void train_one_round(const Fast5Map& name_map, size_t round)
{
    const PoreModelMap& current_models = PoreModelSet::get_models(opt::trained_model_type);

    // Initialize the training summary stats for each kmer for each model
    ModelTrainingMap model_training_data;
    for(auto current_model_iter = current_models.begin(); current_model_iter != current_models.end(); current_model_iter++) {
        // one summary entry per kmer in the model
        std::vector<StateSummary> summaries(current_model_iter->second.get_num_states());
        model_training_data[current_model_iter->first] = summaries;
    }

    // Open the BAM and iterate over reads

    // load bam file
    htsFile* bam_fh = sam_open(opt::bam_file.c_str(), "r");
    assert(bam_fh != NULL);

    // load bam index file
    std::string index_filename = opt::bam_file + ".bai";
    hts_idx_t* bam_idx = bam_index_load(index_filename.c_str());
    assert(bam_idx != NULL);

    // read the bam header
    bam_hdr_t* hdr = sam_hdr_read(bam_fh);

    // load reference fai file
    faidx_t *fai = fai_load(opt::genome_file.c_str());

    hts_itr_t* itr;

    // If processing a region of the genome, only emit events aligned to this window
    int clip_start = -1;
    int clip_end = -1;

    if(opt::region.empty()) {
        // TODO: is this valid?
        itr = sam_itr_queryi(bam_idx, HTS_IDX_START, 0, 0);
    } else {
        fprintf(stderr, "Region: %s\n", opt::region.c_str());
        itr = sam_itr_querys(bam_idx, hdr, opt::region.c_str());
        hts_parse_reg(opt::region.c_str(), &clip_start, &clip_end);
    }

#ifndef H5_HAVE_THREADSAFE
    if(opt::num_threads > 1) {
        fprintf(stderr, "You enabled multi-threading but you do not have a threadsafe HDF5\n");
        fprintf(stderr, "Please recompile nanopolish's built-in libhdf5 or run with -t 1\n");
        exit(1);
    }
#endif

    // Initialize iteration
    std::vector<bam1_t*> records(opt::batch_size, NULL);
    for(size_t i = 0; i < records.size(); ++i) {
        records[i] = bam_init1();
    }

    int result;
    size_t num_reads_realigned = 0;
    size_t num_records_buffered = 0;
    Progress progress("[methyltrain]");

    do {
        assert(num_records_buffered < records.size());
        
        // read a record into the next slot in the buffer
        result = sam_itr_next(bam_fh, itr, records[num_records_buffered]);
        num_records_buffered += result >= 0;

        // realign if we've hit the max buffer size or reached the end of file
        if(num_records_buffered == records.size() || result < 0) {
            #pragma omp parallel for            
            for(size_t i = 0; i < num_records_buffered; ++i) {
                bam1_t* record = records[i];
                size_t read_idx = num_reads_realigned + i;
                if( (record->core.flag & BAM_FUNMAP) == 0) {
                    add_aligned_events(name_map, fai, hdr, record, read_idx, clip_start, clip_end, round, model_training_data);
                }
            }

            num_reads_realigned += num_records_buffered;
            num_records_buffered = 0;
        }

        if(opt::progress) {
            fprintf(stderr, "Realigned %zu reads in %.1lfs\r", num_reads_realigned, progress.get_elapsed_seconds());
        }
    } while(result >= 0);
    
    assert(num_records_buffered == 0);
    progress.end();
    
    // open the summary file
    std::stringstream summary_fn;
    summary_fn << "methyltrain" << opt::out_suffix << ".summary";
    FILE* summary_fp = fopen(summary_fn.str().c_str(), "w");
    fprintf(summary_fp, "model_short_name\tkmer\tnum_matches\tnum_skips\t"
                         "num_stays\tnum_events_for_training\twas_trained\t"
                         "trained_level_mean\ttrained_level_stdv\n");
//.........这里部分代码省略.........

ErrorList topolTest::checkPointInPolygon( double tolerance, QgsVectorLayer *layer1, QgsVectorLayer *layer2, bool isExtent )
{
  Q_UNUSED( tolerance );

  int i = 0;
  ErrorList errorList;

  if ( layer1->geometryType() != QgsWkbTypes::PointGeometry )
  {
    return errorList;
  }

  if ( layer2->geometryType() != QgsWkbTypes::PolygonGeometry )
  {
    return errorList;
  }

  QgsSpatialIndex *index = mLayerIndexes[layer2->id()];

  QgsGeometry canvasExtentPoly = QgsGeometry::fromWkt( qgsInterface->mapCanvas()->extent().asWktPolygon() );

  QList<FeatureLayer>::Iterator it;
  for ( it = mFeatureList1.begin(); it != mFeatureList1.end(); ++it )
  {
    if ( !( ++i % 100 ) )
      emit progress( i );
    if ( testCanceled() )
      break;
    QgsGeometry g1 = it->feature.geometry();
    QgsRectangle bb = g1.boundingBox();
    QList<QgsFeatureId> crossingIds;
    crossingIds = index->intersects( bb );
    QList<QgsFeatureId>::ConstIterator cit = crossingIds.begin();
    QList<QgsFeatureId>::ConstIterator crossingIdsEnd = crossingIds.end();
    bool touched = false;
    for ( ; cit != crossingIdsEnd; ++cit )
    {
      QgsFeature &f = mFeatureMap2[*cit].feature;
      QgsGeometry g2 = f.geometry();
      if ( g2.isNull() || !_canExportToGeos( g2 ) )
      {
        QgsMessageLog::logMessage( tr( "Second geometry missing or GEOS import failed." ), tr( "Topology plugin" ) );
        continue;
      }
      if ( g2.contains( g1 ) )
      {
        touched = true;
        break;
      }
    }
    if ( !touched )
    {
      QgsGeometry conflictGeom = g1;

      if ( isExtent )
      {
        if ( canvasExtentPoly.disjoint( conflictGeom ) )
        {
          continue;
        }
      }

      QList<FeatureLayer> fls;
      fls << *it << *it;
      //bb.scale(10);

      TopolErrorPointNotInPolygon *err = new TopolErrorPointNotInPolygon( bb, conflictGeom, fls );
      errorList << err;
    }
  }

  return errorList;
}

int main() {
    // The physical computations run at about 1500 Hz. 30 consecutive
    // time steps are mixed into a frame buffer for motion blur. But
    // this is not only about motion blur. This higher temporal resolution
    // is necessary to avoid discretization errors to grow too large and
    // to keep the whole thing "stable".
    //
    // The framebuffer is "oversampled" (higher resolution) for
    // anti-aliasing.
    const int num_particles = 10;
    const int substeps = 30; // temporal oversampling
    const int sover = 5; // spatial oversampling

    std::srand(std::time(0));
    std::vector<particle> ps;
    ps.push_back( // bottom border particle that is not moving
        make_particle(
            make_random_color(),
            -1
        )
    );
    for (int i = 0; i < num_particles; ++i) {
        ps.push_back( // almost equidistantly spaced particles
            make_particle(
                make_random_color(),
                (i + 0.9f + 0.2f * uniform_random()) / (1 + num_particles) * (num_leds + 1) - 1
            )
        );
    }
    ps.push_back( // top border particle that is not moving
        make_particle(
            make_random_color(),
            num_leds
        )
    );

    std::vector<int> framebuff (num_leds * 3 * sover);
    std::vector<unsigned char> scratch;
    int time = -1;
    int period = 10000; // time steps until next impulse
    int part_change_color_index = 1;
    color part_change_color_new = {{0}}, part_change_color_old = {{0}};
#ifdef WRITE_PPM
    const int iters = 500; // for debugging purposes
    write_binary_ppm_header(num_leds, iters, std::cout);
    for (int i = 0; i < iters; ++i) {
#else
    for (;;) {
#endif
        // blank frame buffer (black)
        std::fill(framebuff.begin(), framebuff.end(), 0);
        for (int s = 0; s < substeps; ++s) {
            render_frame(ps, sover, substeps, framebuff);
            time = (time + 1) % period;
            if (time <= 1000) { // impulse phase
                if (time == 0) {
                    period = 5000 + std::rand() % 10000;
                    part_change_color_index = (std::rand() % num_particles) + 1;
                    part_change_color_old = ps[part_change_color_index].col;
                    part_change_color_new = make_random_color();
                }
                float s1 = squared(std::sin(time * (3.14159265 / 2000)));
                float s2 = squared(std::sin(time * (3.14159265 / 1000)));
                ps[0].pos = s2 * 15 - 1; // move bottom particle around
                // also change the color of a random particle once in a while
                ps[part_change_color_index].col = fade(
                    part_change_color_old,
                    part_change_color_new, s1);
            }
            update_accels(ps);
            progress(ps);
        }
        write_frame(framebuff, 1.0f/substeps, sover, scratch, std::cout);
#ifndef WRITE_PPM
        usleep(20000); // wait 20 ms (=> about 50 frames/sec)
#endif
    }
    return 0;
}

/**
 * Apply the detector test criterion
 * @param counts1 :: A workspace containing the integrated counts of the first
 * white beam run
 * @param counts2 :: A workspace containing the integrated counts of the first
 * white beam run
 * @param average :: The computed median
 * @param variation :: The allowed variation in terms of number of medians, i.e
 * those spectra where
 * the ratio of the counts outside this range will fail the tests and will be
 * masked on counts1
 * @return number of detectors for which tests failed
 */
int DetectorEfficiencyVariation::doDetectorTests(
    API::MatrixWorkspace_const_sptr counts1,
    API::MatrixWorkspace_const_sptr counts2, const double average,
    double variation) {
  // DIAG in libISIS did this.  A variation of less than 1 doesn't make sense in
  // this algorithm
  if (variation < 1) {
    variation = 1.0 / variation;
  }
  // criterion for if the the first spectrum is larger than expected
  double largest = average * variation;
  // criterion for if the the first spectrum is lower than expected
  double lowest = average / variation;

  const int numSpec = static_cast<int>(counts1->getNumberHistograms());
  const int progStep = static_cast<int>(std::ceil(numSpec / 30.0));

  // Create a workspace for the output
  MaskWorkspace_sptr maskWS = this->generateEmptyMask(counts1);

  bool checkForMask = false;
  Geometry::Instrument_const_sptr instrument = counts1->getInstrument();
  if (instrument != nullptr) {
    checkForMask = ((instrument->getSource() != nullptr) &&
                    (instrument->getSample() != nullptr));
  }

  const double deadValue(1.0);
  int numFailed(0);
  PARALLEL_FOR3(counts1, counts2, maskWS)
  for (int i = 0; i < numSpec; ++i) {
    PARALLEL_START_INTERUPT_REGION
    // move progress bar
    if (i % progStep == 0) {
      advanceProgress(progStep * static_cast<double>(RTMarkDetects) / numSpec);
      progress(m_fracDone);
      interruption_point();
    }

    if (checkForMask) {
      const std::set<detid_t> &detids =
          counts1->getSpectrum(i)->getDetectorIDs();
      if (instrument->isMonitor(detids))
        continue;
      if (instrument->isDetectorMasked(detids)) {
        // Ensure it is masked on the output
        maskWS->dataY(i)[0] = deadValue;
        continue;
      }
    }

    const double signal1 = counts1->readY(i)[0];
    const double signal2 = counts2->readY(i)[0];

    // Mask out NaN and infinite
    if (boost::math::isinf(signal1) || boost::math::isnan(signal1) ||
        boost::math::isinf(signal2) || boost::math::isnan(signal2)) {
      maskWS->dataY(i)[0] = deadValue;
      PARALLEL_ATOMIC
      ++numFailed;
      continue;
    }

    // Check the ratio is within the given range
    const double ratio = signal1 / signal2;
    if (ratio < lowest || ratio > largest) {
      maskWS->dataY(i)[0] = deadValue;
      PARALLEL_ATOMIC
      ++numFailed;
    }

    PARALLEL_END_INTERUPT_REGION
  }
  PARALLEL_CHECK_INTERUPT_REGION

  // Register the results with the ADS
  setProperty("OutputWorkspace", maskWS);

  return numFailed;
}

void DimensionReductionBestPath(Thread* start, Thread* target, int n, vector<Thread*>& traj, vector<vector<VectorXd> >& mot) 
{
  Thread* st = new Thread(*start);
  Thread* en = new Thread(*target); 

  // need to call minimize energy on start from outside this method 
  if (n == 0) {
    glThreads[4]->setThread(new Thread(*start));
    glThreads[4]->updateThreadPoints();
    glThreads[5]->setThread(new Thread(*target));
    glThreads[5]->updateThreadPoints();
    glThreads[6]->setThread(new Thread(*target));
    glThreads[6]->updateThreadPoints();
    planner.initialize(new Thread(*st), new Thread(*en));
    initialized = true; 

    Thread goal_thread; Thread prev_thread; Thread next_thread; 
    while(!interruptEnabled) {
      #pragma omp parallel for num_threads(NUM_CPU_THREADS)
      for (int i = 0; i < 999999; i++) {
        if (!interruptEnabled) {  
          planner.planStep(goal_thread, prev_thread, next_thread);
        }
      }
    }
    
    planner.updateBestPath();
    
    RRTNode* node = planner.getTree()->front();
    node = node->next;
    while (node != NULL) {
      traj.push_back(new Thread(*node->thread));
      vector<VectorXd> wrapper_mot;
      wrapper_mot.push_back(node->motion);
      mot.push_back(wrapper_mot);
      node = node->next;
    }

  } else { 
    Thread* approxStart = planner.halfDimApproximation(st);
    Thread* approxTarget = planner.halfDimApproximation(en); 
    vector<Thread*> path;
    vector<vector<VectorXd> > motions; 
    DimensionReductionBestPath(approxStart, approxTarget, n-1, path, motions);
    /* use Trajectory Follower to follow the path in higher D space. */ 
    
    // transform the path to higher D space 
    vector<Thread*> transformed_path; 
    transformed_path.resize(path.size());
    boost::progress_display progress(path.size()); 
    for (int i = 0; i < path.size(); i++) {
      transformed_path[i] = planner.doubleDimApproximation(path[i]);
      ++progress; 
    }
     
    // follow the trajectory of the transformed approximation
    Trajectory_Follower *pathFollower = 
      new Trajectory_Follower(transformed_path, motions, st);

    pathFollower->control_to_finish();
    pathFollower->getReachedStates(traj);
    cout << traj.size() << endl;
    pathFollower->getMotions(mot);
  }

  apprxNodes[n] = new RRTNode(new Thread(*st));
  curApprxNodes[n] = apprxNodes[n]; 
  RRTNode* prevNode = apprxNodes[n]; 
  for (int i = 0; i < traj.size(); i++) {
    RRTNode* node = new RRTNode(new Thread(*traj[i]));
    node->prev = prevNode;
    prevNode->next = node;
    prevNode = node; 
  }

}

/* Valid sizes, according to FIPS 186-3 are (1024, 160), (2048. 224),
   (2048, 256), (3072, 256). Currenty, we use only q_bits of 160 or
   256. */
int
dsa_generate_keypair(struct dsa_public_key *pub,
		     struct dsa_private_key *key,
		     void *random_ctx, nettle_random_func *random,
		     void *progress_ctx, nettle_progress_func *progress,
		     unsigned p_bits, unsigned q_bits)
{
  mpz_t p0, p0q, r;
  unsigned p0_bits;
  unsigned a;

  switch (q_bits)
    {
    case 160:
      if (p_bits < DSA_SHA1_MIN_P_BITS)
	return 0;
      break;
    case 256:
      if (p_bits < DSA_SHA256_MIN_P_BITS)
	return 0;
      break;
    default:
      return 0;
    }

  mpz_init (p0);
  mpz_init (p0q);
  mpz_init (r);

  nettle_random_prime (pub->q, q_bits, 0, random_ctx, random,
		       progress_ctx, progress);

  p0_bits = (p_bits + 3)/2;
  
  nettle_random_prime (p0, p0_bits, 0,
		       random_ctx, random,
		       progress_ctx, progress);

  if (progress)
    progress (progress_ctx, 'q');
  
  /* Generate p = 2 r q p0 + 1, such that 2^{n-1} < p < 2^n.
   *
   * We select r in the range i + 1 < r <= 2i, with i = floor (2^{n-2} / (p0 q). */

  mpz_mul (p0q, p0, pub->q);

  _nettle_generate_pocklington_prime (pub->p, r, p_bits, 0,
				      random_ctx, random,
				      p0, pub->q, p0q);

  if (progress)
    progress (progress_ctx, 'p');

  mpz_mul (r, r, p0);

  for (a = 2; ; a++)
    {
      mpz_set_ui (pub->g, a);
      mpz_powm (pub->g, pub->g, r, pub->p);
      if (mpz_cmp_ui (pub->g, 1) != 0)
	break;
    }

  if (progress)
    progress (progress_ctx, 'g');

  mpz_set(r, pub->q);
  mpz_sub_ui(r, r, 2);
  nettle_mpz_random(key->x, random_ctx, random, r);

  mpz_add_ui(key->x, key->x, 1);

  mpz_powm(pub->y, pub->g, key->x, pub->p);

  if (progress)
    progress (progress_ctx, '\n');
  
  mpz_clear (p0);
  mpz_clear (p0q);
  mpz_clear (r);

  return 1;
}

int main(int argc, char **argv)
{
  kumy_file_t *kumy;
  miniseed_file_t *mseed[KUMY_FILE_CHANNELS];
  int32_t frame[KUMY_FILE_CHANNELS];
  uint64_t frames, l, frames_per_file, frames_total, frame_count = 0;
  int i;
  char oname[1024], folder[1024];
  uint32_t sample_rate, seconds_per_file;
  int percent = 0, old_percent = -1;
  int compression = 1, show_progress = 1;
  char *infile = 0;

  struct taia start_time; /* 1871 */
  struct taia stop_time;  /* 1951 */
  struct taia sync_time;  /* 2031 */
  struct taia skew_time;  /* 2111 */

  struct caltime ct;
  struct taia tt, dt;

  program = argv[0];
  parse_options(&argc, &argv, OPTIONS(
    FLAG('n', "no-compression", compression, 0),
    FLAG('q', "quiet", show_progress, 0),
    FLAG_CALLBACK('h', "help", usage)
  ));

  if (argc < 2) {
    usage(0, 0, 0);
  }

  infile = argv[1];
  if (!(kumy = kumy_file_open(infile))) {
    fprintf(stderr, "Invalid file: %s.\n", infile);
    return -1;
  }

  parse_text_date(&start_time, kumy->text_header[0].content + 1871);
  parse_text_date(&stop_time,  kumy->text_header[0].content + 1951);
  parse_text_date(&sync_time,  kumy->text_header[0].content + 2031);
  parse_text_date(&skew_time,  kumy->text_header[0].content + 2111);

  sample_rate = 1000000 / kumy->binary_header[0].sample_interval;

  if (sample_rate <= 250) {
    seconds_per_file = 86400;
  } else if (sample_rate <= 500) {
    seconds_per_file = 43200;
  } else if (sample_rate <= 1000) {
    seconds_per_file = 21600;
  } else if (sample_rate <= 2000) {
    seconds_per_file = 10800;
  } else {
    seconds_per_file = 5400;
  }

  frames_per_file = sample_rate * seconds_per_file;
  frames_total = kumy->binary_header[0].num_samples;

  caltime_utc(&ct, &start_time.sec, 0, 0);
  ct.hour = 0;
  ct.minute = 0;
  ct.second = 0;
  caltime_tai(&ct, &tt.sec);
  tt.nano = tt.atto = 0;

  while (!taia_less(&start_time, &tt)) {
    tt.sec.x += seconds_per_file;
  }

  taia_sub(&dt, &tt, &start_time);
  frames = taia_approx(&dt) / seconds_per_file * frames_per_file;

  l = last('.', infile);
  if (l == -1 || l >= sizeof(folder)) return -1;

  /* Create folder. */
  copy(folder, l, infile);
  folder[l] = 0;
  mkdir_p(folder);

  for (i = 0; i < KUMY_FILE_CHANNELS; ++i) {
    caltime_utc(&ct, &start_time.sec, 0, 0);
    snprintf(oname, sizeof(oname), "%s/%lld.%02lld.%02lld.%02lld.%02lld.%02lld.%s.seed",
      folder, (long long)ct.date.year, (long long)ct.date.month, (long long)ct.date.day, (long long)ct.hour, (long long)ct.minute, (long long)ct.second, channel_names[i]);

    if (!(mseed[i] = miniseed_file_create((char*)oname))) {
      fprintf(stderr, "Invalid file: %s.\n", oname);
      return -1;
    }
    miniseed_file_set_sample_rate(mseed[i], sample_rate);
    miniseed_file_set_start_time(mseed[i], &start_time);
    miniseed_file_set_info(mseed[i], "OBS", "DE", channel_names[i], "K");
    miniseed_file_set_compression(mseed[i], compression);
  }

  while (kumy_file_read_int_frame(kumy, frame) >= 0) {
    if (frames == 0) {
      /* Create new files.*/
//.........这里部分代码省略.........

void ProgressReceiver::timeout()
{
	emit progress(mReader->progress() * mScale);
}

void
GrdPlugin::saveTrimmed(QString trimFile,
			    int dmin, int dmax,
			    int wmin, int wmax,
			    int hmin, int hmax)
{
  QProgressDialog progress("Saving trimmed volume",
			   0,
			   0, 100,
			   0);
  progress.setMinimumDuration(0);

  int nX, nY, nZ;
  nX = m_depth;
  nY = m_width;
  nZ = m_height;

  int mX, mY, mZ;
  mX = dmax-dmin+1;
  mY = wmax-wmin+1;
  mZ = hmax-hmin+1;

  int nbytes = nY*nZ*m_bytesPerVoxel;
  uchar *tmp = new uchar[nbytes];

  uchar vt;
  if (m_voxelType == _UChar) vt = 0; // unsigned byte
  if (m_voxelType == _Char) vt = 1; // signed byte
  if (m_voxelType == _UShort) vt = 2; // unsigned short
  if (m_voxelType == _Short) vt = 3; // signed short
  if (m_voxelType == _Int) vt = 4; // int
  if (m_voxelType == _Float) vt = 8; // float
  
  QFile fout(trimFile);
  fout.open(QFile::WriteOnly);

  fout.write((char*)&vt, 1);
  fout.write((char*)&mX, 4);
  fout.write((char*)&mY, 4);
  fout.write((char*)&mZ, 4);

  for(uint i=dmin; i<=dmax; i++)
    {
      //----------------------------
      QFile fin(m_imageList[i]);
      fin.open(QFile::ReadOnly);
      fin.seek(m_headerBytes);
      fin.read((char*)tmp, nbytes);
      fin.close();
      //----------------------------      

      for(uint j=wmin; j<=wmax; j++)
	{
	  memcpy(tmp+(j-wmin)*mZ*m_bytesPerVoxel,
		 tmp+(j*nZ + hmin)*m_bytesPerVoxel,
		 mZ*m_bytesPerVoxel);
	}
	  
      fout.write((char*)tmp, mY*mZ*m_bytesPerVoxel);

      progress.setValue((int)(100*(float)(i-dmin)/(float)mX));
      qApp->processEvents();
    }

  fout.close();

  delete [] tmp;

  m_headerBytes = 13; // to be used for applyMapping function
}

//.........这里部分代码省略.........
                && (getconf_int("c_auth_mode") != AUTHMODE_LDAP)
                && (getconf_int("c_auth_mode") != AUTHMODE_LDAP_AD)
           ) {
            curr += 5;	/* skip LDAP questions if we're not authenticating against LDAP */
        }

        if (curr == eSysAdminName) {
            if (getconf_int("c_auth_mode") == AUTHMODE_NATIVE) {
                /* for native auth mode, fetch the admin's existing pw */
                snprintf(buf, sizeof buf, "AGUP %s", admin_name);
                serv_puts(buf);
                serv_gets(buf);
                if (buf[0] == '2') {
                    extract_token(admin_pass, &buf[4], 1, '|', sizeof admin_pass);
                }
            }
            else {
                ++curr;		/* skip the password question for non-native auth modes */
            }
        }
    }

    if ((pw = getpwuid( getconf_int("c_ctdluid") )) == NULL) {
        gid = getgid();
    } else {
        gid = pw->pw_gid;
    }

    if (create_run_directories(getconf_int("c_ctdluid"), gid) != 0) {
        display_error("%s\n", _("failed to create directories"));
    }

    activity = _("Reconfiguring Citadel server");
    progress(activity, 0, 5);
    sleep(1);					/* Let the message appear briefly */

    /*
     * Create the administrator account.  It's ok if the command fails if this user already exists.
     */
    progress(activity, 1, 5);
    snprintf(buf, sizeof buf, "CREU %s|%s", admin_name, admin_pass);
    serv_puts(buf);
    progress(activity, 2, 5);
    serv_gets(buf);
    progress(activity, 3, 5);

    /*
     * Assign the desired password and access level to the administrator account.
     */
    snprintf(buf, sizeof buf, "AGUP %s", admin_name);
    serv_puts(buf);
    progress(activity, 4, 5);
    serv_gets(buf);
    if (buf[0] == '2') {
        int admin_flags = extract_int(&buf[4], 2);
        int admin_times_called = extract_int(&buf[4], 3);
        int admin_msgs_posted = extract_int(&buf[4], 4);
        snprintf(buf, sizeof buf, "ASUP %s|%s|%d|%d|%d|6",
                 admin_name, admin_pass, admin_flags, admin_times_called, admin_msgs_posted
                );
        serv_puts(buf);
        serv_gets(buf);
    }
    progress(activity, 5, 5);

#ifndef __CYGWIN__

void
GrdPlugin::findMinMaxandGenerateHistogram()
{
  float rSize;
  float rMin;
  m_histogram.clear();
  if (m_voxelType == _UChar ||
      m_voxelType == _Char)
    {
      if (m_voxelType == _UChar) rMin = 0;
      if (m_voxelType == _Char) rMin = -127;
      rSize = 255;
      for(uint i=0; i<256; i++)
	m_histogram.append(0);
    }
  else if (m_voxelType == _UShort ||
      m_voxelType == _Short)
    {
      if (m_voxelType == _UShort) rMin = 0;
      if (m_voxelType == _Short) rMin = -32767;
      rSize = 65535;
      for(uint i=0; i<65536; i++)
	m_histogram.append(0);
    }
  else
    {
      QMessageBox::information(0, "Error", "Why am i here ???");
      return;
    }

//  //==================
//  // do not calculate histogram
//  if (m_voxelType == _UChar)
//    {
//      m_rawMin = 0;
//      m_rawMax = 255;
//      return;
//    }
//  //==================

  int nbytes = m_width*m_height*m_bytesPerVoxel;
  uchar *tmp = new uchar[nbytes];

  m_rawMin = 10000000;
  m_rawMax = -10000000;

  QProgressDialog progress("Generating Histogram",
			   0,
			   0, 100,
			   0);
  progress.setMinimumDuration(0);

  for(uint i=0; i<m_depth; i++)
    {
      progress.setValue((int)(100.0*(float)i/(float)m_depth));
      qApp->processEvents();

      //----------------------------
      QFile fin(m_imageList[i]);
      fin.open(QFile::ReadOnly);
      fin.seek(m_headerBytes);
      fin.read((char*)tmp, nbytes);
      fin.close();
      //----------------------------

      if (m_voxelType == _UChar)
	{
	  uchar *ptr = tmp;
	  MINMAXANDHISTOGRAM();
	}
      else if (m_voxelType == _Char)
	{
	  char *ptr = (char*) tmp;
	  MINMAXANDHISTOGRAM();
	}
      if (m_voxelType == _UShort)
	{
	  ushort *ptr = (ushort*) tmp;
	  MINMAXANDHISTOGRAM();
	}
      else if (m_voxelType == _Short)
	{
	  short *ptr = (short*) tmp;
	  MINMAXANDHISTOGRAM();
	}
      else if (m_voxelType == _Int)
	{
	  int *ptr = (int*) tmp;
	  MINMAXANDHISTOGRAM();
	}
      else if (m_voxelType == _Float)
	{
	  float *ptr = (float*) tmp;
	  MINMAXANDHISTOGRAM();
	}
    }

  delete [] tmp;

//  while(m_histogram.last() == 0)
//.........这里部分代码省略.........

void KeyframeAnimation::animate(CompositeAnimation* animation, RenderObject* renderer, const RenderStyle* currentStyle, 
                                    const RenderStyle* targetStyle, RefPtr<RenderStyle>& animatedStyle)
{
    // If we have not yet started, we will not have a valid start time, so just start the animation if needed.
    if (isNew() && m_animation->playState() == AnimPlayStatePlaying)
        updateStateMachine(AnimationStateInputStartAnimation, -1);

    // If we get this far and the animation is done, it means we are cleaning up a just finished animation.
    // If so, we need to send back the targetStyle.
    if (postActive()) {
        if (!animatedStyle)
            animatedStyle = const_cast<RenderStyle*>(targetStyle);
        return;
    }

    // If we are waiting for the start timer, we don't want to change the style yet.
    // Special case - if the delay time is 0, then we do want to set the first frame of the
    // animation right away. This avoids a flash when the animation starts.
    if (waitingToStart() && m_animation->delay() > 0)
        return;

    // FIXME: we need to be more efficient about determining which keyframes we are animating between.
    // We should cache the last pair or something.

    // Find the first key
    double elapsedTime = (m_startTime > 0) ? ((!paused() ? currentTime() : m_pauseTime) - m_startTime) : 0;
    if (elapsedTime < 0)
        elapsedTime = 0;

    double t = m_animation->duration() ? (elapsedTime / m_animation->duration()) : 1;
    int i = static_cast<int>(t);
    t -= i;
    if (m_animation->direction() && (i & 1))
        t = 1 - t;

    const RenderStyle* fromStyle = 0;
    const RenderStyle* toStyle = 0;
    double scale = 1;
    double offset = 0;
    Vector<KeyframeValue>::const_iterator endKeyframes = m_keyframes.endKeyframes();
    for (Vector<KeyframeValue>::const_iterator it = m_keyframes.beginKeyframes(); it != endKeyframes; ++it) {
        if (t < it->key()) {
            // The first key should always be 0, so we should never succeed on the first key
            if (!fromStyle)
                break;
            scale = 1.0 / (it->key() - offset);
            toStyle = it->style();
            break;
        }

        offset = it->key();
        fromStyle = it->style();
    }

    // If either style is 0 we have an invalid case, just stop the animation.
    if (!fromStyle || !toStyle) {
        updateStateMachine(AnimationStateInputEndAnimation, -1);
        return;
    }

    // Run a cycle of animation.
    // We know we will need a new render style, so make one if needed.
    if (!animatedStyle)
        animatedStyle = RenderStyle::clone(targetStyle);

    const TimingFunction* timingFunction = 0;
    if (fromStyle->animations() && fromStyle->animations()->size() > 0)
        timingFunction = &(fromStyle->animations()->animation(0)->timingFunction());

    double prog = progress(scale, offset, timingFunction);

    HashSet<int>::const_iterator endProperties = m_keyframes.endProperties();
    for (HashSet<int>::const_iterator it = m_keyframes.beginProperties(); it != endProperties; ++it) {
        if (blendProperties(this, *it, animatedStyle.get(), fromStyle, toStyle, prog))
            setAnimating();
    }
}

void ConfigureDiveComputer::progressEvent(int percent)
{
	emit progress(percent);
}

void SyncEngine::slotDiscoveryJobFinished(int discoveryResult)
{
    // To clean the progress info
    emit folderDiscovered(false, QString());

    if (discoveryResult < 0 ) {
        handleSyncError(_csync_ctx, "csync_update");
        return;
    }
    qDebug() << "<<#### Discovery end #################################################### " << _stopWatch.addLapTime(QLatin1String("Discovery Finished"));

    // Sanity check
    if (!_journal->isConnected()) {
        qDebug() << "Bailing out, DB failure";
        emit csyncError(tr("Cannot open the sync journal"));
        finalize();
        return;
    } else {
        // Commits a possibly existing (should not though) transaction and starts a new one for the propagate phase
        _journal->commitIfNeededAndStartNewTransaction("Post discovery");
    }

    if( csync_reconcile(_csync_ctx) < 0 ) {
        handleSyncError(_csync_ctx, "csync_reconcile");
        return;
    }

    _stopWatch.addLapTime(QLatin1String("Reconcile Finished"));

    _progressInfo = Progress::Info();

    _hasNoneFiles = false;
    _hasRemoveFile = false;
    bool walkOk = true;
    _seenFiles.clear();

    if( csync_walk_local_tree(_csync_ctx, &treewalkLocal, 0) < 0 ) {
        qDebug() << "Error in local treewalk.";
        walkOk = false;
    }
    if( walkOk && csync_walk_remote_tree(_csync_ctx, &treewalkRemote, 0) < 0 ) {
        qDebug() << "Error in remote treewalk.";
    }

    if (_csync_ctx->remote.root_perms) {
        _remotePerms[QLatin1String("")] = _csync_ctx->remote.root_perms;
        qDebug() << "Permissions of the root folder: " << _remotePerms[QLatin1String("")];
    }

    // The map was used for merging trees, convert it to a list:
    _syncedItems = _syncItemMap.values().toVector();

    // Adjust the paths for the renames.
    for (SyncFileItemVector::iterator it = _syncedItems.begin();
            it != _syncedItems.end(); ++it) {
        it->_file = adjustRenamedPath(it->_file);
    }

    // Sort items per destination
    std::sort(_syncedItems.begin(), _syncedItems.end());

    // make sure everything is allowed
    checkForPermission();

    // To announce the beginning of the sync
    emit aboutToPropagate(_syncedItems);
    _progressInfo._completedFileCount = ULLONG_MAX; // indicate the start with max
    emit transmissionProgress(_progressInfo);
    _progressInfo._completedFileCount = 0;

    if (!_hasNoneFiles && _hasRemoveFile) {
        qDebug() << Q_FUNC_INFO << "All the files are going to be changed, asking the user";
        bool cancel = false;
        emit aboutToRemoveAllFiles(_syncedItems.first()._direction, &cancel);
        if (cancel) {
            qDebug() << Q_FUNC_INFO << "Abort sync";
            finalize();
            return;
        }
    }

    ne_session_s *session = 0;
    // that call to set property actually is a get which will return the session
    csync_set_module_property(_csync_ctx, "get_dav_session", &session);
    Q_ASSERT(session);

    // post update phase script: allow to tweak stuff by a custom script in debug mode.
    if( !qgetenv("OWNCLOUD_POST_UPDATE_SCRIPT").isEmpty() ) {
#ifndef NDEBUG
        QString script = qgetenv("OWNCLOUD_POST_UPDATE_SCRIPT");

        qDebug() << "OOO => Post Update Script: " << script;
        QProcess::execute(script.toUtf8());
#else
    qDebug() << "**** Attention: POST_UPDATE_SCRIPT installed, but not executed because compiled with NDEBUG";
#endif
    }

    // do a database commit
    _journal->commit("post treewalk");
//.........这里部分代码省略.........

// Scene Methods
void Scene::Render() {
	/*if(!Spectrum::SpectrumTest())
	{
		printf("FAILED spectrum unit test. NO rendering allowed.\n");
		return;
	}else{
		printf("PASSED spectrum unit test. YES!\n");
	}*/
	// Allocate and initialize _sample_
	Sample *sample = new Sample(surfaceIntegrator,
	                            volumeIntegrator,
	                            this);
	// Allow integrators to do pre-processing for the scene
	surfaceIntegrator->Preprocess(this);
	volumeIntegrator->Preprocess(this);
	camera->AutoFocus(this);
	// Trace rays: The main loop
	ProgressReporter progress(sampler->TotalSamples(), "Rendering");
	while (sampler->GetNextSample(sample)) {
		// Find camera ray for _sample_
		RayDifferential ray;
		float rayWeight = camera->GenerateRay(*sample, &ray);
		// Generate ray differentials for camera ray
		++(sample->imageX);
		float wt1 = camera->GenerateRay(*sample, &ray.rx);
		--(sample->imageX);
		++(sample->imageY);
		float wt2 = camera->GenerateRay(*sample, &ray.ry);
		if (wt1 > 0 && wt2 > 0) ray.hasDifferentials = true;
		--(sample->imageY);
		// Evaluate radiance along camera ray
		float alpha = 1.f;//initialized to count rayWeight 0 as opaque black
		Spectrum Ls = 0.f;
		if (rayWeight > 0.f)
		{
		  Ls = rayWeight * Li(ray, sample, &alpha);
		 // Ls = Li(ray, sample, &alpha);
			//printf("Li Value: ");
			//Ls.printSelf();
		}
		// Issue warning if unexpected radiance value returned
		if (Ls.IsNaN()) {
			Error("Not-a-number radiance value returned "
		          "for image sample.  Setting to black.");
			Ls = Spectrum(0.f);
			//printf("NAN ALERT\n");
		}
		else if (Ls.y() < -1e-5) {
			Error("Negative luminance value, %g, returned "
		          "for image sample.  Setting to black.", Ls.y());
			Ls = Spectrum(0.f);
			//printf("NEGATIVE LUMINANCE ALERT\n");
		}
		else if (isinf(Ls.y())) {
			Error("Infinite luminance value returned "
		          "for image sample.  Setting to black.");
			Ls = Spectrum(0.f);
			//printf("INFINITE LUMINANCE ALERT\n");
		}
		// Add sample contribution to image
		camera->film->AddSample(*sample, ray, Ls, alpha);
		// Free BSDF memory from computing image sample value
		BSDF::FreeAll();
		// Report rendering progress
		static StatsCounter cameraRaysTraced("Camera", "Camera Rays Traced");
		++cameraRaysTraced;
		progress.Update();
	}
	// Clean up after rendering and store final image
	delete sample;
	progress.Done();
	camera->film->WriteImage();
}

void CSyncThread::startSync()
{
    if (!_syncMutex.tryLock()) {
        qDebug() << Q_FUNC_INFO << "WARNING: Another sync seems to be running. Not starting a new one.";
        return;
    }

    if( ! _csync_ctx ) {
        qDebug() << "XXXXXXXXXXXXXXXX FAIL: do not have csync_ctx!";
    }
    qDebug() << Q_FUNC_INFO << "Sync started";


    qDebug() << "starting to sync " << qApp->thread() << QThread::currentThread();
    _syncedItems.clear();

    _mutex.lock();
    _needsUpdate = false;
    if (!_abortRequested.fetchAndAddRelease(0)) {
        csync_resume(_csync_ctx);
    }
    _mutex.unlock();


    // maybe move this somewhere else where it can influence a running sync?
    MirallConfigFile cfg;

    int fileRecordCount = 0;
    if (!_journal->exists()) {
        qDebug() << "=====sync looks new (no DB exists), activating recursive PROPFIND if csync supports it";
        bool no_recursive_propfind = false;
        csync_set_module_property(_csync_ctx, "no_recursive_propfind", &no_recursive_propfind);
    } else if ((fileRecordCount = _journal->getFileRecordCount()) < 50) {
        qDebug() << "=====sync DB has only" << fileRecordCount << "items, enable recursive PROPFIND if csync supports it";
        bool no_recursive_propfind = false;
        csync_set_module_property(_csync_ctx, "no_recursive_propfind", &no_recursive_propfind);
    } else {
        qDebug() << "=====sync with existing DB";
    }

    csync_set_module_property(_csync_ctx, "csync_context", _csync_ctx);
    csync_set_userdata(_csync_ctx, this);
    // TODO: This should be a part of this method, but we don't have
    // any way to get "session_key" module property from csync. Had we
    // have it, then we could keep this code and remove it from
    // AbstractCredentials implementations.
    cfg.getCredentials()->syncContextPreStart(_csync_ctx);
    // if (_lastAuthCookies.length() > 0) {
    //     // Stuff cookies inside csync, then we can avoid the intermediate HTTP 401 reply
    //     // when https://github.com/owncloud/core/pull/4042 is merged.
    //     QString cookiesAsString;
    //     foreach(QNetworkCookie c, _lastAuthCookies) {
    //         cookiesAsString += c.name();
    //         cookiesAsString += '=';
    //         cookiesAsString += c.value();
    //         cookiesAsString += "; ";
    //     }
    //     csync_set_module_property(_csync_ctx, "session_key", cookiesAsString.to
    // }

    // csync_set_auth_callback( _csync_ctx, getauth );
    csync_set_log_callback( csyncLogCatcher );
    csync_set_log_level( 11 );

    _syncTime.start();

    QElapsedTimer updateTime;
    updateTime.start();
    qDebug() << "#### Update start #################################################### >>";

    if( csync_update(_csync_ctx) < 0 ) {
        handleSyncError(_csync_ctx, "csync_update");
        return;
    }
    qDebug() << "<<#### Update end #################################################### " << updateTime.elapsed();

    if( csync_reconcile(_csync_ctx) < 0 ) {
        handleSyncError(_csync_ctx, "csync_reconcile");
        return;
    }

    _progressInfo = Progress::Info();

    _hasFiles = false;
    bool walkOk = true;
    if( csync_walk_local_tree(_csync_ctx, &treewalkLocal, 0) < 0 ) {
        qDebug() << "Error in local treewalk.";
        walkOk = false;
    }
    if( walkOk && csync_walk_remote_tree(_csync_ctx, &treewalkRemote, 0) < 0 ) {
        qDebug() << "Error in remote treewalk.";
    }

    // Adjust the paths for the renames.
    for (SyncFileItemVector::iterator it = _syncedItems.begin();
            it != _syncedItems.end(); ++it) {
        it->_file = adjustRenamedPath(it->_file);
    }

    qSort(_syncedItems);
//.........这里部分代码省略.........