List of usage examples for java.io DataInputStream skipBytes
public final int skipBytes(int n) throws IOException
skipBytes
method of DataInput
. From source file:ffx.realspace.CCP4MapFilter.java
/** * {@inheritDoc}// www . j a v a 2 s . c o m */ @Override public Crystal getCrystal(String fileName, CompositeConfiguration properties) { int imapData; int spaceGroup = -1; double cellA = -1.0; double cellB = -1.0; double cellC = -1.0; double cellAlpha = -1.0; double cellBeta = -1.0; double cellGamma = -1.0; ByteOrder byteOrder = ByteOrder.nativeOrder(); FileInputStream fileInputStream; DataInputStream dataInputStream; // first determine byte order of file versus system try { fileInputStream = new FileInputStream(fileName); dataInputStream = new DataInputStream(fileInputStream); dataInputStream.skipBytes(212); byte bytes[] = new byte[4]; dataInputStream.read(bytes, 0, 4); ByteBuffer byteBuffer = ByteBuffer.wrap(bytes); imapData = byteBuffer.order(ByteOrder.BIG_ENDIAN).getInt(); String stampString = Integer.toHexString(imapData); 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; } fileInputStream.close(); } catch (Exception e) { String message = " Fatal exception reading CCP4 map.\n"; logger.log(Level.SEVERE, message, e); } try { fileInputStream = new FileInputStream(fileName); dataInputStream = new DataInputStream(fileInputStream); dataInputStream.skipBytes(40); byte bytes[] = new byte[80]; dataInputStream.read(bytes, 0, 80); ByteBuffer byteBuffer = ByteBuffer.wrap(bytes); cellA = byteBuffer.order(byteOrder).getFloat(); cellB = byteBuffer.order(byteOrder).getFloat(); cellC = byteBuffer.order(byteOrder).getFloat(); cellAlpha = byteBuffer.order(byteOrder).getFloat(); cellBeta = byteBuffer.order(byteOrder).getFloat(); cellGamma = byteBuffer.order(byteOrder).getFloat(); for (int i = 0; i < 3; i++) { byteBuffer.order(byteOrder).getInt(); } for (int i = 0; i < 3; i++) { byteBuffer.order(byteOrder).getFloat(); } spaceGroup = byteBuffer.order(byteOrder).getInt(); fileInputStream.close(); } catch (Exception e) { String message = " Fatal exception reading CCP4 map.\n"; logger.log(Level.SEVERE, message, e); } return new Crystal(cellA, cellB, cellC, cellAlpha, cellBeta, cellGamma, SpaceGroup.spaceGroupNames[spaceGroup - 1]); }
From source file:cn.xiongyihui.wificar.MjpegStream.java
public Bitmap readFrame(DataInputStream in) throws IOException { int mContentLength = -1; in.mark(FRAME_MAX_LENGTH);//from www.ja va 2s . c om int headerLen = getStartOfSequence(in, SOI_MARKER); in.reset(); byte[] header = new byte[headerLen]; in.readFully(header); try { mContentLength = parseContentLength(header); } catch (NumberFormatException nfe) { mContentLength = getEndOfSeqeunce(in, EOF_MARKER); } in.reset(); byte[] frameData = new byte[mContentLength]; in.skipBytes(headerLen); in.readFully(frameData); return BitmapFactory.decodeStream(new ByteArrayInputStream(frameData)); }
From source file:ffx.realspace.CCP4MapFilter.java
/** * {@inheritDoc}/*from w w w. j a va 2s . c o m*/ */ @Override public boolean readFile(String filename, RealSpaceRefinementData refinementdata, CompositeConfiguration properties) { int imapData; double cellA, cellB, cellC, cellAlpha, cellBeta, cellGamma; String stampString; ByteOrder byteOrder = ByteOrder.nativeOrder(); FileInputStream fileInputStream; DataInputStream dataInputStream; double min = Double.POSITIVE_INFINITY; double max = Double.NEGATIVE_INFINITY; double mean = 0.0; double sd = 0.0; double rmsd = 0.0; // First determine byte order of file versus system try { fileInputStream = new FileInputStream(filename); dataInputStream = new DataInputStream(fileInputStream); dataInputStream.skipBytes(212); byte bytes[] = new byte[4]; dataInputStream.read(bytes, 0, 4); ByteBuffer byteBuffer = ByteBuffer.wrap(bytes); imapData = byteBuffer.order(ByteOrder.BIG_ENDIAN).getInt(); stampString = Integer.toHexString(imapData); 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; } if (logger.isLoggable(Level.INFO)) { StringBuilder sb = new StringBuilder(); sb.append(String.format("\n Opening CCP4 map: %s\n", filename)); //sb.append(String.format("file type (machine stamp): %s\n", stampString)); logger.info(sb.toString()); } fileInputStream.close(); } catch (Exception e) { String message = " Fatal exception reading CCP4 map.\n"; logger.log(Level.SEVERE, message, e); } try { fileInputStream = new FileInputStream(filename); dataInputStream = new DataInputStream(fileInputStream); byte bytes[] = new byte[2048]; dataInputStream.read(bytes, 0, 1024); ByteBuffer byteBuffer = ByteBuffer.wrap(bytes); int ext[] = new int[3]; ext[0] = byteBuffer.order(byteOrder).getInt(); ext[1] = byteBuffer.order(byteOrder).getInt(); ext[2] = byteBuffer.order(byteOrder).getInt(); // mode (2 = reals, only one we accept) int mode = byteBuffer.order(byteOrder).getInt(); int ori[] = new int[3]; ori[0] = byteBuffer.order(byteOrder).getInt(); ori[1] = byteBuffer.order(byteOrder).getInt(); ori[2] = byteBuffer.order(byteOrder).getInt(); int ni[] = new int[3]; ni[0] = byteBuffer.order(byteOrder).getInt(); ni[1] = byteBuffer.order(byteOrder).getInt(); ni[2] = byteBuffer.order(byteOrder).getInt(); cellA = byteBuffer.order(byteOrder).getFloat(); cellB = byteBuffer.order(byteOrder).getFloat(); cellC = byteBuffer.order(byteOrder).getFloat(); cellAlpha = byteBuffer.order(byteOrder).getFloat(); cellBeta = byteBuffer.order(byteOrder).getFloat(); cellGamma = byteBuffer.order(byteOrder).getFloat(); int axisi[] = new int[3]; for (int i = 0; i < 3; i++) { int axis = byteBuffer.order(byteOrder).getInt(); switch (axis) { case 1: axisi[0] = i; break; case 2: axisi[1] = i; break; case 3: axisi[2] = i; break; } } min = byteBuffer.order(byteOrder).getFloat(); max = byteBuffer.order(byteOrder).getFloat(); mean = byteBuffer.order(byteOrder).getFloat(); int sg = byteBuffer.order(byteOrder).getInt(); int nsymb = byteBuffer.order(byteOrder).getInt(); int skew = byteBuffer.order(byteOrder).getInt(); for (int i = 0; i < 12; i++) { byteBuffer.order(byteOrder).getFloat(); } for (int i = 0; i < 15; i++) { byteBuffer.order(byteOrder).getInt(); } byte word[] = new byte[2048]; byteBuffer.order(byteOrder).get(word, 0, 4); String mapString = new String(word); sd = byteBuffer.order(byteOrder).getFloat(); rmsd = byteBuffer.order(byteOrder).getFloat(); if (logger.isLoggable(Level.INFO)) { StringBuilder sb = new StringBuilder(); sb.append(String.format(" Column origin: %d\t Extent: %d\n", ori[0], ext[0])); sb.append(String.format(" Row origin: %d\t Extent: %d\n", ori[1], ext[1])); sb.append(String.format(" Section origin: %d\t Extent: %d\n", ori[2], ext[2])); sb.append(String.format(" Axis order: %d %d %d\n", axisi[0], axisi[1], axisi[2])); sb.append(String.format(" Number of X, Y, Z columns: %d %d %d\n", ni[0], ni[1], ni[2])); sb.append(String.format(" Spacegroup: %d (%s)\n", sg, SpaceGroup.spaceGroupNames[sg - 1])); sb.append(String.format(" Cell: %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f\n", cellA, cellB, cellC, cellAlpha, cellBeta, cellGamma)); logger.info(sb.toString()); } int nlabel = byteBuffer.order(byteOrder).getInt(); for (int i = 0; i < 10; i++) { byteBuffer.order(byteOrder).get(word, 0, 80); mapString = new String(word); } if (nsymb > 0) { byteBuffer.rewind(); dataInputStream.read(bytes, 0, nsymb); for (int i = 0; i < nsymb / 80; i += 80) { byteBuffer.order(byteOrder).get(word, 0, 80); mapString = new String(word); } } byteBuffer.rewind(); dataInputStream.read(bytes, 0, 2048); refinementdata.setData(new double[ext[0] * ext[1] * ext[2]]); int ijk[] = new int[3]; int index, x, y, z; refinementdata.setOrigin(ori[axisi[0]], ori[axisi[1]], ori[axisi[2]]); int nx = ext[axisi[0]]; int ny = ext[axisi[1]]; int nz = ext[axisi[2]]; refinementdata.setExtent(nx, ny, nz); refinementdata.setNI(ni[0], ni[1], ni[2]); for (ijk[2] = 0; ijk[2] < ext[2]; ijk[2]++) { for (ijk[1] = 0; ijk[1] < ext[1]; ijk[1]++) { for (ijk[0] = 0; ijk[0] < ext[0]; ijk[0]++) { x = ijk[axisi[0]]; y = ijk[axisi[1]]; z = ijk[axisi[2]]; index = x + nx * (y + ny * z); refinementdata.getData()[index] = byteBuffer.order(byteOrder).getFloat(); if (!byteBuffer.hasRemaining()) { byteBuffer.rewind(); dataInputStream.read(bytes, 0, 2048); } } } } fileInputStream.close(); } catch (Exception e) { String message = " Fatal exception reading CCP4 map.\n"; logger.log(Level.SEVERE, message, e); } return true; }
From source file:ffx.xray.CCP4MapFilter.java
/** * {@inheritDoc}/*from w ww.ja va 2s . co m*/ */ @Override public boolean readFile(String filename, RealSpaceRefinementData refinementdata, CompositeConfiguration properties) { int imapdata; double cella, cellb, cellc, cellalpha, cellbeta, cellgamma; String stampstr; ByteOrder b = ByteOrder.nativeOrder(); FileInputStream fis; DataInputStream dis; double min = Double.POSITIVE_INFINITY; double max = Double.NEGATIVE_INFINITY; double mean = 0.0; double sd = 0.0; double rmsd = 0.0; // first determine byte order of file versus system try { fis = new FileInputStream(filename); dis = new DataInputStream(fis); dis.skipBytes(212); byte bytes[] = new byte[4]; dis.read(bytes, 0, 4); ByteBuffer bb = ByteBuffer.wrap(bytes); imapdata = bb.order(ByteOrder.BIG_ENDIAN).getInt(); stampstr = Integer.toHexString(imapdata); // System.out.println("stamp: " + stampstr); switch (stampstr.charAt(0)) { case '1': case '3': if (b.equals(ByteOrder.LITTLE_ENDIAN)) { b = ByteOrder.BIG_ENDIAN; } break; case '4': if (b.equals(ByteOrder.BIG_ENDIAN)) { b = ByteOrder.LITTLE_ENDIAN; } break; } if (logger.isLoggable(Level.INFO)) { StringBuilder sb = new StringBuilder(); sb.append(String.format("\nOpening CCP4 map: %s\n", filename)); sb.append(String.format("file type (machine stamp): %s\n", stampstr)); logger.info(sb.toString()); } fis.close(); } catch (Exception e) { String message = "Fatal exception reading CCP4 map.\n"; logger.log(Level.SEVERE, message, e); System.exit(-1); } try { fis = new FileInputStream(filename); dis = new DataInputStream(fis); byte bytes[] = new byte[2048]; dis.read(bytes, 0, 1024); ByteBuffer bb = ByteBuffer.wrap(bytes); int ext[] = new int[3]; ext[0] = bb.order(b).getInt(); ext[1] = bb.order(b).getInt(); ext[2] = bb.order(b).getInt(); // mode (2 = reals, only one we accept) int mode = bb.order(b).getInt(); int ori[] = new int[3]; ori[0] = bb.order(b).getInt(); ori[1] = bb.order(b).getInt(); ori[2] = bb.order(b).getInt(); int ni[] = new int[3]; ni[0] = bb.order(b).getInt(); ni[1] = bb.order(b).getInt(); ni[2] = bb.order(b).getInt(); cella = bb.order(b).getFloat(); cellb = bb.order(b).getFloat(); cellc = bb.order(b).getFloat(); cellalpha = bb.order(b).getFloat(); cellbeta = bb.order(b).getFloat(); cellgamma = bb.order(b).getFloat(); int axisi[] = new int[3]; for (int i = 0; i < 3; i++) { int axis = bb.order(b).getInt(); switch (axis) { case 1: axisi[0] = i; break; case 2: axisi[1] = i; break; case 3: axisi[2] = i; break; } } min = bb.order(b).getFloat(); max = bb.order(b).getFloat(); mean = bb.order(b).getFloat(); int sg = bb.order(b).getInt(); int nsymb = bb.order(b).getInt(); int skew = bb.order(b).getInt(); for (int i = 0; i < 12; i++) { bb.order(b).getFloat(); } for (int i = 0; i < 15; i++) { bb.order(b).getInt(); } byte word[] = new byte[2048]; bb.order(b).get(word, 0, 4); String mapstr = new String(word); // System.out.println("MAP?: " + mapstr); sd = bb.order(b).getFloat(); rmsd = bb.order(b).getFloat(); /* System.out.println("col: " + ori[0] + " " + ext[0] + " " + ni[0]); System.out.println("row: " + ori[1] + " " + ext[1] + " " + ni[1]); System.out.println("sec: " + ori[2] + " " + ext[2] + " " + ni[2]); System.out.println("order: " + axisi[0] + " " + axisi[1] + " " + axisi[2]); System.out.println("min: " + min + " max: " + max + " mean: " + mean); System.out.println("sd: " + sd + " rmsd: " + rmsd); System.out.println("sg: " + sg); System.out.println("a: " + cella + " b: " + cellb + " c: " + cellc + " alpha: " + cellalpha + " beta: " + cellbeta + " gamma: " + cellgamma); */ if (logger.isLoggable(Level.INFO)) { StringBuilder sb = new StringBuilder(); sb.append(String.format(" column origin: %d extent: %d\n", ori[0], ext[0])); sb.append(String.format(" row origin: %d extent: %d\n", ori[1], ext[1])); sb.append(String.format(" section origin: %d extent: %d\n", ori[2], ext[2])); sb.append(String.format(" axis order: %d %d %d\n", axisi[0], axisi[1], axisi[2])); sb.append(String.format(" number of X, Y, Z columns: %d %d %d\n", ni[0], ni[1], ni[2])); sb.append(String.format(" spacegroup #: %d (name: %s)\n", sg, SpaceGroup.spaceGroupNames[sg - 1])); sb.append(String.format(" cell: %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f\n", cella, cellb, cellc, cellalpha, cellbeta, cellgamma)); logger.info(sb.toString()); } int nlabel = bb.order(b).getInt(); // System.out.println("nsymb: " + nsymb + " nlabel: " + nlabel); for (int i = 0; i < 10; i++) { bb.order(b).get(word, 0, 80); mapstr = new String(word); // System.out.println("label " + i + " : " + mapstr); } if (nsymb > 0) { bb.rewind(); dis.read(bytes, 0, nsymb); for (int i = 0; i < nsymb / 80; i += 80) { bb.order(b).get(word, 0, 80); mapstr = new String(word); // System.out.println("symm: " + mapstr); } } bb.rewind(); dis.read(bytes, 0, 2048); refinementdata.data = new double[ext[0] * ext[1] * ext[2]]; int ijk[] = new int[3]; int index, x, y, z; refinementdata.ori[0] = ori[axisi[0]]; refinementdata.ori[1] = ori[axisi[1]]; refinementdata.ori[2] = ori[axisi[2]]; int nx = ext[axisi[0]]; int ny = ext[axisi[1]]; int nz = ext[axisi[2]]; refinementdata.ext[0] = nx; refinementdata.ext[1] = ny; refinementdata.ext[2] = nz; refinementdata.ni[0] = ni[0]; refinementdata.ni[1] = ni[1]; refinementdata.ni[2] = ni[2]; for (ijk[2] = 0; ijk[2] < ext[2]; ijk[2]++) { for (ijk[1] = 0; ijk[1] < ext[1]; ijk[1]++) { for (ijk[0] = 0; ijk[0] < ext[0]; ijk[0]++) { x = ijk[axisi[0]]; y = ijk[axisi[1]]; z = ijk[axisi[2]]; index = x + nx * (y + ny * z); refinementdata.data[index] = bb.order(b).getFloat(); if (!bb.hasRemaining()) { bb.rewind(); dis.read(bytes, 0, 2048); } } } } fis.close(); } catch (Exception e) { String message = "Fatal exception reading CCP4 map.\n"; logger.log(Level.SEVERE, message, e); System.exit(-1); } return true; }
From source file:org.bdval.cache.TableCache.java
public ObjectSet<CharSequence> getTableColumnIds(final int splitId, final String splitType, final String datasetName) { final File cachedTableFile = getCachedTableFile(splitId, splitType, datasetName); final ObjectSet<CharSequence> result = new ObjectOpenHashSet<CharSequence>(); DataInputStream dataInput = null; try {/*from ww w .j a v a2s . c o m*/ dataInput = new DataInputStream(new FastBufferedInputStream(new FileInputStream(cachedTableFile))); final int numberOfColumns = dataInput.readInt(); LOG.info("Reading cached table with " + numberOfColumns + " columns"); for (int i = 0; i < numberOfColumns; i++) { final String colType = dataInput.readUTF(); final String colId = dataInput.readUTF(); result.add(colId); if ("s".equals(colType)) { final int numStrings = dataInput.readInt(); for (int j = 0; j < numStrings; j++) { dataInput.readUTF(); } } else if ("d".equals(colType)) { final int numDoubles = dataInput.readInt(); // we don't need to read these doubles, just skip them; final int numBytes = Double.SIZE * numDoubles / 8; final int actualBytes = dataInput.skipBytes(numBytes); if (actualBytes != numBytes) { LOG.warn("actual bytes skipped (" + actualBytes + ") does " + "not equal expected of " + numBytes); } } else { LOG.error("UNKNOWN COLUMN TYPE " + colType + " cannot read cached table from file " + filenameOf(cachedTableFile)); return null; } } return result; } catch (IOException e) { LOG.error("Error getting column ids", e); return null; } finally { IOUtils.closeQuietly(dataInput); } }
From source file:org.bdval.cache.TableCache.java
/** * Retrieve a cached table from the cache. isTableCached should be called * before calling this to verify that the table is cached. Null will * be returned if the table wasn't in the cache or there was a problem * reading the table./*from ww w . ja v a 2s. co m*/ * * @param splitId The split id * @param splitType The Split type * @param datasetName The dataset name * @param geneListFilter A gene list. If not null, the gene list is queried with each double * column identifier to determine if the identifier is contained in the gene list. Columns * that do not match the gene list are not loaded. * @return the table read from the cache (or null if it could not be read) */ public Table getCachedTable(final int splitId, final String splitType, final String datasetName, final GeneList geneListFilter) { final File cachedTableFile = getCachedTableFile(splitId, splitType, datasetName); if (geneListFilter != null && !(geneListFilter instanceof FullGeneList)) { final ObjectSet<CharSequence> tableColumnIds = getTableColumnIds(splitId, splitType, datasetName); geneListFilter.calculateProbeSetSelection(tableColumnIds); } DataInputStream dataInput = null; try { dataInput = new DataInputStream(new FastBufferedInputStream(new FileInputStream(cachedTableFile))); final ArrayTable result = new ArrayTable(); final int numberOfColumns = dataInput.readInt(); LOG.info("Reading cached table with " + numberOfColumns + " columns"); for (int i = 0; i < numberOfColumns; i++) { final String colType = dataInput.readUTF(); final String colId = dataInput.readUTF(); if ("s".equals(colType)) { final int numStrings = dataInput.readInt(); resize(result, numStrings); final int columnIndex = result.addColumn(colId, String.class); for (int j = 0; j < numStrings; j++) { result.appendObject(columnIndex, dataInput.readUTF()); } } else if ("d".equals(colType)) { final int numDoubles = dataInput.readInt(); resize(result, numDoubles); if (geneListFilter != null && !geneListFilter.isProbesetInList(colId)) { // the column does not match the gene list. Skip this column // we don't need to read these doubles, just skip them; final int numBytes = Double.SIZE * numDoubles / 8; final int actualBytes = dataInput.skipBytes(numBytes); if (actualBytes != numBytes) { LOG.warn("actual bytes skipped (" + actualBytes + ") does" + "not equal expected of " + numBytes); } continue; } final int columnIndex = result.addColumn(colId, double.class); for (int j = 0; j < numDoubles; j++) { result.appendDoubleValue(columnIndex, dataInput.readDouble()); } } else { LOG.error("UNKNOWN COLUMN TYPE " + colType + " cannot read cached table from file " + filenameOf(cachedTableFile)); return null; } } return result; } catch (IOException e) { LOG.error(e); return null; } catch (TypeMismatchException e) { LOG.error("TypeMismatchException adding data to Table " + filenameOf(cachedTableFile), e); return null; } finally { IOUtils.closeQuietly(dataInput); } }
From source file:net.sergetk.mobile.lcdui.BitmapFont.java
/** * Creates a new font from the resource. The capacity of the color cache defines maximum size of * the color cache.//from w ww . j av a2 s. co m * * @param fontPath * the resource name * @param colorCacheCapacity * the maximum color cache size */ public BitmapFont(String fontPath, int colorCacheCapacity) { this.style = Font.STYLE_PLAIN; this.currentColor = 0; this.colorCache = new CacheEntry[colorCacheCapacity]; this.colorUsageCounts = new IntHashMap(colorCacheCapacity * 2); try { InputStream input = new Object().getClass().getResourceAsStream(fontPath); if (input == null) { throw new IOException(); } DataInputStream data = new DataInputStream(input); int streamLen = data.available(); this.fontFilePath = fontPath; this.version = data.readByte(); this.height = data.readByte(); this.baseline = data.readByte(); this.xIndent = data.readByte(); this.yIndent = data.readByte(); this.spaceWidth = data.readByte(); characterMap = data.readUTF(); int count = characterMap.length(); // read characters widthes this.widths = new int[count]; this.x = new int[count]; this.y = new int[count]; for (int i = 0; i < count; i++) { widths[i] = data.readByte(); } baseImage = null; // the original implementation supported multiple-images // in the font file, but this is not necessary. Because I do // not want to change the encoding, I am leaving this byte that // used to represent the number of PNGs in the file data.skipBytes(1); short pngLen = data.readShort(); byte[] buffer = new byte[pngLen]; data.read(buffer, 0, pngLen); this.pngOffset = (short) (streamLen - pngLen); baseImage = Image.createImage(buffer, 0, pngLen); currentImage = baseImage; // calculate characters coordinates int curX = 0, curY = 0; for (int i = 0; i < count; i++) { if (widths[i] < 0) { // negative width points to another character int sourceIndex = -widths[i]; widths[i] = widths[sourceIndex]; x[i] = x[sourceIndex]; y[i] = y[sourceIndex]; } else { x[i] = curX; y[i] = curY; curX += widths[i]; } } if (defaultFont == null) defaultFont = this; } catch (IOException e) { // Log.warn("IOException reading font: ", e); System.err.println("IOException reading font: " + e.getMessage()); e.printStackTrace(); } }
From source file:com.serenegiant.media.TLMediaEncoder.java
private void checkLastSequence() { if (DEBUG)/*from ww w.jav a 2 s. c o m*/ Log.v(TAG, "checkLastSequence:"); int sequence = -1; MediaFormat configFormat = null; try { final DataInputStream in = openInputStream(mBaseDir, mType, 0); if (in != null) try { // read MediaFormat data for MediaCodec and for MediaMuxer readHeader(in); configFormat = asMediaFormat(in.readUTF()); // for MediaCodec in.readUTF(); // for MediaMuxer // search last sequence // this is not a effective implementation for large intermediate file. // ex. it may be better to split into multiple files for each sequence // or split into two files; file for control block and file for raw bit stream. final TLMediaFrameHeader header = new TLMediaFrameHeader(); for (; mIsRunning;) { readHeader(in, header); in.skipBytes(header.size); sequence = Math.max(sequence, header.sequence); } } finally { in.close(); } } catch (Exception e) { // ignore } mSequence = sequence; mConfigFormat = configFormat; if (sequence < 0) { // if intermediate files do not exist or invalid, remove them and re-create intermediate directory delete(mBaseDir); mBaseDir.mkdirs(); } if (DEBUG) Log.v(TAG, "checkLastSequence:finished. sequence=" + sequence); }
From source file:ffx.xray.MTZFilter.java
/** * {@inheritDoc}/*from ww w .j a v a 2 s .co m*/ */ @Override public ReflectionList getReflectionList(File mtzFile, CompositeConfiguration properties) { ByteOrder b = ByteOrder.nativeOrder(); FileInputStream fis; DataInputStream dis; try { fis = new FileInputStream(mtzFile); dis = new DataInputStream(fis); byte headeroffset[] = new byte[4]; byte bytes[] = new byte[80]; int offset = 0; // eat "MTZ" title dis.read(bytes, offset, 4); String mtzstr = new String(bytes); // header offset dis.read(headeroffset, offset, 4); // machine stamp dis.read(bytes, offset, 4); ByteBuffer bb = ByteBuffer.wrap(bytes); int stamp = bb.order(ByteOrder.BIG_ENDIAN).getInt(); String stampstr = Integer.toHexString(stamp); switch (stampstr.charAt(0)) { case '1': case '3': if (b.equals(ByteOrder.LITTLE_ENDIAN)) { b = ByteOrder.BIG_ENDIAN; } break; case '4': if (b.equals(ByteOrder.BIG_ENDIAN)) { b = ByteOrder.LITTLE_ENDIAN; } break; } bb = ByteBuffer.wrap(headeroffset); int headeroffseti = bb.order(b).getInt(); // skip to header and parse dis.skipBytes((headeroffseti - 4) * 4); for (Boolean parsing = true; parsing; dis.read(bytes, offset, 80)) { mtzstr = new String(bytes); parsing = parseHeader(mtzstr); } } catch (EOFException eof) { System.out.println("EOF reached "); } catch (IOException ioe) { System.out.println("IO Exception: " + ioe.getMessage()); return null; } // 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; fc = phic = -1; boolean print = false; parseColumns(print); parseFcColumns(print); if (fo < 0 && fplus < 0 && sigfo < 0 && sigfplus < 0 && fc < 0 && phic < 0) { logger.info( " The MTZ header contains insufficient information to generate the reflection list.\n For non-default column labels set fostring/sigfostring in the properties file."); return null; } Column c; if (fo > 0) { c = (Column) columns.get(fo); } else if (fplus > 0) { c = (Column) columns.get(fplus); } else { c = (Column) columns.get(fc); } Dataset d = (Dataset) datasets.get(c.id - dsetoffset); if (logger.isLoggable(Level.INFO)) { StringBuilder sb = new StringBuilder(); sb.append(String.format("\n Reading %s\n\n", mtzFile.getName())); sb.append(String.format(" Setting up reflection list based on MTZ file.\n")); sb.append(String.format(" Space group number: %d (name: %s)\n", sgnum, SpaceGroup.spaceGroupNames[sgnum - 1])); sb.append(String.format(" Resolution: %8.3f\n", 0.999999 * resHigh)); sb.append(String.format(" Cell: %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f\n", d.cell[0], d.cell[1], d.cell[2], d.cell[3], d.cell[4], d.cell[5])); logger.info(sb.toString()); } Crystal crystal = new Crystal(d.cell[0], d.cell[1], d.cell[2], d.cell[3], d.cell[4], d.cell[5], SpaceGroup.spaceGroupNames[sgnum - 1]); double sampling = 0.6; if (properties != null) { sampling = properties.getDouble("sampling", 0.6); } Resolution resolution = new Resolution(0.999999 * resHigh, sampling); return new ReflectionList(crystal, resolution, properties); }
From source file:ffx.xray.MTZFilter.java
public boolean readFcs(File mtzFile, ReflectionList reflectionlist, DiffractionRefinementData fcdata, CompositeConfiguration properties) { int nread, nignore, nres, nfriedel, ncut; ByteOrder b = ByteOrder.nativeOrder(); FileInputStream fis;//from w w w . ja va 2 s.co m DataInputStream dis; StringBuilder sb = new StringBuilder(); try { fis = new FileInputStream(mtzFile); dis = new DataInputStream(fis); byte headeroffset[] = new byte[4]; byte bytes[] = new byte[80]; int offset = 0; // eat "MTZ" title dis.read(bytes, offset, 4); String mtzstr = new String(bytes); // header offset dis.read(headeroffset, offset, 4); // machine stamp dis.read(bytes, offset, 4); ByteBuffer bb = ByteBuffer.wrap(bytes); int stamp = bb.order(ByteOrder.BIG_ENDIAN).getInt(); String stampstr = Integer.toHexString(stamp); switch (stampstr.charAt(0)) { case '1': case '3': if (b.equals(ByteOrder.LITTLE_ENDIAN)) { b = ByteOrder.BIG_ENDIAN; } break; case '4': if (b.equals(ByteOrder.BIG_ENDIAN)) { b = ByteOrder.LITTLE_ENDIAN; } break; } bb = ByteBuffer.wrap(headeroffset); int headeroffseti = bb.order(b).getInt(); // skip to header and parse dis.skipBytes((headeroffseti - 4) * 4); for (Boolean parsing = true; parsing; dis.read(bytes, offset, 80)) { mtzstr = new String(bytes); parsing = parseHeader(mtzstr); } // column identifiers fc = phic = fs = phis = -1; boolean print = true; parseFcColumns(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 fis = new FileInputStream(mtzFile); dis = new DataInputStream(fis); // skip initial header dis.skipBytes(80); float data[] = new float[nColumns]; HKL mate = new HKL(); // read in data ComplexNumber c = new ComplexNumber(); nread = nignore = nres = nfriedel = ncut = 0; for (int i = 0; i < nReflections; i++) { for (int j = 0; j < nColumns; j++) { dis.read(bytes, offset, 4); bb = ByteBuffer.wrap(bytes); data[j] = bb.order(b).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 hkl = reflectionlist.getHKL(mate); if (hkl != null) { if (fc > 0 && phic > 0) { c.re(data[fc] * cos(toRadians(data[phic]))); c.im(data[fc] * sin(toRadians(data[phic]))); fcdata.setFc(hkl.index(), c); } if (fs > 0 && phis > 0) { c.re(data[fs] * cos(toRadians(data[phis]))); c.im(data[fs] * sin(toRadians(data[phis]))); fcdata.setFs(hkl.index(), c); } nread++; } else { HKL tmp = new HKL(ih, ik, il); if (!reflectionlist.resolution .inInverseResSqRange(Crystal.invressq(reflectionlist.crystal, tmp))) { nres++; } else { nignore++; } } } sb.append(String.format(" MTZ file type (machine stamp): %s\n", stampstr)); sb.append(String.format(" Fc HKL read in: %d\n", nread)); sb.append(String.format(" Fc HKL read as friedel mates: %d\n", nfriedel)); sb.append(String.format(" Fc HKL NOT read in (too high resolution): %d\n", nres)); sb.append(String.format(" Fc HKL NOT read in (not in internal list?): %d\n", nignore)); sb.append(String.format(" Fc HKL NOT read in (F/sigF cutoff): %d\n", ncut)); sb.append(String.format(" HKL in internal list: %d\n", reflectionlist.hkllist.size())); if (logger.isLoggable(Level.INFO)) { logger.info(sb.toString()); } } catch (EOFException eof) { System.out.println("EOF reached "); return false; } catch (IOException ioe) { System.out.println("IO Exception: " + ioe.getMessage()); return false; } return true; }