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

Example 36 with Location

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

the class VolocityReader 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);
    int[] zct = getZCTCoords(no);
    Stack stack = stacks.get(getSeries());
    if (!new Location(stack.pixelsFiles[zct[1]]).exists()) {
        Arrays.fill(buf, (byte) 0);
        return buf;
    }
    RandomAccessInputStream pix = new RandomAccessInputStream(stack.pixelsFiles[zct[1]]);
    int padding = zct[2] * stack.planePadding;
    long planeSize = FormatTools.getPlaneSize(this);
    int planesInFile = (int) (pix.length() / planeSize);
    int planeIndex = no / getEffectiveSizeC();
    if (planesInFile == getSizeT()) {
        planeIndex = zct[2];
        int block = stack.blockSize;
        padding = block - (int) (planeSize % block);
        if (padding == block) {
            padding = 0;
        }
        padding *= zct[2];
    }
    long offset = (long) stack.blockSize + planeIndex * planeSize + padding;
    if (offset >= pix.length()) {
        pix.close();
        return buf;
    }
    pix.seek(offset);
    if (stack.clippingData) {
        pix.seek(offset - 3);
        ByteArrayHandle v = new ByteArrayHandle();
        while (v.length() < FormatTools.getPlaneSize(this) && pix.getFilePointer() < pix.length()) {
            try {
                byte[] b = new LZOCodec().decompress(pix, null);
                pix.skipBytes(4);
                v.write(b);
            } catch (IOException e) {
            }
        }
        RandomAccessInputStream s = new RandomAccessInputStream(v);
        s.seek(0);
        readPlane(s, x, y, w, h, buf);
        s.close();
    } else {
        if (pix.getFilePointer() + planeSize > pix.length()) {
            pix.close();
            return buf;
        }
        readPlane(pix, x, y, w, h, buf);
    }
    pix.close();
    if (getRGBChannelCount() == 4) {
        // stored as ARGB, need to swap to RGBA
        for (int i = 0; i < buf.length / 4; i++) {
            byte a = buf[i * 4];
            buf[i * 4] = buf[i * 4 + 1];
            buf[i * 4 + 1] = buf[i * 4 + 2];
            buf[i * 4 + 2] = buf[i * 4 + 3];
            buf[i * 4 + 3] = a;
        }
    }
    return buf;
}

Example 37 with Location

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

the class TillVisionReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    if (!checkSuffix(id, "vws")) {
        Location pst = new Location(id).getAbsoluteFile();
        String name = pst.getParentFile().getName();
        Location parent = pst.getParentFile().getParentFile();
        Location vwsFile = new Location(parent, name.replaceAll(".pst", ".vws"));
        if (vwsFile.exists() && !vwsFile.isDirectory()) {
            id = vwsFile.getAbsolutePath();
        } else if (vwsFile.isDirectory()) {
            parent = pst.getParentFile();
            String[] list = parent.list(true);
            boolean foundVWS = false;
            for (String f : list) {
                if (checkSuffix(f, "vws")) {
                    id = new Location(parent, f).getAbsolutePath();
                    foundVWS = true;
                    break;
                }
            }
            if (!foundVWS) {
                throw new FormatException("Could not find .vws file.");
            }
        } else
            throw new FormatException("Could not find .vws file.");
    }
    super.initFile(id);
    exposureTimes = new HashMap<Integer, Double>();
    POIService poi = null;
    try {
        ServiceFactory factory = new ServiceFactory();
        poi = factory.getInstance(POIService.class);
    } catch (DependencyException de) {
        throw new FormatException("POI library not found", de);
    }
    poi.initialize(id);
    Vector<String> documents = poi.getDocumentList();
    int nImages = 0;
    final Hashtable<String, Object> tmpSeriesMetadata = new Hashtable<String, Object>();
    for (String name : documents) {
        LOGGER.debug("Reading {}", name);
        if (name.equals("Root Entry" + File.separator + "Contents")) {
            RandomAccessInputStream s = poi.getDocumentStream(name);
            s.order(true);
            boolean specialCImage = false;
            int nFound = 0;
            Long[] cimages = null;
            Location dir = new Location(id).getAbsoluteFile().getParentFile();
            String[] list = dir.list(true);
            boolean hasPST = false;
            for (String f : list) {
                if (checkSuffix(f, "pst")) {
                    hasPST = true;
                    break;
                }
            }
            if (!hasPST) {
                cimages = findImages(s);
                nFound = cimages.length;
                if (nFound == 0) {
                    s.seek(13);
                    int len = s.readShort();
                    String type = s.readString(len);
                    if (type.equals("CImage")) {
                        nFound = 1;
                        cimages = new Long[] { s.getFilePointer() + 6 };
                        specialCImage = true;
                    }
                }
                embeddedImages = nFound > 0;
            }
            LOGGER.debug("Images are {}embedded", embeddedImages ? "" : "not ");
            if (embeddedImages) {
                core.clear();
                embeddedOffset = new long[nFound];
                for (int i = 0; i < nFound; i++) {
                    CoreMetadata ms = new CoreMetadata();
                    core.add(ms);
                    s.seek(cimages[i]);
                    int len = s.read();
                    String imageName = s.readString(len);
                    imageNames.add(imageName);
                    if (specialCImage) {
                        s.seek(1280);
                    } else {
                        while (true) {
                            if (s.readString(2).equals("sB")) {
                                break;
                            } else
                                s.seek(s.getFilePointer() - 1);
                        }
                    }
                    s.skipBytes(20);
                    ms.sizeX = s.readInt();
                    ms.sizeY = s.readInt();
                    ms.sizeZ = s.readInt();
                    ms.sizeC = s.readInt();
                    ms.sizeT = s.readInt();
                    ms.pixelType = convertPixelType(s.readInt());
                    if (specialCImage) {
                        embeddedOffset[i] = s.getFilePointer() + 27;
                    } else {
                        embeddedOffset[i] = s.getFilePointer() + 31;
                    }
                }
                if (in != null)
                    in.close();
                in = poi.getDocumentStream(name);
                s.close();
                break;
            }
            s.seek(0);
            int lowerBound = 0;
            int upperBound = 0x1000;
            while (s.getFilePointer() < s.length() - 2) {
                LOGGER.debug("  Looking for image at {}", s.getFilePointer());
                s.order(false);
                int nextOffset = findNextOffset(s);
                if (nextOffset < 0 || nextOffset >= s.length())
                    break;
                s.seek(nextOffset);
                s.skipBytes(3);
                int len = s.readShort();
                if (len <= 0)
                    continue;
                imageNames.add(s.readString(len));
                if (s.getFilePointer() + 8 >= s.length())
                    break;
                s.skipBytes(6);
                s.order(true);
                len = s.readShort();
                if (nImages == 0 && len > upperBound * 2 && len < upperBound * 4) {
                    lowerBound = 512;
                    upperBound = 0x4000;
                }
                if (len < lowerBound || len > upperBound)
                    continue;
                String description = s.readString(len);
                LOGGER.debug("Description: {}", description);
                // parse key/value pairs from description
                String dateTime = "";
                String[] lines = description.split("[\r\n]");
                for (String line : lines) {
                    line = line.trim();
                    int colon = line.indexOf(':');
                    if (colon != -1 && !line.startsWith(";")) {
                        String key = line.substring(0, colon).trim();
                        String value = line.substring(colon + 1).trim();
                        String metaKey = "Series " + nImages + " " + key;
                        addMeta(metaKey, value, tmpSeriesMetadata);
                        if (key.equals("Start time of experiment")) {
                            // HH:mm:ss aa OR HH:mm:ss.sss aa
                            dateTime += " " + value;
                        } else if (key.equals("Date")) {
                            // mm/dd/yy ?
                            dateTime = value + " " + dateTime;
                        } else if (key.equals("Exposure time [ms]")) {
                            double exp = Double.parseDouble(value) / 1000;
                            exposureTimes.put(nImages, exp);
                        } else if (key.equals("Image type")) {
                            types.add(value);
                        }
                    }
                }
                dateTime = dateTime.trim();
                if (!dateTime.equals("")) {
                    boolean success = false;
                    for (String format : DATE_FORMATS) {
                        try {
                            dateTime = DateTools.formatDate(dateTime, format, ".");
                            success = true;
                        } catch (NullPointerException e) {
                        }
                    }
                    dates.add(success ? dateTime : "");
                }
                nImages++;
            }
            s.close();
        }
    }
    Location directory = new Location(currentId).getAbsoluteFile().getParentFile();
    String[] pixelsFile = new String[nImages];
    if (!embeddedImages) {
        if (nImages == 0) {
            throw new FormatException("No images found.");
        }
        // look for appropriate pixels files
        String[] files = directory.list(true);
        String name = currentId.substring(currentId.lastIndexOf(File.separator) + 1, currentId.lastIndexOf("."));
        int nextFile = 0;
        for (String f : files) {
            if (checkSuffix(f, "pst")) {
                Location pst = new Location(directory, f);
                if (pst.isDirectory() && f.startsWith(name)) {
                    String[] subfiles = pst.list(true);
                    Arrays.sort(subfiles);
                    for (String q : subfiles) {
                        if (checkSuffix(q, "pst") && nextFile < nImages) {
                            pixelsFile[nextFile++] = f + File.separator + q;
                        }
                    }
                }
            }
        }
        if (nextFile == 0) {
            for (String f : files) {
                if (checkSuffix(f, "pst")) {
                    pixelsFile[nextFile++] = new Location(directory, f).getAbsolutePath();
                }
            }
            if (nextFile == 0)
                throw new FormatException("No image files found.");
        }
    }
    Arrays.sort(pixelsFile);
    int nSeries = core.size();
    if (!embeddedImages) {
        core.clear();
        nSeries = nImages;
    }
    pixelsFiles = new String[nSeries];
    infFiles = new String[nSeries];
    Object[] metadataKeys = tmpSeriesMetadata.keySet().toArray();
    IniParser parser = new IniParser();
    for (int i = 0; i < nSeries; i++) {
        CoreMetadata ms;
        if (!embeddedImages) {
            ms = new CoreMetadata();
            core.add(ms);
            setSeries(i);
            // make sure that pixels file exists
            String file = pixelsFile[i];
            file = file.replace('/', File.separatorChar);
            file = file.replace('\\', File.separatorChar);
            String oldFile = file;
            Location f = new Location(directory, oldFile);
            if (!f.exists()) {
                oldFile = oldFile.substring(oldFile.lastIndexOf(File.separator) + 1);
                f = new Location(directory, oldFile);
                if (!f.exists()) {
                    throw new FormatException("Could not find pixels file '" + file);
                }
            }
            file = f.getAbsolutePath();
            pixelsFiles[i] = file;
            // read key/value pairs from .inf files
            int dot = file.lastIndexOf(".");
            String inf = file.substring(0, dot) + ".inf";
            infFiles[i] = inf;
            BufferedReader reader = new BufferedReader(new InputStreamReader(new FileInputStream(inf), Constants.ENCODING));
            IniList data = parser.parseINI(reader);
            reader.close();
            IniTable infoTable = data.getTable("Info");
            ms.sizeX = Integer.parseInt(infoTable.get("Width"));
            ms.sizeY = Integer.parseInt(infoTable.get("Height"));
            ms.sizeC = Integer.parseInt(infoTable.get("Bands"));
            ms.sizeZ = Integer.parseInt(infoTable.get("Slices"));
            ms.sizeT = Integer.parseInt(infoTable.get("Frames"));
            int dataType = Integer.parseInt(infoTable.get("Datatype"));
            ms.pixelType = convertPixelType(dataType);
            if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
                HashMap<String, String> iniMap = data.flattenIntoHashMap();
                ms.seriesMetadata.putAll(iniMap);
            }
        } else {
            ms = core.get(i);
            setSeries(i);
        }
        ms.imageCount = ms.sizeZ * ms.sizeC * ms.sizeT;
        ms.rgb = false;
        ms.littleEndian = true;
        ms.dimensionOrder = "XYCZT";
        ms.seriesMetadata = new Hashtable<String, Object>();
        for (Object key : metadataKeys) {
            String keyName = key.toString();
            if (keyName.startsWith("Series " + i + " ")) {
                keyName = keyName.replaceAll("Series " + i + " ", "");
                ms.seriesMetadata.put(keyName, tmpSeriesMetadata.get(key));
            }
        }
    }
    setSeries(0);
    populateMetadataStore();
    poi.close();
    poi = null;
}

Example 38 with Location

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

the class TrestleReader method isThisType.

// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(String, boolean) */
@Override
public boolean isThisType(String name, boolean open) {
    if (super.isThisType(name, open))
        return true;
    if (!checkSuffix(name, "tif") && open) {
        Location current = new Location(name).getAbsoluteFile();
        Location parent = current.getParentFile();
        String tiff = current.getName();
        int index = tiff.lastIndexOf(".");
        if (index >= 0) {
            tiff = tiff.substring(0, index);
        }
        tiff += ".tif";
        Location tiffFile = new Location(parent, tiff);
        return tiffFile.exists() && isThisType(tiffFile.getAbsolutePath(), open);
    }
    return false;
}

Example 39 with Location

use of loci.common.Location 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());
        }
    }
}

Example 40 with Location

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

the class VarianFDFReader method parseFDF.

// -- Helper methods --
private void parseFDF(String file) throws FormatException, IOException {
    in = new RandomAccessInputStream(file);
    CoreMetadata m = core.get(0);
    boolean storedFloats = false;
    boolean multifile = false;
    String data = in.readString(Character.toString((char) 0x0c));
    String[] lines = data.split("\n");
    for (String line : lines) {
        line = line.trim();
        if (line.length() == 0)
            break;
        if (line.startsWith("#"))
            continue;
        int space = line.indexOf(' ');
        int eq = line.indexOf('=');
        String type = line.substring(0, space).trim();
        String var = line.substring(space, eq).trim();
        String value = line.substring(eq + 1, line.indexOf(';')).trim();
        if (var.equals("*storage")) {
            storedFloats = value.equals("\"float\"");
        }
        if (var.equals("bits")) {
            m.bitsPerPixel = Integer.parseInt(value);
            if (value.equals("8")) {
                m.pixelType = FormatTools.UINT8;
            } else if (value.equals("16")) {
                m.pixelType = FormatTools.UINT16;
            } else if (value.equals("32")) {
                if (storedFloats) {
                    m.pixelType = FormatTools.FLOAT;
                } else
                    m.pixelType = FormatTools.UINT32;
            } else
                throw new FormatException("Unsupported bits: " + value);
        } else if (var.equals("matrix[]")) {
            String[] values = parseArray(value);
            m.sizeX = (int) Double.parseDouble(values[0]);
            m.sizeY = (int) Double.parseDouble(values[1]);
            if (values.length > 2) {
                m.sizeZ = (int) Double.parseDouble(values[2]);
            }
        } else if (var.equals("slices")) {
            m.sizeZ = Integer.parseInt(value);
            multifile = true;
        } else if (var.equals("echoes")) {
            m.sizeT = Integer.parseInt(value);
            multifile = true;
        } else if (var.equals("span[]")) {
            String[] values = parseArray(value);
            if (values.length > 0) {
                pixelSizeX = computePhysicalSize(getSizeX(), values[0], units[0]);
            }
            if (values.length > 1) {
                pixelSizeY = computePhysicalSize(getSizeY(), values[1], units[1]);
            }
            if (values.length > 2) {
                pixelSizeZ = computePhysicalSize(getSizeZ(), values[2], units[2]);
            }
        } else if (var.equals("origin[]")) {
            String[] values = parseArray(value);
            if (values.length > 0) {
                final double size = computePhysicalSize(1, values[0], units[0]);
                originX = new Length(size, UNITS.REFERENCEFRAME);
                addGlobalMeta("X position for position #1", originX);
            }
            if (values.length > 1) {
                final double size = computePhysicalSize(1, values[1], units[1]);
                originY = new Length(size, UNITS.REFERENCEFRAME);
                addGlobalMeta("Y position for position #1", originY);
            }
            if (values.length > 2) {
                final double size = computePhysicalSize(1, values[2], units[2]);
                originZ = new Length(size, UNITS.REFERENCEFRAME);
                addGlobalMeta("Z position for position #1", originZ);
            }
        } else if (var.equals("*abscissa[]")) {
            units = parseArray(value);
        } else if (var.equals("bigendian")) {
            m.littleEndian = value.equals("0");
            in.order(isLittleEndian());
        }
        addGlobalMeta(var, value);
    }
    if (multifile && files.isEmpty()) {
        Location thisFile = new Location(file).getAbsoluteFile();
        Location parent = thisFile.getParentFile();
        String[] list = parent.list(true);
        Arrays.sort(list);
        for (String f : list) {
            if (checkSuffix(f, "fdf") && f.length() == thisFile.getName().length()) {
                files.add(new Location(parent, f).getAbsolutePath());
            }
        }
    }
}