Examples with ByteOrder java.nio.ByteOrder used on opensource projects

Example 76 with ByteOrder

use of java.nio.ByteOrder in project ffx by mjschnie.

the class MTZFilter method readFile.

/**
 * {@inheritDoc}
 */
@Override
public boolean readFile(File mtzFile, ReflectionList reflectionList, DiffractionRefinementData refinementData, CompositeConfiguration properties) {
    int nRead, nIgnore, nRes, nFriedel, nCut;
    ByteOrder byteOrder = ByteOrder.nativeOrder();
    FileInputStream fileInputStream;
    DataInputStream dataInputStream;
    boolean transpose = false;
    StringBuilder sb = new StringBuilder();
    try {
        fileInputStream = new FileInputStream(mtzFile);
        dataInputStream = new DataInputStream(fileInputStream);
        byte[] headerOffset = new byte[4];
        byte[] bytes = new byte[80];
        int offset = 0;
        // Eat "MTZ" title.
        dataInputStream.read(bytes, offset, 4);
        String mtzstr = null;
        // Header offset.
        dataInputStream.read(headerOffset, offset, 4);
        // Machine stamp.
        dataInputStream.read(bytes, offset, 4);
        ByteBuffer byteBuffer = ByteBuffer.wrap(bytes);
        int stamp = byteBuffer.order(ByteOrder.BIG_ENDIAN).getInt();
        String stampString = Integer.toHexString(stamp);
        switch(stampString.charAt(0)) {
            case '1':
            case '3':
                if (byteOrder.equals(ByteOrder.LITTLE_ENDIAN)) {
                    byteOrder = ByteOrder.BIG_ENDIAN;
                }
                break;
            case '4':
                if (byteOrder.equals(ByteOrder.BIG_ENDIAN)) {
                    byteOrder = ByteOrder.LITTLE_ENDIAN;
                }
                break;
        }
        byteBuffer = ByteBuffer.wrap(headerOffset);
        int headerOffsetI = byteBuffer.order(byteOrder).getInt();
        // skip to header and parse
        dataInputStream.skipBytes((headerOffsetI - 4) * 4);
        for (Boolean parsing = true; parsing; dataInputStream.read(bytes, offset, 80)) {
            mtzstr = new String(bytes);
            parsing = parseHeader(mtzstr);
        }
        // column identifiers
        foString = sigFoString = rFreeString = null;
        if (properties != null) {
            foString = properties.getString("fostring", null);
            sigFoString = properties.getString("sigfostring", null);
            rFreeString = properties.getString("rfreestring", null);
        }
        h = k = l = fo = sigFo = rFree = -1;
        fPlus = sigFPlus = fMinus = sigFMinus = rFreePlus = rFreeMinus = -1;
        boolean print = true;
        parseColumns(print);
        if (h < 0 || k < 0 || l < 0) {
            String message = "Fatal error in MTZ file - no H K L indexes?\n";
            logger.log(Level.SEVERE, message);
            return false;
        }
        // Reopen to start at beginning.
        fileInputStream = new FileInputStream(mtzFile);
        dataInputStream = new DataInputStream(fileInputStream);
        // Skip initial header.
        dataInputStream.skipBytes(80);
        // Check if HKLs need to be transposed or not.
        float[] data = new float[nColumns];
        HKL mate = new HKL();
        int nPosIgnore = 0;
        int nTransIgnore = 0;
        int nZero = 0;
        int none = 0;
        for (int i = 0; i < nReflections; i++) {
            for (int j = 0; j < nColumns; j++) {
                dataInputStream.read(bytes, offset, 4);
                byteBuffer = ByteBuffer.wrap(bytes);
                data[j] = byteBuffer.order(byteOrder).getFloat();
            }
            int ih = (int) data[h];
            int ik = (int) data[k];
            int il = (int) data[l];
            boolean friedel = reflectionList.findSymHKL(ih, ik, il, mate, false);
            HKL hklpos = reflectionList.getHKL(mate);
            if (hklpos == null) {
                nPosIgnore++;
            }
            friedel = reflectionList.findSymHKL(ih, ik, il, mate, true);
            HKL hkltrans = reflectionList.getHKL(mate);
            if (hkltrans == null) {
                nTransIgnore++;
            }
            if (rFree > 0) {
                if (((int) data[rFree]) == 0) {
                    nZero++;
                } else if (((int) data[rFree]) == 1) {
                    none++;
                }
            }
            if (rFreePlus > 0) {
                if (((int) data[rFreePlus]) == 0) {
                    nZero++;
                } else if (((int) data[rFreePlus]) == 1) {
                    none++;
                }
            }
            if (rFreeMinus > 0) {
                if (((int) data[rFreeMinus]) == 0) {
                    nZero++;
                } else if (((int) data[rFreeMinus]) == 1) {
                    none++;
                }
            }
        }
        if (nPosIgnore > nTransIgnore) {
            transpose = true;
        }
        if (none > (nZero * 2) && refinementData.rfreeflag < 0) {
            refinementData.setFreeRFlag(0);
            sb.append(format(" Setting R free flag to %d based on MTZ file data.\n", refinementData.rfreeflag));
        } else if (nZero > (none * 2) && refinementData.rfreeflag < 0) {
            refinementData.setFreeRFlag(1);
            sb.append(format(" Setting R free flag to %d based on MTZ file data.\n", refinementData.rfreeflag));
        } else if (refinementData.rfreeflag < 0) {
            refinementData.setFreeRFlag(0);
            sb.append(format(" Setting R free flag to MTZ default: %d\n", refinementData.rfreeflag));
        }
        // reopen to start at beginning
        fileInputStream = new FileInputStream(mtzFile);
        dataInputStream = new DataInputStream(fileInputStream);
        // skip initial header
        dataInputStream.skipBytes(80);
        // read in data
        double[][] anofSigF = new double[refinementData.n][4];
        for (int i = 0; i < refinementData.n; i++) {
            anofSigF[i][0] = anofSigF[i][1] = anofSigF[i][2] = anofSigF[i][3] = Double.NaN;
        }
        nRead = nIgnore = nRes = nFriedel = nCut = 0;
        for (int i = 0; i < nReflections; i++) {
            for (int j = 0; j < nColumns; j++) {
                dataInputStream.read(bytes, offset, 4);
                byteBuffer = ByteBuffer.wrap(bytes);
                data[j] = byteBuffer.order(byteOrder).getFloat();
            }
            int ih = (int) data[h];
            int ik = (int) data[k];
            int il = (int) data[l];
            boolean friedel = reflectionList.findSymHKL(ih, ik, il, mate, transpose);
            HKL hkl = reflectionList.getHKL(mate);
            if (hkl != null) {
                if (fo > 0 && sigFo > 0) {
                    if (refinementData.fsigfcutoff > 0.0) {
                        if ((data[fo] / data[sigFo]) < refinementData.fsigfcutoff) {
                            nCut++;
                            continue;
                        }
                    }
                    if (friedel) {
                        anofSigF[hkl.index()][2] = data[fo];
                        anofSigF[hkl.index()][3] = data[sigFo];
                        nFriedel++;
                    } else {
                        anofSigF[hkl.index()][0] = data[fo];
                        anofSigF[hkl.index()][1] = data[sigFo];
                    }
                } else {
                    if (fPlus > 0 && sigFPlus > 0) {
                        if (refinementData.fsigfcutoff > 0.0) {
                            if ((data[fPlus] / data[sigFPlus]) < refinementData.fsigfcutoff) {
                                nCut++;
                                continue;
                            }
                        }
                        anofSigF[hkl.index()][0] = data[fPlus];
                        anofSigF[hkl.index()][1] = data[sigFPlus];
                    }
                    if (fMinus > 0 && sigFMinus > 0) {
                        if (refinementData.fsigfcutoff > 0.0) {
                            if ((data[fMinus] / data[sigFMinus]) < refinementData.fsigfcutoff) {
                                nCut++;
                                continue;
                            }
                        }
                        anofSigF[hkl.index()][2] = data[fMinus];
                        anofSigF[hkl.index()][3] = data[sigFMinus];
                    }
                }
                if (rFree > 0) {
                    refinementData.setFreeR(hkl.index(), (int) data[rFree]);
                } else {
                    if (rFreePlus > 0 && rFreeMinus > 0) {
                        // not sure what the correct thing to do here is?
                        refinementData.setFreeR(hkl.index(), (int) data[rFreePlus]);
                    } else if (rFreePlus > 0) {
                        refinementData.setFreeR(hkl.index(), (int) data[rFreePlus]);
                    } else if (rFreeMinus > 0) {
                        refinementData.setFreeR(hkl.index(), (int) data[rFreeMinus]);
                    }
                }
                nRead++;
            } else {
                HKL tmp = new HKL(ih, ik, il);
                if (!reflectionList.resolution.inInverseResSqRange(Crystal.invressq(reflectionList.crystal, tmp))) {
                    nRes++;
                } else {
                    nIgnore++;
                }
            }
        }
        // Set up fsigf from F+ and F-.
        refinementData.generate_fsigf_from_anofsigf(anofSigF);
        // Log results.
        if (logger.isLoggable(Level.INFO)) {
            sb.append(format(" MTZ file type (machine stamp): %s\n", stampString));
            sb.append(format(" HKL data is %s\n", transpose ? "transposed" : "not transposed"));
            sb.append(format(" HKL read in:                             %d\n", nRead));
            sb.append(format(" HKL read as friedel mates:               %d\n", nFriedel));
            sb.append(format(" HKL NOT read in (too high resolution):   %d\n", nRes));
            sb.append(format(" HKL NOT read in (not in internal list?): %d\n", nIgnore));
            sb.append(format(" HKL NOT read in (F/sigF cutoff):         %d\n", nCut));
            sb.append(format(" HKL in internal list:                    %d\n", reflectionList.hkllist.size()));
            logger.info(sb.toString());
        }
        if (rFree < 0 && rFreePlus < 0 && rFreeMinus < 0) {
            refinementData.generateRFree();
        }
    } catch (EOFException e) {
        String message = " MTZ end of file reached.";
        logger.log(Level.WARNING, message, e);
        return false;
    } catch (IOException e) {
        String message = " MTZ IO Exception.";
        logger.log(Level.WARNING, message, e);
        return false;
    }
    return true;
}

Example 77 with ByteOrder

use of java.nio.ByteOrder in project openj9 by eclipse.

the class ELFFileReader method getELFFileReaderWithOffset.

public static ELFFileReader getELFFileReaderWithOffset(ImageInputStream in, long offset) throws IOException, InvalidDumpFormatException {
    // mark the stream as the validation and bitsize determinations move the underlying pointer
    in.mark();
    in.seek(offset);
    if (!isFormatValid(in)) {
        throw new InvalidDumpFormatException("The input stream is not an ELF file");
    }
    int bitness = in.read();
    ByteOrder byteOrder = getByteOrder(in);
    in.setByteOrder(byteOrder);
    // reset the stream so that the reader reads from the start
    in.reset();
    if (ELFCLASS64 == bitness) {
        return new ELF64FileReader(in, offset);
    } else {
        return new ELF32FileReader(in, offset);
    }
}

Example 78 with ByteOrder

use of java.nio.ByteOrder in project openj9 by eclipse.

the class ELFFileReader method getELFFileReaderWithOffset.

// ELF files can be either Big Endian (for example on Linux/PPC) or Little
// Endian (Linux/IA).
// Let's check whether it's actually an ELF file. We'll sort out the byte
// order later.
public static ELFFileReader getELFFileReaderWithOffset(File f, long offset) throws IOException, InvalidDumpFormatException {
    // Figure out which combination of bitness and architecture we are
    ImageInputStream in = new FileImageInputStream(f);
    if (!isFormatValid(in)) {
        throw new InvalidDumpFormatException("File " + f.getAbsolutePath() + " is not an ELF file");
    }
    int bitness = in.read();
    ByteOrder byteOrder = getByteOrder(in);
    // no longer need the input stream as passing the File descriptor into the reader
    in.close();
    if (ELFCLASS64 == bitness) {
        return new ELF64FileReader(f, byteOrder, offset);
    } else {
        return new ELF32FileReader(f, byteOrder, offset);
    }
}

Example 79 with ByteOrder

use of java.nio.ByteOrder in project openj9 by eclipse.

the class ELFFileReader method getByteOrder.

private static ByteOrder getByteOrder(ImageInputStream in) throws IOException {
    int endian = in.read();
    ByteOrder byteOrder = null;
    if (ELFDATA2MSB == endian) {
        byteOrder = ByteOrder.BIG_ENDIAN;
    } else {
        byteOrder = ByteOrder.LITTLE_ENDIAN;
    }
    return byteOrder;
}

Example 80 with ByteOrder

use of java.nio.ByteOrder in project openj9 by eclipse.

the class FileSniffer method isZipFile.

/**
 * Checks to see if the input stream is for a zip file, assumes that the stream is correctly positioned.
 * This method will reset the stream if possible to it's starting position. The reason for using this
 * method over just trying java.util.zip.ZipFile(File) and catching errors is that on some platforms
 * the zip support is provided by native libraries. It is possible to cause the native library to
 * crash when speculatively passing files into it.
 *
 * @param in stream to analyze
 * @return true if it is a zip file
 * @throws IOException
 */
/*
	 * zip format
	 * 
	 A.  Local file header:

        local file header signature     4 bytes  (0x04034b50)
        version needed to extract       2 bytes
        general purpose bit flag        2 bytes
        compression method              2 bytes
        last mod file time              2 bytes
        last mod file date              2 bytes
	 */
public static boolean isZipFile(ImageInputStream iis) throws IOException {
    ByteOrder byteOrder = iis.getByteOrder();
    try {
        // zip file format is in little endian format
        iis.setByteOrder(ByteOrder.LITTLE_ENDIAN);
        iis.mark();
        int sig = iis.readInt();
        if (sig != ZIP_ID) {
            // header doesn't match
            return false;
        }
        // date time starts at the 10th byte
        iis.seek(10);
        // validate the time stamp for the first local header entry
        // read an MS-DOS date time format
        int time = iis.readUnsignedShort();
        int seconds = (time & 0x1F) / 2;
        if ((seconds < 0) || (seconds > 60)) {
            return false;
        }
        int minutes = (time & 0x7E0) >> 5;
        if ((minutes < 0) || (minutes > 60)) {
            return false;
        }
        int hours = (time & 0xF800) >> 11;
        if ((hours < 0) || (hours > 23)) {
            return false;
        }
        // validate the date stamp for the first local header entry
        // read an MS-DOS date time format
        int date = iis.readUnsignedShort();
        int day = date & 0x1F;
        if ((day < 1) || (day > 31)) {
            return false;
        }
        int month = (date & 0x1E0) >> 5;
        if ((month < 1) || (month > 12)) {
            return false;
        }
        int year = ((date & 0xFE00) >> 9) + 1980;
        if ((year < 1980) || (year > 2500)) {
            return false;
        }
    } finally {
        // restore the byte order
        iis.setByteOrder(byteOrder);
        // reset the stream position
        iis.reset();
    }
    return true;
}