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

Example 81 with RandomAccessInputStream

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

the class BioRadGelReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    String check = in.readString(48);
    if (check.indexOf("Intel Format") != -1) {
        in.order(true);
    }
    in.seek(START_OFFSET);
    boolean codeFound = false;
    int skip = 0;
    long baseFP = 0;
    while (!codeFound) {
        short code = in.readShort();
        if (code == 0x81)
            codeFound = true;
        short length = in.readShort();
        in.skipBytes(2 + 2 * length);
        if (codeFound) {
            baseFP = in.getFilePointer() + 2;
            if (length > 1) {
                in.seek(in.getFilePointer() - 2);
            }
            skip = in.readInt() - 32;
        } else {
            if (length == 1)
                in.skipBytes(12);
            else if (length == 2)
                in.skipBytes(10);
        }
    }
    diff = BASE_OFFSET - baseFP;
    skip += diff;
    double physicalWidth = 0d, physicalHeight = 0d;
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        if (baseFP + skip - 8187 > 0) {
            in.seek(baseFP + skip - 8187);
            String scannerName = in.readCString();
            in.skipBytes(8);
            in.readCString();
            in.skipBytes(8);
            String imageArea = in.readCString();
            imageArea = imageArea.substring(imageArea.indexOf(':') + 1).trim();
            int xIndex = imageArea.indexOf('x');
            if (xIndex > 0) {
                int space = imageArea.indexOf(' ');
                if (space >= 0) {
                    String width = imageArea.substring(1, space);
                    int nextSpace = imageArea.indexOf(" ", xIndex + 2);
                    if (nextSpace > xIndex) {
                        String height = imageArea.substring(xIndex + 1, nextSpace);
                        physicalWidth = Double.parseDouble(width.trim()) * 1000;
                        physicalHeight = Double.parseDouble(height.trim()) * 1000;
                    }
                }
            }
        }
    }
    in.seek(baseFP + skip - 298);
    String date = in.readString(17);
    date = DateTools.formatDate(date, "dd-MMM-yyyy HH:mm");
    in.skipBytes(73);
    String scannerName = in.readCString();
    addGlobalMeta("Scanner name", scannerName);
    in.seek(baseFP + skip);
    CoreMetadata m = core.get(0);
    m.sizeX = in.readShort() & 0xffff;
    m.sizeY = in.readShort() & 0xffff;
    if (getSizeX() * getSizeY() > in.length()) {
        in.order(true);
        in.seek(in.getFilePointer() - 4);
        m.sizeX = in.readShort();
        m.sizeY = in.readShort();
    }
    in.skipBytes(2);
    int bpp = in.readShort();
    m.pixelType = FormatTools.pixelTypeFromBytes(bpp, false, false);
    offset = in.getFilePointer();
    m.sizeZ = 1;
    m.sizeC = 1;
    m.sizeT = 1;
    m.imageCount = 1;
    m.dimensionOrder = "XYCZT";
    m.rgb = false;
    m.interleaved = false;
    m.indexed = false;
    m.littleEndian = in.isLittleEndian();
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    if (date != null) {
        store.setImageAcquisitionDate(new Timestamp(date), 0);
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        Length sizeX = FormatTools.getPhysicalSizeX(physicalWidth / getSizeX());
        Length sizeY = FormatTools.getPhysicalSizeY(physicalHeight / getSizeY());
        if (sizeX != null) {
            store.setPixelsPhysicalSizeX(sizeX, 0);
        }
        if (sizeY != null) {
            store.setPixelsPhysicalSizeY(sizeY, 0);
        }
    }
}

Example 82 with RandomAccessInputStream

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

the class CanonRawReader 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);
    if (plane == null) {
        plane = new byte[FormatTools.getPlaneSize(this)];
        ImageTools.interpolate(pix, plane, COLOR_MAP, getSizeX(), getSizeY(), isLittleEndian());
    }
    RandomAccessInputStream s = new RandomAccessInputStream(plane);
    readPlane(s, x, y, w, h, buf);
    s.close();
    return buf;
}

Example 83 with RandomAccessInputStream

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

the class BioRadSCNReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    CoreMetadata m = core.get(0);
    String line = in.readLine();
    String currentBoundary = "";
    String currentType = "";
    int currentLength = 0;
    ArrayList<String> xml = new ArrayList<String>();
    while (in.getFilePointer() < in.length() && line != null) {
        line = line.trim();
        if (line.startsWith("Content-Type")) {
            currentType = line.substring(line.indexOf(' ') + 1);
            int boundary = currentType.indexOf("boundary");
            if (boundary > 0) {
                currentBoundary = currentType.substring(boundary + 10, currentType.length() - 1);
            }
            if (currentType.indexOf(';') > 0) {
                currentType = currentType.substring(0, currentType.indexOf(';'));
            }
        } else if (line.equals("--" + currentBoundary)) {
            currentLength = 0;
        } else if (line.startsWith("Content-Length")) {
            currentLength = Integer.parseInt(line.substring(line.indexOf(' ') + 1));
        } else if (line.length() == 0) {
            if (currentType.equals("application/octet-stream")) {
                pixelsOffset = in.getFilePointer();
                in.skipBytes(currentLength);
            } else if (currentType.equals("text/xml")) {
                String xmlBlock = in.readString(currentLength);
                xml.add(xmlBlock);
            }
        }
        line = in.readLine();
    }
    SCNHandler handler = new SCNHandler();
    for (String block : xml) {
        XMLTools.parseXML(block, handler);
    }
    m.sizeZ = 1;
    m.sizeT = 1;
    m.imageCount = 1;
    m.dimensionOrder = "XYCZT";
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, exposureTime != null);
    store.setInstrumentID(MetadataTools.createLSID("Instrument", 0), 0);
    if (serialNumber != null) {
        store.setMicroscopeSerialNumber(serialNumber, 0);
    }
    if (model != null) {
        store.setMicroscopeModel(model, 0);
    }
    if (imageName != null) {
        store.setImageName(imageName, 0);
    }
    if (acquisitionDate != null) {
        store.setImageAcquisitionDate(new Timestamp(acquisitionDate), 0);
    }
    if (gain != null || binning != null) {
        String detector = MetadataTools.createLSID("Detector", 0, 0);
        store.setDetectorID(detector, 0, 0);
        store.setDetectorSettingsID(detector, 0, 0);
    }
    if (gain != null) {
        store.setDetectorSettingsGain(gain, 0, 0);
    }
    if (binning != null) {
        store.setDetectorSettingsBinning(getBinning(binning), 0, 0);
    }
    if (exposureTime != null) {
        store.setPlaneExposureTime(new Time(exposureTime, UNITS.SECOND), 0, 0);
    }
    if (physicalSizeX != null) {
        store.setPixelsPhysicalSizeX(FormatTools.createLength(physicalSizeX, UNITS.MICROMETER), 0);
    }
    if (physicalSizeY != null) {
        store.setPixelsPhysicalSizeY(FormatTools.createLength(physicalSizeY, UNITS.MICROMETER), 0);
    }
}

Example 84 with RandomAccessInputStream

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

the class BurleighReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    CoreMetadata m = core.get(0);
    m.littleEndian = true;
    in.order(isLittleEndian());
    int version = (int) in.readFloat() - 1;
    m.sizeX = in.readShort();
    m.sizeY = in.readShort();
    double xSize = 0d, ySize = 0d, zSize = 0d;
    pixelsOffset = version == 1 ? 8 : 260;
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        double timePerPixel = 0d;
        int mode = 0, gain = 0, mag = 0;
        double sampleVolts = 0d, tunnelCurrent = 0d;
        if (version == 1) {
            in.seek(in.length() - 40);
            in.skipBytes(12);
            xSize = in.readInt();
            ySize = in.readInt();
            zSize = in.readInt();
            timePerPixel = in.readShort() * 50;
            mag = in.readShort();
            switch(mag) {
                case 3:
                    mag = 10;
                    break;
                case 4:
                    mag = 50;
                    break;
                case 5:
                    mag = 250;
                    break;
            }
            xSize /= mag;
            ySize /= mag;
            zSize /= mag;
            mode = in.readShort();
            gain = in.readShort();
            sampleVolts = in.readFloat() / 1000;
            tunnelCurrent = in.readFloat();
        } else if (version == 2) {
            in.skipBytes(14);
            xSize = in.readInt();
            ySize = in.readInt();
            zSize = in.readInt();
            mode = in.readShort();
            in.skipBytes(4);
            gain = in.readShort();
            timePerPixel = in.readShort() * 50;
            in.skipBytes(12);
            sampleVolts = in.readFloat();
            tunnelCurrent = in.readFloat();
            addGlobalMeta("Force", in.readFloat());
        }
        addGlobalMeta("Version", version);
        addGlobalMeta("Image mode", mode);
        addGlobalMeta("Z gain", gain);
        addGlobalMeta("Time per pixel (s)", timePerPixel);
        addGlobalMeta("Sample volts", sampleVolts);
        addGlobalMeta("Tunnel current", tunnelCurrent);
        addGlobalMeta("Magnification", mag);
    }
    m.pixelType = FormatTools.UINT16;
    m.sizeZ = 1;
    m.sizeC = 1;
    m.sizeT = 1;
    m.imageCount = 1;
    m.dimensionOrder = "XYZCT";
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        Length sizeX = FormatTools.getPhysicalSizeX(xSize / getSizeX());
        Length sizeY = FormatTools.getPhysicalSizeY(ySize / getSizeY());
        Length sizeZ = FormatTools.getPhysicalSizeZ(zSize / getSizeZ());
        if (sizeX != null) {
            store.setPixelsPhysicalSizeX(sizeX, 0);
        }
        if (sizeY != null) {
            store.setPixelsPhysicalSizeY(sizeY, 0);
        }
        if (sizeZ != null) {
            store.setPixelsPhysicalSizeZ(sizeZ, 0);
        }
    }
}

Example 85 with RandomAccessInputStream

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

the class CellSensReader method parseETSFile.

private void parseETSFile(String file, int s) throws FormatException, IOException {
    fileMap.put(core.size() - 1, file);
    RandomAccessInputStream etsFile = new RandomAccessInputStream(file);
    etsFile.order(true);
    CoreMetadata ms = core.get(getCoreIndex());
    // read the volume header
    String magic = etsFile.readString(4).trim();
    if (!magic.equals("SIS")) {
        throw new FormatException("Unknown magic bytes: " + magic);
    }
    int headerSize = etsFile.readInt();
    int version = etsFile.readInt();
    nDimensions.add(etsFile.readInt());
    long additionalHeaderOffset = etsFile.readLong();
    int additionalHeaderSize = etsFile.readInt();
    // reserved
    etsFile.skipBytes(4);
    long usedChunkOffset = etsFile.readLong();
    int nUsedChunks = etsFile.readInt();
    // reserved
    etsFile.skipBytes(4);
    // read the additional header
    etsFile.seek(additionalHeaderOffset);
    String moreMagic = etsFile.readString(4).trim();
    if (!moreMagic.equals("ETS")) {
        throw new FormatException("Unknown magic bytes: " + moreMagic);
    }
    // extra version number
    etsFile.skipBytes(4);
    int pixelType = etsFile.readInt();
    ms.sizeC = etsFile.readInt();
    int colorspace = etsFile.readInt();
    compressionType.add(etsFile.readInt());
    int compressionQuality = etsFile.readInt();
    tileX.add(etsFile.readInt());
    tileY.add(etsFile.readInt());
    int tileZ = etsFile.readInt();
    // pixel info hints
    etsFile.skipBytes(4 * 17);
    byte[] color = new byte[ms.sizeC * FormatTools.getBytesPerPixel(convertPixelType(pixelType))];
    etsFile.read(color);
    backgroundColor.put(getCoreIndex(), color);
    // background color
    etsFile.skipBytes(4 * 10 - color.length);
    // component order
    etsFile.skipBytes(4);
    boolean usePyramid = etsFile.readInt() != 0;
    ms.rgb = ms.sizeC > 1;
    // read the used chunks
    etsFile.seek(usedChunkOffset);
    tileOffsets.add(new Long[nUsedChunks]);
    ArrayList<TileCoordinate> tmpTiles = new ArrayList<TileCoordinate>();
    for (int chunk = 0; chunk < nUsedChunks; chunk++) {
        etsFile.skipBytes(4);
        int dimensions = nDimensions.get(nDimensions.size() - 1);
        TileCoordinate t = new TileCoordinate(dimensions);
        for (int i = 0; i < dimensions; i++) {
            t.coordinate[i] = etsFile.readInt();
        }
        tileOffsets.get(tileOffsets.size() - 1)[chunk] = etsFile.readLong();
        int nBytes = etsFile.readInt();
        etsFile.skipBytes(4);
        tmpTiles.add(t);
    }
    int maxResolution = 0;
    if (usePyramid) {
        for (TileCoordinate t : tmpTiles) {
            if (t.coordinate[t.coordinate.length - 1] > maxResolution) {
                maxResolution = t.coordinate[t.coordinate.length - 1];
            }
        }
    }
    maxResolution++;
    int[] maxX = new int[maxResolution];
    int[] maxY = new int[maxResolution];
    int[] maxZ = new int[maxResolution];
    int[] maxC = new int[maxResolution];
    int[] maxT = new int[maxResolution];
    HashMap<String, Integer> dimOrder = pyramids.get(s).dimensionOrdering;
    for (TileCoordinate t : tmpTiles) {
        int resolution = usePyramid ? t.coordinate[t.coordinate.length - 1] : 0;
        Integer tv = dimOrder.get("T");
        Integer zv = dimOrder.get("Z");
        Integer cv = dimOrder.get("C");
        int tIndex = tv == null ? -1 : tv + 2;
        int zIndex = zv == null ? -1 : zv + 2;
        int cIndex = cv == null ? -1 : cv + 2;
        if (usePyramid && tIndex == t.coordinate.length - 1) {
            tv = null;
            tIndex = -1;
        }
        if (usePyramid && zIndex == t.coordinate.length - 1) {
            zv = null;
            zIndex = -1;
        }
        int upperLimit = usePyramid ? t.coordinate.length - 1 : t.coordinate.length;
        if ((tIndex < 0 || tIndex >= upperLimit) && (zIndex < 0 || zIndex >= upperLimit) && (cIndex < 0 || cIndex >= upperLimit)) {
            tIndex--;
            zIndex--;
            cIndex--;
            if (dimOrder.containsKey("T")) {
                dimOrder.put("T", tIndex - 2);
            }
            if (dimOrder.containsKey("Z")) {
                dimOrder.put("Z", zIndex - 2);
            }
            if (dimOrder.containsKey("C")) {
                dimOrder.put("C", cIndex - 2);
            }
        }
        if (tv == null && zv == null) {
            if (t.coordinate.length > 4 && cv == null) {
                cIndex = 2;
                dimOrder.put("C", cIndex - 2);
            }
            if (t.coordinate.length > 4) {
                if (cv == null) {
                    tIndex = 3;
                } else {
                    tIndex = cIndex + 2;
                }
                if (tIndex < t.coordinate.length) {
                    dimOrder.put("T", tIndex - 2);
                } else {
                    tIndex = -1;
                }
            }
            if (t.coordinate.length > 5) {
                if (cv == null) {
                    zIndex = 4;
                } else {
                    zIndex = cIndex + 1;
                }
                if (zIndex < t.coordinate.length) {
                    dimOrder.put("Z", zIndex - 2);
                } else {
                    zIndex = -1;
                }
            }
        }
        if (t.coordinate[0] > maxX[resolution]) {
            maxX[resolution] = t.coordinate[0];
        }
        if (t.coordinate[1] > maxY[resolution]) {
            maxY[resolution] = t.coordinate[1];
        }
        if (tIndex >= 0 && t.coordinate[tIndex] > maxT[resolution]) {
            maxT[resolution] = t.coordinate[tIndex];
        }
        if (zIndex >= 0 && t.coordinate[zIndex] > maxZ[resolution]) {
            maxZ[resolution] = t.coordinate[zIndex];
        }
        if (cIndex >= 0 && t.coordinate[cIndex] > maxC[resolution]) {
            maxC[resolution] = t.coordinate[cIndex];
        }
    }
    if (pyramids.get(s).width != null) {
        ms.sizeX = pyramids.get(s).width;
    }
    if (pyramids.get(s).height != null) {
        ms.sizeY = pyramids.get(s).height;
    }
    ms.sizeZ = maxZ[0] + 1;
    if (maxC[0] > 0) {
        ms.sizeC *= (maxC[0] + 1);
    }
    ms.sizeT = maxT[0] + 1;
    if (ms.sizeZ == 0) {
        ms.sizeZ = 1;
    }
    ms.imageCount = ms.sizeZ * ms.sizeT;
    if (maxC[0] > 0) {
        ms.imageCount *= (maxC[0] + 1);
    }
    if (maxY[0] >= 1) {
        rows.add(maxY[0] + 1);
    } else {
        rows.add(1);
    }
    if (maxX[0] >= 1) {
        cols.add(maxX[0] + 1);
    } else {
        cols.add(1);
    }
    ArrayList<TileCoordinate> map = new ArrayList<TileCoordinate>();
    for (int i = 0; i < tmpTiles.size(); i++) {
        map.add(tmpTiles.get(i));
    }
    tileMap.add(map);
    ms.pixelType = convertPixelType(pixelType);
    if (usePyramid) {
        int finalResolution = 1;
        int initialCoreSize = core.size();
        for (int i = 1; i < maxResolution; i++) {
            CoreMetadata newResolution = new CoreMetadata(ms);
            int previousX = core.get(core.size() - 1).sizeX;
            int previousY = core.get(core.size() - 1).sizeY;
            int maxSizeX = tileX.get(tileX.size() - 1) * (maxX[i] < 1 ? 1 : maxX[i] + 1);
            int maxSizeY = tileY.get(tileY.size() - 1) * (maxY[i] < 1 ? 1 : maxY[i] + 1);
            newResolution.sizeX = previousX / 2;
            if (previousX % 2 == 1 && newResolution.sizeX < maxSizeX) {
                newResolution.sizeX++;
            } else if (newResolution.sizeX > maxSizeX) {
                newResolution.sizeX = maxSizeX;
            }
            newResolution.sizeY = previousY / 2;
            if (previousY % 2 == 1 && newResolution.sizeY < maxSizeY) {
                newResolution.sizeY++;
            } else if (newResolution.sizeY > maxSizeY) {
                newResolution.sizeY = maxSizeY;
            }
            newResolution.sizeZ = maxZ[i] + 1;
            if (maxC[i] > 0 && newResolution.sizeC != (maxC[i] + 1)) {
                newResolution.sizeC *= (maxC[i] + 1);
            }
            newResolution.sizeT = maxT[i] + 1;
            if (newResolution.sizeZ == 0) {
                newResolution.sizeZ = 1;
            }
            newResolution.imageCount = newResolution.sizeZ * newResolution.sizeT;
            if (maxC[i] > 0) {
                newResolution.imageCount *= (maxC[i] + 1);
            }
            newResolution.metadataComplete = true;
            newResolution.dimensionOrder = "XYCZT";
            core.add(newResolution);
            rows.add(maxY[i] >= 1 ? maxY[i] + 1 : 1);
            cols.add(maxX[i] >= 1 ? maxX[i] + 1 : 1);
            fileMap.put(core.size() - 1, file);
            finalResolution = core.size() - initialCoreSize + 1;
            tileX.add(tileX.get(tileX.size() - 1));
            tileY.add(tileY.get(tileY.size() - 1));
            compressionType.add(compressionType.get(compressionType.size() - 1));
            tileMap.add(map);
            nDimensions.add(nDimensions.get(nDimensions.size() - 1));
            tileOffsets.add(tileOffsets.get(tileOffsets.size() - 1));
            backgroundColor.put(core.size() - 1, color);
        }
        ms.resolutionCount = finalResolution;
    }
    etsFile.close();
}