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

Example 91 with IFD

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

the class IonpathMIBITiffReader method initStandardMetadata.

// -- Internal BaseTiffReader API methods --
/* @see loci.formats.BaseTiffReader#initStandardMetadata() */
@Override
protected void initStandardMetadata() throws FormatException, IOException {
    super.initStandardMetadata();
    ifds = tiffParser.getIFDs();
    int seriesIndex;
    String imageType = null;
    core.clear();
    for (int i = 0; i < ifds.size(); i++) {
        IFD ifd = ifds.get(i);
        Object description = ifd.get(IFD.IMAGE_DESCRIPTION);
        if (description == null) {
            throw new FormatException("Image description is mandatory.");
        }
        String imageDescription = null;
        if (description instanceof TiffIFDEntry) {
            Object value = tiffParser.getIFDValue((TiffIFDEntry) description);
            if (value != null) {
                imageDescription = value.toString();
            }
        } else if (description instanceof String) {
            imageDescription = (String) description;
        }
        JSONObject jsonDescription;
        try {
            jsonDescription = new JSONObject(imageDescription);
            imageType = jsonDescription.getString("image.type");
            if (imageType.equals("SIMS")) {
                String mass = jsonDescription.getString("channel.mass");
                if (mass == null) {
                    throw new FormatException("Channel masses are mandatory.");
                }
                String target = jsonDescription.getString("channel.target");
                channelIDs.add(mass);
                channelNames.add(target != null && target != "null" ? target : mass);
            }
        } catch (JSONException e) {
            throw new FormatException("Unexpected format in SIMS description JSON.");
        }
        if (seriesTypes.containsKey(imageType)) {
            if (!imageType.equals("SIMS")) {
                throw new FormatException("Only type 'SIMS' can have >1 image per file.");
            }
            seriesIndex = seriesTypes.get(imageType);
            CoreMetadata ms = core.get(seriesIndex);
            ms.sizeC += 1;
            ms.imageCount += 1;
        } else {
            seriesIndex = seriesTypes.size();
            seriesTypes.put(imageType, seriesIndex);
            seriesIFDs.add(i);
            core.add(new CoreMetadata());
            setSeries(seriesIndex);
            tiffParser.setDoCaching(true);
            tiffParser.fillInIFD(ifd);
            if (imageType.equals("SIMS")) {
                try {
                    Iterator<?> keySet = jsonDescription.keys();
                    while (keySet.hasNext()) {
                        String key = (String) keySet.next();
                        if (key.startsWith("mibi.")) {
                            simsDescription.put(key, jsonDescription.getString(key));
                        }
                    }
                } catch (JSONException e) {
                    throw new FormatException("Unexpected format in SIMS description JSON.");
                }
            }
            CoreMetadata ms = core.get(seriesIndex);
            PhotoInterp p = ifd.getPhotometricInterpretation();
            int samples = ifd.getSamplesPerPixel();
            ms.rgb = samples > 1 || p == PhotoInterp.RGB;
            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 = false;
            ms.imageCount = 1;
            if (imageType.equals("SIMS")) {
                ms.seriesMetadata = simsDescription;
            }
        }
    }
}

Example 92 with IFD

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

the class IonpathMIBITiffReader method isThisType.

// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
    TiffParser tiffParser = new TiffParser(stream);
    IFD ifd = tiffParser.getFirstIFD();
    if (ifd == null)
        return false;
    String software = ifd.getIFDTextValue(IFD.SOFTWARE);
    if (software == null)
        return false;
    return software.startsWith(IONPATH_MIBI_SOFTWARE_PREFIX);
}

Example 93 with IFD

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

the class FlexReader method getOptimalTileWidth.

/* @see loci.formats.IFormatReader#getOptimalTileWidth() */
@Override
public int getOptimalTileWidth() {
    FormatTools.assertId(currentId, true, 1);
    FlexFile file = lookupFile(0);
    IFD ifd = file.ifds.get(0);
    try {
        return (int) ifd.getTileWidth();
    } catch (FormatException e) {
        LOGGER.debug("Could not retrieve tile width", e);
    }
    return super.getOptimalTileWidth();
}

Example 94 with IFD

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

the class FlexReader method openBytes.

/**
 * @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
 */
@Override
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, IOException {
    FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
    FlexFile firstFile = lookupFile(0);
    FlexFile file = lookupFile(getSeries());
    int[] lengths = new int[] { fieldCount / effectiveFieldCount, wellCount, plateCount };
    int[] pos = FormatTools.rasterToPosition(lengths, getSeries());
    int imageNumber = file.offsets == null ? getImageCount() * pos[0] + no : 0;
    RandomAccessInputStream s = new RandomAccessInputStream(getFileHandle(file.file));
    IFD ifd;
    double factor;
    if (file.offsets == null) {
        ifd = file.ifds.get(imageNumber);
        factor = 1d;
    } else {
        // Only the first IFD was read. Hack the IFD to adjust the offset.
        final IFD firstIFD = firstFile.ifds.get(0);
        ifd = new IFD(firstIFD);
        int tag = IFD.STRIP_OFFSETS;
        if (firstIFD.isTiled() && firstIFD.getIFDLongArray(IFD.TILE_OFFSETS) != null) {
            tag = IFD.TILE_OFFSETS;
        }
        long[] offsets = ifd.getIFDLongArray(tag);
        final int planeSize = getSizeX() * getSizeY() * getRGBChannelCount() * ifd.getBitsPerSample()[0] / 8;
        final int index = getImageCount() * pos[0] + no;
        long offset = (index == file.offsets.length - 1 ? s.length() : file.offsets[index + 1]) - offsets[0] - planeSize;
        for (int i = 0; i < offsets.length; i++) {
            offsets[i] += offset;
        }
        ifd.putIFDValue(tag, offsets);
    }
    int nBytes = ifd.getBitsPerSample()[0] / 8;
    int bpp = FormatTools.getBytesPerPixel(getPixelType());
    // read pixels from the file
    TiffParser tp = new TiffParser(s);
    tp.fillInIFD(ifd);
    // log the first offset used
    LOGGER.trace("first offset for series={} no={}: {}", getCoreIndex(), no, ifd.getStripOffsets()[0]);
    tp.getSamples(ifd, buf, x, y, w, h);
    factor = file.factors == null ? 1d : file.factors[imageNumber];
    LOGGER.trace("  using factor = {}", factor);
    tp.getStream().close();
    // expand pixel values with multiplication by factor[no]
    int num = buf.length / bpp;
    if (factor != 1d || nBytes != bpp) {
        for (int i = num - 1; i >= 0; i--) {
            int q = nBytes == 1 ? buf[i] & 0xff : DataTools.bytesToInt(buf, i * nBytes, nBytes, isLittleEndian());
            q = (int) (q * factor);
            DataTools.unpackBytes(q, buf, i * bpp, bpp, isLittleEndian());
        }
    }
    s.close();
    return buf;
}

Example 95 with IFD

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

the class FlexReader method populateCoreMetadata.

/**
 * Populate core metadata using the given list of image names.
 */
private void populateCoreMetadata(int wellRow, int wellCol, int field, List<String> imageNames) throws FormatException {
    LOGGER.info("Populating core metadata for well row " + wellRow + ", column " + wellCol);
    CoreMetadata ms0 = core.get(0);
    if (getSizeC() == 0 && getSizeT() == 0) {
        if (fieldCount == 0 || (imageNames.size() % fieldCount) != 0) {
            fieldCount = 1;
        }
        final List<String> uniqueChannels = new ArrayList<String>();
        for (int i = 0; i < imageNames.size(); i++) {
            String name = imageNames.get(i);
            String[] tokens = name.split("_");
            if (tokens.length > 1) {
                // fields are indexed from 1
                int fieldIndex = Integer.parseInt(tokens[0]);
                if (fieldIndex > fieldCount)
                    fieldCount = fieldIndex;
            } else
                tokens = name.split(":");
            String channel = tokens[tokens.length - 1];
            if (!uniqueChannels.contains(channel))
                uniqueChannels.add(channel);
        }
        if (fieldCount == 0)
            fieldCount = 1;
        ms0.sizeC = (int) Math.max(uniqueChannels.size(), 1);
        if (getSizeZ() == 0)
            ms0.sizeZ = 1;
        ms0.sizeT = imageNames.size() / (fieldCount * getSizeC() * getSizeZ());
    }
    if (getSizeC() == 0) {
        ms0.sizeC = (int) Math.max(channelNames.length, 1);
    }
    if (getSizeZ() == 0)
        ms0.sizeZ = 1;
    if (getSizeT() == 0)
        ms0.sizeT = 1;
    if (plateCount == 0)
        plateCount = 1;
    if (wellCount == 0)
        wellCount = 1;
    if (fieldCount == 0)
        fieldCount = 1;
    // adjust dimensions if the number of IFDs doesn't match the number
    // of reported images
    FlexFile file = lookupFile(wellRow, wellCol, field);
    IFD ifd = file.ifds.get(0);
    int nPlanes = file.ifds.size();
    if (file.offsets != null) {
        nPlanes = file.offsets.length;
    }
    ms0.imageCount = getSizeZ() * getSizeC() * getSizeT();
    if (getImageCount() == imageNames.size()) {
        fieldCount = 1;
    }
    // otherwise assume that fields are stored within the files
    if (getImageCount() * fieldCount != nPlanes && ((getImageCount() != nPlanes && nFiles > 1) || nFiles == 1)) {
        ms0.imageCount = nPlanes / fieldCount;
        ms0.sizeZ = 1;
        ms0.sizeT = nPlanes / fieldCount;
        if (getSizeT() % getSizeC() == 0) {
            ms0.sizeT /= getSizeC();
        } else {
            ms0.sizeC = 1;
        }
    }
    ms0.sizeX = (int) ifd.getImageWidth();
    ms0.sizeY = (int) ifd.getImageLength();
    ms0.dimensionOrder = "XYCZT";
    ms0.rgb = false;
    ms0.interleaved = false;
    ms0.indexed = false;
    ms0.littleEndian = ifd.isLittleEndian();
    ms0.pixelType = ifd.getPixelType();
    if (fieldCount == 1) {
        fieldCount *= nFiles;
    }
    int seriesCount = plateCount * wellCount * fieldCount;
    if (seriesCount > 1) {
        core.clear();
        for (int i = 0; i < seriesCount; i++) {
            core.add(ms0);
        }
    }
}