void operator()( boost::property_tree::ptree & s, object_type & obj ) {
boost::property_tree::ptree tr;
state_getter< typename object_type::trait_space_type > tr_logger;
tr_logger( tr, obj.m_trait_space );
boost::property_tree::ptree fr;
state_getter< typename object_type::free_space_type > free_logger;
free_logger( fr, obj.m_free_space );
boost::property_tree::ptree fx, alls;
state_getter< typename object_type::allele_type > all_logger;
all_logger( fx, obj.m_fixed );
all_logger( alls, obj.m_allele_space );
boost::property_tree::ptree c_pop;
state_getter< typename object_type::sequence_space_type > pop_logger;
pop_logger( c_pop, *(obj.m_pop.back()) );
boost::property_tree::ptree ft;
clotho::utility::add_value_array( ft, obj.m_fits.back()->begin(), obj.m_fits.back()->end() );
c_pop.put_child( "fitness", ft );
s.put_child( "free_space", fr );
s.put_child( "allele_space", alls );
s.put_child( "trait_space", tr );
s.put_child( "fixed_alleles", fx );
s.put_child( "child", c_pop );
}
void operator()( boost::property_tree::ptree & s, object_type & obj ) {
boost::property_tree::ptree tr;
state_getter< typename object_type::trait_space_type > tr_logger;
tr_logger( tr, obj.m_trait_space );
boost::property_tree::ptree ph;
state_getter< typename object_type::phenotype_eval_type > pheno_logger;
pheno_logger( ph, obj.m_pheno );
boost::property_tree::ptree fr;
state_getter< typename object_type::free_space_type > free_logger;
free_logger( fr, obj.m_free_space );
boost::property_tree::ptree fx, alls;
state_getter< typename object_type::allele_type > all_logger;
all_logger( fx, obj.m_fixed );
all_logger( alls, obj.m_allele_space );
// boost::property_tree::ptree c_pop;
// state_getter< typename object_type::sequence_space_type > pop_logger;
// pop_logger( c_pop, *(obj.m_child) );
s.put_child( "phenotypes", ph );
s.put_child( "free_space", fr );
s.put_child( "allele_space", alls );
s.put_child( "trait_space", tr );
s.put_child( "fixed_alleles", fx );
// s.put_child( "child", c_pop );
}
void operator()( boost::property_tree::ptree & s, object_type & obj ) {
boost::property_tree::ptree al;
state_getter< typename object_type::allele_type > a_log;
a_log( al, obj.getAlleleSpace() );
boost::property_tree::ptree ft;
clotho::utility::add_value_array( ft, obj.fitness_begin(), obj.fitness_end() );
s.put_child( "alleles" , al );
s.put_child( "fitness", ft );
}
void get_state( boost::property_tree::ptree & state ) {
boost::property_tree::ptree a, s, f, p;
alleles.get_state( a );
sequences.get_state( s );
get_device_object_state( f, free_space );
get_device_object_state( p, pheno_space );
state.put_child( "alleles", a );
state.put_child( "sequences", s );
state.put_child( "free_space", f );
state.put_child( "phenotypes", p );
}
void recordResults( boost::property_tree::ptree & log ) {
typedef ac::accumulator_set< size_type, ac::stats< ac::tag::min, ac::tag::mean, ac::tag::max, ac::tag::variance, ac::tag::median, ac::tag::count > > accumulator_t;
accumulator_t col_accum, row_accum;
boost::property_tree::ptree dist, lfreq;
// maximum frequency for an allele is bounded by the number of sequences (rows) in the population
std::vector< size_type > freq( m_indices.size(), 0 );
// evaluate allele (column) statistics
size_type i = 0;
while( i < m_column_margin_size ) {
size_type v = m_column_margin[i++];
clotho::utility::add_value_array( dist, v );
col_accum( v );
freq[v]++;
}
clotho::utility::add_value_array(lfreq, freq.begin(), freq.end() );
log.put_child( "distribution", dist );
log.put_child( "frequency_distribution", lfreq );
log.put( "stats.sequences_per_allele.min", ac::min( col_accum ) );
log.put( "stats.sequences_per_allele.max", ac::max( col_accum ) );
log.put( "stats.sequences_per_allele.mean", ac::mean( col_accum ) );
log.put( "stats.sequences_per_allele.median", ac::median( col_accum ) );
log.put( "stats.sequences_per_allele.variance", ac::variance( col_accum ) );
log.put( "stats.sequences_per_allele.total", ac::count(col_accum) );
// evaluate sequence (row) statistics
i = 0;
while( i < m_row_margin_size ) {
if( m_indices.test(i) ) {
row_accum( m_row_margin[ i ] );
}
++i;
}
log.put( "stats.alleles_per_sequence.min", ac::min( row_accum ) );
log.put( "stats.alleles_per_sequence.max", ac::max( row_accum ) );
log.put( "stats.alleles_per_sequence.mean", ac::mean( row_accum ) );
log.put( "stats.alleles_per_sequence.median", ac::median( row_accum ) );
log.put( "stats.alleles_per_sequence.variance", ac::variance( row_accum ) );
log.put( "stats.alleles_per_sequence.total", ac::count(row_accum) );
}
bool upgrade_json (unsigned version_a, boost::property_tree::ptree & tree_a)
{
auto result (false);
switch (version_a)
{
case 1:
{
rai::account account;
account.decode_account (tree_a.get<std::string> ("account"));
tree_a.erase ("account");
tree_a.put ("account", account.to_account ());
tree_a.erase ("version");
tree_a.put ("version", "2");
result = true;
}
case 2:
{
boost::property_tree::ptree rpc_l;
rpc.serialize_json (rpc_l);
tree_a.put ("rpc_enable", "false");
tree_a.put_child ("rpc", rpc_l);
tree_a.erase ("version");
tree_a.put ("version", "3");
result = true;
}
case 3:
{
auto opencl_enable_l (tree_a.get_optional<bool> ("opencl_enable"));
if (!opencl_enable_l)
{
tree_a.put ("opencl_enable", "false");
}
auto opencl_l (tree_a.get_child_optional ("opencl"));
if (!opencl_l)
{
boost::property_tree::ptree opencl_l;
opencl.serialize_json (opencl_l);
tree_a.put_child ("opencl", opencl_l);
}
tree_a.put ("version", "4");
result = true;
}
case 4:
break;
default:
throw std::runtime_error ("Unknown qt_wallet_config version");
}
return result;
}
bool rai_daemon::daemon_config::upgrade_json (unsigned version_a, boost::property_tree::ptree & tree_a)
{
auto result (false);
switch (version_a)
{
case 1:
{
auto opencl_enable_l (tree_a.get_optional <bool> ("opencl_enable"));
if (!opencl_enable_l)
{
tree_a.put ("opencl_enable", "false");
}
auto opencl_l (tree_a.get_child_optional ("opencl"));
if (!opencl_l)
{
boost::property_tree::ptree opencl_l;
opencl.serialize_json (opencl_l);
tree_a.put_child ("opencl", opencl_l);
}
tree_a.put ("version", "2");
result = true;
}
case 2:
break;
default:
throw std::runtime_error ("Unknown daemon_config version");
}
return result;
}
void merge( boost::property_tree::ptree& pt, const boost::property_tree::ptree& updates )
{
BOOST_FOREACH( auto& update, updates )
{
printf("boost foreach\n");
pt.put_child( update.first, update.second );
}
void operator()( boost::property_tree::ptree & s, object_type & obj ) {
boost::property_tree::ptree fr;
clotho::utility::add_value_array( fr, obj.free_begin(), obj.free_end() );
s.put_child( "free", fr );
s.add( "free_size", obj.free_size() );
s.add( "variable_count", obj.variable_count() );
}
void init( size_t aN, boost::property_tree::ptree & config ) {
size_t pN = 0;
if( m_pop_growth ) {
pN = m_pop_growth->operator()( pN, m_generation );
}
boost::property_tree::ptree lconfig;
lconfig = config.get_child( "generations", lconfig);
unsigned int intermed = lconfig.get< unsigned int>( "intermediates", 0 );
lconfig.put("intermediates", intermed );
config.put_child( "generations", lconfig );
for( unsigned int i = 0; i < intermed + 2; ++i ) {
sequence_space_type * ss = new sequence_space_type();
m_pop.push_back( ss );
fitness_type * f = new fitness_type( config );
assert( f->isEmpty() );
m_fits.push_back( f );
mutation_pool_type * p = new mutation_pool_type();
m_mut_pools.push_back( p );
mutation_distribution_type * d = new mutation_distribution_type();
m_mut_dists.push_back( d );
}
if( m_thread_count.m_tc > 0 ) {
m_worker_rng = new random_engine_type * [ m_thread_count.m_tc ];
m_worker_off_gens = new offspring_generator_type * [ m_thread_count.m_tc ];
for( int offset = 0; offset < m_thread_count.m_tc; ++offset ) {
m_worker_rng[ offset ] = new random_engine_type( (*m_rand)());
m_worker_off_gens[ offset ] = new offspring_generator_type( m_worker_rng[ offset ], &m_allele_space, &m_trait_space, config );
}
}
#ifdef USE_ROW_VECTOR
m_pop1.getSequenceSpace().fill_empty();
m_pop1.getSequenceSpace().finalize();
#endif // USE_ROW_VECTOR
++m_generation;
}
void buildTimeVectorLog( boost::property_tree::ptree & log, time_map & times ) {
for( typename time_map::iterator it = times.begin(); it != times.end(); it++ ) {
boost::property_tree::ptree starts, stops;
for( typename time_vector::iterator iter = it->second.begin(); iter != it->second.end(); ++iter ) {
clotho::utility::add_value_array( starts, iter->first );
clotho::utility::add_value_array( stops, iter->second );
}
boost::property_tree::ptree tmp;
tmp.put_child( "start", starts );
tmp.put_child( "stop", stops );
log.put_child( it->first, tmp );
}
}
quadratic_fitness_parameter( boost::property_tree::ptree & config ) :
m_scale( 1.0 ) {
boost::property_tree::ptree fblock;
fblock = config.get_child( FITNESS_BLOCK_K, fblock );
boost::property_tree::ptree pblock;
pblock = fblock.get_child( PARAM_K, pblock );
m_scale = pblock.get< RealType >( SCALE_K, m_scale );
pblock.put( SCALE_K, m_scale );
fblock.put( NAME_K, QUAD_NAME );
fblock.put_child( PARAM_K, pblock );
config.put_child( FITNESS_BLOCK_K, fblock );
}
void record( boost::property_tree::ptree & xo, boost::property_tree::ptree & mt, boost::property_tree::ptree & ph, boost::property_tree::ptree & fx ) {
boost::property_tree::ptree xo_begins, xo_ends;
buildTimeLog( xo_begins, xo_ends, m_crossover_times );
xo.put_child( "start", xo_begins);
xo.put_child( "stop", xo_ends);
boost::property_tree::ptree mt_begins, mt_ends;
buildTimeLog( mt_begins, mt_ends, m_mutate_times );
mt.put_child( "start", mt_begins);
mt.put_child( "stop", mt_ends);
boost::property_tree::ptree ph_begins, ph_ends;
buildTimeLog( ph_begins, ph_ends, m_phenotype_times );
ph.put_child( "start", ph_begins);
ph.put_child( "stop", ph_ends);
boost::property_tree::ptree fx_begins, fx_ends;
buildTimeLog( fx_begins, fx_ends, m_fixed_times );
fx.put_child( "start", fx_begins);
fx.put_child( "stop", fx_ends);
}
void NetworkManagerHandler::wifiScan(boost::property_tree::ptree &responsePt)
{
std::vector<WirelessManager::ScanResult> scanResult = qpcrApp.wirelessManager()->scanResult();
boost::property_tree::ptree array;
for (const WirelessManager::ScanResult &result: scanResult)
{
boost::property_tree::ptree ptree;
ptree.put("ssid", result.ssid);
ptree.put("quality", result.quality);
ptree.put("siganl_level", result.siganlLevel);
switch (result.encryption)
{
case WirelessManager::ScanResult::WepEncryption:
ptree.put("encryption", "wep");
break;
case WirelessManager::ScanResult::Wpa1Ecryption:
ptree.put("encryption", "wpa1");
break;
case WirelessManager::ScanResult::Wpa2PSKEcryption:
ptree.put("encryption", "wpa2 psk");
break;
case WirelessManager::ScanResult::Wpa28021xEcryption:
ptree.put("encryption", "wpa2 802.1x");
break;
default:
ptree.put("encryption", "none");
break;
}
array.push_back(std::make_pair("", ptree));
}
responsePt.put_child("scan_result", array);
}
void parse_configuration( boost::property_tree::ptree & config ) {
boost::property_tree::ptree lconfig;
if( config.get_child_optional( "mutation" ) != boost::none ) {
lconfig = config.get_child( "mutation" );
}
if( lconfig.get_child_optional( "mutation_per_sequence" ) == boost::none ) {
lconfig.put("mutation_per_sequence", m_mutation_rate );
} else {
m_mutation_rate = lconfig.get< real_type >( "mutation_per_sequence", m_mutation_rate );
}
if( lconfig.get_child_optional( "rng.seed" ) != boost::none ) {
m_seed = lconfig.get< seed_type >( "rng.seed", m_seed );
}
if( m_seed == 0 ) {
m_seed = clotho::utility::clock_type::now().time_since_epoch().count();
lconfig.put("rng.seed", m_seed );
}
config.put_child( "mutation", lconfig );
}
void to_ptree(const details::global_kernel_state_t &state, ::boost::property_tree::ptree &ptree, int level)
{
{
::boost::property_tree::ptree init;
state.initialization_parameters_ref().to_ptree(init);
ptree.put_child("initialization", init);
}
{
::boost::property_tree::ptree last_collect;
last_collect.put("clear_mark_time", ::std::to_string(state.clear_mark_time_span().count()));
last_collect.put("mark_time", ::std::to_string(state.mark_time_span().count()));
last_collect.put("sweep_time", ::std::to_string(state.sweep_time_span().count()));
last_collect.put("notify_time", ::std::to_string(state.notify_time_span().count()));
last_collect.put("total_time", ::std::to_string(state.total_collect_time_span().count()));
ptree.put_child("last_collect", last_collect);
}
{
::boost::property_tree::ptree slab_allocator;
state._internal_slab_allocator().to_ptree(slab_allocator, level);
ptree.put_child("slab_allocator", slab_allocator);
}
{
::boost::property_tree::ptree cgc_allocator;
state._internal_allocator().to_ptree(cgc_allocator, level);
ptree.put_child("cgc_allocator", cgc_allocator);
}
{
::boost::property_tree::ptree gc_allocator;
state.gc_allocator().to_ptree(gc_allocator, level);
ptree.put_child("gc_allocator", gc_allocator);
}
{
::boost::property_tree::ptree packed_allocator;
state._bitmap_allocator().to_ptree(packed_allocator, level);
ptree.put_child("packed_allocator", packed_allocator);
}
}
void getPerformanceResults( boost::property_tree::ptree & log ) {
for( int i = 0; i < m_thread_count.m_tc; ++i ) {
std::ostringstream oss;
oss << "W_" << (i + 1);
boost::property_tree::ptree mut, xo, ph, fx, ft;
m_worker_off_gens[ i ]->record( xo, mut, ph, fx, ft );
log.put_child( "performance.mutate." + oss.str(), mut );
log.put_child( "performance.crossover." + oss.str(), xo );
log.put_child( "performance.fixed." + oss.str(), fx );
log.put_child( "performance.phenotype." + oss.str(), ph );
log.put_child( "performance.fitness." + oss.str(), ft );
}
boost::property_tree::ptree mut, xo, ph, fx, ft;
m_main_off_gen.record( xo, mut, ph, fx, ft );
log.put_child( "performance.mutate.main", mut );
log.put_child( "performance.crossover.main", xo );
log.put_child( "performance.fixed.main", fx );
log.put_child( "performance.phenotype.main", ph );
log.put_child( "performance.fitness.main", ft );
log.put_child( "memory.free_count", free_sizes );
log.put_child( "memory.variable_count", var_sizes );
log.put_child( "memory.fixed_count", fixed_sizes );
}
