Examples with Location loci.common.Location used on opensource projects

Example 41 with Location

use of loci.common.Location in project bioformats by openmicroscopy.

the class VisitechReader method isThisType.

/* @see loci.formats.IFormatReader#isThisType(String, boolean) */
@Override
public boolean isThisType(String name, boolean open) {
    if (checkSuffix(name, "xys"))
        return true;
    // verify that there is an .xys file in the same directory
    if (name.indexOf(' ') == -1)
        return false;
    if (!open)
        return false;
    String prefix = name.substring(0, name.lastIndexOf(" "));
    Location xys = new Location(prefix + " 1.xys");
    return xys.exists();
}

Example 42 with Location

use of loci.common.Location in project bioformats by openmicroscopy.

the class ScanrReader 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 (metadataFiles.size() > 0) {
        // this dataset has already been initialized
        return;
    }
    // make sure we have the .xml file
    if (!checkSuffix(id, "xml") && isGroupFiles()) {
        Location parent = new Location(id).getAbsoluteFile().getParentFile();
        if (checkSuffix(id, "tif") && parent.getName().equalsIgnoreCase("Data")) {
            parent = parent.getParentFile();
        }
        String[] list = parent.list();
        for (String file : list) {
            if (file.equals(XML_FILE)) {
                id = new Location(parent, file).getAbsolutePath();
                super.initFile(id);
                break;
            }
        }
        if (!checkSuffix(id, "xml")) {
            throw new FormatException("Could not find " + XML_FILE + " in " + parent.getAbsolutePath());
        }
    } else if (!isGroupFiles() && checkSuffix(id, "tif")) {
        TiffReader r = new TiffReader();
        r.setMetadataStore(getMetadataStore());
        r.setId(id);
        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();
        tiffs = new String[] { id };
        reader = new MinimalTiffReader();
        return;
    }
    Location dir = new Location(id).getAbsoluteFile().getParentFile();
    String[] list = dir.list(true);
    for (String file : list) {
        Location f = new Location(dir, file);
        if (checkSuffix(file, METADATA_SUFFIXES) && !f.isDirectory()) {
            metadataFiles.add(f.getAbsolutePath());
        }
    }
    // parse XML metadata
    String xml = DataTools.readFile(id).trim();
    if (xml.startsWith("<?")) {
        xml = xml.substring(xml.indexOf("?>") + 2);
    }
    xml = "<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>" + xml;
    XMLTools.parseXML(xml, new ScanrHandler());
    final List<String> uniqueRows = new ArrayList<String>();
    final List<String> uniqueColumns = new ArrayList<String>();
    if (wellRows == 0 || wellColumns == 0) {
        for (String well : wellLabels.keySet()) {
            if (!Character.isLetter(well.charAt(0)))
                continue;
            String row = well.substring(0, 1).trim();
            String column = well.substring(1).trim();
            if (!uniqueRows.contains(row) && row.length() > 0)
                uniqueRows.add(row);
            if (!uniqueColumns.contains(column) && column.length() > 0) {
                uniqueColumns.add(column);
            }
        }
        wellRows = uniqueRows.size();
        wellColumns = uniqueColumns.size();
        if (wellRows * wellColumns != wellCount) {
            adjustWellDimensions();
        }
    }
    int nChannels = getSizeC() == 0 ? channelNames.size() : (int) Math.min(channelNames.size(), getSizeC());
    if (nChannels == 0)
        nChannels = 1;
    int nSlices = getSizeZ() == 0 ? 1 : getSizeZ();
    int nTimepoints = getSizeT();
    int nWells = wellCount;
    int nPos = 0;
    if (foundPositions)
        nPos = fieldPositionX.length;
    else
        nPos = fieldRows * fieldColumns;
    if (nPos == 0)
        nPos = 1;
    // get list of TIFF files
    Location dataDir = new Location(dir, "data");
    list = dataDir.list(true);
    if (list == null) {
        // try to find the TIFFs in the current directory
        list = dir.list(true);
    } else
        dir = dataDir;
    if (nTimepoints == 0 || list.length < nTimepoints * nChannels * nSlices * nWells * nPos) {
        nTimepoints = list.length / (nChannels * nWells * nPos * nSlices);
        if (nTimepoints == 0)
            nTimepoints = 1;
    }
    tiffs = new String[nChannels * nWells * nPos * nTimepoints * nSlices];
    Arrays.sort(list, new Comparator<String>() {

        @Override
        public int compare(String s1, String s2) {
            int lastSeparator1 = s1.lastIndexOf(File.separator) + 1;
            int lastSeparator2 = s2.lastIndexOf(File.separator) + 1;
            String dir1 = s1.substring(0, lastSeparator1);
            String dir2 = s2.substring(0, lastSeparator2);
            if (!dir1.equals(dir2)) {
                return dir1.compareTo(dir2);
            }
            int dash1 = s1.indexOf("-", lastSeparator1);
            int dash2 = s2.indexOf("-", lastSeparator2);
            String label1 = dash1 < 0 ? "" : s1.substring(lastSeparator1, dash1);
            String label2 = dash2 < 0 ? "" : s2.substring(lastSeparator2, dash2);
            if (label1.equals(label2)) {
                String remainder1 = dash1 < 0 ? s1 : s1.substring(dash1);
                String remainder2 = dash2 < 0 ? s2 : s2.substring(dash2);
                return remainder1.compareTo(remainder2);
            }
            Integer index1 = wellLabels.get(label1);
            Integer index2 = wellLabels.get(label2);
            if (index1 == null && index2 != null) {
                return 1;
            } else if (index1 != null && index2 == null) {
                return -1;
            }
            return index1.compareTo(index2);
        }
    });
    int lastListIndex = 0;
    int next = 0;
    String[] keys = wellLabels.keySet().toArray(new String[wellLabels.size()]);
    Arrays.sort(keys, new Comparator<String>() {

        @Override
        public int compare(String s1, String s2) {
            char row1 = s1.charAt(0);
            char row2 = s2.charAt(0);
            final Integer col1 = new Integer(s1.substring(1));
            final Integer col2 = new Integer(s2.substring(1));
            if (row1 < row2) {
                return -1;
            } else if (row1 > row2) {
                return 1;
            }
            return col1.compareTo(col2);
        }
    });
    int realPosCount = 0;
    for (int well = 0; well < nWells; well++) {
        int missingWellFiles = 0;
        int wellIndex = wellNumbers.get(well);
        String wellPos = getBlock(wellIndex, "W");
        int originalIndex = next;
        for (int pos = 0; pos < nPos; pos++) {
            String posPos = getBlock(pos + 1, "P");
            int posIndex = next;
            for (int z = 0; z < nSlices; z++) {
                String zPos = getBlock(z, "Z");
                for (int t = 0; t < nTimepoints; t++) {
                    String tPos = getBlock(t, "T");
                    for (int c = 0; c < nChannels; c++) {
                        for (int i = lastListIndex; i < list.length; i++) {
                            String file = list[i];
                            if (file.indexOf(wellPos) != -1 && file.indexOf(zPos) != -1 && file.indexOf(posPos) != -1 && file.indexOf(tPos) != -1 && file.indexOf(channelNames.get(c)) != -1) {
                                tiffs[next++] = new Location(dir, file).getAbsolutePath();
                                if (c == nChannels - 1) {
                                    lastListIndex = i;
                                }
                                break;
                            }
                        }
                        if (next == originalIndex) {
                            missingWellFiles++;
                        }
                    }
                }
            }
            if (posIndex != next)
                realPosCount++;
        }
        if (next == originalIndex && well < keys.length) {
            wellLabels.remove(keys[well]);
        }
        if (next == originalIndex && missingWellFiles == nSlices * nTimepoints * nChannels * nPos) {
            wellNumbers.remove(well);
        }
    }
    nWells = wellNumbers.size();
    if (wellLabels.size() > 0 && wellLabels.size() != nWells) {
        uniqueRows.clear();
        uniqueColumns.clear();
        for (String well : wellLabels.keySet()) {
            if (!Character.isLetter(well.charAt(0)))
                continue;
            String row = well.substring(0, 1).trim();
            String column = well.substring(1).trim();
            if (!uniqueRows.contains(row) && row.length() > 0)
                uniqueRows.add(row);
            if (!uniqueColumns.contains(column) && column.length() > 0) {
                uniqueColumns.add(column);
            }
        }
        nWells = uniqueRows.size() * uniqueColumns.size();
        adjustWellDimensions();
    }
    if (realPosCount < nPos) {
        nPos = realPosCount;
    }
    reader = new MinimalTiffReader();
    reader.setId(tiffs[0]);
    int sizeX = reader.getSizeX();
    int sizeY = reader.getSizeY();
    int pixelType = reader.getPixelType();
    tileWidth = reader.getOptimalTileWidth();
    tileHeight = reader.getOptimalTileHeight();
    switch(pixelType) {
        case FormatTools.INT8:
            pixelType = FormatTools.UINT8;
            break;
        case FormatTools.INT16:
            pixelType = FormatTools.UINT16;
            break;
    }
    boolean rgb = reader.isRGB();
    boolean interleaved = reader.isInterleaved();
    boolean indexed = reader.isIndexed();
    boolean littleEndian = reader.isLittleEndian();
    reader.close();
    int seriesCount = nWells * nPos;
    core.clear();
    for (int i = 0; i < seriesCount; i++) {
        CoreMetadata ms = new CoreMetadata();
        core.add(ms);
        ms.sizeC = nChannels;
        ms.sizeZ = nSlices;
        ms.sizeT = nTimepoints;
        ms.sizeX = sizeX;
        ms.sizeY = sizeY;
        ms.pixelType = pixelType;
        ms.rgb = rgb;
        ms.interleaved = interleaved;
        ms.indexed = indexed;
        ms.littleEndian = littleEndian;
        ms.dimensionOrder = "XYCTZ";
        ms.imageCount = nSlices * nTimepoints * nChannels;
        ms.bitsPerPixel = 12;
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    store.setPlateID(MetadataTools.createLSID("Plate", 0), 0);
    store.setPlateColumns(new PositiveInteger(wellColumns), 0);
    store.setPlateRows(new PositiveInteger(wellRows), 0);
    String plateAcqID = MetadataTools.createLSID("PlateAcquisition", 0, 0);
    store.setPlateAcquisitionID(plateAcqID, 0, 0);
    int nFields = 0;
    if (foundPositions) {
        nFields = fieldPositionX.length;
    } else {
        nFields = fieldRows * fieldColumns;
    }
    PositiveInteger fieldCount = FormatTools.getMaxFieldCount(nFields);
    if (fieldCount != null) {
        store.setPlateAcquisitionMaximumFieldCount(fieldCount, 0, 0);
    }
    for (int i = 0; i < getSeriesCount(); i++) {
        int field = i % nFields;
        int well = i / nFields;
        int index = well;
        while (wellNumbers.get(index) == null && index < wellNumbers.size()) {
            index++;
        }
        int wellIndex = wellNumbers.get(index) == null ? index : wellNumbers.get(index) - 1;
        int wellRow = wellIndex / wellColumns;
        int wellCol = wellIndex % wellColumns;
        if (field == 0) {
            store.setWellID(MetadataTools.createLSID("Well", 0, well), 0, well);
            store.setWellColumn(new NonNegativeInteger(wellCol), 0, well);
            store.setWellRow(new NonNegativeInteger(wellRow), 0, well);
        }
        String wellSample = MetadataTools.createLSID("WellSample", 0, well, field);
        store.setWellSampleID(wellSample, 0, well, field);
        store.setWellSampleIndex(new NonNegativeInteger(i), 0, well, field);
        String imageID = MetadataTools.createLSID("Image", i);
        store.setWellSampleImageRef(imageID, 0, well, field);
        store.setImageID(imageID, i);
        String name = "Well " + (well + 1) + ", Field " + (field + 1) + " (Spot " + (i + 1) + ")";
        store.setImageName(name, i);
        store.setPlateAcquisitionWellSampleRef(wellSample, 0, 0, i);
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        for (int i = 0; i < getSeriesCount(); i++) {
            for (int c = 0; c < getSizeC(); c++) {
                store.setChannelName(channelNames.get(c), i, c);
            }
            Length x = FormatTools.getPhysicalSizeX(pixelSize);
            Length y = FormatTools.getPhysicalSizeY(pixelSize);
            if (x != null) {
                store.setPixelsPhysicalSizeX(x, i);
            }
            if (y != null) {
                store.setPixelsPhysicalSizeY(y, i);
            }
            if (fieldPositionX != null && fieldPositionY != null) {
                int field = i % nFields;
                int well = i / nFields;
                final Length posX = fieldPositionX[field];
                final Length posY = fieldPositionY[field];
                store.setWellSamplePositionX(posX, 0, well, field);
                store.setWellSamplePositionY(posY, 0, well, field);
                for (int c = 0; c < getSizeC(); c++) {
                    int image = getIndex(0, c, 0);
                    store.setPlaneTheZ(new NonNegativeInteger(0), i, image);
                    store.setPlaneTheC(new NonNegativeInteger(c), i, image);
                    store.setPlaneTheT(new NonNegativeInteger(0), i, image);
                    store.setPlanePositionX(fieldPositionX[field], i, image);
                    store.setPlanePositionY(fieldPositionY[field], i, image);
                    // exposure time is stored in milliseconds
                    // convert to seconds before populating MetadataStore
                    Double time = exposures.get(c);
                    if (time != null) {
                        time /= 1000;
                        store.setPlaneExposureTime(new Time(time, UNITS.SECOND), i, image);
                    }
                    if (deltaT != null) {
                        store.setPlaneDeltaT(new Time(deltaT, UNITS.SECOND), i, image);
                    }
                }
            }
        }
        String row = wellRows > 26 ? "Number" : "Letter";
        String col = wellRows > 26 ? "Letter" : "Number";
        store.setPlateRowNamingConvention(getNamingConvention(row), 0);
        store.setPlateColumnNamingConvention(getNamingConvention(col), 0);
        store.setPlateName(plateName, 0);
    }
}

Example 43 with Location

use of loci.common.Location in project bioformats by openmicroscopy.

the class ScanrReader method isSingleFile.

// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isSingleFile(String) */
@Override
public boolean isSingleFile(String id) throws FormatException, IOException {
    Location file = new Location(id).getAbsoluteFile();
    String name = file.getName();
    if (name.equals(XML_FILE) || name.equals(EXPERIMENT_FILE) || name.equals(ACQUISITION_FILE)) {
        return true;
    }
    Location parent = file.getParentFile();
    if (parent != null) {
        parent = parent.getParentFile();
    }
    return new Location(parent, XML_FILE).exists();
}

Example 44 with Location

use of loci.common.Location in project bioformats by openmicroscopy.

the class SPCReader method isThisType.

/* @see loci.formats.IFormatReader#isThisType(String, boolean) */
@Override
public boolean isThisType(String name, boolean open) {
    if (!(checkSuffix(name, "spc") || checkSuffix(name, "set")))
        return false;
    String extension = name.substring(name.lastIndexOf(".") + 1);
    String baseName = name.substring(0, name.lastIndexOf("."));
    if (!new Location(baseName + ".spc").exists())
        return false;
    return new Location(baseName + ".set").exists();
}

Example 45 with Location

use of loci.common.Location in project bioformats by openmicroscopy.

the class SPCReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    allFiles = new ArrayList<String>();
    // get the working directory
    Location tmpFile = new Location(id).getAbsoluteFile();
    Location workingDir = tmpFile.getParentFile();
    if (workingDir == null)
        workingDir = new Location(".");
    String workingDirPath = workingDir.getPath();
    if (!workingDirPath.equals(""))
        workingDirPath += File.separator;
    String[] ls = workingDir.list(true);
    if (!new Location(id).exists()) {
        ls = Location.getIdMap().keySet().toArray(new String[0]);
        workingDirPath = "";
    }
    String name = tmpFile.getName();
    // generate the name of the two matching files
    String setName = null;
    String spcName = null;
    int pos = name.lastIndexOf(".");
    if (pos != -1) {
        setName = tmpFile.getName().substring(0, pos) + ".set";
        spcName = tmpFile.getName().substring(0, pos) + ".spc";
        for (String l : ls) {
            if (l.equalsIgnoreCase(setName))
                setName = l;
            if (l.equalsIgnoreCase(spcName))
                spcName = l;
        }
    }
    if (setName == null) {
        throw new FormatException("Failed to find a matching .set file!");
    }
    if (spcName == null) {
        throw new FormatException("Failed to find a matching .spc file!");
    }
    frameClockList = new ArrayList<>();
    endOfFrameList = new ArrayList<>();
    allFiles.add(workingDirPath + setName);
    allFiles.add(workingDirPath + spcName);
    in = new RandomAccessInputStream(workingDirPath + setName);
    LOGGER.info("Reading info from .set file");
    in.order(true);
    in.skip(8);
    Integer setuppos = in.readInt();
    Short setupcount = in.readShort();
    String module = "";
    try {
        // Arbitrary length established by trial and error
        String header = in.readString(600);
        int index = header.indexOf("module SPC-");
        module = header.substring(index + 7, index + 14);
    } catch (IOException exc) {
        LOGGER.debug("Failed to read header from .set file!", exc);
    }
    if (!module.equalsIgnoreCase("SPC-134") && !module.equalsIgnoreCase("SPC-144") && !module.equalsIgnoreCase("SPC-154") && !module.equalsIgnoreCase("SPC-830")) {
        throw new FormatException("Failed to find a matching .set file!");
    }
    // goto start of setup information
    in.seek(setuppos);
    String setup = in.readString(setupcount);
    in.close();
    // get the tac range from the setup information
    double tacRange = parseSetup(TAC_RANGE, setup);
    // get the tac range from the setup information
    double tacGain = parseSetup(TAC_GAIN, setup);
    double timeBase;
    if (tacGain != 0.0 && tacRange != 0.0) {
        timeBase = 4095 * tacRange / (tacGain * 4096);
        // convert from s to ps
        timeBase *= 1.000e12;
    } else {
        throw new FormatException("Failed to parse setup file!");
    }
    LOGGER.debug("timeBase = " + Double.toString(timeBase));
    // Now read .spc file
    spcId = workingDirPath + spcName;
    in = new RandomAccessInputStream(spcId);
    in.order(true);
    LOGGER.info("Reading info from .spc file");
    /* The first 3 bytes in the file contain information about the 
     * macro time clock in 0.1 ns units ("500" for 50ns clock)
    */
    in.skip(3);
    /*
     * The 4th byte contains information about the number of 
     * routing channels in bits 3 to 6.
     * Bits 0-2 reserved bit 7 = 1 ("Data invalid")
    */
    byte routing = in.readByte();
    if ((routing & 0x10) != 0) {
        throw new FormatException("Invalid data!");
    }
    nChannels = (routing & 0x78) >> 3;
    currentPixel = 0;
    currentLine = -1;
    currentFrame = -1;
    rawBuf = new byte[bufLength];
    endOfFrameFlag = false;
    nBuffers = 0;
    bufLength = 1024;
    rawBuf = new byte[bufLength];
    int noOfBytes;
    nBuffers = 0;
    byte adcL;
    byte adcLM;
    while ((noOfBytes = in.read(rawBuf)) != -1) {
        for (int bb = 3; bb < noOfBytes; bb += 4) {
            // even nybble adc
            // get upper byte containing ADC data
            adcL = rawBuf[bb];
            // mask out upper 4 bits
            adcLM = (byte) (adcL & 0xF0);
            // at this point only the various clocks are of interest
            switch(adcLM) {
                case (byte) 0x90:
                    invalidAndMarkInit(bb);
                    break;
                case // Invalid, Mark and MTOV all set.
                (byte) 0xd0:
                    // Unsure about this-- Not well documented!
                    invalidAndMarkInit(bb);
                    break;
                default:
                    break;
            }
        // end switch
        }
        // end for
        nBuffers++;
    }
    nTimebins = (0xFFF >> adcResShift) + 1;
    nFrames = currentFrame - 1;
    addGlobalMeta("time bins", nTimebins);
    addGlobalMeta("nChannels", nChannels);
    addGlobalMeta("time base", timeBase);
    LOGGER.info("Populating metadata");
    CoreMetadata m = core.get(0);
    // Duplicates the behaviour of U.Lorenzo's Matlab code.
    if (nLines < 530) {
        // return an image
        lineMode = false;
        m.sizeY = nLines;
    } else {
        LOGGER.info("Single line mode");
        // return a single line
        lineMode = true;
        m.sizeY = 1;
    }
    Integer frameLength;
    Integer maxFrameLength = 0;
    for (int T = 0; T < nFrames; T++) {
        frameLength = (int) (endOfFrameList.get(T + 1) - frameClockList.get(T));
        if (frameLength > maxFrameLength)
            maxFrameLength = frameLength;
    }
    rawBuf = new byte[maxFrameLength];
    m.sizeX = nPixels;
    m.sizeZ = 1;
    m.sizeT = nTimebins * nFrames;
    m.sizeC = nChannels;
    m.dimensionOrder = "XYZTC";
    m.pixelType = FormatTools.UINT16;
    m.rgb = false;
    m.littleEndian = true;
    m.imageCount = m.sizeZ * m.sizeC * m.sizeT;
    m.indexed = false;
    m.falseColor = false;
    m.metadataComplete = true;
    m.moduloT.type = FormatTools.LIFETIME;
    m.moduloT.parentType = FormatTools.SPECTRA;
    m.moduloT.typeDescription = "TCSPC";
    m.moduloT.start = 0;
    m.moduloT.step = timeBase / nTimebins;
    m.moduloT.end = m.moduloT.step * (nTimebins - 1);
    m.moduloT.unit = "ps";
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
}