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

Example 86 with TiffParser

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

the class NikonTiffReader method isThisType.

// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
    TiffParser tp = new TiffParser(stream);
    IFD ifd = tp.getFirstIFD();
    if (ifd == null)
        return false;
    String software = ifd.getIFDTextValue(IFD.SOFTWARE);
    return software != null && software.toString().indexOf("EZ-C1") != -1;
}

Example 87 with TiffParser

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

the class OperettaReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    if (!checkSuffix(id, "xml")) {
        Location parent = new Location(id).getAbsoluteFile().getParentFile();
        Location xml = new Location(parent, XML_FILE);
        if (!xml.exists()) {
            throw new FormatException("Could not find XML file " + xml.getAbsolutePath());
        }
        initFile(xml.getAbsolutePath());
        return;
    } else {
        super.initFile(id);
    }
    // parse plate layout and image dimensions from the XML file
    String xmlData = DataTools.readFile(id);
    OperettaHandler handler = new OperettaHandler();
    XMLTools.parseXML(xmlData, handler);
    // sort the list of images by well and field indices
    ArrayList<Plane> planeList = handler.getPlanes();
    ArrayList<Integer> uniqueRows = new ArrayList<Integer>();
    ArrayList<Integer> uniqueCols = new ArrayList<Integer>();
    ArrayList<Integer> uniqueFields = new ArrayList<Integer>();
    ArrayList<Integer> uniqueZs = new ArrayList<Integer>();
    ArrayList<Integer> uniqueTs = new ArrayList<Integer>();
    ArrayList<Integer> uniqueCs = new ArrayList<Integer>();
    for (Plane p : planeList) {
        if (!uniqueRows.contains(p.row)) {
            uniqueRows.add(p.row);
        }
        if (!uniqueCols.contains(p.col)) {
            uniqueCols.add(p.col);
        }
        if (!uniqueFields.contains(p.field)) {
            uniqueFields.add(p.field);
        }
        if (!uniqueZs.contains(p.z)) {
            uniqueZs.add(p.z);
        }
        if (!uniqueCs.contains(p.c)) {
            uniqueCs.add(p.c);
        }
        if (!uniqueTs.contains(p.t)) {
            uniqueTs.add(p.t);
        }
    }
    Integer[] rows = uniqueRows.toArray(new Integer[uniqueRows.size()]);
    Integer[] cols = uniqueCols.toArray(new Integer[uniqueCols.size()]);
    Integer[] fields = uniqueFields.toArray(new Integer[uniqueFields.size()]);
    Integer[] zs = uniqueZs.toArray(new Integer[uniqueZs.size()]);
    Integer[] cs = uniqueCs.toArray(new Integer[uniqueCs.size()]);
    Integer[] ts = uniqueTs.toArray(new Integer[uniqueTs.size()]);
    Arrays.sort(rows);
    Arrays.sort(cols);
    Arrays.sort(fields);
    Arrays.sort(zs);
    Arrays.sort(ts);
    Arrays.sort(cs);
    int seriesCount = rows.length * cols.length * fields.length;
    core.clear();
    planes = new Plane[seriesCount][zs.length * cs.length * ts.length];
    int nextSeries = 0;
    for (int row = 0; row < rows.length; row++) {
        for (int col = 0; col < cols.length; col++) {
            for (int field = 0; field < fields.length; field++) {
                int nextPlane = 0;
                for (int t = 0; t < ts.length; t++) {
                    for (int z = 0; z < zs.length; z++) {
                        for (int c = 0; c < cs.length; c++) {
                            for (Plane p : planeList) {
                                if (p.row == rows[row] && p.col == cols[col] && p.field == fields[field] && p.t == ts[t] && p.z == zs[z] && p.c == cs[c]) {
                                    planes[nextSeries][nextPlane] = p;
                                    break;
                                }
                            }
                            nextPlane++;
                        }
                    }
                }
                nextSeries++;
            }
        }
    }
    reader = new MinimalTiffReader();
    for (int i = 0; i < seriesCount; i++) {
        CoreMetadata ms = new CoreMetadata();
        core.add(ms);
        ms.sizeZ = uniqueZs.size();
        ms.sizeC = uniqueCs.size();
        ms.sizeT = uniqueTs.size();
        ms.dimensionOrder = "XYCZT";
        ms.rgb = false;
        ms.imageCount = getSizeZ() * getSizeC() * getSizeT();
        int planeIndex = 0;
        while (planeIndex < planes[i].length && planes[i][planeIndex] == null) {
            LOGGER.debug("skipping null plane series = {}, plane = {}", i, planeIndex);
            planeIndex++;
        }
        if (planeIndex >= planes[i].length) {
            if (i > 0) {
                ms.sizeX = core.get(i - 1).sizeX;
                ms.sizeY = core.get(i - 1).sizeY;
                ms.pixelType = core.get(i - 1).pixelType;
                ms.littleEndian = core.get(i - 1).littleEndian;
            } else {
                LOGGER.warn("Could not find valid plane for series 0");
            }
        } else {
            ms.sizeX = planes[i][planeIndex].x;
            ms.sizeY = planes[i][planeIndex].y;
            String filename = planes[i][planeIndex].filename;
            while ((filename == null || !new Location(filename).exists()) && planeIndex < planes[i].length - 1) {
                LOGGER.debug("Missing TIFF file: {}", filename);
                planeIndex++;
                filename = planes[i][planeIndex].filename;
            }
            if (filename != null && new Location(filename).exists()) {
                RandomAccessInputStream s = new RandomAccessInputStream(filename, 16);
                TiffParser parser = new TiffParser(s);
                parser.setDoCaching(false);
                IFD firstIFD = parser.getFirstIFD();
                ms.littleEndian = firstIFD.isLittleEndian();
                ms.pixelType = firstIFD.getPixelType();
                s.close();
            } else if (i > 0) {
                LOGGER.warn("Could not find valid TIFF file for series {}", i);
                ms.littleEndian = core.get(0).littleEndian;
                ms.pixelType = core.get(0).pixelType;
            } else {
                LOGGER.warn("Could not find valid TIFF file for series 0; pixel type may be wrong");
            }
        }
    }
    addGlobalMeta("Plate name", handler.getPlateName());
    addGlobalMeta("Plate description", handler.getPlateDescription());
    addGlobalMeta("Plate ID", handler.getPlateIdentifier());
    addGlobalMeta("Measurement ID", handler.getMeasurementID());
    // populate the MetadataStore
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, true);
    String instrument = MetadataTools.createLSID("Instrument", 0);
    store.setInstrumentID(instrument, 0);
    String objective = MetadataTools.createLSID("Objective", 0, 0);
    store.setObjectiveID(objective, 0, 0);
    if (planes[0][0] != null) {
        store.setObjectiveNominalMagnification(planes[0][0].magnification, 0, 0);
        store.setObjectiveLensNA(planes[0][0].lensNA, 0, 0);
    }
    store.setPlateID(MetadataTools.createLSID("Plate", 0), 0);
    store.setPlateRows(new PositiveInteger(handler.getPlateRows()), 0);
    store.setPlateColumns(new PositiveInteger(handler.getPlateColumns()), 0);
    String plateAcqID = MetadataTools.createLSID("PlateAcquisition", 0, 0);
    store.setPlateAcquisitionID(plateAcqID, 0, 0);
    PositiveInteger fieldCount = FormatTools.getMaxFieldCount(fields.length);
    if (fieldCount != null) {
        store.setPlateAcquisitionMaximumFieldCount(fieldCount, 0, 0);
    }
    for (int row = 0; row < rows.length; row++) {
        for (int col = 0; col < cols.length; col++) {
            int well = row * cols.length + col;
            store.setWellID(MetadataTools.createLSID("Well", 0, well), 0, well);
            store.setWellRow(new NonNegativeInteger(rows[row]), 0, well);
            store.setWellColumn(new NonNegativeInteger(cols[col]), 0, well);
            for (int field = 0; field < fields.length; field++) {
                int imageIndex = well * fields.length + field;
                String wellSampleID = MetadataTools.createLSID("WellSample", 0, well, field);
                store.setWellSampleID(wellSampleID, 0, well, field);
                store.setWellSampleIndex(new NonNegativeInteger(imageIndex), 0, well, field);
                String imageID = MetadataTools.createLSID("Image", imageIndex);
                store.setImageID(imageID, imageIndex);
                store.setWellSampleImageRef(imageID, 0, well, field);
                store.setImageInstrumentRef(instrument, imageIndex);
                store.setObjectiveSettingsID(objective, imageIndex);
                String name = "Well " + (well + 1) + ", Field " + (field + 1);
                store.setImageName(name, imageIndex);
                store.setPlateAcquisitionWellSampleRef(wellSampleID, 0, 0, imageIndex);
                if (planes[imageIndex][0] != null && planes[imageIndex][0].absoluteTime != null) {
                    store.setImageAcquisitionDate(planes[imageIndex][0].absoluteTime, imageIndex);
                }
            }
        }
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        store.setPlateName(handler.getPlateName(), 0);
        store.setPlateDescription(handler.getPlateDescription(), 0);
        store.setPlateExternalIdentifier(handler.getPlateIdentifier(), 0);
        String experimenterID = MetadataTools.createLSID("Experimenter", 0);
        store.setExperimenterID(experimenterID, 0);
        store.setExperimenterLastName(handler.getExperimenterName(), 0);
        for (int i = 0; i < getSeriesCount(); i++) {
            store.setImageExperimenterRef(experimenterID, i);
            for (int c = 0; c < getSizeC(); c++) {
                if (planes[i][c] != null && planes[i][c].channelName != null) {
                    store.setChannelName(planes[i][c].channelName, i, c);
                }
                if (planes[i][c] != null) {
                    store.setChannelEmissionWavelength(FormatTools.getEmissionWavelength(planes[i][c].emWavelength), i, c);
                    store.setChannelExcitationWavelength(FormatTools.getExcitationWavelength(planes[i][c].exWavelength), i, c);
                }
            }
            if (planes[i][0] != null) {
                store.setPixelsPhysicalSizeX(FormatTools.getPhysicalSizeX(planes[i][0].resolutionX), i);
                store.setPixelsPhysicalSizeY(FormatTools.getPhysicalSizeY(planes[i][0].resolutionY), i);
            }
            for (int p = 0; p < getImageCount(); p++) {
                if (planes[i][p] != null) {
                    store.setPlanePositionX(planes[i][p].positionX, i, p);
                    store.setPlanePositionY(planes[i][p].positionY, i, p);
                    store.setPlanePositionZ(planes[i][p].positionZ, i, p);
                    store.setPlaneExposureTime(planes[i][p].exposureTime, i, p);
                    store.setPlaneDeltaT(planes[i][p].deltaT, i, p);
                }
            }
        }
    }
}

Example 88 with TiffParser

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

the class PCIReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    imageFiles = new HashMap<Integer, String>();
    timestamps = new HashMap<Integer, Double>();
    uniqueZ = new ArrayList<Double>();
    CoreMetadata m = core.get(0);
    initPOIService();
    double scaleFactor = 1;
    final List<String> allFiles = poi.getDocumentList();
    if (allFiles.isEmpty()) {
        throw new FormatException("No files were found - the .cxd may be corrupt.");
    }
    double firstZ = 0d, secondZ = 0d;
    int mode = 0;
    for (String name : allFiles) {
        int separator = name.lastIndexOf(File.separator);
        String parent = name.substring(0, separator);
        String relativePath = name.substring(separator + 1);
        RandomAccessInputStream stream = null;
        if (!(relativePath.startsWith("Bitmap") || (relativePath.equals("Data") && parent.indexOf("Image") != -1))) {
            stream = poi.getDocumentStream(name);
            stream.order(true);
        }
        if (stream != null && stream.length() == 8) {
            double value = stream.readDouble();
            stream.seek(0);
            String key = name.replace(File.separatorChar, ' ');
            key = key.replaceAll("Root Entry ", "");
            key = key.replaceAll("Field Data ", "");
            key = key.replaceAll("Details ", "");
            addGlobalMeta(key, value);
        }
        if (relativePath.equals("Field Count")) {
            m.imageCount = stream.readInt();
        } else if (relativePath.equals("File Has Image")) {
            if (stream.readShort() == 0) {
                throw new FormatException("This file does not contain image data.");
            }
        } else if (relativePath.startsWith("Bitmap") || (relativePath.equals("Data") && parent.indexOf("Image") != -1)) {
            imageFiles.put(imageFiles.size(), name);
            if (getSizeX() != 0 && getSizeY() != 0) {
                int bpp = FormatTools.getBytesPerPixel(getPixelType());
                int plane = getSizeX() * getSizeY() * bpp;
                if (getSizeC() == 0 || getSizeC() * plane > poi.getFileSize(name)) {
                    m.sizeC = poi.getFileSize(name) / plane;
                }
            }
        } else if (relativePath.indexOf("Image_Depth") != -1) {
            boolean firstBits = m.bitsPerPixel == 0;
            int bits = (int) stream.readDouble();
            m.bitsPerPixel = bits;
            while (bits % 8 != 0 || bits == 0) bits++;
            if (bits % 3 == 0) {
                m.sizeC = 3;
                bits /= 3;
                m.bitsPerPixel /= 3;
            }
            bits /= 8;
            m.pixelType = FormatTools.pixelTypeFromBytes(bits, false, false);
            if (getSizeC() > 1 && firstBits) {
                m.sizeC /= bits;
            }
        } else if (relativePath.indexOf("Image_Height") != -1 && getSizeY() == 0) {
            m.sizeY = (int) stream.readDouble();
        } else if (relativePath.indexOf("Image_Width") != -1 && getSizeX() == 0) {
            m.sizeX = (int) stream.readDouble();
        } else if (relativePath.indexOf("Time_From_Start") != -1) {
            timestamps.put(getTimestampIndex(parent), stream.readDouble());
        } else if (relativePath.indexOf("Position_Z") != -1) {
            double zPos = stream.readDouble();
            if (!uniqueZ.contains(zPos) && getSizeZ() <= 1) {
                uniqueZ.add(zPos);
            }
            if (name.indexOf("Field 1" + File.separator) != -1)
                firstZ = zPos;
            else if (name.indexOf("Field 2" + File.separator) != -1)
                secondZ = zPos;
        } else if (relativePath.equals("First Field Date & Time")) {
            long date = (long) stream.readDouble() * 1000;
            creationDate = DateTools.convertDate(date, DateTools.COBOL);
        } else if (relativePath.equals("GroupMode")) {
            mode = stream.readInt();
        } else if (relativePath.equals("GroupSelectedFields")) {
            m.sizeZ = (int) (stream.length() / 8);
        } else if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
            if (relativePath.equals("Binning")) {
                binning = (int) stream.readDouble();
            } else if (relativePath.equals("Comments")) {
                String comments = stream.readString((int) stream.length());
                String[] lines = comments.split("\n");
                for (String line : lines) {
                    int eq = line.indexOf('=');
                    if (eq != -1) {
                        String key = line.substring(0, eq).trim();
                        String value = line.substring(eq + 1).trim();
                        addGlobalMeta(key, value);
                        if (key.equals("factor")) {
                            if (value.indexOf(';') != -1) {
                                value = value.substring(0, value.indexOf(';'));
                            }
                            scaleFactor = Double.parseDouble(value.trim());
                        }
                    }
                }
            }
        }
        if (stream != null) {
            stream.close();
        }
    }
    boolean zFirst = Math.abs(firstZ - secondZ) > Constants.EPSILON;
    if (getSizeC() == 0)
        m.sizeC = 1;
    if (mode == 0) {
        m.sizeZ = 0;
    }
    if (getSizeZ() <= 1 || (getImageCount() % getSizeZ()) != 0) {
        m.sizeZ = uniqueZ.isEmpty() ? 1 : uniqueZ.size();
    }
    m.sizeT = getImageCount() / getSizeZ();
    while (getSizeZ() * getSizeT() < getImageCount()) {
        m.sizeZ++;
        m.sizeT = getImageCount() / getSizeZ();
    }
    m.rgb = getSizeC() > 1;
    if (imageFiles.size() > getImageCount() && getSizeC() == 1) {
        m.sizeC = imageFiles.size() / getImageCount();
        m.imageCount *= getSizeC();
    } else {
        m.imageCount = getSizeZ() * getSizeT();
    }
    m.interleaved = false;
    m.dimensionOrder = zFirst ? "XYCZT" : "XYCTZ";
    m.littleEndian = true;
    m.indexed = false;
    m.falseColor = false;
    m.metadataComplete = true;
    // re-index image files
    String[] files = imageFiles.values().toArray(new String[imageFiles.size()]);
    for (String file : files) {
        int separator = file.lastIndexOf(File.separator);
        String parent = file.substring(0, separator);
        imageFiles.put(getImageIndex(parent), file);
    }
    int bpp = FormatTools.getBytesPerPixel(m.pixelType);
    int expectedPlaneSize = m.sizeX * m.sizeY * bpp * m.sizeC;
    String file = imageFiles.get(0);
    RandomAccessInputStream s = poi.getDocumentStream(file);
    TiffParser tp = new TiffParser(s);
    // don't correct the image width if it's stored as a TIFF
    if (!tp.isValidHeader() && s.length() > expectedPlaneSize) {
        m.sizeX += (s.length() - expectedPlaneSize) / (m.sizeY * bpp * m.sizeC);
    }
    s.close();
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, true);
    if (creationDate != null) {
        store.setImageAcquisitionDate(new Timestamp(creationDate), 0);
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        Length sizeX = FormatTools.getPhysicalSizeX(scaleFactor);
        Length sizeY = FormatTools.getPhysicalSizeY(scaleFactor);
        if (sizeX != null) {
            store.setPixelsPhysicalSizeX(sizeX, 0);
        }
        if (sizeY != null) {
            store.setPixelsPhysicalSizeY(sizeY, 0);
        }
        for (int i = 0; i < timestamps.size(); i++) {
            if (i >= getImageCount()) {
                break;
            }
            Double timestamp = timestamps.get(i);
            if (timestamp != null) {
                store.setPlaneDeltaT(new Time(timestamp, UNITS.SECOND), 0, i);
            }
            if (i == 2) {
                Double first = timestamps.get(1);
                Double increment = timestamp - first;
                if (increment != null) {
                    store.setPixelsTimeIncrement(new Time(increment, UNITS.SECOND), 0);
                }
            }
        }
        if (binning > 0) {
            String instrumentID = MetadataTools.createLSID("Instrument", 0);
            String detectorID = MetadataTools.createLSID("Detector", 0);
            store.setInstrumentID(instrumentID, 0);
            store.setDetectorID(detectorID, 0, 0);
            store.setDetectorType(getDetectorType("Other"), 0, 0);
            store.setImageInstrumentRef(instrumentID, 0);
            Binning binningEnum = getBinning(binning + "x" + binning);
            for (int c = 0; c < getEffectiveSizeC(); c++) {
                store.setDetectorSettingsID(detectorID, 0, c);
                store.setDetectorSettingsBinning(binningEnum, 0, c);
            }
        }
    }
}

Example 89 with TiffParser

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

the class PyramidTiffReader method isThisType.

// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
    TiffParser parser = new TiffParser(stream);
    parser.setAssumeEqualStrips(equalStrips);
    IFD ifd = parser.getFirstIFD();
    if (ifd == null)
        return false;
    String software = ifd.getIFDTextValue(IFD.SOFTWARE);
    if (software == null)
        return false;
    return software.indexOf("Faas") >= 0;
}

Example 90 with TiffParser

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

the class LeicaSCNReader method isThisType.

// -- IFormatReader API methods --
/* (non-Javadoc)
   * @see loci.formats.FormatReader#isThisType(java.lang.String, boolean)
   */
@Override
public boolean isThisType(String name, boolean open) {
    if (super.isThisType(name, open) && open) {
        RandomAccessInputStream stream = null;
        try {
            stream = new RandomAccessInputStream(name);
            TiffParser tiffParser = new TiffParser(stream);
            if (!tiffParser.isValidHeader()) {
                return false;
            }
            String imageDescription = tiffParser.getComment();
            if (imageDescription != null) {
                try {
                    // Test if XML is valid SCN metadata
                    LeicaSCNHandler handler = new LeicaSCNHandler();
                    XMLTools.parseXML(imageDescription, handler);
                    return true;
                } catch (Exception se) {
                    LOGGER.debug("XML parsing failed", se);
                }
            }
        } catch (IOException e) {
            LOGGER.debug("I/O exception during isThisType() evaluation.", e);
        } finally {
            try {
                if (stream != null) {
                    stream.close();
                }
            } catch (IOException e) {
                LOGGER.debug("I/O exception during stream closure.", e);
            }
        }
    }
    return false;
}