Ejemplo n.º 1
0
float KernelKmeansClusterer::distanceToCluster(int sampleId,
		const boost::unordered_set<int>& clusterIdSet) {
	if (clusterIdSet.empty()) {
		return FLT_MAX;
	}
	// the sum of weight of the cluster
	float weightSum = 0.0f;
	// the sum of kernels from the sample to all samples in the cluster, multiplied by the weight
	float kernelSum = 0.0f;
	// the sum of kernels from each pair of samples in the cluster, multiplied by weights
	float kernelPairSum = 0.0f;
	for (boost::unordered_set<int>::const_iterator iter = clusterIdSet.begin();
			iter != clusterIdSet.end(); ++iter) {
		float weight = mWeightArray[*iter];
		weightSum += weight;
		float kernelResult = (*mpKernel)(sampleId, *iter);
		kernelSum += weight * kernelResult;
		for (boost::unordered_set<int>::const_iterator _iter =
				clusterIdSet.begin(); _iter != clusterIdSet.end(); ++_iter) {
			float _kernelResult = (*mpKernel)(*iter, *_iter);
			kernelPairSum += weight * mWeightArray[*_iter] * _kernelResult;
		}
	}
	float kernelSelf = (*mpKernel)(sampleId, sampleId);
	if (weightSum == 0.0f) {
		return FLT_MAX;
	}
	return kernelSelf - 2 * kernelSum / weightSum
			+ kernelPairSum / (weightSum * weightSum);
}
Ejemplo n.º 2
0
 inline Observer& Observer::operator=(const Observer& o) {
     iterator i;
     for (i=observables_.begin(); i!=observables_.end(); ++i)
         (*i)->unregisterObserver(this);
     observables_ = o.observables_;
     for (i=observables_.begin(); i!=observables_.end(); ++i)
         (*i)->registerObserver(this);
     return *this;
 }
Ejemplo n.º 3
0
    inline void ObservableSettings::registerDeferredObservers(boost::unordered_set<Observer*>& observers) {
        if (updatesDeferred())
	{
		QL_TRACE("adding " << observers.size() << " observers to the deferred list");
        	deferredObservers_.insert(observers.begin(), observers.end());
	}
    }
Ejemplo n.º 4
0
//calculates average of vectors
boost::unordered_map<string, double> Cluster::_centroid(boost::unordered_set<int>& cluster_list) {

  unordered_string_map centroid;

  int cluster_size = cluster_list.size();
  
  for (boost::unordered_set<int>::iterator it = cluster_list.begin(); it != cluster_list.end(); ++it) {

    //add each element of vector to centroid
    for (unordered_string_map::iterator ivec = doc_term_index[ *it ].begin(); ivec != doc_term_index[ *it ].end(); ++ivec) {
  
      //element (term) doesn't exist, we add it to the map
      if ( centroid.count ( ivec->first ) == 0) {
	//cout << "ivec second: " << ivec->second <<endl;
	//cout << "cluster_size: " << cluster_size <<endl;

	centroid.insert(unordered_string_map::value_type( ivec->first, double( (double)ivec->second / cluster_size ) ));
      }
      else {
	centroid[ivec->first] += double( ((double)ivec->second / cluster_size) );
      }

    }
  }    
  return centroid;
}
Ejemplo n.º 5
0
    inline void ObservableSettings::enableUpdates() {
    	updatesEnabled_  = true;
    	updatesDeferred_ = false;

    	// if there are outstanding deferred updates, do the notification
        if (deferredObservers_.size() > 0)
        {
            bool successful = true;
            std::string errMsg;

            QL_TRACE("deferred notification of " << deferredObservers_.size() << " observers");
            for (iterator i=deferredObservers_.begin(); i!=deferredObservers_.end(); ++i) {
                try {
                    (*i)->update();
                } catch (std::exception& e) {
                    successful = false;
                    errMsg = e.what();
                } catch (...) {
                    successful = false;
                }
            }

            deferredObservers_.clear();

            QL_ENSURE(successful,
                  "could not notify one or more observers: " << errMsg);
        }
    }
Ejemplo n.º 6
0
		static void serialize(storage_type& s, const boost::unordered_set<T>& o)
			{
			uint32_t sz = o.size();
			s.serialize(sz);

			for (auto it = o.begin(), it_end = o.end(); it != it_end; ++it)
				s.serialize(*it);
			}
Ejemplo n.º 7
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Strings get_live_object_names() {
  IMP::Vector<std::string> ret;
  for (boost::unordered_set<Object*>::const_iterator it = live_.begin();
       it != live_.end(); ++it) {
    ret.push_back((*it)->get_name());
  }
  return ret;
}
Ejemplo n.º 8
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IMPKERNEL_END_NAMESPACE
IMPKERNEL_BEGIN_INTERNAL_NAMESPACE
void check_live_objects() {
  for (boost::unordered_set<Object*>::const_iterator it = live_.begin();
       it != live_.end(); ++it) {
    IMP_USAGE_CHECK((*it)->get_ref_count() > 0,
                    "Object " << (*it)->get_name() << " is not ref counted.");
  }
}
Ejemplo n.º 9
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IMPKERNEL_END_NAMESPACE
IMPKERNEL_BEGIN_INTERNAL_NAMESPACE
void check_live_objects() {
  for (boost::unordered_set<Object*>::const_iterator it = live_.begin();
       it != live_.end(); ++it) {
    IMP_USAGE_CHECK((*it)->get_ref_count() > 0,
                    "Object " << (*it)->get_name()
                    << " is alive but not ref counted - memory leakage possible."
                    << " This usually happens if an owning pointer is released"
                    << " without being either deleted manually or assigned to"
                    << " another owning pointer.");
  }
}
Ejemplo n.º 10
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void save(Archive & ar, const boost::unordered_set<T> & t, unsigned int version)
{
    // write the size
    // TODO: should we handle bucket size as well?
    typedef typename boost::unordered_set<T>::size_type size_type;
    typedef typename boost::unordered_set<T>::const_iterator const_iterator;
    size_type size = t.size();
    ar & BOOST_SERIALIZATION_NVP(size);
    unsigned int count = 0;
    for (const_iterator it = t.begin(); it != t.end(); it++) {
        ar & boost::serialization::make_nvp("item" + count, *it);
        count++;
    }
}
Ejemplo n.º 11
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    inline void Observable::notifyObservers() {
    	// check whether the notifications should be triggered
    	if (!settings_.updatesEnabled())
    	{
    	    // if updates are only deferred, flag this for later notification
    	    // these are held centrally by the settings singleton
            if (settings_.updatesDeferred())
    		settings_.registerDeferredObservers(observers_);

    	    return;
    	}

        if (observers_.size() > 0)
        {
            bool successful = true;
            std::string errMsg;

            QL_TRACE("direct notification of " << observers_.size() << " observers");
            for (iterator i=observers_.begin(); i!=observers_.end(); ++i) {
                try {
                   (*i)->update();
                } catch (std::exception& e) {
                    // quite a dilemma. If we don't catch the exception,
                    // other observers will not receive the notification
                    // and might be left in an incorrect state. If we do
                    // catch it and continue the loop (as we do here) we
                    // lose the exception. The least evil might be to try
                    // and notify all observers, while raising an
                    // exception if something bad happened.
                    successful = false;
                    errMsg = e.what();
                } catch (...) {
                    successful = false;
                }
            }
            QL_ENSURE(successful,
                  "could not notify one or more observers: " << errMsg);
        }
    }
Ejemplo n.º 12
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Objects get_live_objects() {
  Objects ret(live_.begin(), live_.end());
  return ret;
}
Ejemplo n.º 13
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 static void exec(OutArcType& oarc, const boost::unordered_set<T>& vec){
   serialize_iterator(oarc,
                      vec.begin(), vec.end(), vec.size());
 }
Ejemplo n.º 14
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		void insert(const boost::unordered_set<key_type>& inKeys, const boost::unordered_set<value_type>& inValues)
			{
			for (auto it = inValues.begin(); it != inValues.end();++it)
				insert(inKeys, *it);
			}
 /**
   * Return the mirror information of the vertex in the i'th position.
   */
  inline const std::vector<graph_shard_id_t> mirrors(size_t i) const {
    const boost::unordered_set<graph_shard_id_t> mirrorset = shard_impl.vertex_mirrors[i];
    std::vector<graph_shard_id_t> ret(mirrorset.begin(), mirrorset.end());
    return ret;
  }
Ejemplo n.º 16
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 inline void Observer::unregisterWithAll() {
     for (iterator i=observables_.begin(); i!=observables_.end(); ++i)
         (*i)->unregisterObserver(this);
     observables_.clear();
 }
Ejemplo n.º 17
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 inline Observer::~Observer() {
     for (iterator i=observables_.begin(); i!=observables_.end(); ++i)
         (*i)->unregisterObserver(this);
 }
Ejemplo n.º 18
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		void drop(const boost::unordered_set<key_type>& inKey, const value_type& inValue)
			{
			for (auto it = inKey.begin(); it != inKey.end();++it)
				drop(*it, inValue);
			}
Ejemplo n.º 19
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 inline Observer::Observer(const Observer& o)
 : observables_(o.observables_) {
     for (iterator i=observables_.begin(); i!=observables_.end(); ++i)
         (*i)->registerObserver(this);
 }
Ejemplo n.º 20
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 inline void ObservableSettings::registerDeferredObservers(
     const boost::unordered_set<Observer*>& observers) {
     if (updatesDeferred()) {
         deferredObservers_.insert(observers.begin(), observers.end());
     }
 }
Ejemplo n.º 21
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		void drop(const key_type& inKey, const boost::unordered_set<value_type>& inValue)
			{
			for (auto it = inValue.begin(); it != inValue.end();++it)
				drop(inKey, *it);
			}