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

Example 61 with CoreMetadata

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

the class WlzReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    try {
        ServiceFactory factory = new ServiceFactory();
        wlz = factory.getInstance(WlzService.class);
    } catch (DependencyException e) {
        throw new FormatException(NO_WLZ_MSG, e);
    }
    if (wlz != null) {
        wlz.open(id, "r");
        CoreMetadata md = core.get(0);
        MetadataStore store = makeFilterMetadata();
        md.rgb = wlz.isRGB();
        md.interleaved = false;
        md.indexed = false;
        md.sizeX = wlz.getSizeX();
        md.sizeY = wlz.getSizeY();
        md.sizeZ = wlz.getSizeZ();
        md.sizeC = wlz.getSizeC();
        md.sizeT = wlz.getSizeT();
        md.dimensionOrder = "XYZCT";
        md.imageCount = wlz.getSizeZ();
        md.pixelType = wlz.getPixelType();
        PositiveFloat x = new PositiveFloat(Math.abs(wlz.getVoxSzX()));
        PositiveFloat y = new PositiveFloat(Math.abs(wlz.getVoxSzY()));
        PositiveFloat z = new PositiveFloat(Math.abs(wlz.getVoxSzZ()));
        store.setPixelsPhysicalSizeX(FormatTools.createLength(x, UNITS.MICROMETER), 0);
        store.setPixelsPhysicalSizeY(FormatTools.createLength(y, UNITS.MICROMETER), 0);
        store.setPixelsPhysicalSizeZ(FormatTools.createLength(z, UNITS.MICROMETER), 0);
        store.setStageLabelName(wlz.getWlzOrgLabelName(), 0);
        store.setStageLabelX(new Length(wlz.getOrgX(), UNITS.REFERENCEFRAME), 0);
        store.setStageLabelY(new Length(wlz.getOrgY(), UNITS.REFERENCEFRAME), 0);
        store.setStageLabelZ(new Length(wlz.getOrgZ(), UNITS.REFERENCEFRAME), 0);
        MetadataTools.populatePixels(store, this);
    }
}

Example 62 with CoreMetadata

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

the class ZeissCZIReader method calculateDimensions.

private void calculateDimensions(int coreIndex, boolean xyOnly) {
    // calculate the dimensions
    CoreMetadata ms0 = core.get(coreIndex);
    int previousCoreIndex = getCoreIndex();
    setCoreIndex(coreIndex);
    ArrayList<Integer> uniqueT = new ArrayList<Integer>();
    for (SubBlock plane : planes) {
        if (xyOnly && plane.coreIndex != coreIndex) {
            continue;
        }
        for (DimensionEntry dimension : plane.directoryEntry.dimensionEntries) {
            if (dimension == null) {
                continue;
            }
            if (xyOnly && dimension.dimension.charAt(0) != 'X' && dimension.dimension.charAt(0) != 'Y') {
                continue;
            }
            switch(dimension.dimension.charAt(0)) {
                case 'X':
                    plane.x = dimension.size;
                    plane.col = dimension.start;
                    if ((prestitched == null || prestitched) && getSizeX() > 0 && dimension.size != getSizeX() && allowAutostitching()) {
                        prestitched = true;
                        continue;
                    }
                    if (allowAutostitching() || ms0.sizeX == 0 || dimension.size == dimension.storedSize) {
                        ms0.sizeX = dimension.size;
                    }
                    break;
                case 'Y':
                    plane.y = dimension.size;
                    plane.row = dimension.start;
                    if ((prestitched == null || prestitched) && getSizeY() > 0 && dimension.size != getSizeY() && allowAutostitching()) {
                        prestitched = true;
                        continue;
                    }
                    if (allowAutostitching() || ms0.sizeY == 0 || dimension.size == dimension.storedSize) {
                        ms0.sizeY = dimension.size;
                    }
                    break;
                case 'C':
                    if (dimension.start >= getSizeC()) {
                        ms0.sizeC = dimension.start + 1;
                    }
                    break;
                case 'Z':
                    if (dimension.start > 0 && dimension.start >= getSizeZ()) {
                        ms0.sizeZ = dimension.start + 1;
                    } else if (dimension.size > getSizeZ()) {
                        ms0.sizeZ = dimension.size;
                    }
                    break;
                case 'T':
                    if (!uniqueT.contains(dimension.start)) {
                        uniqueT.add(dimension.start);
                        ms0.sizeT = uniqueT.size();
                    }
                    if (dimension.size > getSizeT()) {
                        ms0.sizeT = dimension.size;
                    }
                    break;
                case 'R':
                    if (dimension.start >= rotations) {
                        rotations = dimension.start + 1;
                    }
                    break;
                case 'S':
                    if (dimension.start >= positions) {
                        positions = dimension.start + 1;
                    }
                    break;
                case 'I':
                    if (dimension.start >= illuminations) {
                        illuminations = dimension.start + 1;
                    }
                    break;
                case 'B':
                    if (dimension.start >= acquisitions) {
                        acquisitions = dimension.start + 1;
                    }
                    break;
                case 'M':
                    if (dimension.start >= mosaics) {
                        mosaics = dimension.start + 1;
                    }
                    break;
                case 'H':
                    if (dimension.start >= phases) {
                        phases = dimension.start + 1;
                    }
                    break;
                case 'V':
                    if (dimension.start >= angles) {
                        angles = dimension.start + 1;
                    }
                    break;
                default:
                    LOGGER.warn("Unknown dimension '{}'", dimension.dimension);
            }
        }
    }
    setCoreIndex(previousCoreIndex);
}

Example 63 with CoreMetadata

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

the class ZeissLMSReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
public void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    CoreMetadata m = core.get(0);
    CoreMetadata thumb = new CoreMetadata();
    m.littleEndian = true;
    thumb.littleEndian = true;
    in.order(m.littleEndian);
    in.seek(18);
    double magnification = in.readInt();
    // all assumed to be constant based upon the CSM 700 data sheet
    thumb.sizeX = 1280;
    thumb.sizeY = 1024;
    thumb.pixelType = FormatTools.UINT8;
    thumb.sizeC = 3;
    thumb.rgb = true;
    thumb.interleaved = true;
    thumb.dimensionOrder = "XYCZT";
    m.sizeX = 1280;
    m.sizeY = 1024;
    m.pixelType = FormatTools.UINT16;
    m.sizeC = 1;
    m.rgb = false;
    m.dimensionOrder = "XYCZT";
    m.indexed = true;
    // each image can be found using the "BM6" marker
    seekToNextMarker();
    in.skipBytes(50);
    offsets.add(in.getFilePointer());
    in.skipBytes(thumb.sizeX * thumb.sizeY * thumb.sizeC);
    seekToNextMarker();
    in.skipBytes(50);
    lut = new byte[3][256];
    for (int i = 0; i < lut[0].length; i++) {
        for (int j = 0; j < lut.length; j++) {
            lut[j][i] = in.readByte();
        }
        // skip alpha channel
        in.skipBytes(1);
    }
    offsets.add(in.getFilePointer());
    // again, Z stack is assumed based upon the CSM 700 data sheet
    thumb.sizeZ = 1;
    thumb.sizeT = 1;
    thumb.imageCount = thumb.sizeZ * thumb.sizeT;
    long availableBytes = in.length() - offsets.get(1);
    int planeSize = m.sizeX * m.sizeY * FormatTools.getBytesPerPixel(m.pixelType);
    m.sizeZ = (int) (availableBytes / planeSize);
    m.sizeT = 1;
    m.imageCount = m.sizeZ * m.sizeT;
    core.add(thumb);
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    store.setInstrumentID(MetadataTools.createLSID("Instrument", 0), 0);
    String objective = MetadataTools.createLSID("Objective", 0, 0);
    store.setObjectiveID(objective, 0, 0);
    store.setObjectiveNominalMagnification(magnification, 0, 0);
    store.setObjectiveSettingsID(objective, 0);
    store.setObjectiveSettingsID(objective, 1);
}

Example 64 with CoreMetadata

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

the class TillVisionReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    if (!checkSuffix(id, "vws")) {
        Location pst = new Location(id).getAbsoluteFile();
        String name = pst.getParentFile().getName();
        Location parent = pst.getParentFile().getParentFile();
        Location vwsFile = new Location(parent, name.replaceAll(".pst", ".vws"));
        if (vwsFile.exists() && !vwsFile.isDirectory()) {
            id = vwsFile.getAbsolutePath();
        } else if (vwsFile.isDirectory()) {
            parent = pst.getParentFile();
            String[] list = parent.list(true);
            boolean foundVWS = false;
            for (String f : list) {
                if (checkSuffix(f, "vws")) {
                    id = new Location(parent, f).getAbsolutePath();
                    foundVWS = true;
                    break;
                }
            }
            if (!foundVWS) {
                throw new FormatException("Could not find .vws file.");
            }
        } else
            throw new FormatException("Could not find .vws file.");
    }
    super.initFile(id);
    exposureTimes = new HashMap<Integer, Double>();
    POIService poi = null;
    try {
        ServiceFactory factory = new ServiceFactory();
        poi = factory.getInstance(POIService.class);
    } catch (DependencyException de) {
        throw new FormatException("POI library not found", de);
    }
    poi.initialize(id);
    Vector<String> documents = poi.getDocumentList();
    int nImages = 0;
    final Hashtable<String, Object> tmpSeriesMetadata = new Hashtable<String, Object>();
    for (String name : documents) {
        LOGGER.debug("Reading {}", name);
        if (name.equals("Root Entry" + File.separator + "Contents")) {
            RandomAccessInputStream s = poi.getDocumentStream(name);
            s.order(true);
            boolean specialCImage = false;
            int nFound = 0;
            Long[] cimages = null;
            Location dir = new Location(id).getAbsoluteFile().getParentFile();
            String[] list = dir.list(true);
            boolean hasPST = false;
            for (String f : list) {
                if (checkSuffix(f, "pst")) {
                    hasPST = true;
                    break;
                }
            }
            if (!hasPST) {
                cimages = findImages(s);
                nFound = cimages.length;
                if (nFound == 0) {
                    s.seek(13);
                    int len = s.readShort();
                    String type = s.readString(len);
                    if (type.equals("CImage")) {
                        nFound = 1;
                        cimages = new Long[] { s.getFilePointer() + 6 };
                        specialCImage = true;
                    }
                }
                embeddedImages = nFound > 0;
            }
            LOGGER.debug("Images are {}embedded", embeddedImages ? "" : "not ");
            if (embeddedImages) {
                core.clear();
                embeddedOffset = new long[nFound];
                for (int i = 0; i < nFound; i++) {
                    CoreMetadata ms = new CoreMetadata();
                    core.add(ms);
                    s.seek(cimages[i]);
                    int len = s.read();
                    String imageName = s.readString(len);
                    imageNames.add(imageName);
                    if (specialCImage) {
                        s.seek(1280);
                    } else {
                        while (true) {
                            if (s.readString(2).equals("sB")) {
                                break;
                            } else
                                s.seek(s.getFilePointer() - 1);
                        }
                    }
                    s.skipBytes(20);
                    ms.sizeX = s.readInt();
                    ms.sizeY = s.readInt();
                    ms.sizeZ = s.readInt();
                    ms.sizeC = s.readInt();
                    ms.sizeT = s.readInt();
                    ms.pixelType = convertPixelType(s.readInt());
                    if (specialCImage) {
                        embeddedOffset[i] = s.getFilePointer() + 27;
                    } else {
                        embeddedOffset[i] = s.getFilePointer() + 31;
                    }
                }
                if (in != null)
                    in.close();
                in = poi.getDocumentStream(name);
                s.close();
                break;
            }
            s.seek(0);
            int lowerBound = 0;
            int upperBound = 0x1000;
            while (s.getFilePointer() < s.length() - 2) {
                LOGGER.debug("  Looking for image at {}", s.getFilePointer());
                s.order(false);
                int nextOffset = findNextOffset(s);
                if (nextOffset < 0 || nextOffset >= s.length())
                    break;
                s.seek(nextOffset);
                s.skipBytes(3);
                int len = s.readShort();
                if (len <= 0)
                    continue;
                imageNames.add(s.readString(len));
                if (s.getFilePointer() + 8 >= s.length())
                    break;
                s.skipBytes(6);
                s.order(true);
                len = s.readShort();
                if (nImages == 0 && len > upperBound * 2 && len < upperBound * 4) {
                    lowerBound = 512;
                    upperBound = 0x4000;
                }
                if (len < lowerBound || len > upperBound)
                    continue;
                String description = s.readString(len);
                LOGGER.debug("Description: {}", description);
                // parse key/value pairs from description
                String dateTime = "";
                String[] lines = description.split("[\r\n]");
                for (String line : lines) {
                    line = line.trim();
                    int colon = line.indexOf(':');
                    if (colon != -1 && !line.startsWith(";")) {
                        String key = line.substring(0, colon).trim();
                        String value = line.substring(colon + 1).trim();
                        String metaKey = "Series " + nImages + " " + key;
                        addMeta(metaKey, value, tmpSeriesMetadata);
                        if (key.equals("Start time of experiment")) {
                            // HH:mm:ss aa OR HH:mm:ss.sss aa
                            dateTime += " " + value;
                        } else if (key.equals("Date")) {
                            // mm/dd/yy ?
                            dateTime = value + " " + dateTime;
                        } else if (key.equals("Exposure time [ms]")) {
                            double exp = Double.parseDouble(value) / 1000;
                            exposureTimes.put(nImages, exp);
                        } else if (key.equals("Image type")) {
                            types.add(value);
                        }
                    }
                }
                dateTime = dateTime.trim();
                if (!dateTime.equals("")) {
                    boolean success = false;
                    for (String format : DATE_FORMATS) {
                        try {
                            dateTime = DateTools.formatDate(dateTime, format, ".");
                            success = true;
                        } catch (NullPointerException e) {
                        }
                    }
                    dates.add(success ? dateTime : "");
                }
                nImages++;
            }
            s.close();
        }
    }
    Location directory = new Location(currentId).getAbsoluteFile().getParentFile();
    String[] pixelsFile = new String[nImages];
    if (!embeddedImages) {
        if (nImages == 0) {
            throw new FormatException("No images found.");
        }
        // look for appropriate pixels files
        String[] files = directory.list(true);
        String name = currentId.substring(currentId.lastIndexOf(File.separator) + 1, currentId.lastIndexOf("."));
        int nextFile = 0;
        for (String f : files) {
            if (checkSuffix(f, "pst")) {
                Location pst = new Location(directory, f);
                if (pst.isDirectory() && f.startsWith(name)) {
                    String[] subfiles = pst.list(true);
                    Arrays.sort(subfiles);
                    for (String q : subfiles) {
                        if (checkSuffix(q, "pst") && nextFile < nImages) {
                            pixelsFile[nextFile++] = f + File.separator + q;
                        }
                    }
                }
            }
        }
        if (nextFile == 0) {
            for (String f : files) {
                if (checkSuffix(f, "pst")) {
                    pixelsFile[nextFile++] = new Location(directory, f).getAbsolutePath();
                }
            }
            if (nextFile == 0)
                throw new FormatException("No image files found.");
        }
    }
    Arrays.sort(pixelsFile);
    int nSeries = core.size();
    if (!embeddedImages) {
        core.clear();
        nSeries = nImages;
    }
    pixelsFiles = new String[nSeries];
    infFiles = new String[nSeries];
    Object[] metadataKeys = tmpSeriesMetadata.keySet().toArray();
    IniParser parser = new IniParser();
    for (int i = 0; i < nSeries; i++) {
        CoreMetadata ms;
        if (!embeddedImages) {
            ms = new CoreMetadata();
            core.add(ms);
            setSeries(i);
            // make sure that pixels file exists
            String file = pixelsFile[i];
            file = file.replace('/', File.separatorChar);
            file = file.replace('\\', File.separatorChar);
            String oldFile = file;
            Location f = new Location(directory, oldFile);
            if (!f.exists()) {
                oldFile = oldFile.substring(oldFile.lastIndexOf(File.separator) + 1);
                f = new Location(directory, oldFile);
                if (!f.exists()) {
                    throw new FormatException("Could not find pixels file '" + file);
                }
            }
            file = f.getAbsolutePath();
            pixelsFiles[i] = file;
            // read key/value pairs from .inf files
            int dot = file.lastIndexOf(".");
            String inf = file.substring(0, dot) + ".inf";
            infFiles[i] = inf;
            BufferedReader reader = new BufferedReader(new InputStreamReader(new FileInputStream(inf), Constants.ENCODING));
            IniList data = parser.parseINI(reader);
            reader.close();
            IniTable infoTable = data.getTable("Info");
            ms.sizeX = Integer.parseInt(infoTable.get("Width"));
            ms.sizeY = Integer.parseInt(infoTable.get("Height"));
            ms.sizeC = Integer.parseInt(infoTable.get("Bands"));
            ms.sizeZ = Integer.parseInt(infoTable.get("Slices"));
            ms.sizeT = Integer.parseInt(infoTable.get("Frames"));
            int dataType = Integer.parseInt(infoTable.get("Datatype"));
            ms.pixelType = convertPixelType(dataType);
            if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
                HashMap<String, String> iniMap = data.flattenIntoHashMap();
                ms.seriesMetadata.putAll(iniMap);
            }
        } else {
            ms = core.get(i);
            setSeries(i);
        }
        ms.imageCount = ms.sizeZ * ms.sizeC * ms.sizeT;
        ms.rgb = false;
        ms.littleEndian = true;
        ms.dimensionOrder = "XYCZT";
        ms.seriesMetadata = new Hashtable<String, Object>();
        for (Object key : metadataKeys) {
            String keyName = key.toString();
            if (keyName.startsWith("Series " + i + " ")) {
                keyName = keyName.replaceAll("Series " + i + " ", "");
                ms.seriesMetadata.put(keyName, tmpSeriesMetadata.get(key));
            }
        }
    }
    setSeries(0);
    populateMetadataStore();
    poi.close();
    poi = null;
}

Example 65 with CoreMetadata

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

the class TrestleReader method initStandardMetadata.

// -- Internal BaseTiffReader API methods --
/* @see loci.formats.in.BaseTiffReader#initStandardMetadata() */
@Override
protected void initStandardMetadata() throws FormatException, IOException {
    super.initStandardMetadata();
    ifds = tiffParser.getIFDs();
    for (IFD ifd : ifds) {
        tiffParser.fillInIFD(ifd);
    }
    String comment = ifds.get(0).getComment();
    String[] values = comment.split(";");
    for (String v : values) {
        int eq = v.indexOf('=');
        if (eq < 0)
            continue;
        String key = v.substring(0, eq).trim();
        String value = v.substring(eq + 1).trim();
        addGlobalMeta(key, value);
        if (key.equals("OverlapsXY")) {
            String[] overlapValues = value.split(" ");
            overlaps = new int[ifds.size() * 2];
            for (int i = 0; i < overlapValues.length; i++) {
                overlaps[i] = Integer.parseInt(overlapValues[i]);
            }
        }
    }
    int seriesCount = ifds.size();
    core.clear();
    for (int i = 0; i < seriesCount; i++) {
        CoreMetadata c = new CoreMetadata();
        if (i == 0 && !hasFlattenedResolutions()) {
            c.resolutionCount = seriesCount;
        }
        core.add(c);
    }
    for (int s = 0; s < core.size(); s++) {
        CoreMetadata ms = core.get(s);
        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;
        int overlapX = overlaps[s * 2];
        int overlapY = overlaps[s * 2 + 1];
        ms.sizeX = (int) (ifd.getImageWidth() - (numTileCols * overlapX));
        ms.sizeY = (int) (ifd.getImageLength() - (numTileRows * overlapY));
        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;
    }
    // look for all of the other associated metadata files
    files = new ArrayList<String>();
    Location baseFile = new Location(currentId).getAbsoluteFile();
    Location parent = baseFile.getParentFile();
    String name = baseFile.getName();
    if (name.indexOf('.') >= 0) {
        name = name.substring(0, name.indexOf('.') + 1);
    }
    roiFile = new Location(parent, name + "ROI").getAbsolutePath();
    roiDrawFile = new Location(parent, name + "ROI-draw").getAbsolutePath();
    String[] list = parent.list(true);
    for (String f : list) {
        if (!f.equals(baseFile.getName())) {
            files.add(new Location(parent, f).getAbsolutePath());
        }
    }
}