/* @see BaseTiffReader#initMetadataStore() */
  protected void initMetadataStore() throws FormatException {
    super.initMetadataStore();
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, true);

    if (date != null) {
      date = DateTools.formatDate(date, DATE_FORMAT);
      if (date != null) {
        store.setImageAcquisitionDate(new Timestamp(date), 0);
      }
    }

    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
      store.setImageDescription(MAGIC_STRING, 0);
      if (scaling > 0) {
        store.setPixelsPhysicalSizeX(new PositiveFloat(scaling), 0);
        store.setPixelsPhysicalSizeY(new PositiveFloat(scaling), 0);
      } else {
        LOGGER.warn("Expected positive value for PhysicalSize; got {}", scaling);
      }

      String instrument = MetadataTools.createLSID("Instrument", 0);
      store.setInstrumentID(instrument, 0);
      store.setImageInstrumentRef(instrument, 0);

      store.setObjectiveID(MetadataTools.createLSID("Objective", 0, 0), 0, 0);
      if (magnification > 0) {
        store.setObjectiveNominalMagnification(new PositiveInteger(magnification), 0, 0);
      } else {
        LOGGER.warn("Expected positive value for NominalMagnification; got {}", magnification);
      }
      store.setObjectiveImmersion(getImmersion(immersion), 0, 0);

      String detector = MetadataTools.createLSID("Detector", 0, 0);
      store.setDetectorID(detector, 0, 0);
      store.setDetectorModel(cameraType + " " + cameraName, 0, 0);
      store.setDetectorType(getDetectorType("CCD"), 0, 0);

      for (int i = 0; i < getSizeC(); i++) {
        store.setDetectorSettingsID(detector, 0, i);
        store.setDetectorSettingsBinning(getBinning(binning), 0, i);
      }

      for (int i = 0; i < getImageCount(); i++) {
        int[] zct = getZCTCoords(i);
        store.setPlaneExposureTime(exposureTimes.get(zct[1]) / 1000000, 0, i);
      }
    }
  }
Esempio n. 2
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  /* @see loci.formats.FormatReader#initFile(String) */
  protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    CoreMetadata m = core.get(0);

    m.littleEndian = true;
    in.order(isLittleEndian());

    while (in.getFilePointer() < MAX_HEADER_SIZE) {
      readVariable();
    }

    in.seek(pixelsOffset);
    m.sizeX = in.readShort();
    pixelsOffset += 2;

    m.sizeY = getSizeX();
    m.pixelType = FormatTools.UINT16;

    m.sizeZ = 1;
    m.sizeC = 1;
    m.sizeT = 1;
    m.imageCount = 1;
    m.dimensionOrder = "XYZCT";

    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    if (date != null) {
      date = DateTools.formatDate(date, "MMM dd yyyy HH:mm:ssSSS");
      if (date != null) {
        store.setImageAcquisitionDate(new Timestamp(date), 0);
      }
    }

    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
      store.setImageDescription(comment, 0);

      PositiveFloat sizeX = FormatTools.getPhysicalSizeX((double) xSize / getSizeX());
      PositiveFloat sizeY = FormatTools.getPhysicalSizeY((double) xSize / getSizeY());

      if (sizeX != null) {
        store.setPixelsPhysicalSizeX(sizeX, 0);
      }
      if (sizeY != null) {
        store.setPixelsPhysicalSizeY(sizeY, 0);
      }
    }
  }
Esempio n. 3
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  /**
   * Populates the metadata store using the data parsed in {@link #initStandardMetadata()} along
   * with some further parsing done in the method itself.
   *
   * <p>All calls to the active <code>MetadataStore</code> should be made in this method and
   * <b>only</b> in this method. This is especially important for sub-classes that override the
   * getters for pixel set array size, etc.
   */
  protected void initMetadataStore() throws FormatException {
    LOGGER.info("Populating OME metadata");

    // the metadata store we're working with
    MetadataStore store = makeFilterMetadata();

    IFD firstIFD = ifds.get(0);
    IFD exif = null;

    if (ifds.get(0).containsKey(IFD.EXIF)) {
      try {
        IFDList exifIFDs = tiffParser.getExifIFDs();
        if (exifIFDs.size() > 0) {
          exif = exifIFDs.get(0);
        }
        tiffParser.fillInIFD(exif);
      } catch (IOException e) {
        LOGGER.debug("Could not read EXIF IFDs", e);
      }
    }

    MetadataTools.populatePixels(store, this, exif != null);

    // format the creation date to ISO 8601

    String creationDate = getImageCreationDate();
    String date = DateTools.formatDate(creationDate, DATE_FORMATS);
    if (creationDate != null && date == null) {
      LOGGER.warn("unknown creation date format: {}", creationDate);
    }
    creationDate = date;

    // populate Image

    if (creationDate != null) {
      store.setImageAcquisitionDate(new Timestamp(creationDate), 0);
    }

    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
      // populate Experimenter
      String artist = firstIFD.getIFDTextValue(IFD.ARTIST);

      if (artist != null) {
        String firstName = null, lastName = null;
        int ndx = artist.indexOf(" ");
        if (ndx < 0) lastName = artist;
        else {
          firstName = artist.substring(0, ndx);
          lastName = artist.substring(ndx + 1);
        }
        String email = firstIFD.getIFDStringValue(IFD.HOST_COMPUTER);
        store.setExperimenterFirstName(firstName, 0);
        store.setExperimenterLastName(lastName, 0);
        store.setExperimenterEmail(email, 0);
        store.setExperimenterID(MetadataTools.createLSID("Experimenter", 0), 0);
      }

      store.setImageDescription(firstIFD.getComment(), 0);

      // set the X and Y pixel dimensions

      double pixX = firstIFD.getXResolution();
      double pixY = firstIFD.getYResolution();

      PositiveFloat sizeX = FormatTools.getPhysicalSizeX(pixX);
      PositiveFloat sizeY = FormatTools.getPhysicalSizeY(pixY);

      if (sizeX != null) {
        store.setPixelsPhysicalSizeX(sizeX, 0);
      }
      if (sizeY != null) {
        store.setPixelsPhysicalSizeY(sizeY, 0);
      }
      store.setPixelsPhysicalSizeZ(null, 0);

      if (exif != null) {
        if (exif.containsKey(IFD.EXPOSURE_TIME)) {
          Object exp = exif.get(IFD.EXPOSURE_TIME);
          if (exp instanceof TiffRational) {
            Double exposure = ((TiffRational) exp).doubleValue();
            for (int i = 0; i < getImageCount(); i++) {
              store.setPlaneExposureTime(exposure, 0, i);
            }
          }
        }
      }
    }
  }
Esempio n. 4
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  /* @see loci.formats.FormatReader#initFile(String) */
  public void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    MetadataLevel level = getMetadataOptions().getMetadataLevel();

    LOGGER.info("Reading header");

    // check endianness

    in.seek(ENDIANNESS_OFFSET);
    core[0].littleEndian = in.read() == 68;

    // read dimension information from 1024 byte header

    in.seek(0);
    in.order(isLittleEndian());

    core[0].sizeX = in.readInt();
    core[0].sizeY = in.readInt();
    core[0].sizeZ = in.readInt();

    // We are using BigInteger here because of the very real possiblity
    // of not just an int overflow but also a long overflow when multiplying
    // sizeX * sizeY * sizeZ.
    BigInteger v = BigInteger.valueOf(getSizeX());
    v = v.multiply(BigInteger.valueOf(getSizeY()));
    v = v.multiply(BigInteger.valueOf(getSizeZ()));
    if (getSizeX() < 0
        || getSizeY() < 0
        || getSizeZ() < 0
        || (v.compareTo(BigInteger.valueOf(in.length())) > 0)) {
      LOGGER.debug("Detected endianness is wrong, swapping");
      core[0].littleEndian = !isLittleEndian();
      in.seek(0);
      in.order(isLittleEndian());
      core[0].sizeX = in.readInt();
      core[0].sizeY = in.readInt();
      core[0].sizeZ = in.readInt();
    }

    core[0].sizeC = 1;

    int mode = in.readInt();
    switch (mode) {
      case 0:
        core[0].pixelType = FormatTools.UINT8;
        break;
      case 1:
        core[0].pixelType = FormatTools.INT16;
        break;
      case 6:
        core[0].pixelType = FormatTools.UINT16;
        break;
      case 2:
        core[0].pixelType = FormatTools.FLOAT;
        break;
      case 3:
        core[0].pixelType = FormatTools.UINT32;
        break;
      case 4:
        core[0].pixelType = FormatTools.DOUBLE;
        break;
      case 16:
        core[0].sizeC = 3;
        core[0].pixelType = FormatTools.UINT16;
        break;
    }

    in.skipBytes(12);

    // pixel size = xlen / mx

    double xSize = 0d, ySize = 0d, zSize = 0d;

    if (level != MetadataLevel.MINIMUM) {
      int mx = in.readInt();
      int my = in.readInt();
      int mz = in.readInt();

      // physical sizes are stored in ångströms, we want them in µm
      xSize = (in.readFloat() / mx) / 10000.0;
      ySize = (in.readFloat() / my) / 10000.0;
      zSize = (in.readFloat() / mz) / 10000.0;

      addGlobalMeta("Pixel size (X)", xSize);
      addGlobalMeta("Pixel size (Y)", ySize);
      addGlobalMeta("Pixel size (Z)", zSize);

      addGlobalMeta("Alpha angle", in.readFloat());
      addGlobalMeta("Beta angle", in.readFloat());
      addGlobalMeta("Gamma angle", in.readFloat());

      in.skipBytes(12);

      // min, max and mean pixel values
    } else in.skipBytes(48);

    double minValue = in.readFloat();
    double maxValue = in.readFloat();

    addGlobalMeta("Minimum pixel value", minValue);
    addGlobalMeta("Maximum pixel value", maxValue);
    addGlobalMeta("Mean pixel value", in.readFloat());

    int bytes = FormatTools.getBytesPerPixel(getPixelType());
    double range = Math.pow(2, bytes * 8) - 1;
    double pixelTypeMin = 0;
    boolean signed = FormatTools.isSigned(getPixelType());
    if (signed) {
      pixelTypeMin -= (range / 2);
    }
    double pixelTypeMax = pixelTypeMin + range;

    if (pixelTypeMax < maxValue || pixelTypeMin > minValue && signed) {
      // make the pixel type unsigned
      switch (getPixelType()) {
        case FormatTools.INT8:
          core[0].pixelType = FormatTools.UINT8;
          break;
        case FormatTools.INT16:
          core[0].pixelType = FormatTools.UINT16;
          break;
        case FormatTools.INT32:
          core[0].pixelType = FormatTools.UINT32;
          break;
      }
    }

    in.skipBytes(4);

    extHeaderSize = in.readInt();

    if (level != MetadataLevel.MINIMUM) {
      in.skipBytes(64);

      int idtype = in.readShort();

      String type = "unknown";
      if (idtype >= 0 && idtype < TYPES.length) type = TYPES[idtype];

      addGlobalMeta("Series type", type);
      addGlobalMeta("Lens", in.readShort());
      addGlobalMeta("ND1", in.readShort());
      addGlobalMeta("ND2", in.readShort());
      addGlobalMeta("VD1", in.readShort());
      addGlobalMeta("VD2", in.readShort());

      for (int i = 0; i < 6; i++) {
        addGlobalMeta("Angle " + (i + 1), in.readFloat());
      }

      in.skipBytes(24);

      addGlobalMeta("Number of useful labels", in.readInt());

      for (int i = 0; i < 10; i++) {
        addGlobalMeta("Label " + (i + 1), in.readString(80));
      }
    }

    LOGGER.info("Populating metadata");

    core[0].sizeT = 1;
    core[0].dimensionOrder = "XYZTC";
    core[0].imageCount = getSizeZ();
    core[0].rgb = false;
    core[0].interleaved = true;
    core[0].indexed = false;
    core[0].falseColor = false;
    core[0].metadataComplete = true;

    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);

    if (level != MetadataLevel.MINIMUM) {
      if (xSize - Constants.EPSILON > 0) {
        store.setPixelsPhysicalSizeX(new PositiveFloat(xSize), 0);
      } else {
        LOGGER.warn("xSize {} not a positive float skipping", xSize);
      }
      if (ySize - Constants.EPSILON > 0) {
        store.setPixelsPhysicalSizeY(new PositiveFloat(ySize), 0);
      } else {
        LOGGER.warn("ySize {} not a positive float skipping", ySize);
      }
      if (zSize - Constants.EPSILON > 0) {
        store.setPixelsPhysicalSizeZ(new PositiveFloat(zSize), 0);
      } else {
        LOGGER.warn("zSize {} not a positive float skipping", zSize);
      }
    }
  }
Esempio n. 5
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  @Override
  protected void initFile(String id) throws FormatException, IOException {
    LOGGER.debug("OmeroReader.initFile({})", id);

    super.initFile(id);

    if (!id.startsWith("omero:")) {
      throw new IllegalArgumentException("Not an OMERO id: " + id);
    }

    // parse credentials from id string

    LOGGER.info("Parsing credentials");

    String address = server, user = username, pass = password;
    int port = thePort;
    long iid = -1;

    final String[] tokens = id.substring(6).split("\n");
    for (String token : tokens) {
      final int equals = token.indexOf("=");
      if (equals < 0) continue;
      final String key = token.substring(0, equals);
      final String val = token.substring(equals + 1);
      if (key.equals("server")) address = val;
      else if (key.equals("user")) user = val;
      else if (key.equals("pass")) pass = val;
      else if (key.equals("port")) {
        try {
          port = Integer.parseInt(val);
        } catch (NumberFormatException exc) {
        }
      } else if (key.equals("session")) {
        sessionID = val;
      } else if (key.equals("groupName")) {
        group = val;
      } else if (key.equals("groupID")) {
        groupID = new Long(val);
      } else if (key.equals("iid")) {
        try {
          iid = Long.parseLong(val);
        } catch (NumberFormatException exc) {
        }
      }
    }

    if (address == null) {
      throw new FormatException("Invalid server address");
    }
    if (user == null && sessionID == null) {
      throw new FormatException("Invalid username");
    }
    if (pass == null && sessionID == null) {
      throw new FormatException("Invalid password");
    }
    if (iid < 0) {
      throw new FormatException("Invalid image ID");
    }

    try {
      // authenticate with OMERO server

      LOGGER.info("Logging in");

      client = new omero.client(address, port);
      ServiceFactoryPrx serviceFactory = null;
      if (user != null && pass != null) {
        serviceFactory = client.createSession(user, pass);
      } else {
        serviceFactory = client.createSession(sessionID, sessionID);
      }

      if (!encrypted) {
        client = client.createClient(false);
        serviceFactory = client.getSession();
      }

      if (group != null || groupID != null) {
        IAdminPrx iAdmin = serviceFactory.getAdminService();
        IQueryPrx iQuery = serviceFactory.getQueryService();
        EventContext eventContext = iAdmin.getEventContext();
        ExperimenterGroup defaultGroup = iAdmin.getDefaultGroup(eventContext.userId);
        if (!defaultGroup.getName().getValue().equals(group)
            && !new Long(defaultGroup.getId().getValue()).equals(groupID)) {
          Experimenter exp = iAdmin.getExperimenter(eventContext.userId);

          ParametersI p = new ParametersI();
          p.addId(eventContext.userId);
          List<IObject> groupList =
              iQuery.findAllByQuery(
                  "select distinct g from ExperimenterGroup as g "
                      + "join fetch g.groupExperimenterMap as map "
                      + "join fetch map.parent e "
                      + "left outer join fetch map.child u "
                      + "left outer join fetch u.groupExperimenterMap m2 "
                      + "left outer join fetch m2.parent p "
                      + "where g.id in "
                      + "  (select m.parent from GroupExperimenterMap m "
                      + "  where m.child.id = :id )",
                  p);

          Iterator<IObject> i = groupList.iterator();

          ExperimenterGroup g = null;

          boolean in = false;
          while (i.hasNext()) {
            g = (ExperimenterGroup) i.next();
            if (g.getName().getValue().equals(group)
                || new Long(g.getId().getValue()).equals(groupID)) {
              in = true;
              groupID = g.getId().getValue();
              break;
            }
          }
          if (in) {
            iAdmin.setDefaultGroup(exp, iAdmin.getGroup(groupID));
            serviceFactory.setSecurityContext(new ExperimenterGroupI(groupID, false));
          }
        }
      }

      // get raw pixels store and pixels

      store = serviceFactory.createRawPixelsStore();

      final GatewayPrx gateway = serviceFactory.createGateway();
      img = gateway.getImage(iid);

      if (img == null) {
        throw new FormatException(
            "Could not find Image with ID=" + iid + " in group '" + group + "'.");
      }

      long pixelsId = img.getPixels(0).getId().getValue();

      store.setPixelsId(pixelsId, false);

      pix = gateway.getPixels(pixelsId);
      final int sizeX = pix.getSizeX().getValue();
      final int sizeY = pix.getSizeY().getValue();
      final int sizeZ = pix.getSizeZ().getValue();
      final int sizeC = pix.getSizeC().getValue();
      final int sizeT = pix.getSizeT().getValue();
      final String pixelType = pix.getPixelsType().getValue().getValue();

      // populate metadata

      LOGGER.info("Populating metadata");

      core[0].sizeX = sizeX;
      core[0].sizeY = sizeY;
      core[0].sizeZ = sizeZ;
      core[0].sizeC = sizeC;
      core[0].sizeT = sizeT;
      core[0].rgb = false;
      core[0].littleEndian = false;
      core[0].dimensionOrder = "XYZCT";
      core[0].imageCount = sizeZ * sizeC * sizeT;
      core[0].pixelType = FormatTools.pixelTypeFromString(pixelType);

      RDouble x = pix.getPhysicalSizeX();
      Double px = x == null ? null : x.getValue();
      RDouble y = pix.getPhysicalSizeY();
      Double py = y == null ? null : y.getValue();
      RDouble z = pix.getPhysicalSizeZ();
      Double pz = z == null ? null : z.getValue();
      RDouble t = pix.getTimeIncrement();
      Double time = t == null ? null : t.getValue();

      RString imageName = img.getName();
      String name = imageName == null ? null : imageName.getValue();

      if (name != null) {
        currentId = name;
      } else {
        currentId = "Image ID " + iid;
      }

      RString imgDescription = img.getDescription();
      String description = imgDescription == null ? null : imgDescription.getValue();
      RTime date = img.getAcquisitionDate();

      MetadataStore store = getMetadataStore();
      MetadataTools.populatePixels(store, this);
      store.setImageName(name, 0);
      store.setImageDescription(description, 0);
      if (date != null) {
        store.setImageAcquisitionDate(
            new Timestamp(DateTools.convertDate(date.getValue(), (int) DateTools.UNIX_EPOCH)), 0);
      }

      if (px != null && px > 0) {
        store.setPixelsPhysicalSizeX(new PositiveFloat(px), 0);
      }
      if (py != null && py > 0) {
        store.setPixelsPhysicalSizeY(new PositiveFloat(py), 0);
      }
      if (pz != null && pz > 0) {
        store.setPixelsPhysicalSizeZ(new PositiveFloat(pz), 0);
      }
      if (time != null) {
        store.setPixelsTimeIncrement(time, 0);
      }

      List<Channel> channels = pix.copyChannels();
      for (int c = 0; c < channels.size(); c++) {
        LogicalChannel channel = channels.get(c).getLogicalChannel();

        RInt emWave = channel.getEmissionWave();
        RInt exWave = channel.getExcitationWave();
        RDouble pinholeSize = channel.getPinHoleSize();
        RString cname = channel.getName();

        Integer emission = emWave == null ? null : emWave.getValue();
        Integer excitation = exWave == null ? null : exWave.getValue();
        String channelName = cname == null ? null : cname.getValue();
        Double pinhole = pinholeSize == null ? null : pinholeSize.getValue();

        if (channelName != null) {
          store.setChannelName(channelName, 0, c);
        }
        if (pinhole != null) {
          store.setChannelPinholeSize(pinhole, 0, c);
        }
        if (emission != null && emission > 0) {
          store.setChannelEmissionWavelength(new PositiveInteger(emission), 0, c);
        }
        if (excitation != null && excitation > 0) {
          store.setChannelExcitationWavelength(new PositiveInteger(excitation), 0, c);
        }
      }
    } catch (CannotCreateSessionException e) {
      throw new FormatException(e);
    } catch (PermissionDeniedException e) {
      throw new FormatException(e);
    } catch (ServerError e) {
      throw new FormatException(e);
    }
  }
Esempio n. 6
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  private void populateMetadata() throws FormatException, IOException {
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, true);

    String instrumentID = MetadataTools.createLSID("Instrument", 0);
    store.setInstrumentID(instrumentID, 0);

    for (int i = 0; i < positions.size(); i++) {
      Position p = positions.get(i);
      if (p.time != null) {
        String date = DateTools.formatDate(p.time, DATE_FORMAT);
        if (date != null) {
          store.setImageAcquisitionDate(new Timestamp(date), i);
        }
      }

      if (positions.size() > 1) {
        Location parent = new Location(p.metadataFile).getParentFile();
        store.setImageName(parent.getName(), i);
      }

      if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        store.setImageDescription(p.comment, i);

        // link Instrument and Image
        store.setImageInstrumentRef(instrumentID, i);

        for (int c = 0; c < p.channels.length; c++) {
          store.setChannelName(p.channels[c], i, c);
        }

        if (p.pixelSize != null && p.pixelSize > 0) {
          store.setPixelsPhysicalSizeX(new PositiveFloat(p.pixelSize), i);
          store.setPixelsPhysicalSizeY(new PositiveFloat(p.pixelSize), i);
        } else {
          LOGGER.warn("Expected positive value for PhysicalSizeX; got {}", p.pixelSize);
        }
        if (p.sliceThickness != null && p.sliceThickness > 0) {
          store.setPixelsPhysicalSizeZ(new PositiveFloat(p.sliceThickness), i);
        } else {
          LOGGER.warn("Expected positive value for PhysicalSizeZ; got {}", p.sliceThickness);
        }

        int nextStamp = 0;
        for (int q = 0; q < getImageCount(); q++) {
          store.setPlaneExposureTime(p.exposureTime, i, q);
          String tiff = positions.get(getSeries()).getFile(q);
          if (tiff != null && new Location(tiff).exists() && nextStamp < p.timestamps.length) {
            store.setPlaneDeltaT(p.timestamps[nextStamp++], i, q);
          }
        }

        String serialNumber = p.detectorID;
        p.detectorID = MetadataTools.createLSID("Detector", 0, i);

        for (int c = 0; c < p.channels.length; c++) {
          store.setDetectorSettingsBinning(getBinning(p.binning), i, c);
          store.setDetectorSettingsGain(new Double(p.gain), i, c);
          if (c < p.voltage.size()) {
            store.setDetectorSettingsVoltage(p.voltage.get(c), i, c);
          }
          store.setDetectorSettingsID(p.detectorID, i, c);
        }

        store.setDetectorID(p.detectorID, 0, i);
        if (p.detectorModel != null) {
          store.setDetectorModel(p.detectorModel, 0, i);
        }

        if (serialNumber != null) {
          store.setDetectorSerialNumber(serialNumber, 0, i);
        }

        if (p.detectorManufacturer != null) {
          store.setDetectorManufacturer(p.detectorManufacturer, 0, i);
        }

        if (p.cameraMode == null) p.cameraMode = "Other";
        store.setDetectorType(getDetectorType(p.cameraMode), 0, i);
        store.setImagingEnvironmentTemperature(p.temperature, i);
      }
    }
  }
  /* @see loci.formats.FormatReader#initFile(String) */
  protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);

    Vector<String> uniqueChannels = new Vector<String>();
    Vector<Double> uniqueZs = new Vector<Double>();
    Vector<Double> stageX = new Vector<Double>();
    Vector<Double> stageY = new Vector<Double>();

    String filename = id.substring(id.lastIndexOf(File.separator) + 1);
    filename = filename.substring(0, filename.indexOf("."));
    boolean integerFilename = true;
    try {
      Integer.parseInt(filename);
    } catch (NumberFormatException e) {
      integerFilename = false;
    }

    if (integerFilename
        && ifds.size() == 1
        && ifds.get(0).getIFDIntValue(IFD.NEW_SUBFILE_TYPE) == 2) {
      // look for other files in the dataset

      findTIFFs();

      String stageLabel = null;

      for (String tiff : files) {
        MetamorphHandler handler = new MetamorphHandler();
        parseFile(tiff, handler);

        String label = handler.getStageLabel();
        if (stageLabel == null) {
          stageLabel = label;
        } else if (!label.equals(stageLabel)) {
          break;
        }

        if (!uniqueChannels.contains(handler.getChannelName())) {
          uniqueChannels.add(handler.getChannelName());
        }

        Vector<Double> zPositions = handler.getZPositions();
        Double pos = Math.rint(zPositions.get(0));

        if (!uniqueZs.contains(pos)) {
          uniqueZs.add(pos);
        }
      }

      MetamorphHandler handler = new MetamorphHandler();
      parseFile(files[files.length - 1], handler);

      String lastStageLabel = handler.getStageLabel();
      int lastField = getField(lastStageLabel);
      int lastWellRow = getWellRow(lastStageLabel);
      int lastWellColumn = getWellColumn(lastStageLabel);

      int field = getField(stageLabel);
      int fieldRow = getWellRow(stageLabel);
      int fieldColumn = getWellColumn(stageLabel);

      wellCount = lastField - field + 1;
      fieldRowCount = lastWellRow - fieldRow + 1;
      fieldColumnCount = lastWellColumn - fieldColumn + 1;
      core[0].sizeC = uniqueChannels.size();
      core[0].sizeZ = uniqueZs.size();
    } else {
      files = new String[] {id};
      wellCount = 1;
      fieldRowCount = 1;
      fieldColumnCount = 1;
      core[0].sizeC = 0;
    }

    // parse XML comment

    MetamorphHandler handler = new MetamorphHandler(getGlobalMetadata());
    Vector<Double> xPositions = new Vector<Double>();
    Vector<Double> yPositions = new Vector<Double>();

    for (IFD ifd : ifds) {
      String xml = XMLTools.sanitizeXML(ifd.getComment());
      XMLTools.parseXML(xml, handler);

      double x = handler.getStagePositionX();
      double y = handler.getStagePositionY();

      if (xPositions.size() == 0) {
        xPositions.add(x);
        yPositions.add(y);
      } else {
        double previousX = xPositions.get(xPositions.size() - 1);
        double previousY = yPositions.get(yPositions.size() - 1);

        if (Math.abs(previousX - x) > 0.21 || Math.abs(previousY - y) > 0.21) {
          xPositions.add(x);
          yPositions.add(y);
        }
      }
    }

    if (xPositions.size() > 1) {
      fieldRowCount = xPositions.size();
    }

    Vector<Integer> wavelengths = handler.getWavelengths();
    Vector<Double> zPositions = handler.getZPositions();

    // calculate axis sizes

    Vector<Integer> uniqueC = new Vector<Integer>();
    for (Integer c : wavelengths) {
      if (!uniqueC.contains(c)) {
        uniqueC.add(c);
      }
    }
    int effectiveC = uniqueC.size();
    if (effectiveC == 0) effectiveC = 1;
    if (getSizeC() == 0) core[0].sizeC = 1;
    int samples = ifds.get(0).getSamplesPerPixel();
    core[0].sizeC *= effectiveC * samples;

    Vector<Double> uniqueZ = new Vector<Double>();
    for (Double z : zPositions) {
      if (!uniqueZ.contains(z)) uniqueZ.add(z);
    }
    if (getSizeZ() == 0) core[0].sizeZ = 1;
    core[0].sizeZ *= uniqueZ.size();

    int totalPlanes = files.length * ifds.size();
    effectiveC = getSizeC() / samples;
    core[0].sizeT =
        totalPlanes / (wellCount * fieldRowCount * fieldColumnCount * getSizeZ() * effectiveC);
    if (getSizeT() == 0) core[0].sizeT = 1;

    int seriesCount = wellCount * fieldRowCount * fieldColumnCount;

    if (seriesCount > 1 && getSizeZ() > totalPlanes / seriesCount) {
      core[0].sizeZ = 1;
      core[0].sizeT = totalPlanes / (seriesCount * getSizeT() * effectiveC);
    }

    core[0].imageCount = getSizeZ() * getSizeT() * effectiveC;

    if (seriesCount > 1) {
      CoreMetadata oldCore = core[0];
      core = new CoreMetadata[seriesCount];
      for (int i = 0; i < seriesCount; i++) {
        core[i] = oldCore;
      }
    }

    for (int s = 0; s < wellCount * fieldRowCount * fieldColumnCount; s++) {
      if (files.length > 1) {
        int[] lengths =
            new int[] {
              getSizeZ(),
              getEffectiveSizeC(),
              fieldColumnCount,
              fieldRowCount,
              wellCount,
              getSizeT()
            };

        Well well = getWell(s);
        int[] position = new int[] {0, 0, well.fieldCol, well.fieldRow, well.well, 0};

        int fileIndex = FormatTools.positionToRaster(lengths, position);
        parseFile(files[fileIndex], handler);

        stageX.add(handler.getStagePositionX());
        stageY.add(handler.getStagePositionY());
      } else {
        stageX.add(xPositions.get(s));
        stageY.add(yPositions.get(s));
      }
    }

    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);

    store.setPlateID(MetadataTools.createLSID("Plate", 0), 0);
    store.setPlateRowNamingConvention(NamingConvention.LETTER, 0);
    store.setPlateColumnNamingConvention(NamingConvention.NUMBER, 0);

    for (int well = 0; well < wellCount; well++) {
      store.setWellID(MetadataTools.createLSID("Well", 0, well), 0, well);
      store.setWellRow(new NonNegativeInteger(0), 0, well);
      store.setWellColumn(new NonNegativeInteger(well), 0, well);

      for (int row = 0; row < fieldRowCount; row++) {
        for (int col = 0; col < fieldColumnCount; col++) {
          int field = row * fieldColumnCount + col;
          String wellSampleID = MetadataTools.createLSID("WellSample", 0, well, field);
          store.setWellSampleID(wellSampleID, 0, well, field);

          int seriesIndex = getSeriesIndex(row, col, well);
          String imageID = MetadataTools.createLSID("Image", seriesIndex);
          store.setImageID(imageID, seriesIndex);
          store.setWellSampleImageRef(imageID, 0, well, field);
          store.setWellSampleIndex(new NonNegativeInteger(seriesIndex), 0, well, field);
        }
      }
    }

    for (int s = 0; s < seriesCount; s++) {
      setSeries(s);
      Well well = getWell(s);

      String name = handler.getImageName();
      if (seriesCount > 1) {
        name =
            "Field "
                + (char) (well.fieldRow + 'A')
                + (well.fieldCol + 1)
                + ", Well "
                + (well.well + 1)
                + ": "
                + name;
      }

      store.setImageName(name, s);

      String date = DateTools.formatDate(handler.getDate(), DateTools.ISO8601_FORMAT);
      store.setImageAcquiredDate(date, s);

      if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        Vector<String> timestamps = handler.getTimestamps();
        Vector<Double> exposures = handler.getExposures();

        for (int i = 0; i < timestamps.size(); i++) {
          long timestamp = DateTools.getTime(timestamps.get(i), DATE_FORMAT);
          addSeriesMeta("timestamp " + i, timestamp);
        }
        for (int i = 0; i < exposures.size(); i++) {
          addSeriesMeta("exposure time " + i + " (ms)", exposures.get(i).floatValue() * 1000);
        }

        long startDate = 0;
        if (timestamps.size() > 0) {
          startDate = DateTools.getTime(timestamps.get(0), DATE_FORMAT);
        }

        store.setImageDescription("", s);

        int image = 0;
        for (int c = 0; c < getEffectiveSizeC(); c++) {
          for (int t = 0; t < getSizeT(); t++) {
            store.setPlaneTheZ(new NonNegativeInteger(0), s, image);
            store.setPlaneTheC(new NonNegativeInteger(c), s, image);
            store.setPlaneTheT(new NonNegativeInteger(t), s, image);

            if (t < timestamps.size()) {
              String stamp = timestamps.get(t);
              long ms = DateTools.getTime(stamp, DATE_FORMAT);
              store.setPlaneDeltaT((ms - startDate) / 1000.0, s, image);
            }
            if (image < exposures.size()) {
              store.setPlaneExposureTime(exposures.get(image), s, image);
            }

            if (s < stageX.size()) {
              store.setPlanePositionX(stageX.get(s), s, image);
            }
            if (s < stageY.size()) {
              store.setPlanePositionY(stageY.get(s), s, image);
            }
            image++;
          }
        }

        store.setImagingEnvironmentTemperature(handler.getTemperature(), s);
        store.setPixelsPhysicalSizeX(new PositiveFloat(handler.getPixelSizeX()), s);
        store.setPixelsPhysicalSizeY(new PositiveFloat(handler.getPixelSizeY()), s);

        for (int c = 0; c < getEffectiveSizeC(); c++) {
          if (uniqueChannels.size() > c) {
            store.setChannelName(uniqueChannels.get(c), s, c);
          } else store.setChannelName(handler.getChannelName(), s, c);
        }
      }
    }
  }
Esempio n. 8
0
  /* @see loci.formats.FormatReader#initFile(String) */
  protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    core[0].littleEndian = true;
    in.order(isLittleEndian());

    String comment = null;

    MetadataLevel level = getMetadataOptions().getMetadataLevel();
    if (level != MetadataLevel.MINIMUM) {
      in.seek(49);
      comment = in.readString(33);
    }

    in.seek(211);
    int year = in.readInt();
    int month = in.readInt();
    int day = in.readInt();
    int hour = in.readInt();
    int min = in.readInt();
    String date = year + "-" + month + "-" + day + "T" + hour + ":" + min;
    date = DateTools.formatDate(date, "yyyy-MM-dd'T'HH:mm");

    in.skipBytes(8);

    double xSize = in.readInt() / 100d;
    double ySize = in.readInt() / 100d;
    double zSize = in.readInt() / 100d;

    core[0].sizeX = in.readInt();
    core[0].sizeY = in.readInt();

    if (level != MetadataLevel.MINIMUM) {
      double tunnelCurrent = in.readInt() / 1000d;
      double sampleVolts = in.readInt() / 1000d;

      in.skipBytes(180);

      int originalZMax = in.readInt();
      int originalZMin = in.readInt();
      int zMax = in.readInt();
      int zMin = in.readInt();

      addGlobalMeta("Comment", comment);
      addGlobalMeta("X size (in um)", xSize);
      addGlobalMeta("Y size (in um)", ySize);
      addGlobalMeta("Z size (in um)", zSize);
      addGlobalMeta("Tunnel current (in amps)", tunnelCurrent);
      addGlobalMeta("Sample volts", sampleVolts);
      addGlobalMeta("Acquisition date", date);
    }

    core[0].pixelType = FormatTools.INT16;
    core[0].sizeC = 1;
    core[0].sizeZ = 1;
    core[0].sizeT = 1;
    core[0].imageCount = 1;
    core[0].dimensionOrder = "XYZCT";
    core[0].rgb = false;

    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);

    if (date != null) {
      store.setImageAcquisitionDate(new Timestamp(date), 0);
    }

    if (level != MetadataLevel.MINIMUM) {
      store.setImageDescription(comment, 0);
      if (xSize > 0) {
        store.setPixelsPhysicalSizeX(new PositiveFloat((double) xSize / getSizeX()), 0);
      } else {
        LOGGER.warn(
            "Expected positive value for PhysicalSizeX; got {}", (double) xSize / getSizeX());
      }
      if (ySize > 0) {
        store.setPixelsPhysicalSizeY(new PositiveFloat((double) ySize / getSizeY()), 0);
      } else {
        LOGGER.warn(
            "Expected positive value for PhysicalSizeY; got {}", (double) ySize / getSizeY());
      }
    }
  }
Esempio n. 9
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  /* @see BaseTiffReader#initMetadataStore() */
  @Override
  protected void initMetadataStore() throws FormatException {
    super.initMetadataStore();
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);

    if (date != null) {
      date = DateTools.formatDate(date, DATE_FORMAT);
      if (date != null) {
        store.setImageAcquisitionDate(new Timestamp(date), 0);
      }
    }

    if (imageName != null) {
      store.setImageName(imageName, 0);
    }

    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
      if (imageDescription != null) {
        store.setImageDescription(imageDescription, 0);
      }
      if (userName != null) {
        store.setExperimenterID(MetadataTools.createLSID("Experimenter", 0), 0);
        store.setExperimenterLastName(userName, 0);
      }
      if (microscopeModel != null) {
        String instrument = MetadataTools.createLSID("Instrument", 0);
        store.setInstrumentID(instrument, 0);
        store.setImageInstrumentRef(instrument, 0);
        store.setMicroscopeModel(microscopeModel, 0);
      }
      if (detectors != null && detectors.size() > 0) {
        String instrument = MetadataTools.createLSID("Instrument", 0);
        store.setInstrumentID(instrument, 0);
        store.setImageInstrumentRef(instrument, 0);

        for (int i = 0; i < detectors.size(); i++) {
          String detectorID = MetadataTools.createLSID("Detector", 0, i);
          store.setDetectorID(detectorID, 0, i);
          store.setDetectorModel(detectors.get(i), 0, i);
          store.setDetectorType(getDetectorType("Other"), 0, i);
        }
      }
      if (magnification != null) {
        store.setObjectiveID(MetadataTools.createLSID("Objective", 0, 0), 0, 0);
        store.setObjectiveNominalMagnification(magnification, 0, 0);
        store.setObjectiveCorrection(getCorrection("Other"), 0, 0);
        store.setObjectiveImmersion(getImmersion("Other"), 0, 0);
      }

      store.setStageLabelX(stageX, 0);
      store.setStageLabelY(stageY, 0);
      store.setStageLabelZ(stageZ, 0);
      store.setStageLabelName("", 0);

      Length physicalSizeX = FormatTools.getPhysicalSizeX(sizeX);
      Length physicalSizeY = FormatTools.getPhysicalSizeY(sizeY);

      if (physicalSizeX != null) {
        store.setPixelsPhysicalSizeX(physicalSizeX, 0);
      }
      if (physicalSizeY != null) {
        store.setPixelsPhysicalSizeY(physicalSizeY, 0);
      }
      if (timeIncrement != null) {
        store.setPixelsTimeIncrement(new Time(timeIncrement, UNITS.S), 0);
      }
    }
  }