public void close() throws IOException {
   datas.close();
   if (sums != null) {
     sums.close();
   }
   set(fs.verifyChecksum, null, 1, 0);
 }
Exemplo n.º 2
0
  /*
   * Fetch a file that is in a Hadoop file system. Return a local File.
   * Interruptible.
   */
  private File hdfsFetch(Path fromPath, Reporter reporter)
      throws IOException, InterruptedException {
    UUID uniqueId = UUID.randomUUID();
    File toFile = new File(tempDir, uniqueId.toString() + "/" + fromPath.getName());
    File toDir = new File(toFile.getParent());
    if (toDir.exists()) {
      FileUtils.deleteDirectory(toDir);
    }
    toDir.mkdirs();
    Path toPath = new Path(toFile.getCanonicalPath());

    FileSystem fS = fromPath.getFileSystem(hadoopConf);
    FileSystem tofS = FileSystem.getLocal(hadoopConf);

    Throttler throttler = new Throttler((double) bytesPerSecThrottle);
    try {
      for (FileStatus fStatus : fS.globStatus(fromPath)) {
        log.info("Copying " + fStatus.getPath() + " to " + toPath);
        long bytesSoFar = 0;

        FSDataInputStream iS = fS.open(fStatus.getPath());
        FSDataOutputStream oS = tofS.create(toPath);

        byte[] buffer = new byte[downloadBufferSize];

        int nRead;
        while ((nRead = iS.read(buffer, 0, buffer.length)) != -1) {
          // Needed to being able to be interrupted at any moment.
          if (Thread.interrupted()) {
            iS.close();
            oS.close();
            cleanDirNoExceptions(toDir);
            throw new InterruptedException();
          }
          bytesSoFar += nRead;
          oS.write(buffer, 0, nRead);
          throttler.incrementAndThrottle(nRead);
          if (bytesSoFar >= bytesToReportProgress) {
            reporter.progress(bytesSoFar);
            bytesSoFar = 0l;
          }
        }

        if (reporter != null) {
          reporter.progress(bytesSoFar);
        }

        oS.close();
        iS.close();
      }

      return toDir;
    } catch (ClosedByInterruptException e) {
      // This can be thrown by the method read.
      cleanDirNoExceptions(toDir);
      throw new InterruptedIOException();
    }
  }
Exemplo n.º 3
0
    public void map(Text key, Text value, Context context)
        throws InterruptedException, IOException {

      String filename = key.toString();
      String json = value.toString();

      // Make sure the input is valid
      if (!(filename.isEmpty() || json.isEmpty())) {

        // Change the json-type feature to Mat-type feature
        Mat descriptor = json2mat(json);
        if (descriptor != null) {
          // Read the query feature from the cache in Hadoop
          Mat query_features;
          String pathStr = context.getConfiguration().get("featureFilePath");
          FileSystem fs = FileSystem.get(context.getConfiguration());
          FSDataInputStream fsDataInputStream = fs.open(new Path(pathStr));
          StringBuilder sb = new StringBuilder();

          // Use a buffer to read the query_feature
          int remain = fsDataInputStream.available();
          while (remain > 0) {
            int read;
            byte[] buf = new byte[BUF_SIZE];
            read = fsDataInputStream.read(buf, fsDataInputStream.available() - remain, BUF_SIZE);
            sb.append(new String(buf, 0, read, StandardCharsets.UTF_8));
            remain = remain - read;
            System.out.println("remain:" + remain + "\tread:" + read + "\tsb.size:" + sb.length());
          }

          // Read the query_feature line by line
          //                    Scanner sc = new Scanner(fsDataInputStream, "UTF-8");
          //                    StringBuilder sb = new StringBuilder();
          //                    while (sc.hasNextLine()) {
          //                        sb.append(sc.nextLine());
          //                    }
          //                    String query_json = sb.toString();
          //                    String query_json = new String(buf, StandardCharsets.UTF_8);

          String query_json = sb.toString();
          fsDataInputStream.close();
          query_features = json2mat(query_json);

          // Get the similarity of the current database image against the query image
          DescriptorMatcher matcher = DescriptorMatcher.create(DescriptorMatcher.FLANNBASED);
          MatOfDMatch matches = new MatOfDMatch();

          // Ensure the two features have same length of cols (the feature extracted are all 128
          // cols(at least in this case))
          if (query_features.cols() == descriptor.cols()) {

            matcher.match(query_features, descriptor, matches);
            DMatch[] dMatches = matches.toArray();

            // Calculate the max/min distances
            //                    double max_dist = Double.MAX_VALUE;
            //                    double min_dist = Double.MIN_VALUE;
            double max_dist = 0;
            double min_dist = 100;
            for (int i = 0; i < dMatches.length; i++) {
              double dist = dMatches[i].distance;
              if (min_dist > dist) min_dist = dist;
              if (max_dist < dist) max_dist = dist;
            }
            // Only distances ≤ threshold are good matches
            double threshold = max_dist * THRESHOLD_FACTOR;
            //                    double threshold = min_dist * 2;
            LinkedList<DMatch> goodMatches = new LinkedList<DMatch>();

            for (int i = 0; i < dMatches.length; i++) {
              if (dMatches[i].distance <= threshold) {
                goodMatches.addLast(dMatches[i]);
              }
            }

            // Get the ratio of good_matches to all_matches
            double ratio = (double) goodMatches.size() / (double) dMatches.length;

            System.out.println("*** current_record_filename:" + filename + " ***");
            System.out.println("feature:" + descriptor + "\nquery_feature:" + query_features);
            System.out.println(
                "min_dist of keypoints:" + min_dist + "  max_dist of keypoints:" + max_dist);
            System.out.println(
                "total_matches:" + dMatches.length + "\tgood_matches:" + goodMatches.size());
            //                    System.out.println("type:" + descriptor.type() + " channels:" +
            // descriptor.channels() + " rows:" + descriptor.rows() + " cols:" + descriptor.cols());
            //                    System.out.println("qtype:" + query_features.type() + "
            // qchannels:" + query_features.channels() + " qrows:" + query_features.rows() + "
            // qcols:" + query_features.cols());
            System.out.println();

            if (ratio > PERCENTAGE_THRESHOLD) {
              // Key:1        Value:filename|ratio
              context.write(ONE, new Text(filename + "|" + ratio));
              //                        context.write(ONE, new Text(filename + "|" +
              // String.valueOf(goodMatches.size())));
            }
          } else {
            System.out.println("The size of the features are not equal");
          }
        } else {
          // a null pointer, do nothing
          System.out.println("A broken/null feature:" + filename);
          System.out.println();
        }
      }
    }
  /**
   * Check how prefetch override works.
   *
   * @throws Exception IF failed.
   */
  public void testOpenPrefetchOverride() throws Exception {
    create(igfsSecondary, paths(DIR, SUBDIR), paths(FILE));

    // Write enough data to the secondary file system.
    final int blockSize = IGFS_BLOCK_SIZE;

    IgfsOutputStream out = igfsSecondary.append(FILE, false);

    int totalWritten = 0;

    while (totalWritten < blockSize * 2 + chunk.length) {
      out.write(chunk);

      totalWritten += chunk.length;
    }

    out.close();

    awaitFileClose(igfsSecondary.asSecondary(), FILE);

    // Instantiate file system with overridden "seq reads before prefetch" property.
    Configuration cfg = new Configuration();

    cfg.addResource(U.resolveIgniteUrl(PRIMARY_CFG));

    int seqReads = SEQ_READS_BEFORE_PREFETCH + 1;

    cfg.setInt(String.format(PARAM_IGFS_SEQ_READS_BEFORE_PREFETCH, "igfs:grid@"), seqReads);

    FileSystem fs = FileSystem.get(new URI(PRIMARY_URI), cfg);

    // Read the first two blocks.
    Path fsHome = new Path(PRIMARY_URI);
    Path dir = new Path(fsHome, DIR.name());
    Path subdir = new Path(dir, SUBDIR.name());
    Path file = new Path(subdir, FILE.name());

    FSDataInputStream fsIn = fs.open(file);

    final byte[] readBuf = new byte[blockSize * 2];

    fsIn.readFully(0, readBuf, 0, readBuf.length);

    // Wait for a while for prefetch to finish (if any).
    IgfsMetaManager meta = igfs.context().meta();

    IgfsFileInfo info = meta.info(meta.fileId(FILE));

    IgfsBlockKey key = new IgfsBlockKey(info.id(), info.affinityKey(), info.evictExclude(), 2);

    IgniteCache<IgfsBlockKey, byte[]> dataCache =
        igfs.context().kernalContext().cache().jcache(igfs.configuration().getDataCacheName());

    for (int i = 0; i < 10; i++) {
      if (dataCache.containsKey(key)) break;
      else U.sleep(100);
    }

    fsIn.close();

    // Remove the file from the secondary file system.
    igfsSecondary.delete(FILE, false);

    // Try reading the third block. Should fail.
    GridTestUtils.assertThrows(
        log,
        new Callable<Object>() {
          @Override
          public Object call() throws Exception {
            IgfsInputStream in0 = igfs.open(FILE);

            in0.seek(blockSize * 2);

            try {
              in0.read(readBuf);
            } finally {
              U.closeQuiet(in0);
            }

            return null;
          }
        },
        IOException.class,
        "Failed to read data due to secondary file system exception: /dir/subdir/file");
  }