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

Example 41 with CoreMetadata

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

the class PDSReader 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")) {
        String headerFile = id.substring(0, id.lastIndexOf(".")) + ".hdr";
        if (!new Location(headerFile).exists()) {
            headerFile = id.substring(0, id.lastIndexOf(".")) + ".HDR";
            if (!new Location(headerFile).exists()) {
                throw new FormatException("Could not find matching .hdr file.");
            }
        }
        initFile(headerFile);
        return;
    }
    super.initFile(id);
    String[] headerData = DataTools.readFile(id).split("\r\n");
    if (headerData.length == 1) {
        headerData = headerData[0].split("\r");
    }
    Length xPos = null, yPos = null;
    Double deltaX = null, deltaY = null;
    String date = null;
    CoreMetadata m = core.get(0);
    for (String line : headerData) {
        int eq = line.indexOf('=');
        if (eq < 0)
            continue;
        int end = line.indexOf('/');
        if (end < 0)
            end = line.length();
        String key = line.substring(0, eq).trim();
        String value = line.substring(eq + 1, end).trim();
        if (key.equals("NXP")) {
            m.sizeX = Integer.parseInt(value);
        } else if (key.equals("NYP")) {
            m.sizeY = Integer.parseInt(value);
        } else if (key.equals("XPOS")) {
            final Double number = Double.valueOf(value);
            xPos = new Length(number, UNITS.REFERENCEFRAME);
            addGlobalMeta("X position for position #1", xPos);
        } else if (key.equals("YPOS")) {
            final Double number = Double.valueOf(value);
            yPos = new Length(number, UNITS.REFERENCEFRAME);
            addGlobalMeta("Y position for position #1", yPos);
        } else if (key.equals("SIGNX")) {
            reverseX = value.replaceAll("'", "").trim().equals("-");
        } else if (key.equals("SIGNY")) {
            reverseY = value.replaceAll("'", "").trim().equals("-");
        } else if (key.equals("DELTAX")) {
            deltaX = new Double(value);
        } else if (key.equals("DELTAY")) {
            deltaY = new Double(value);
        } else if (key.equals("COLOR")) {
            int color = Integer.parseInt(value);
            if (color == 4) {
                m.sizeC = 3;
                m.rgb = true;
            } else {
                m.sizeC = 1;
                m.rgb = false;
                lutIndex = color - 1;
                m.indexed = lutIndex >= 0;
            }
        } else if (key.equals("SCAN TIME")) {
            long modTime = new Location(currentId).getAbsoluteFile().lastModified();
            String year = DateTools.convertDate(modTime, DateTools.UNIX, "yyyy");
            date = value.replaceAll("'", "") + " " + year;
            date = DateTools.formatDate(date, DATE_FORMAT);
        } else if (key.equals("FILE REC LEN")) {
            recordWidth = Integer.parseInt(value) / 2;
        }
        addGlobalMeta(key, value);
    }
    m.sizeZ = 1;
    m.sizeT = 1;
    m.imageCount = 1;
    m.dimensionOrder = "XYCZT";
    m.pixelType = FormatTools.UINT16;
    m.littleEndian = true;
    String base = currentId.substring(0, currentId.lastIndexOf("."));
    pixelsFile = base + ".IMG";
    if (!new Location(pixelsFile).exists()) {
        pixelsFile = base + ".img";
    }
    boolean minimumMetadata = getMetadataOptions().getMetadataLevel() == MetadataLevel.MINIMUM;
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, !minimumMetadata);
    if (date != null) {
        store.setImageAcquisitionDate(new Timestamp(date), 0);
    }
    if (!minimumMetadata) {
        store.setPlanePositionX(xPos, 0, 0);
        store.setPlanePositionY(yPos, 0, 0);
        Length sizeX = FormatTools.getPhysicalSizeX(deltaX);
        Length sizeY = FormatTools.getPhysicalSizeY(deltaY);
        if (sizeX != null) {
            store.setPixelsPhysicalSizeX(sizeX, 0);
        }
        if (sizeY != null) {
            store.setPixelsPhysicalSizeY(sizeY, 0);
        }
    }
}

Example 42 with CoreMetadata

use of loci.formats.CoreMetadata 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 43 with CoreMetadata

use of loci.formats.CoreMetadata 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 44 with CoreMetadata

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

the class PrairieReader method populateCoreMetadata.

/**
 * This step populates the {@link CoreMetadata} by extracting relevant values
 * from the parsed {@link #meta} structure.
 */
private void populateCoreMetadata() throws FormatException, IOException {
    LOGGER.info("Populating core metadata");
    // NB: Both stage positions and time points are rasterized into the list
    // of Sequences. So by definition: sequenceCount = sizeT * seriesCount.
    final int sequenceCount = sequences.size();
    final int sizeT = computeSizeT(sequenceCount);
    final int seriesCount = sequenceCount / sizeT;
    final Integer bitDepth = meta.getBitDepth();
    int bpp = bitDepth == null ? -1 : bitDepth;
    core.clear();
    framesAreTime = new boolean[seriesCount];
    for (int s = 0; s < seriesCount; s++) {
        final Sequence sequence = sequence(0, s, seriesCount);
        final Frame frame = sequence.getFirstFrame();
        final PFile file = frame == null ? null : frame.getFirstFile();
        if (frame == null || file == null) {
            throw new FormatException("No metadata for series #" + s);
        }
        // should remedy any resultant inaccuracies in the metadata.
        if (s == 0) {
            tiff.setId(getPath(file));
            if (bpp <= 0)
                bpp = tiff.getBitsPerPixel();
        }
        final Integer linesPerFrame = frame.getLinesPerFrame();
        final Integer pixelsPerLine = frame.getPixelsPerLine();
        final int indexCount = sequence.getIndexCount();
        final int sizeX = pixelsPerLine == null ? tiff.getSizeX() : pixelsPerLine;
        final int sizeY = linesPerFrame == null ? tiff.getSizeY() : linesPerFrame;
        framesAreTime[s] = sequence.isTimeSeries() && sizeT == 1;
        final CoreMetadata cm = new CoreMetadata();
        cm.sizeX = sizeX;
        cm.sizeY = sizeY;
        cm.sizeZ = framesAreTime[s] ? 1 : indexCount;
        cm.sizeC = channels.length;
        cm.sizeT = framesAreTime[s] ? indexCount : sizeT;
        cm.pixelType = tiff.getPixelType();
        cm.bitsPerPixel = bpp;
        cm.imageCount = cm.sizeZ * cm.sizeC * cm.sizeT;
        cm.dimensionOrder = "XYCZT";
        cm.orderCertain = true;
        cm.rgb = false;
        cm.littleEndian = tiff.isLittleEndian();
        cm.interleaved = false;
        cm.indexed = tiff.isIndexed();
        cm.falseColor = false;
        core.add(cm);
    }
}

Example 45 with CoreMetadata

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

the class PyramidTiffReader method initStandardMetadata.

// -- Internal BaseTiffReader API methods --
/* @see loci.formats.in.BaseTiffReader#initStandardMetadata() */
@Override
protected void initStandardMetadata() throws FormatException, IOException {
    int seriesCount = ifds.size();
    // repopulate core metadata
    core.clear();
    for (int s = 0; s < seriesCount; s++) {
        CoreMetadata ms = new CoreMetadata();
        core.add(ms);
        if (s == 0) {
            ms.resolutionCount = seriesCount;
        }
        IFD ifd = ifds.get(s);
        PhotoInterp p = ifd.getPhotometricInterpretation();
        int samples = ifd.getSamplesPerPixel();
        ms.rgb = samples > 1 || p == PhotoInterp.RGB;
        long numTileRows = ifd.getTilesPerColumn() - 1;
        long numTileCols = ifd.getTilesPerRow() - 1;
        ms.sizeX = (int) ifd.getImageWidth();
        ms.sizeY = (int) ifd.getImageLength();
        ms.sizeZ = 1;
        ms.sizeT = 1;
        ms.sizeC = ms.rgb ? samples : 1;
        ms.littleEndian = ifd.isLittleEndian();
        ms.indexed = p == PhotoInterp.RGB_PALETTE && (get8BitLookupTable() != null || get16BitLookupTable() != null);
        ms.imageCount = 1;
        ms.pixelType = ifd.getPixelType();
        ms.metadataComplete = true;
        ms.interleaved = false;
        ms.falseColor = false;
        ms.dimensionOrder = "XYCZT";
        ms.thumbnail = s > 0;
    }
}