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

Example 21 with IFD

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

the class PCORAWReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    if (checkSuffix(id, "rec")) {
        paramFile = new Location(id).getAbsolutePath();
        String base = new Location(id).getAbsoluteFile().getAbsolutePath();
        base = base.substring(0, base.lastIndexOf("."));
        id = base + ".pcoraw";
        if (!new Location(id).exists()) {
            throw new FormatException("Could not find image file.");
        }
    }
    super.initFile(id);
    imageFile = new Location(id).getAbsolutePath();
    reader.close();
    reader.setMetadataStore(getMetadataStore());
    reader.setId(id);
    core = reader.getCoreMetadataList();
    metadata = reader.getGlobalMetadata();
    in = new RandomAccessInputStream(id);
    try {
        if (in.length() >= Math.pow(2, 32)) {
            // even though BigTIFF is likely being used, the offsets
            // are still recorded as though only 32 bits are available
            long add = 0;
            long prevOffset = 0;
            for (IFD ifd : reader.ifds) {
                long[] offsets = ifd.getStripOffsets();
                for (int i = 0; i < offsets.length; i++) {
                    offsets[i] += add;
                    if (offsets[i] < prevOffset) {
                        add += 0x100000000L;
                        offsets[i] += 0x100000000L;
                    }
                    prevOffset = offsets[i];
                }
                ifd.put(IFD.STRIP_OFFSETS, offsets);
            }
        }
    } finally {
        in.close();
    }
    if (paramFile == null) {
        String base = imageFile.substring(0, imageFile.lastIndexOf("."));
        base += ".rec";
        if (new Location(base).exists()) {
            paramFile = base;
        }
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, true);
    if (paramFile != null) {
        // parse extra metadata from the parameter file
        store.setInstrumentID(MetadataTools.createLSID("Instrument", 0), 0);
        String detector = MetadataTools.createLSID("Detector", 0, 0);
        store.setDetectorID(detector, 0, 0);
        String[] lines = DataTools.readFile(paramFile).split("\n");
        for (int i = 0; i < lines.length; i++) {
            String line = lines[i];
            int sep = line.indexOf(':');
            if (sep < 0) {
                continue;
            }
            String key = line.substring(0, sep).trim();
            String value = line.substring(sep + 1).trim();
            addGlobalMeta(key, value);
            if (key.equals("Exposure / Delay")) {
                // set the exposure time
                String exp = value.substring(0, value.indexOf(' '));
                Double parsedExp = new Double(exp);
                Time exposure = null;
                if (parsedExp != null) {
                    exposure = new Time(parsedExp / 1000, UNITS.SECOND);
                }
                for (int plane = 0; plane < getImageCount(); plane++) {
                    store.setPlaneExposureTime(exposure, 0, plane);
                }
            } else if (key.equals("Camera serial number")) {
                // set the serial number
                store.setDetectorSerialNumber(value, 0, 0);
            } else if (key.equals("Binning horz./vert.")) {
                store.setDetectorSettingsID(detector, 0, 0);
                value = value.charAt(1) + value;
                value = value.substring(0, 3);
                store.setDetectorSettingsBinning(getBinning(value), 0, 0);
            } else if (key.equals("Comment")) {
                final StringBuilder description = new StringBuilder();
                for (int j = i + 1; j < lines.length; j++) {
                    lines[j] = lines[j].trim();
                    if (lines[j].length() > 0) {
                        description.append(lines[j]);
                        description.append(" ");
                    }
                }
                store.setImageDescription(description.toString().trim(), 0);
                break;
            }
        }
    }
}

Example 22 with IFD

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

the class PhotoshopTiffReader method isThisType.

// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
    TiffParser tp = new TiffParser(stream);
    tp.setDoCaching(false);
    IFD ifd = tp.getFirstIFD();
    if (ifd == null)
        return false;
    return ifd.containsKey(IMAGE_SOURCE_DATA);
}

Example 23 with IFD

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

the class PrairieReader method isThisType.

@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
    final int blockLen = (int) Math.min(1048608, stream.length());
    if (!FormatTools.validStream(stream, blockLen, false))
        return false;
    String s = stream.readString(blockLen);
    if (s.indexOf("xml") != -1 && s.indexOf("PV") != -1)
        return true;
    TiffParser tp = new TiffParser(stream);
    IFD ifd = tp.getFirstIFD();
    if (ifd == null)
        return false;
    String software = null;
    try {
        software = ifd.getIFDStringValue(IFD.SOFTWARE);
    } catch (FormatException exc) {
        // no software tag, or tag is wrong type
        return false;
    }
    if (software == null)
        return false;
    // not Prairie software
    if (software.indexOf("Prairie") < 0)
        return false;
    return ifd.containsKey(new Integer(PRAIRIE_TAG_1)) && ifd.containsKey(new Integer(PRAIRIE_TAG_2)) && ifd.containsKey(new Integer(PRAIRIE_TAG_3));
}

Example 24 with IFD

use of loci.formats.tiff.IFD 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 25 with IFD

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

the class IPWReader method getOptimalTileWidth.

/* @see loci.formats.IFormatReader#getOptimalTileWidth() */
@Override
public int getOptimalTileWidth() {
    FormatTools.assertId(currentId, true, 1);
    try {
        RandomAccessInputStream stream = poi.getDocumentStream(imageFiles.get(0));
        TiffParser tp = new TiffParser(stream);
        IFD ifd = tp.getFirstIFD();
        stream.close();
        return (int) ifd.getTileWidth();
    } catch (FormatException e) {
        LOGGER.debug("Could not retrieve tile width", e);
    } catch (IOException e) {
        LOGGER.debug("Could not retrieve tile height", e);
    }
    return super.getOptimalTileWidth();
}