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

Example 26 with CoreMetadata

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

the class OxfordInstrumentsReader 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 = true;
    in.order(isLittleEndian());
    in.seek(48);
    String comment = in.readString(32);
    String dateTime = readDate();
    in.skipBytes(8);
    double xSize = -in.readFloat() + in.readFloat();
    in.skipBytes(20);
    double ySize = -in.readFloat() + in.readFloat();
    in.skipBytes(24);
    double zMin = in.readFloat();
    double zMax = in.readFloat();
    in.skipBytes(864);
    m.sizeX = in.readInt();
    m.sizeY = in.readInt();
    in.skipBytes(28);
    if (getSizeX() == 0 && getSizeY() == 0) {
        m.sizeX = in.readInt();
        m.sizeY = in.readInt();
        in.skipBytes(196);
    } else
        in.skipBytes(204);
    m.pixelType = FormatTools.UINT16;
    m.sizeZ = 1;
    m.sizeC = 1;
    m.sizeT = 1;
    m.imageCount = 1;
    m.rgb = false;
    m.indexed = false;
    m.dimensionOrder = "XYZCT";
    m.interleaved = false;
    if (FormatTools.getPlaneSize(this) + in.getFilePointer() > in.length()) {
        m.sizeY = 1;
    }
    int lutSize = in.readInt();
    in.skipBytes(lutSize);
    headerSize = in.getFilePointer();
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        in.skipBytes(FormatTools.getPlaneSize(this));
        int nMetadataStrings = in.readInt();
        for (int i = 0; i < nMetadataStrings; i++) {
            int length = in.readInt();
            String s = in.readString(length);
            if (s.indexOf(':') != -1) {
                String key = s.substring(0, s.indexOf(':')).trim();
                String value = s.substring(s.indexOf(':') + 1).trim();
                if (!value.equals("-")) {
                    addGlobalMeta(key, value);
                }
            }
        }
        addGlobalMeta("Description", comment);
        addGlobalMeta("Acquisition date", dateTime);
        addGlobalMeta("X size (um)", xSize);
        addGlobalMeta("Y size (um)", ySize);
        addGlobalMeta("Z minimum (um)", zMin);
        addGlobalMeta("Z maximum (um)", zMax);
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    store.setImageDescription(comment, 0);
    if (dateTime != null) {
        store.setImageAcquisitionDate(new Timestamp(dateTime), 0);
    }
    double physicalSizeX = xSize / getSizeX();
    double physicalSizeY = ySize / getSizeY();
    Length sizeX = FormatTools.getPhysicalSizeX(physicalSizeX);
    Length sizeY = FormatTools.getPhysicalSizeY(physicalSizeY);
    if (sizeX != null) {
        store.setPixelsPhysicalSizeX(sizeX, 0);
    }
    if (sizeY != null) {
        store.setPixelsPhysicalSizeY(sizeY, 0);
    }
}

Example 27 with CoreMetadata

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

the class LeicaHandler method endElement.

// -- DefaultHandler API methods --
@Override
public void endElement(String uri, String localName, String qName) {
    if (!nameStack.isEmpty() && nameStack.peek().equals(qName))
        nameStack.pop();
    if (qName.equals("ImageDescription")) {
        CoreMetadata coreMeta = core.get(numDatasets);
        if (numChannels == 0)
            numChannels = 1;
        coreMeta.sizeC = numChannels;
        if (extras > 1) {
            if (coreMeta.sizeZ == 1)
                coreMeta.sizeZ = extras;
            else {
                if (coreMeta.sizeT == 0)
                    coreMeta.sizeT = extras;
                else
                    coreMeta.sizeT *= extras;
            }
        }
        if (coreMeta.sizeX == 0 && coreMeta.sizeY == 0) {
            if (numDatasets > 0)
                numDatasets--;
        } else {
            if (coreMeta.sizeX == 0)
                coreMeta.sizeX = 1;
            if (coreMeta.sizeZ == 0)
                coreMeta.sizeZ = 1;
            if (coreMeta.sizeT == 0)
                coreMeta.sizeT = 1;
            coreMeta.orderCertain = true;
            coreMeta.metadataComplete = true;
            coreMeta.littleEndian = true;
            coreMeta.interleaved = coreMeta.rgb;
            coreMeta.imageCount = coreMeta.sizeZ * coreMeta.sizeT;
            if (!coreMeta.rgb)
                coreMeta.imageCount *= coreMeta.sizeC;
            coreMeta.indexed = !coreMeta.rgb;
            coreMeta.falseColor = true;
            Integer[] bytes = bytesPerAxis.keySet().toArray(new Integer[0]);
            Arrays.sort(bytes);
            coreMeta.dimensionOrder = "XY";
            for (Integer nBytes : bytes) {
                String axis = bytesPerAxis.get(nBytes);
                if (coreMeta.dimensionOrder.indexOf(axis) == -1) {
                    coreMeta.dimensionOrder += axis;
                }
            }
            String[] axes = new String[] { "Z", "C", "T" };
            for (String axis : axes) {
                if (coreMeta.dimensionOrder.indexOf(axis) == -1) {
                    coreMeta.dimensionOrder += axis;
                }
            }
            core.set(numDatasets, coreMeta);
        }
        if (level != MetadataLevel.MINIMUM) {
            int nChannels = coreMeta.rgb ? 0 : numChannels;
            for (int c = 0; c < nChannels; c++) {
                store.setChannelPinholeSize(new Length(pinhole, UNITS.MICROMETER), numDatasets, c);
            }
            for (int i = 0; i < xPos.size(); i++) {
                int pos = i + 1;
                globalMetadata.put("X position for position #" + pos, xPos.get(i));
                globalMetadata.put("Y position for position #" + pos, yPos.get(i));
                globalMetadata.put("Z position for position #" + pos, zPos.get(i));
                for (int image = 0; image < coreMeta.imageCount; image++) {
                    store.setPlanePositionX(xPos.get(i), numDatasets, image);
                    store.setPlanePositionY(yPos.get(i), numDatasets, image);
                    store.setPlanePositionZ(zPos.get(i), numDatasets, image);
                }
            }
            for (int c = 0; c < nChannels; c++) {
                int index = c < detectorIndices.size() ? detectorIndices.get(c).intValue() : detectorIndices.size() - 1;
                if (index < 0 || index >= nChannels || index >= 0)
                    break;
                String id = MetadataTools.createLSID("Detector", numDatasets, index);
                store.setDetectorSettingsID(id, numDatasets, c);
            }
            String[] keys = channels.keySet().toArray(new String[0]);
            Arrays.sort(keys);
            for (int c = 0; c < keys.length; c++) {
                Channel ch = channels.get(keys[c]);
                store.setDetectorSettingsID(ch.detector, numDatasets, c);
                store.setChannelExcitationWavelength(ch.exWave, numDatasets, c);
                store.setChannelName(ch.name, numDatasets, c);
                store.setDetectorSettingsGain(ch.gain, numDatasets, c);
            }
        }
        channels.clear();
        xPos.clear();
        yPos.clear();
        zPos.clear();
        detectorIndices.clear();
    } else if (qName.equals("Element") && level != MetadataLevel.MINIMUM) {
        multiBands.clear();
        nextROI = 0;
        if (numDatasets >= 0) {
            int nChannels = core.get(numDatasets).rgb ? 1 : numChannels;
            for (int c = 0; c < detectorIndices.size(); c++) {
                int index = detectorIndices.get(c).intValue();
                if (c >= nChannels || index >= nChannels || index >= 0)
                    break;
                String id = MetadataTools.createLSID("Detector", numDatasets, index);
                store.setDetectorSettingsID(id, numDatasets, index);
            }
            for (int c = 0; c < nChannels; c++) {
                store.setChannelPinholeSize(new Length(pinhole, UNITS.MICROMETER), numDatasets, c);
            }
        }
    } else if (qName.equals("Image")) {
        nextChannel = 0;
    } else if (qName.equals("LDM_Block_Sequential_Master")) {
        canParse = true;
    } else if (qName.equals("Annotation") && level != MetadataLevel.MINIMUM) {
        roi.storeROI(store, numDatasets, nextROI++);
    }
}

Example 28 with CoreMetadata

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

the class LeicaSCNReader method initStandardMetadata.

/* @see loci.formats.BaseTiffReader#initStandardMetadata() */
@Override
protected void initStandardMetadata() throws FormatException, IOException {
    super.initStandardMetadata();
    // Otherwise getComment() doesn't return the comment.
    tiffParser.setDoCaching(true);
    String imageDescription = tiffParser.getComment();
    handler = new LeicaSCNHandler();
    if (imageDescription != null) {
        try {
            // parse the XML description
            XMLTools.parseXML(imageDescription, handler);
        } catch (Exception se) {
            throw new FormatException("Failed to parse XML", se);
        }
    }
    int count = handler.count();
    ifds = tiffParser.getIFDs();
    if (ifds.size() < count) {
        count = ifds.size();
    }
    core.clear();
    int resolution = 0;
    int parent = 0;
    for (int i = 0; i < count; i++) {
        if (resolution == 0) {
            parent = i;
        }
        CoreMetadata ms = new CoreMetadata();
        core.add(ms);
        tiffParser.fillInIFD(ifds.get(handler.IFDMap.get(i)));
        initCoreMetadata(i, resolution);
        resolution++;
        if (resolution == core.get(parent).resolutionCount) {
            resolution = 0;
        }
    }
}

Example 29 with CoreMetadata

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

the class LeicaSCNReader method initMetadataStore.

/* @see loci.formats.BaseTiffReader#initMetadataStore() */
@Override
protected void initMetadataStore() throws FormatException {
    super.initMetadataStore();
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, true);
    HashMap<String, Integer> instrumentIDs = new HashMap<String, Integer>();
    int instrumentidno = 0;
    HashMap<String, String> objectives = new HashMap<String, String>();
    int objectiveidno = 0;
    int parent = 0;
    for (int s = 0; s < getSeriesCount(); s++) {
        int coreIndex = seriesToCoreIndex(s);
        ImageCollection c = handler.collection;
        Image i = handler.imageMap.get(coreIndex);
        int subresolution = coreIndex - parent;
        if (!hasFlattenedResolutions()) {
            subresolution = 0;
        }
        if (core.get(s).resolutionCount > 1) {
            parent = s;
        } else if (core.get(parent).resolutionCount - 1 == subresolution) {
            parent = s + 1;
        }
        Dimension dimension = i.pixels.lookupDimension(0, 0, subresolution);
        if (dimension == null) {
            throw new FormatException("No dimension information for subresolution=" + subresolution);
        }
        // Leica units are nanometres; convert to µm
        double sizeX = i.vSizeX / 1000.0;
        double sizeY = i.vSizeY / 1000.0;
        final Length offsetX = new Length(i.vOffsetX, UNITS.REFERENCEFRAME);
        final Length offsetY = new Length(i.vOffsetY, UNITS.REFERENCEFRAME);
        double sizeZ = i.vSpacingZ / 1000.0;
        store.setPixelsPhysicalSizeX(FormatTools.getPhysicalSizeX(sizeX / dimension.sizeX), s);
        store.setPixelsPhysicalSizeY(FormatTools.getPhysicalSizeY(sizeY / dimension.sizeY), s);
        store.setPixelsPhysicalSizeZ(FormatTools.getPhysicalSizeZ(sizeZ), s);
        if (instrumentIDs.get(i.devModel) == null) {
            String instrumentID = MetadataTools.createLSID("Instrument", instrumentidno);
            instrumentIDs.put(i.devModel, instrumentidno);
            store.setInstrumentID(instrumentID, instrumentidno);
            instrumentidno++;
        }
        int inst = instrumentIDs.get(i.devModel);
        String objectiveName = i.devModel + ":" + i.objMag;
        if (objectives.get(objectiveName) == null) {
            String objectiveID = MetadataTools.createLSID("Objective", inst, objectiveidno);
            objectives.put(objectiveName, objectiveID);
            store.setObjectiveID(objectiveID, inst, objectiveidno);
            Double mag = Double.parseDouble(i.objMag);
            store.setObjectiveNominalMagnification(mag, inst, objectiveidno);
            store.setObjectiveCalibratedMagnification(mag, inst, objectiveidno);
            store.setObjectiveLensNA(new Double(i.illumNA), inst, objectiveidno);
            objectiveidno++;
        }
        store.setImageInstrumentRef(MetadataTools.createLSID("Instrument", inst), s);
        store.setObjectiveSettingsID(objectives.get(objectiveName), s);
        // TODO: Only "brightfield" has been seen in example files
        if (i.illumSource.equals("brightfield")) {
            store.setChannelIlluminationType(IlluminationType.TRANSMITTED, s, 0);
        } else {
            store.setChannelIlluminationType(IlluminationType.OTHER, s, 0);
            LOGGER.debug("Unknown illumination source {}", i.illumSource);
        }
        CoreMetadata ms = core.get(s);
        for (int q = 0; q < ms.imageCount; q++) {
            store.setPlanePositionX(offsetX, s, q);
            store.setPlanePositionY(offsetY, s, q);
        }
        store.setImageName(i.name + " (R" + subresolution + ")", s);
        store.setImageDescription("Collection " + c.name, s);
        store.setImageAcquisitionDate(new Timestamp(i.creationDate), s);
        // Original metadata...
        addSeriesMeta("collection.name", c.name);
        addSeriesMeta("collection.uuid", c.uuid);
        addSeriesMeta("collection.barcode", c.barcode);
        addSeriesMeta("collection.ocr", c.ocr);
        addSeriesMeta("creationDate", i.creationDate);
        addSeriesMeta("device.model for image", i.devModel);
        addSeriesMeta("device.version for image", i.devVersion);
        addSeriesMeta("view.sizeX for image", i.vSizeX);
        addSeriesMeta("view.sizeY for image", i.vSizeY);
        addSeriesMeta("view.offsetX for image", i.vOffsetX);
        addSeriesMeta("view.offsetY for image", i.vOffsetY);
        addSeriesMeta("view.spacingZ for image", i.vSpacingZ);
        addSeriesMeta("scanSettings.objectiveSettings.objective for image", i.objMag);
        addSeriesMeta("scanSettings.illuminationSettings.numericalAperture for image", i.illumNA);
        addSeriesMeta("scanSettings.illuminationSettings.illuminationSource for image", i.illumSource);
    }
}

Example 30 with CoreMetadata

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

the class MIASReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    if (checkSuffix(id, "txt")) {
        // first need to find a relevant TIFF file
        Location base = new Location(id).getAbsoluteFile();
        Location plate = null;
        if (base.getParentFile().getName().equals("Batchresults")) {
            Location experiment = base.getParentFile().getParentFile();
            String[] plates = experiment.list(true);
            Arrays.sort(plates);
            plate = new Location(experiment, plates[0]);
        } else {
            plate = base.getParentFile();
            if (plate.getName().equals("results"))
                plate = plate.getParentFile();
        }
        String[] list = plate.list(true);
        for (String f : list) {
            if (f.startsWith("Well")) {
                Location well = new Location(plate, f);
                String[] wellList = well.list(true);
                for (String file : wellList) {
                    String path = new Location(well, file).getAbsolutePath();
                    if (isThisType(path) && checkSuffix(path, new String[] { "tif", "tiff" })) {
                        initFile(path);
                        return;
                    }
                }
            }
        }
        throw new FormatException("Could not locate an appropriate TIFF file.");
    }
    if (!isGroupFiles()) {
        tiffs = new String[][] { { id } };
        readers = new MinimalTiffReader[1][1];
        readers[0][0] = new MinimalTiffReader();
        TiffReader r = new TiffReader();
        r.setMetadataStore(getMetadataStore());
        r.setId(tiffs[0][0]);
        core = new ArrayList<CoreMetadata>(r.getCoreMetadataList());
        metadataStore = r.getMetadataStore();
        final Map<String, Object> globalMetadata = r.getGlobalMetadata();
        for (final Map.Entry<String, Object> entry : globalMetadata.entrySet()) {
            addGlobalMeta(entry.getKey(), entry.getValue());
        }
        r.close();
        tileRows = 1;
        tileCols = 1;
        return;
    }
    analysisFiles = new ArrayList<AnalysisFile>();
    // MIAS is a high content screening format which supports multiple plates,
    // wells and fields.
    // Most of the metadata comes from the directory hierarchy, as very little
    // metadata is present in the actual files.
    // 
    // The directory hierarchy is either:
    // 
    // <experiment name>                        top level experiment directory
    // Batchresults                           analysis results for experiment
    // <plate number>_<plate barcode>         one directory for each plate
    // results                              analysis results for plate
    // Well<xxxx>                           one directory for each well
    // mode<x>_z<xxx>_t<xxx>_im<x>_<x>.tif
    // 
    // or:
    // 
    // <experiment name>                        top level experiment directory
    // <plate number>                         plate directory (3 digits)
    // <well number>                        well directory (4 digits)
    // <channel number>                   channel directory (1 digit)
    // <tile row>_<tile col>_<Z>_<T>.tif
    // 
    // Each TIFF file contains a single grayscale plane.  The "mode" block
    // refers to the channel number; the "z" and "t" blocks refer to the
    // Z section and timepoint, respectively.  The "im<x>_<x>" block gives
    // the row and column coordinates of the image within a mosaic.
    // 
    // We are initially given one of these TIFF files; from there, we need
    // to find the top level experiment directory and work our way down to
    // determine how many plates and wells are present.
    LOGGER.info("Building list of TIFF files");
    Location baseFile = new Location(id).getAbsoluteFile();
    Location plate = baseFile.getParentFile().getParentFile();
    String plateName = plate.getName();
    if (!(plateName.length() == 3 || (plateName.length() > 3 && plateName.replaceAll("\\d", "").startsWith("-")))) {
        plate = plate.getParentFile();
        plateName = plate.getName();
    }
    int plateNumber = Integer.parseInt(plateName.substring(0, 3));
    Location experiment = plate.getParentFile();
    String[] directories = experiment.list(true);
    Arrays.sort(directories);
    for (String dir : directories) {
        Location f = new Location(experiment, dir);
        if (dir.equals("Batchresults")) {
            String[] results = f.list(true);
            for (String result : results) {
                Location file = new Location(f, result);
                if (result.startsWith("NEO_Results")) {
                    resultFile = file.getAbsolutePath();
                    AnalysisFile af = new AnalysisFile();
                    af.filename = resultFile;
                    analysisFiles.add(af);
                } else if (result.startsWith("NEO_PlateOutput_")) {
                    int plateIndex = Integer.parseInt(result.substring(16, 19));
                    if (plateIndex == plateNumber) {
                        AnalysisFile af = new AnalysisFile();
                        af.filename = file.getAbsolutePath();
                        af.plate = 0;
                        analysisFiles.add(af);
                    }
                }
            }
        }
    }
    String[] list = plate.list(true);
    Arrays.sort(list);
    final List<String> wellDirectories = new ArrayList<String>();
    for (String dir : list) {
        Location f = new Location(plate, dir);
        if (f.getName().startsWith("Well") || f.getName().length() == 4) {
            // directory name is valid, but we need to make sure that the
            // directory contains a TIFF or a subdirectory
            String[] wellList = f.list(true);
            if (wellList != null) {
                boolean validWell = false;
                for (String potentialTIFF : wellList) {
                    if (potentialTIFF.toLowerCase().endsWith(".tif") || new Location(f, potentialTIFF).isDirectory()) {
                        validWell = true;
                        break;
                    }
                }
                if (validWell)
                    wellDirectories.add(f.getAbsolutePath());
            }
        } else if (f.getName().equals("results")) {
            String[] resultsList = f.list(true);
            for (String result : resultsList) {
                // exclude proprietary program state files
                if (!result.endsWith(".sav") && !result.endsWith(".dsv") && !result.endsWith(".dat")) {
                    Location r = new Location(f, result);
                    AnalysisFile af = new AnalysisFile();
                    af.filename = r.getAbsolutePath();
                    af.plate = 0;
                    if (result.toLowerCase().startsWith("well")) {
                        af.well = Integer.parseInt(result.substring(4, 8)) - 1;
                    }
                    analysisFiles.add(af);
                }
            }
        } else if (f.getName().equals("Nugenesistemplate.txt")) {
            templateFile = f.getAbsolutePath();
        }
    }
    int nWells = wellDirectories.size();
    LOGGER.debug("Found {} wells.", nWells);
    readers = new MinimalTiffReader[nWells][];
    tiffs = new String[nWells][];
    int[] zCount = new int[nWells];
    int[] cCount = new int[nWells];
    int[] tCount = new int[nWells];
    String[] order = new String[nWells];
    wellNumber = new int[nWells];
    String[] wells = wellDirectories.toArray(new String[nWells]);
    Arrays.sort(wells);
    for (int j = 0; j < nWells; j++) {
        Location well = new Location(wells[j]);
        String wellName = well.getName().replaceAll("Well", "");
        wellNumber[j] = Integer.parseInt(wellName) - 1;
        String[] tiffFiles = well.list(true);
        final List<String> tmpFiles = new ArrayList<String>();
        for (String tiff : tiffFiles) {
            String name = tiff.toLowerCase();
            if (name.endsWith(".tif") || name.endsWith(".tiff")) {
                tmpFiles.add(new Location(well, tiff).getAbsolutePath());
            }
        }
        if (tmpFiles.size() == 0) {
            LOGGER.debug("No TIFFs in well directory {}", wells[j]);
            // directories which contain the TIFFs
            for (String dir : tiffFiles) {
                Location file = new Location(well, dir);
                if (dir.length() == 1 && file.isDirectory()) {
                    cCount[j]++;
                    String[] tiffs = file.list(true);
                    for (String tiff : tiffs) {
                        String name = tiff.toLowerCase();
                        if (name.endsWith(".tif") || name.endsWith(".tiff")) {
                            tmpFiles.add(new Location(file, tiff).getAbsolutePath());
                        }
                    }
                }
            }
        }
        tiffFiles = tmpFiles.toArray(new String[0]);
        if (ArrayUtils.isEmpty(tiffFiles)) {
            throw new FormatException("Empty dataset - No tiff files were found.");
        }
        Location firstTiff = new Location(tiffFiles[0]);
        List<String> names = new ArrayList<String>();
        for (Location f : firstTiff.getParentFile().listFiles()) {
            names.add(f.getName());
        }
        FilePattern fp = new FilePattern(FilePattern.findPattern(firstTiff.getName(), null, names.toArray(new String[names.size()])));
        String[] blocks = fp.getPrefixes();
        order[j] = "XY";
        int[] count = fp.getCount();
        for (int block = blocks.length - 1; block >= 0; block--) {
            blocks[block] = blocks[block].toLowerCase();
            blocks[block] = blocks[block].substring(blocks[block].lastIndexOf("_") + 1);
            if (blocks[block].equals("z")) {
                zCount[j] = count[block];
                order[j] += 'Z';
            } else if (blocks[block].equals("t")) {
                tCount[j] = count[block];
                order[j] += 'T';
            } else if (blocks[block].equals("mode")) {
                cCount[j] = count[block];
                order[j] += 'C';
            } else if (blocks[block].equals("im"))
                tileRows = count[block];
            else if (blocks[block].equals(""))
                tileCols = count[block];
            else if (blocks[block].replaceAll("\\d", "").length() == 0) {
                if (block == 3)
                    tileRows = count[block];
                else if (block == 2)
                    tileCols = count[block];
                else if (block == 0) {
                    zCount[j] = count[block];
                    order[j] += 'Z';
                } else if (block == 1) {
                    tCount[j] = count[block];
                    order[j] += 'T';
                }
            } else {
                throw new FormatException("Unsupported block '" + blocks[block]);
            }
        }
        Arrays.sort(tiffFiles);
        tiffs[j] = tiffFiles;
        LOGGER.debug("Well {} has {} files.", j, tiffFiles.length);
        readers[j] = new MinimalTiffReader[tiffFiles.length];
        for (int k = 0; k < tiffFiles.length; k++) {
            readers[j][k] = new MinimalTiffReader();
        }
    }
    // Populate core metadata
    LOGGER.info("Populating core metadata");
    int nSeries = tiffs.length;
    bpp = new int[nSeries];
    if (readers.length == 0) {
        throw new FormatException("No wells were found.");
    }
    // assume that all wells have the same width, height, and pixel type
    readers[0][0].setId(tiffs[0][0]);
    tileWidth = readers[0][0].getSizeX();
    tileHeight = readers[0][0].getSizeY();
    if (tileCols == 0)
        tileCols = 1;
    if (tileRows == 0)
        tileRows = 1;
    core.clear();
    for (int i = 0; i < nSeries; i++) {
        CoreMetadata ms = new CoreMetadata();
        core.add(ms);
        ms.sizeZ = zCount[i];
        ms.sizeC = cCount[i];
        ms.sizeT = tCount[i];
        if (ms.sizeZ == 0)
            ms.sizeZ = 1;
        if (ms.sizeC == 0)
            ms.sizeC = 1;
        if (ms.sizeT == 0)
            ms.sizeT = 1;
        ms.sizeX = tileWidth * tileCols;
        ms.sizeY = tileHeight * tileRows;
        ms.pixelType = readers[0][0].getPixelType();
        ms.sizeC *= readers[0][0].getSizeC();
        ms.rgb = readers[0][0].isRGB();
        ms.littleEndian = readers[0][0].isLittleEndian();
        ms.interleaved = readers[0][0].isInterleaved();
        ms.indexed = readers[0][0].isIndexed();
        ms.falseColor = readers[0][0].isFalseColor();
        ms.dimensionOrder = order[i];
        if (ms.dimensionOrder.indexOf('Z') == -1) {
            ms.dimensionOrder += 'Z';
        }
        if (ms.dimensionOrder.indexOf('C') == -1) {
            ms.dimensionOrder += 'C';
        }
        if (ms.dimensionOrder.indexOf('T') == -1) {
            ms.dimensionOrder += 'T';
        }
        ms.imageCount = ms.sizeZ * ms.sizeT * cCount[i];
        if (ms.imageCount == 0) {
            ms.imageCount = 1;
        }
        bpp[i] = FormatTools.getBytesPerPixel(ms.pixelType);
    }
    // Populate metadata hashtable
    LOGGER.info("Populating metadata hashtable");
    if (resultFile != null && getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        String[] cols = null;
        final List<String> rows = new ArrayList<String>();
        boolean doKeyValue = true;
        int nStarLines = 0;
        String analysisResults = DataTools.readFile(resultFile);
        String[] lines = analysisResults.split("\n");
        for (String line : lines) {
            line = line.trim();
            if (line.length() == 0)
                continue;
            if (line.startsWith("******") && line.endsWith("******"))
                nStarLines++;
            if (doKeyValue) {
                String[] n = line.split("\t");
                if (n[0].endsWith(":"))
                    n[0] = n[0].substring(0, n[0].length() - 1);
                if (n.length >= 2)
                    addGlobalMeta(n[0], n[1]);
            } else {
                if (cols == null)
                    cols = line.split("\t");
                else
                    rows.add(line);
            }
            if (nStarLines == 2)
                doKeyValue = false;
        }
        for (String row : rows) {
            String[] d = row.split("\t");
            for (int col = 3; col < cols.length; col++) {
                addGlobalMeta("Plate " + d[0] + ", Well " + d[2] + " " + cols[col], d[col]);
                if (cols[col].equals("AreaCode")) {
                    String wellID = d[col].replaceAll("\\D", "");
                    wellColumns = Integer.parseInt(wellID);
                }
            }
        }
    }
    // Populate MetadataStore
    LOGGER.info("Populating MetadataStore");
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, true);
    // assume that a 96 well plate is 8x12, and a 384 well plate is 16x24
    if (wellColumns == 0) {
        if (nWells == 96) {
            wellColumns = 12;
        } else if (nWells == 384) {
            wellColumns = 24;
        } else {
            LOGGER.warn("Could not determine the plate dimensions.");
            wellColumns = 24;
        }
    }
    store.setPlateID(MetadataTools.createLSID("Plate", 0), 0);
    String plateAcqId = MetadataTools.createLSID("PlateAcquisition", 0, 0);
    store.setPlateAcquisitionID(plateAcqId, 0, 0);
    store.setPlateAcquisitionMaximumFieldCount(new PositiveInteger(1), 0, 0);
    for (int well = 0; well < nWells; well++) {
        int wellIndex = wellNumber[well];
        int row = wellIndex / wellColumns;
        int wellCol = (wellIndex % wellColumns) + 1;
        char wellRow = (char) ('A' + row);
        store.setWellID(MetadataTools.createLSID("Well", 0, well), 0, well);
        store.setWellRow(new NonNegativeInteger(row), 0, well);
        store.setWellColumn(new NonNegativeInteger(wellCol - 1), 0, well);
        String imageID = MetadataTools.createLSID("Image", well);
        String wellSampleID = MetadataTools.createLSID("WellSample", 0, well, 0);
        store.setWellSampleID(wellSampleID, 0, well, 0);
        store.setWellSampleIndex(new NonNegativeInteger(well), 0, well, 0);
        store.setImageID(imageID, well);
        store.setImageName("Well " + wellRow + wellCol, well);
        store.setWellSampleImageRef(imageID, 0, well, 0);
        store.setPlateAcquisitionWellSampleRef(wellSampleID, 0, 0, well);
    }
    MetadataLevel level = getMetadataOptions().getMetadataLevel();
    if (level != MetadataLevel.MINIMUM) {
        String experimentID = MetadataTools.createLSID("Experiment", 0);
        store.setExperimentID(experimentID, 0);
        store.setExperimentType(getExperimentType("Other"), 0);
        store.setExperimentDescription(experiment.getName(), 0);
        // populate SPW metadata
        store.setPlateColumnNamingConvention(getNamingConvention("Number"), 0);
        store.setPlateRowNamingConvention(getNamingConvention("Letter"), 0);
        parseTemplateFile(store);
        plateName = plateName.substring(plateName.indexOf('-') + 1);
        store.setPlateName(plateName, 0);
        store.setPlateExternalIdentifier(plateName, 0);
        for (int well = 0; well < nWells; well++) {
            // populate Image/Pixels metadata
            store.setImageExperimentRef(experimentID, well);
            String instrumentID = MetadataTools.createLSID("Instrument", 0);
            store.setInstrumentID(instrumentID, 0);
            store.setImageInstrumentRef(instrumentID, well);
        }
        roiFiles = new ArrayList<AnalysisFile>();
        for (AnalysisFile af : analysisFiles) {
            String file = af.filename;
            String name = new Location(file).getName();
            if (!name.startsWith("Well"))
                continue;
            if (name.endsWith("AllModesOverlay.tif")) {
                roiFiles.add(af);
            } else if (name.endsWith("overlay.tif")) {
                roiFiles.add(af);
            }
        }
        if (level != MetadataLevel.NO_OVERLAYS) {
            // populate image-level ROIs
            Color[] colors = new Color[getSizeC()];
            int nextROI = 0;
            for (AnalysisFile af : analysisFiles) {
                String file = af.filename;
                String name = new Location(file).getName();
                if (!name.startsWith("Well"))
                    continue;
                int[] position = getPositionFromFile(file);
                int well = position[0];
                if (name.endsWith("detail.txt")) {
                    String data = DataTools.readFile(file);
                    String[] lines = data.split("\n");
                    int start = 0;
                    while (start < lines.length && !lines[start].startsWith("Label")) {
                        start++;
                    }
                    if (start >= lines.length)
                        continue;
                    String[] columns = lines[start].split("\t");
                    List<String> columnNames = Arrays.asList(columns);
                    for (int j = start + 1; j < lines.length; j++) {
                        populateROI(columnNames, lines[j].split("\t"), well, nextROI++, position[1], position[2], store);
                    }
                } else if (name.endsWith("AllModesOverlay.tif")) {
                    // results/Well<nnnn>_mode<n>_z<nnn>_t<nnn>_AllModesOverlay.tif
                    if (colors[position[3]] != null)
                        continue;
                    try {
                        colors[position[3]] = getChannelColorFromFile(file);
                    } catch (IOException e) {
                    }
                    if (colors[position[3]] == null)
                        continue;
                    for (int s = 0; s < getSeriesCount(); s++) {
                        store.setChannelColor(colors[position[3]], s, position[3]);
                    }
                    if (position[3] == 0) {
                        nextROI += parseMasks(store, well, nextROI, file);
                    }
                } else if (name.endsWith("overlay.tif")) {
                    nextROI += parseMasks(store, well, nextROI, file);
                }
            }
        }
    }
}