Examples with PhotoInterp loci.formats.tiff.PhotoInterp used on opensource projects

Example 1 with PhotoInterp

use of loci.formats.tiff.PhotoInterp in project bioformats by openmicroscopy.

the class MetamorphReader method initStandardMetadata.

// -- Internal BaseTiffReader API methods --
/* @see BaseTiffReader#initStandardMetadata() */
@Override
protected void initStandardMetadata() throws FormatException, IOException {
    super.initStandardMetadata();
    CoreMetadata ms0 = core.get(0);
    ms0.sizeZ = 1;
    ms0.sizeT = 0;
    int rgbChannels = getSizeC();
    // Now that the base TIFF standard metadata has been parsed, we need to
    // parse out the STK metadata from the UIC4TAG.
    TiffIFDEntry uic1tagEntry = null;
    TiffIFDEntry uic2tagEntry = null;
    TiffIFDEntry uic4tagEntry = null;
    try {
        uic1tagEntry = tiffParser.getFirstIFDEntry(UIC1TAG);
        uic2tagEntry = tiffParser.getFirstIFDEntry(UIC2TAG);
        uic4tagEntry = tiffParser.getFirstIFDEntry(UIC4TAG);
    } catch (IllegalArgumentException exc) {
        LOGGER.debug("Unknown tag", exc);
    }
    try {
        if (uic4tagEntry != null) {
            mmPlanes = uic4tagEntry.getValueCount();
        }
        if (mmPlanes == 0) {
            mmPlanes = ifds.size();
        }
        if (uic2tagEntry != null) {
            parseUIC2Tags(uic2tagEntry.getValueOffset());
        }
        if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
            if (uic4tagEntry != null) {
                parseUIC4Tags(uic4tagEntry.getValueOffset());
            }
            if (uic1tagEntry != null) {
                parseUIC1Tags(uic1tagEntry.getValueOffset(), uic1tagEntry.getValueCount());
            }
        }
        in.seek(uic4tagEntry.getValueOffset());
    } catch (NullPointerException exc) {
        LOGGER.debug("", exc);
    } catch (IOException exc) {
        LOGGER.debug("Failed to parse proprietary tags", exc);
    }
    try {
        // copy ifds into a new array of Hashtables that will accommodate the
        // additional image planes
        IFD firstIFD = ifds.get(0);
        long[] uic2 = firstIFD.getIFDLongArray(UIC2TAG);
        if (uic2 == null) {
            throw new FormatException("Invalid Metamorph file. Tag " + UIC2TAG + " not found.");
        }
        ms0.imageCount = uic2.length;
        Object entry = firstIFD.getIFDValue(UIC3TAG);
        TiffRational[] uic3 = entry instanceof TiffRational[] ? (TiffRational[]) entry : new TiffRational[] { (TiffRational) entry };
        wave = new double[uic3.length];
        final List<Double> uniqueWavelengths = new ArrayList<Double>();
        for (int i = 0; i < uic3.length; i++) {
            wave[i] = uic3[i].doubleValue();
            addSeriesMeta("Wavelength [" + intFormatMax(i, mmPlanes) + "]", wave[i]);
            final Double v = wave[i];
            if (!uniqueWavelengths.contains(v))
                uniqueWavelengths.add(v);
        }
        if (getSizeC() == 1) {
            ms0.sizeC = uniqueWavelengths.size();
            if (getSizeC() < getImageCount() && getSizeC() > (getImageCount() - getSizeC()) && (getImageCount() % getSizeC()) != 0) {
                ms0.sizeC = getImageCount();
            }
        }
        IFDList tempIFDs = new IFDList();
        long[] oldOffsets = firstIFD.getStripOffsets();
        long[] stripByteCounts = firstIFD.getStripByteCounts();
        int rowsPerStrip = (int) firstIFD.getRowsPerStrip()[0];
        int stripsPerImage = getSizeY() / rowsPerStrip;
        if (stripsPerImage * rowsPerStrip != getSizeY())
            stripsPerImage++;
        PhotoInterp check = firstIFD.getPhotometricInterpretation();
        if (check == PhotoInterp.RGB_PALETTE) {
            firstIFD.putIFDValue(IFD.PHOTOMETRIC_INTERPRETATION, PhotoInterp.BLACK_IS_ZERO);
        }
        emWavelength = firstIFD.getIFDLongArray(UIC3TAG);
        // for each image plane, construct an IFD hashtable
        IFD temp;
        for (int i = 0; i < getImageCount(); i++) {
            // copy data from the first IFD
            temp = new IFD(firstIFD);
            // now we need a StripOffsets entry - the original IFD doesn't have this
            long[] newOffsets = new long[stripsPerImage];
            if (stripsPerImage * (i + 1) <= oldOffsets.length) {
                System.arraycopy(oldOffsets, stripsPerImage * i, newOffsets, 0, stripsPerImage);
            } else {
                System.arraycopy(oldOffsets, 0, newOffsets, 0, stripsPerImage);
                long image = (stripByteCounts[0] / rowsPerStrip) * getSizeY();
                for (int q = 0; q < stripsPerImage; q++) {
                    newOffsets[q] += i * image;
                }
            }
            temp.putIFDValue(IFD.STRIP_OFFSETS, newOffsets);
            long[] newByteCounts = new long[stripsPerImage];
            if (stripsPerImage * i < stripByteCounts.length) {
                System.arraycopy(stripByteCounts, stripsPerImage * i, newByteCounts, 0, stripsPerImage);
            } else {
                Arrays.fill(newByteCounts, stripByteCounts[0]);
            }
            temp.putIFDValue(IFD.STRIP_BYTE_COUNTS, newByteCounts);
            tempIFDs.add(temp);
        }
        ifds = tempIFDs;
    } catch (IllegalArgumentException exc) {
        LOGGER.debug("Unknown tag", exc);
    } catch (NullPointerException exc) {
        LOGGER.debug("", exc);
    } catch (FormatException exc) {
        LOGGER.debug("Failed to build list of IFDs", exc);
    }
    // parse (mangle) TIFF comment
    String descr = ifds.get(0).getComment();
    if (descr != null) {
        String[] lines = descr.split("\n");
        final StringBuilder sb = new StringBuilder();
        for (int i = 0; i < lines.length; i++) {
            String line = lines[i].trim();
            if (line.startsWith("<") && line.endsWith(">")) {
                // XML comment; this will have already been parsed so can be ignored
                break;
            }
            int colon = line.indexOf(':');
            if (colon < 0) {
                // normal line (not a key/value pair)
                if (line.length() > 0) {
                    // not a blank line
                    sb.append(line);
                    sb.append("  ");
                }
            } else {
                String descrValue = null;
                if (i == 0) {
                    // first line could be mangled; make a reasonable guess
                    int dot = line.lastIndexOf(".", colon);
                    if (dot >= 0) {
                        descrValue = line.substring(0, dot + 1);
                    }
                    line = line.substring(dot + 1);
                    colon -= dot + 1;
                }
                // append value to description
                if (descrValue != null) {
                    sb.append(descrValue);
                    if (!descrValue.endsWith("."))
                        sb.append(".");
                    sb.append("  ");
                }
                // add key/value pair embedded in comment as separate metadata
                String key = line.substring(0, colon);
                String value = line.substring(colon + 1).trim();
                addSeriesMeta(key, value);
                if (key.equals("Exposure")) {
                    if (value.indexOf('=') != -1) {
                        value = value.substring(value.indexOf('=') + 1).trim();
                    }
                    if (value.indexOf(' ') != -1) {
                        value = value.substring(0, value.indexOf(' '));
                    }
                    try {
                        value = value.replace(',', '.');
                        double exposure = Double.parseDouble(value);
                        exposureTime = exposure / 1000;
                    } catch (NumberFormatException e) {
                    }
                } else if (key.equals("Bit Depth")) {
                    if (value.indexOf('-') != -1) {
                        value = value.substring(0, value.indexOf('-'));
                    }
                    try {
                        ms0.bitsPerPixel = Integer.parseInt(value);
                    } catch (NumberFormatException e) {
                    }
                } else if (key.equals("Gain")) {
                    int space = value.indexOf(' ');
                    if (space != -1) {
                        int nextSpace = value.indexOf(" ", space + 1);
                        if (nextSpace < 0) {
                            nextSpace = value.length();
                        }
                        try {
                            gain = new Double(value.substring(space, nextSpace));
                        } catch (NumberFormatException e) {
                        }
                    }
                }
            }
        }
        // replace comment with trimmed version
        descr = sb.toString().trim();
        if (descr.equals(""))
            metadata.remove("Comment");
        else
            addSeriesMeta("Comment", descr);
    }
    ms0.sizeT = getImageCount() / (getSizeZ() * (getSizeC() / rgbChannels));
    if (getSizeT() * getSizeZ() * (getSizeC() / rgbChannels) != getImageCount()) {
        ms0.sizeT = 1;
        ms0.sizeZ = getImageCount() / (getSizeC() / rgbChannels);
    }
    // if '_t' is present in the file name, swap Z and T sizes
    // this file was probably part of a larger dataset, but the .nd file is
    // missing
    String filename = currentId.substring(currentId.lastIndexOf(File.separator) + 1);
    if (filename.contains("_t") && getSizeT() > 1) {
        int z = getSizeZ();
        ms0.sizeZ = getSizeT();
        ms0.sizeT = z;
    }
    if (getSizeZ() == 0)
        ms0.sizeZ = 1;
    if (getSizeT() == 0)
        ms0.sizeT = 1;
    if (getSizeZ() * getSizeT() * (isRGB() ? 1 : getSizeC()) != getImageCount()) {
        ms0.sizeZ = getImageCount();
        ms0.sizeT = 1;
        if (!isRGB())
            ms0.sizeC = 1;
    }
}

Example 2 with PhotoInterp

use of loci.formats.tiff.PhotoInterp in project bioformats by openmicroscopy.

the class NDPIReader method initStandardMetadata.

// -- Internal BaseTiffReader API methods --
/* @see loci.formats.BaseTiffReader#initStandardMetadata() */
@Override
protected void initStandardMetadata() throws FormatException, IOException {
    super.initStandardMetadata();
    ifds = tiffParser.getIFDs();
    // fix the offsets for > 4 GB files
    RandomAccessInputStream stream = new RandomAccessInputStream(currentId);
    for (int i = 0; i < ifds.size(); i++) {
        IFD ifd = ifds.get(i);
        long[] stripOffsets = ifd.getStripOffsets();
        boolean neededAdjustment = false;
        for (int j = 0; j < stripOffsets.length; j++) {
            long prevOffset = i == 0 ? 0 : ifds.get(i - 1).getStripOffsets()[0];
            long prevByteCount = i == 0 ? 0 : ifds.get(i - 1).getStripByteCounts()[0];
            long currentOffset = (int) stripOffsets[j];
            while (currentOffset < prevOffset || currentOffset < prevOffset + prevByteCount) {
                long newOffset = currentOffset + 0x100000000L;
                if (newOffset < stream.length() && ((j > 0 && (currentOffset < stripOffsets[j - 1])) || (i > 0 && currentOffset < prevOffset + prevByteCount))) {
                    stripOffsets[j] = newOffset;
                    currentOffset = stripOffsets[j];
                    neededAdjustment = true;
                }
            }
        }
        if (neededAdjustment) {
            ifd.putIFDValue(IFD.STRIP_OFFSETS, stripOffsets);
        }
        neededAdjustment = false;
        long[] stripByteCounts = ifd.getStripByteCounts();
        for (int j = 0; j < stripByteCounts.length; j++) {
            long currentCount = (int) stripByteCounts[j];
            long newByteCount = currentCount + 0x100000000L;
            if (currentCount < 0 || neededAdjustment || newByteCount + stripOffsets[j] < in.length()) {
                if (newByteCount < ifd.getImageWidth() * ifd.getImageLength()) {
                    stripByteCounts[j] = newByteCount;
                    neededAdjustment = true;
                }
            }
        }
        if (neededAdjustment) {
            ifd.putIFDValue(IFD.STRIP_BYTE_COUNTS, stripByteCounts);
        }
    }
    stream.close();
    for (int i = 1; i < ifds.size(); i++) {
        IFD ifd = ifds.get(i);
        if (ifd.getImageWidth() == ifds.get(0).getImageWidth() && ifd.getImageLength() == ifds.get(0).getImageLength()) {
            sizeZ++;
        } else if (sizeZ == 1) {
            boolean isPyramid;
            Object source_lens_value = ifd.getIFDValue(SOURCE_LENS);
            if (source_lens_value != null) {
                float source_lens = (Float) source_lens_value;
                // A value of -1 correspond to the macro image and a value of -2
                // correspond to the map image
                isPyramid = (source_lens != -1 && source_lens != -2);
            } else {
                // Assume the last IFD is the macro image
                isPyramid = i < ifds.size() - 1;
            }
            if (isPyramid)
                pyramidHeight++;
        }
    }
    // repopulate core metadata
    int seriesCount = pyramidHeight + (ifds.size() - pyramidHeight * sizeZ);
    for (int i = 0; i < ifds.size(); i++) {
        IFD ifd = ifds.get(i);
        ifd.remove(THUMB_TAG_2);
        ifds.set(i, ifd);
        TiffIFDEntry markerTag = (TiffIFDEntry) ifd.get(MARKER_TAG);
        if (markerTag != null) {
            if (markerTag.getValueOffset() > in.length()) {
                // can't rely upon the MARKER_TAG to be detected correctly
                ifds.get(i).remove(MARKER_TAG);
            } else {
                Object value = tiffParser.getIFDValue(markerTag);
                ifds.get(i).putIFDValue(MARKER_TAG, value);
            }
        }
        tiffParser.fillInIFD(ifds.get(i));
        int[] bpp = ifds.get(i).getBitsPerSample();
        for (int q = 0; q < bpp.length; q++) {
            if (bpp[q] < 8) {
                bpp[q] = 8;
            }
        }
        ifds.get(i).putIFDValue(IFD.BITS_PER_SAMPLE, bpp);
    }
    core.clear();
    for (int s = 0; s < seriesCount; s++) {
        CoreMetadata ms = new CoreMetadata();
        core.add(ms);
        if (s == 0) {
            ms.resolutionCount = pyramidHeight;
        }
    }
    for (int s = 0; s < core.size(); s++) {
        IFD ifd = ifds.get(getIFDIndex(s, 0));
        PhotoInterp p = ifd.getPhotometricInterpretation();
        int samples = ifd.getSamplesPerPixel();
        CoreMetadata ms = core.get(s);
        ms.rgb = samples > 1 || p == PhotoInterp.RGB;
        ms.sizeX = (int) ifd.getImageWidth();
        ms.sizeY = (int) ifd.getImageLength();
        ms.sizeZ = s < pyramidHeight ? 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 = ms.sizeZ * ms.sizeT;
        ms.pixelType = ifd.getPixelType();
        ms.metadataComplete = true;
        ms.interleaved = ms.sizeX > MAX_SIZE && ms.sizeY > MAX_SIZE;
        ms.falseColor = false;
        ms.dimensionOrder = "XYCZT";
        ms.thumbnail = s != 0;
    }
    String metadataTag = ifds.get(0).getIFDStringValue(METADATA_TAG);
    if (metadataTag != null) {
        String[] entries = metadataTag.split("\n");
        for (String entry : entries) {
            int eq = entry.indexOf('=');
            if (eq < 0) {
                continue;
            }
            String key = entry.substring(0, eq).trim();
            String value = entry.substring(eq + 1).trim();
            addGlobalMeta(key, value);
            if (key.equals("Objective.Lens.Magnificant")) {
                // not a typo
                magnification = new Double(value);
            } else if (key.equals("NDP.S/N")) {
                serialNumber = value;
            } else if (key.equals("Product")) {
                instrumentModel = value;
            }
        }
    }
}

Example 3 with PhotoInterp

use of loci.formats.tiff.PhotoInterp in project bioformats by openmicroscopy.

the class NikonReader method initStandardMetadata.

// -- Internal BaseTiffReader API methods --
/* @see BaseTiffReader#initStandardMetadata() */
@Override
protected void initStandardMetadata() throws FormatException, IOException {
    super.initStandardMetadata();
    // reset image dimensions
    // the actual image data is stored in IFDs referenced by the SubIFD tag
    // in the 'real' IFD
    CoreMetadata m = core.get(0);
    m.imageCount = ifds.size();
    IFD firstIFD = ifds.get(0);
    PhotoInterp photo = firstIFD.getPhotometricInterpretation();
    int samples = firstIFD.getSamplesPerPixel();
    m.rgb = samples > 1 || photo == PhotoInterp.RGB || photo == PhotoInterp.CFA_ARRAY;
    if (photo == PhotoInterp.CFA_ARRAY)
        samples = 3;
    m.sizeX = (int) firstIFD.getImageWidth();
    m.sizeY = (int) firstIFD.getImageLength();
    m.sizeZ = 1;
    m.sizeC = isRGB() ? samples : 1;
    m.sizeT = ifds.size();
    m.pixelType = firstIFD.getPixelType();
    m.indexed = false;
    // now look for the EXIF IFD pointer
    IFDList exifIFDs = tiffParser.getExifIFDs();
    if (exifIFDs.size() > 0) {
        IFD exifIFD = exifIFDs.get(0);
        tiffParser.fillInIFD(exifIFD);
        for (Integer key : exifIFD.keySet()) {
            int tag = key.intValue();
            String name = IFD.getIFDTagName(tag);
            if (tag == IFD.CFA_PATTERN) {
                byte[] cfa = (byte[]) exifIFD.get(key);
                int[] colorMap = new int[cfa.length];
                for (int i = 0; i < cfa.length; i++) colorMap[i] = (int) cfa[i];
                addGlobalMeta(name, colorMap);
                cfaPattern = colorMap;
            } else {
                addGlobalMeta(name, exifIFD.get(key));
                if (name.equals("MAKER_NOTE")) {
                    byte[] b = (byte[]) exifIFD.get(key);
                    int extra = new String(b, 0, 10, Constants.ENCODING).startsWith("Nikon") ? 10 : 0;
                    byte[] buf = new byte[b.length];
                    System.arraycopy(b, extra, buf, 0, buf.length - extra);
                    RandomAccessInputStream makerNote = new RandomAccessInputStream(buf);
                    TiffParser tp = new TiffParser(makerNote);
                    IFD note = null;
                    try {
                        note = tp.getFirstIFD();
                    } catch (Exception e) {
                        LOGGER.debug("Failed to parse first IFD", e);
                    }
                    if (note != null) {
                        for (Integer nextKey : note.keySet()) {
                            int nextTag = nextKey.intValue();
                            addGlobalMeta(name, note.get(nextKey));
                            if (nextTag == 150) {
                                b = (byte[]) note.get(nextKey);
                                RandomAccessInputStream s = new RandomAccessInputStream(b);
                                byte check1 = s.readByte();
                                byte check2 = s.readByte();
                                lossyCompression = check1 != 0x46;
                                vPredictor = new int[4];
                                for (int q = 0; q < vPredictor.length; q++) {
                                    vPredictor[q] = s.readShort();
                                }
                                curve = new int[16385];
                                int bps = ifds.get(0).getBitsPerSample()[0];
                                int max = 1 << bps & 0x7fff;
                                int step = 0;
                                int csize = s.readShort();
                                if (csize > 1) {
                                    step = max / (csize - 1);
                                }
                                if (check1 == 0x44 && check2 == 0x20 && step > 0) {
                                    for (int i = 0; i < csize; i++) {
                                        curve[i * step] = s.readShort();
                                    }
                                    for (int i = 0; i < max; i++) {
                                        int n = i % step;
                                        curve[i] = (curve[i - n] * (step - n) + curve[i - n + step] * n) / step;
                                    }
                                    s.seek(562);
                                    split = s.readShort();
                                } else {
                                    int maxValue = (int) Math.pow(2, bps) - 1;
                                    Arrays.fill(curve, maxValue);
                                    int nElements = (int) (s.length() - s.getFilePointer()) / 2;
                                    if (nElements < 100) {
                                        for (int i = 0; i < curve.length; i++) {
                                            curve[i] = (short) i;
                                        }
                                    } else {
                                        for (int q = 0; q < nElements; q++) {
                                            curve[q] = s.readShort();
                                        }
                                    }
                                }
                                s.close();
                            } else if (nextTag == WHITE_BALANCE_RGB_COEFFS) {
                                whiteBalance = (TiffRational[]) note.get(nextKey);
                            }
                        }
                    }
                    makerNote.close();
                }
            }
        }
    }
}

Example 4 with PhotoInterp

use of loci.formats.tiff.PhotoInterp in project bioformats by openmicroscopy.

the class PyramidTiffReader method initStandardMetadata.

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

Example 5 with PhotoInterp

use of loci.formats.tiff.PhotoInterp 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());
        }
    }
}