInt();
        in.skipBytes(120);
        float angle = in.readFloat();
        float voltage = in.readFloat();
        float sphericalAberration = in.readFloat();
        float partialCoherence = in.readFloat();
        float ccc = in.readFloat();
        float errar = in.readFloat();
        float err3d = in.readFloat();
        int ref = in.readInt();
        float classNumber = in.readFloat();
        in.skipBytes(4);
        float representationQuality = in.readFloat();
        float eqZShift = in.readFloat();
        float xShift = in.readFloat();
        float yShift = in.readFloat();
        float numcls = in.readFloat();
        float overallQuality = in.readFloat();
        float equivalentAngle = in.readFloat();
        float eqXShift = in.readFloat();
        float eqYShift = in.readFloat();
        float cmToVar = in.readFloat();
        float informat = in.readFloat();
        int nEigenvalues = in.readInt();
        int nActiveImages = in.readInt();
        physicalXSize = in.readFloat();
        physicalYSize = in.readFloat();
        physicalZSize = in.readFloat();
        addGlobalMeta("IXOLD", ixold);
        addGlobalMeta("IYOLD", iyold);
        addGlobalMeta("Average density (AVDENS)", averageDensity);
        addGlobalMeta("SIGMA", sigma);
        addGlobalMeta("Maximum density (DENSMAX)", maxDensity);
        addGlobalMeta("Minimum density (DENSMIN)", minDensity);
        addGlobalMeta("DEFOCUS1", defocus1);
        addGlobalMeta("DEFOCUS2", defocus2);
        addGlobalMeta("Defocus angle (DEFANGLE)", defocusAngle);
        addGlobalMeta("SINOSTRT", startAngle);
        addGlobalMeta("SINOEND", endAngle);
        addGlobalMeta("Image name", imageName);
        addGlobalMeta("CCC3D", ccc3d);
        addGlobalMeta("REF3D", ref3d);
        addGlobalMeta("MIDENT", micrographID);
        addGlobalMeta("EZSHIFT", zShift);
        addGlobalMeta("EALPHA", alpha);
        addGlobalMeta("EBETA", beta);
        addGlobalMeta("EGAMMA", gamma);
        addGlobalMeta("NALISUM", nAliSum);
        addGlobalMeta("PGROUP", pointGroup);
        addGlobalMeta("IMAGIC Version (IMAVERS)", version);
        addGlobalMeta("REALTYPE", stamp);
        addGlobalMeta("ANGLE", angle);
        addGlobalMeta("VOLTAGE (in kV)", voltage);
        addGlobalMeta("SPABERR (in mm)", sphericalAberration);
        addGlobalMeta("PCOHER", partialCoherence);
        addGlobalMeta("CCC", ccc);
        addGlobalMeta("ERRAR", errar);
        addGlobalMeta("ERR3D", err3d);
        addGlobalMeta("REF", ref);
        addGlobalMeta("CLASSNO", classNumber);
        addGlobalMeta("REPQUAL", representationQuality);
        addGlobalMeta("ZSHIFT", eqZShift);
        addGlobalMeta("XSHIFT", xShift);
        addGlobalMeta("YSHIFT", yShift);
        addGlobalMeta("NUMCLS", numcls);
        addGlobalMeta("OVQUAL", overallQuality);
        addGlobalMeta("EANGLE", equivalentAngle);
        addGlobalMeta("EXSHIFT", eqXShift);
        addGlobalMeta("EYSHIFT", eqYShift);
        addGlobalMeta("CMTOTVAR", cmToVar);
        addGlobalMeta("INFORMAT", informat);
        addGlobalMeta("NUMEIGEN", nEigenvalues);
        addGlobalMeta("NIACTIVE", nActiveImages);
        addGlobalMeta("RESOLX", physicalXSize);
        addGlobalMeta("RESOLY", physicalYSize);
        addGlobalMeta("RESOLZ", physicalZSize);
    }
    m.sizeZ = nImages;
    m.sizeC = 1;
    m.sizeT = 1;
    m.imageCount = nImages;
    m.dimensionOrder = "XYZCT";
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    store.setImageName(imageName.trim(), 0);
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        Length sizeX = FormatTools.getPhysicalSizeX(physicalXSize * 0.0001);
        Length sizeY = FormatTools.getPhysicalSizeY(physicalYSize * 0.0001);
        Length sizeZ = FormatTools.getPhysicalSizeZ(physicalZSize * 0.0001);
        if (sizeX != null) {
            store.setPixelsPhysicalSizeX(sizeX, 0);
        }
        if (sizeY != null) {
            store.setPixelsPhysicalSizeY(sizeY, 0);
        }
        if (sizeZ != null) {
            store.setPixelsPhysicalSizeZ(sizeZ, 0);
        }
    }
}

Example 34 with MetadataStore

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

the class InveonReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    if (!checkSuffix(id, "hdr")) {
        id += ".hdr";
    }
    super.initFile(id);
    String headerData = DataTools.readFile(id);
    String[] lines = headerData.split("\n");
    String date = null;
    String institution = null, investigator = null;
    String model = null;
    String description = null;
    Double pixelSizeX = null;
    Double pixelSizeY = null;
    Double pixelSizeZ = null;
    int frames = 0;
    for (String line : lines) {
        line = line.trim();
        if (!line.startsWith("#")) {
            int space = line.indexOf(' ');
            if (space < 0) {
                continue;
            }
            String key = line.substring(0, space);
            String value = line.substring(space + 1);
            if (key.equals("institution")) {
                institution = value;
            } else if (key.equals("investigator")) {
                investigator = value;
            } else if (key.equals("study")) {
                description = value;
            } else if (key.equals("model")) {
                value = transformModel(value);
                model = value;
            } else if (key.equals("modality")) {
                value = transformModality(value);
            } else if (key.equals("modality_configuration")) {
                value = transformModalityConfiguration(value);
            } else if (key.equals("file_type")) {
                value = transformFileType(value);
            } else if (key.equals("acquisition_mode")) {
                value = transformAcquisitionMode(value);
            } else if (key.equals("bed_control")) {
                value = transformBedControl(value);
            } else if (key.equals("bed_motion")) {
                value = transformBedMotion(value);
            } else if (key.equals("registration_available")) {
                value = transformRegistrationAvailable(value);
            } else if (key.equals("normalization_applied")) {
                value = transformNormalizationApplied(value);
            } else if (key.equals("recon_algorithm")) {
                value = transformReconAlgorithm(value);
            } else if (key.equals("x_filter")) {
                value = transformFilter(value);
            } else if (key.equals("y_filter")) {
                value = transformFilter(value);
            } else if (key.equals("z_filter")) {
                value = transformFilter(value);
            } else if (key.equals("subject_orientation")) {
                value = transformSubjectOrientation(value);
            } else if (key.equals("subject_length_units")) {
                value = transformSubjectLengthUnits(value);
            } else if (key.equals("subject_weight_units")) {
                value = transformSubjectWeightUnits(value);
            } else if (key.equals("gantry_rotation")) {
                value = transformGantryRotation(value);
            } else if (key.equals("rotation_direction")) {
                value = transformRotationDirection(value);
            } else if (key.equals("ct_warping")) {
                value = transformCTWarping(value);
            } else if (key.equals("ct_projection_interpolation")) {
                value = transformCTProjectionInterpolation(value);
            } else if (key.equals("event_type")) {
                value = transformEventType(value);
            } else if (key.equals("projection") || key.equals("ct_projection_center_offset") || key.equals("ct_projection_horizontal_bed_offset")) {
                space = value.indexOf(' ');
                int index = Integer.parseInt(value.substring(0, space));
                value = value.substring(space + 1);
                key += " " + index;
            } else if (key.equals("user")) {
                space = value.indexOf(' ');
                key = value.substring(0, space);
                value = value.substring(space + 1);
            } else if (key.equals("file_name")) {
                // remove path from stored file name, if present
                value = value.replace('/', File.separatorChar);
                value = value.replace('\\', File.separatorChar);
                value = value.substring(value.lastIndexOf(File.separator) + 1);
                Location header = new Location(currentId).getAbsoluteFile();
                datFile = new Location(header.getParent(), value).getAbsolutePath();
            } else if (key.equals("time_frames")) {
                int sizeT = Integer.parseInt(value);
                for (int i = 0; i < core.size(); i++) {
                    core.get(i).sizeT = sizeT;
                }
            } else if (key.equals("total_frames")) {
                frames = Integer.parseInt(value);
            } else if (key.equals("number_of_bed_positions")) {
                int nPos = (int) Math.min(frames, Integer.parseInt(value));
                if (nPos > 1) {
                    CoreMetadata original = core.get(0);
                    core.clear();
                    for (int i = 0; i < nPos; i++) {
                        core.add(original);
                    }
                }
            } else if (key.equals("data_type")) {
                setDataType(value);
            } else if (key.equals("x_dimension")) {
                int sizeX = Integer.parseInt(value);
                for (int i = 0; i < core.size(); i++) {
                    core.get(i).sizeX = sizeX;
                }
            } else if (key.equals("y_dimension")) {
                int sizeY = Integer.parseInt(value);
                for (int i = 0; i < core.size(); i++) {
                    core.get(i).sizeY = sizeY;
                }
            } else if (key.equals("z_dimension")) {
                int sizeZ = Integer.parseInt(value);
                for (int i = 0; i < core.size(); i++) {
                    core.get(i).sizeZ = sizeZ;
                }
            } else if (key.equals("scan_time")) {
                date = value;
            } else if (key.equals("data_file_pointer")) {
                String[] values = value.split(" ");
                int[] ints = new int[values.length];
                for (int i = 0; i < ints.length; i++) {
                    ints[i] = Integer.parseInt(values[i]);
                }
                byte[] b = DataTools.intsToBytes(ints, false);
                dataPointers.add(DataTools.bytesToLong(b, false));
            } else // pixel sizes stored in mm
            if (key.equals("pixel_size_x")) {
                pixelSizeX = new Double(value) * 1000;
            } else if (key.equals("pixel_size_y")) {
                pixelSizeY = new Double(value) * 1000;
            } else if (key.equals("pixel_size_z")) {
                pixelSizeZ = new Double(value) * 1000;
            }
            addGlobalMeta(key, value);
        }
    }
    for (int i = 0; i < core.size(); i++) {
        CoreMetadata ms = core.get(i);
        if (ms.sizeZ == 0) {
            ms.sizeZ = 1;
        }
        if (ms.sizeT == 0) {
            ms.sizeT = 1;
        }
        ms.sizeC = 1;
        ms.rgb = false;
        ms.interleaved = false;
        ms.indexed = false;
        ms.dimensionOrder = "XYZCT";
        ms.imageCount = ms.sizeZ * ms.sizeC * ms.sizeT;
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    String experimenter = null, instrument = null;
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        experimenter = MetadataTools.createLSID("Experimenter", 0);
        store.setExperimenterID(experimenter, 0);
        store.setExperimenterUserName(investigator, 0);
        store.setExperimenterInstitution(institution, 0);
        instrument = MetadataTools.createLSID("Instrument", 0);
        store.setInstrumentID(instrument, 0);
        store.setMicroscopeModel(model, 0);
    }
    for (int i = 0; i < core.size(); i++) {
        if (date != null) {
            String newDate = DateTools.formatDate(date, "EEE MMM dd HH:mm:ss yyyy");
            if (newDate != null) {
                store.setImageAcquisitionDate(new Timestamp(newDate), i);
            }
        }
        if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
            if (experimenter != null) {
                store.setImageExperimenterRef(experimenter, i);
            }
            if (instrument != null) {
                store.setImageInstrumentRef(instrument, i);
            }
            store.setImageDescription(description, i);
            Length sizeX = FormatTools.getPhysicalSizeX(pixelSizeX);
            Length sizeY = FormatTools.getPhysicalSizeY(pixelSizeY);
            Length sizeZ = FormatTools.getPhysicalSizeZ(pixelSizeZ);
            if (sizeX != null) {
                store.setPixelsPhysicalSizeX(sizeX, i);
            }
            if (sizeY != null) {
                store.setPixelsPhysicalSizeY(sizeY, i);
            }
            if (sizeZ != null) {
                store.setPixelsPhysicalSizeZ(sizeZ, i);
            }
        }
    }
}

Example 35 with MetadataStore

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

the class IvisionReader 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);
    LOGGER.info("Populating metadata");
    String version = in.readString(4);
    addGlobalMeta("Version", version);
    int fileFormat = in.read();
    int dataType = in.read();
    CoreMetadata m = core.get(0);
    m.sizeC = 1;
    switch(dataType) {
        case 0:
            m.pixelType = FormatTools.UINT8;
            break;
        case 1:
            m.pixelType = FormatTools.INT16;
            break;
        case 2:
            m.pixelType = FormatTools.INT32;
            break;
        case 3:
            m.pixelType = FormatTools.FLOAT;
            break;
        case 4:
            m.pixelType = FormatTools.UINT8;
            m.sizeC = 3;
            color16 = true;
            break;
        case 5:
            m.pixelType = FormatTools.UINT8;
            m.sizeC = 3;
            hasPaddingByte = true;
            break;
        case 6:
            m.pixelType = FormatTools.UINT16;
            break;
        case 7:
            m.pixelType = FormatTools.FLOAT;
            squareRoot = true;
            break;
        case 8:
            m.pixelType = FormatTools.UINT16;
            m.sizeC = 3;
            break;
    }
    m.sizeX = in.readInt();
    m.sizeY = in.readInt();
    in.skipBytes(6);
    m.sizeZ = in.readShort();
    in.skipBytes(50);
    m.sizeT = 1;
    if (getSizeX() > 1 && getSizeY() > 1) {
        lut = new byte[2048];
        in.read(lut);
    }
    imageOffset = in.getFilePointer();
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        in.skipBytes(getSizeZ() * getSizeC() * getSizeT() * getSizeX() * getSizeY() * FormatTools.getBytesPerPixel(getPixelType()));
        // look for block of XML data
        LOGGER.info("Looking for XML metadata");
        in.findString(false, "<?xml");
        if (in.getFilePointer() < in.length()) {
            in.seek(in.getFilePointer() - 5);
            String xml = in.readString((int) (in.length() - in.getFilePointer()));
            xml = xml.substring(xml.indexOf('<'), xml.lastIndexOf("plist>") + 6);
            IvisionHandler handler = new IvisionHandler();
            try {
                XMLTools.parseXML(xml, handler);
            } catch (IOException e) {
                LOGGER.debug("", e);
            }
        } else
            LOGGER.debug("XML metadata not found");
    }
    LOGGER.info("Populating core metadata");
    m.rgb = getSizeC() > 1;
    m.dimensionOrder = "XYCZT";
    m.littleEndian = false;
    m.interleaved = true;
    m.indexed = false;
    m.imageCount = getSizeZ() * getSizeT();
    LOGGER.info("Populating MetadataStore");
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, true);
    if (creationDate != null) {
        String date = DateTools.formatDate(creationDate, DATE_FORMAT);
        if (date != null) {
            store.setImageAcquisitionDate(new Timestamp(date), 0);
        }
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        String instrumentID = MetadataTools.createLSID("Instrument", 0);
        store.setInstrumentID(instrumentID, 0);
        store.setImageInstrumentRef(instrumentID, 0);
        if (deltaT != null) {
            Double increment = 0d;
            try {
                increment = new Double(deltaT);
            } catch (NumberFormatException e) {
                LOGGER.debug("Failed to parse time increment", e);
            }
            if (increment != null) {
                store.setPixelsTimeIncrement(new Time(increment, UNITS.SECOND), 0);
            }
        }
        String objectiveID = MetadataTools.createLSID("Objective", 0, 0);
        store.setObjectiveID(objectiveID, 0, 0);
        store.setObjectiveSettingsID(objectiveID, 0);
        store.setObjectiveCorrection(getCorrection("Other"), 0, 0);
        store.setObjectiveImmersion(getImmersion("Other"), 0, 0);
        if (lensNA != null)
            store.setObjectiveLensNA(lensNA, 0, 0);
        if (magnification != null) {
            store.setObjectiveNominalMagnification(magnification, 0, 0);
        }
        if (refractiveIndex != null) {
            store.setObjectiveSettingsRefractiveIndex(refractiveIndex, 0);
        }
        String detectorID = MetadataTools.createLSID("Detector", 0, 0);
        store.setDetectorID(detectorID, 0, 0);
        store.setDetectorSettingsID(detectorID, 0, 0);
        store.setDetectorType(getDetectorType("Other"), 0, 0);
        store.setDetectorSettingsBinning(getBinning(binX + "x" + binY), 0, 0);
        if (gain != null) {
            try {
                store.setDetectorSettingsGain(new Double(gain), 0, 0);
            } catch (NumberFormatException e) {
                LOGGER.debug("Failed to parse detector gain", e);
            }
        }
    }
}