--- a/examples/CMakeLists.txt Sun Feb 17 08:47:20 2008 -0500
+++ b/examples/CMakeLists.txt Sun Feb 17 09:16:30 2008 -0500
@@ -1,5 +1,6 @@
add_subdirectory (alphashapes)
add_subdirectory (ar-vineyard)
add_subdirectory (cech-complex)
+add_subdirectory (fitness)
add_subdirectory (grid)
add_subdirectory (triangle)
--- a/examples/cech-complex/cech-complex.cpp Sun Feb 17 08:47:20 2008 -0500
+++ b/examples/cech-complex/cech-complex.cpp Sun Feb 17 09:16:30 2008 -0500
@@ -14,18 +14,7 @@
typedef SimplexWithValue<PointIndex> Simplex;
typedef std::vector<Simplex> SimplexVector;
typedef Filtration<Simplex> CechFiltration;
-
-class DimensionValueComparison
-{
- public:
- bool operator()(const Simplex& s1, const Simplex& s2) const
- {
- if (s1.dimension() == s2.dimension())
- return s1.get_value() < s2.get_value();
- else
- return s1.dimension() < s2.dimension();
- }
-};
+typedef DimensionValueComparison<Simplex> DimValComparison;
int choose(int n, int k)
{
@@ -109,7 +98,7 @@
add_simplices(sv, i, points);
std::cout << "Size of SimplexVector: " << sv.size() << std::endl;
- std::sort(sv.begin(), sv.end(), DimensionValueComparison());
+ std::sort(sv.begin(), sv.end(), DimValComparison());
for (SimplexVector::const_iterator cur = sv.begin(); cur != sv.end(); ++cur)
cf.append(*cur);
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/fitness/CMakeLists.txt Sun Feb 17 09:16:30 2008 -0500
@@ -0,0 +1,8 @@
+set (targets
+ avida-distance
+ avida-landscape)
+
+foreach (t ${targets})
+ add_executable (${t} ${t}.cpp)
+ target_link_libraries (${t} ${libraries})
+endforeach (t ${targets})
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/fitness/avida-distance.cpp Sun Feb 17 09:16:30 2008 -0500
@@ -0,0 +1,94 @@
+#include <iostream>
+#include <vector>
+#include <algorithm>
+#include "avida-population-detail.h"
+
+#include <topology/filtration.h>
+#include <topology/simplex.h>
+
+
+typedef SimplexWithValue<AvidaOrganismDetail::IDType> Simplex;
+typedef std::vector<Simplex> SimplexVector;
+typedef Filtration<Simplex> SimplexFiltration;
+
+int main(int argc, char** argv)
+{
+#ifdef LOGGING
+ rlog::RLogInit(argc, argv);
+ //stdoutLog.subscribeTo(RLOG_CHANNEL("info"));
+#endif
+
+ if (argc < 2)
+ {
+ std::cout << "USAGE: avida FILENAME" << std::endl;
+ return 0;
+ }
+
+ AvidaPopulationDetail population(argv[1]);
+ const AvidaPopulationDetail::OrganismVector& organisms = population.get_organisms();
+
+ rInfo("Number of organisms: %d", organisms.size());
+ for (int i = 0; i < population.get_organisms().size(); ++i)
+ rInfo("%d (%s) %f %d %d", organisms[i].id(),
+ organisms[i].genome().c_str(),
+ organisms[i].fitness(),
+ organisms[i].length(),
+ organisms[i].genome().size());
+
+ // Distance function filtration
+ SimplexVector simplices;
+
+ // Insert edges
+ AvidaOrganismDetail::DistanceType avg_distance = 0;
+ for (AvidaOrganismDetail::CountType i = 0; i < organisms.size(); ++i)
+ {
+ simplices.push_back(0);
+ simplices.back().add(organisms[i].id());
+
+ for (AvidaOrganismDetail::CountType j = i+1; j < organisms.size(); ++j)
+ {
+ avg_distance += organisms[i].genome_distance(organisms[j]);
+ simplices.push_back(Simplex(organisms[i].genome_distance(organisms[j])));
+ simplices.back().add(organisms[i].id());
+ simplices.back().add(organisms[j].id());
+ }
+ }
+ std::sort(simplices.begin(), simplices.end(), DimensionValueComparison<Simplex>());
+ rInfo("Average distance: %f", float(avg_distance)/
+ ((organisms.size()*organisms.size() - organisms.size())/2));
+
+ SimplexFiltration filtration;
+ for (SimplexVector::const_iterator cur = simplices.begin(); cur != simplices.end(); ++cur)
+ {
+ rInfo("Simplex: %s", tostring(*cur).c_str());
+ filtration.append(*cur);
+ }
+
+ filtration.fill_simplex_index_map();
+ filtration.pair_simplices(false); // pair simplices without storing trails
+
+ std::cout << "Outputting histogram of death values" << std::endl;
+ typedef std::vector<RealType> DeathVector;
+ DeathVector deaths;
+ for (SimplexFiltration::Index i = filtration.begin(); i != filtration.end(); ++i)
+ {
+ if (i->is_paired())
+ if (i->sign())
+ {
+ AssertMsg(i->dimension() == 0, "Expecting only 0-dimensional diagram");
+ AssertMsg(i->get_value() == 0, "Expecting only 0 birth values in 0-D diagram ");
+ deaths.push_back(i->pair()->get_value());
+ }
+ }
+
+ // Produce histogram
+ std::sort(deaths.begin(), deaths.end());
+ for (DeathVector::iterator cur = deaths.begin(); cur != deaths.end(); )
+ {
+ DeathVector::iterator nw = std::find_if(cur, deaths.end(),
+ std::bind2nd(std::greater<RealType>(), *cur));
+ std::cout << *cur << "\t" << (nw - cur) << std::endl;
+ cur = nw;
+ }
+ std::cout << "Total: " << deaths.size() + 1; // +1 for the unpaired
+}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/fitness/avida-landscape.cpp Sun Feb 17 09:16:30 2008 -0500
@@ -0,0 +1,113 @@
+#include <iostream>
+#include <vector>
+#include <algorithm>
+#include <sstream>
+#include "avida-population-detail.h"
+
+#include <topology/lowerstarfiltration.h>
+
+
+typedef AvidaPopulationDetail::OrganismIndex OrganismIndex;
+struct OrganismVertexType;
+typedef std::vector<OrganismVertexType> VertexVector;
+typedef VertexVector::iterator VertexIndex;
+typedef LowerStarFiltration<VertexIndex> LSFiltration;
+struct OrganismVertexType: public LSFiltration::VertexType<OrganismIndex> {};
+
+struct OrganismVertexComparison
+{
+ public:
+ bool operator()(VertexIndex i, VertexIndex j) const
+ { return i->index()->fitness() < j->index()->fitness(); }
+};
+
+
+int main(int argc, char** argv)
+{
+#ifdef LOGGING
+ rlog::RLogInit(argc, argv);
+ //stdoutLog.subscribeTo(RLOG_CHANNEL("info"));
+#endif
+
+ if (argc < 3)
+ {
+ std::cout << "USAGE: avida FILENAME DISTANCE" << std::endl;
+ return 0;
+ }
+
+ AvidaPopulationDetail population(argv[1]);
+ AvidaPopulationDetail::DistanceType connected_distance;
+ std::istringstream(argv[2]) >> connected_distance;
+ const AvidaPopulationDetail::OrganismVector& organisms = population.get_organisms();
+
+ rInfo("Number of organisms: %d", organisms.size());
+ for (int i = 0; i < population.get_organisms().size(); ++i)
+ rInfo("%d (%s) %f %d %d", organisms[i].id(),
+ organisms[i].genome().c_str(),
+ organisms[i].fitness(),
+ organisms[i].length(),
+ organisms[i].genome().size());
+
+ // Order vertices
+ VertexVector vertices(organisms.begin(), organisms.end());
+ LSFiltration fitness_filtration(vertices.begin(), vertices.end(), OrganismVertexComparison());
+
+#if 0
+ //
+ for (AvidaOrganismDetail::CountType i = 0; i < organisms.size(); ++i)
+ {
+ Simplex s(2, v);
+
+ filtration.append(s);
+
+ simplices.push_back(organisms[i].fitness());
+ simplices.back().add(organisms[i].id());
+
+ for (AvidaOrganismDetail::CountType j = i+1; j < organisms.size(); ++j)
+ {
+ avg_distance += organisms[i].genome_distance(organisms[j]);
+ simplices.push_back(Simplex(organisms[i].genome_distance(organisms[j])));
+ simplices.back().add(organisms[i].id());
+ simplices.back().add(organisms[j].id());
+ }
+ }
+ std::sort(simplices.begin(), simplices.end(), DimensionValueComparison<Simplex>());
+ rInfo("Average distance: %f", float(avg_distance)/
+ ((organisms.size()*organisms.size() - organisms.size())/2));
+
+ SimplexFiltration filtration;
+ for (SimplexVector::const_iterator cur = simplices.begin(); cur != simplices.end(); ++cur)
+ {
+ rInfo("Simplex: %s", tostring(*cur).c_str());
+ filtration.append(*cur);
+ }
+
+ filtration.fill_simplex_index_map();
+ filtration.pair_simplices(false); // pair simplices without storing trails
+
+ std::cout << "Outputting histogram of death values" << std::endl;
+ typedef std::vector<RealType> DeathVector;
+ DeathVector deaths;
+ for (SimplexFiltration::Index i = filtration.begin(); i != filtration.end(); ++i)
+ {
+ if (i->is_paired())
+ if (i->sign())
+ {
+ AssertMsg(i->dimension() == 0, "Expecting only 0-dimensional diagram");
+ AssertMsg(i->get_value() == 0, "Expecting only 0 birth values in 0-D diagram ");
+ deaths.push_back(i->pair()->get_value());
+ }
+ }
+
+ // Produce histogram
+ std::sort(deaths.begin(), deaths.end());
+ for (DeathVector::iterator cur = deaths.begin(); cur != deaths.end(); )
+ {
+ DeathVector::iterator nw = std::find_if(cur, deaths.end(),
+ std::bind2nd(std::greater<RealType>(), *cur));
+ std::cout << *cur << "\t" << (nw - cur) << std::endl;
+ cur = nw;
+ }
+ std::cout << "Total: " << deaths.size() + 1; // +1 for the unpaired
+#endif
+}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/fitness/avida-population-detail.h Sun Feb 17 09:16:30 2008 -0500
@@ -0,0 +1,65 @@
+/**
+ * Author: Dmitriy Morozov
+ * Department of Computer Science, Duke University, 2007
+ */
+
+#ifndef __AVIDA_POPULATION_DETAIL_H__
+#define __AVIDA_POPULATION_DETAIL_H__
+
+#include <string>
+#include <vector>
+
+/**
+ * Stores organism details stored in a single line of a population detail file in data/
+ * directory of Avida's output.
+ */
+class AvidaOrganismDetail
+{
+ public:
+ typedef int IDType;
+ /// Distance between two genomes
+ typedef unsigned int DistanceType;
+ typedef unsigned int CountType;
+
+ AvidaOrganismDetail(std::string line);
+
+ DistanceType genome_distance(const AvidaOrganismDetail& other) const;
+
+ IDType id() const { return id_; }
+ float fitness() const { return fitness_; }
+ CountType length() const { return genome_length_; }
+ std::string genome() const { return genome_; }
+
+ private:
+ IDType id_, parent_id_;
+ int parent_distance_;
+ CountType num_organisms_alive_, num_organisms_ever_;
+ CountType genome_length_;
+ float merit_, gestation_time_;
+ float fitness_;
+ int update_born_, update_deactivated_, depth_phylogenetic_tree_;
+ std::string genome_;
+};
+
+/**
+ * Stores entire population details (all organisms in a given time step), i.e., stores
+ * an entire population detail file in data/ directory of Avida's ouptut.
+ */
+class AvidaPopulationDetail
+{
+ public:
+ typedef std::vector<AvidaOrganismDetail> OrganismVector;
+ typedef OrganismVector::const_iterator OrganismIndex;
+
+ AvidaPopulationDetail(std::string filename);
+
+ const OrganismVector& get_organisms() const { return organisms_; }
+
+ private:
+ OrganismVector organisms_;
+};
+
+
+#include "avida-population-detail.hpp"
+
+#endif //__AVIDA_POPULATION_DETAIL_H__
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/fitness/avida-population-detail.hpp Sun Feb 17 09:16:30 2008 -0500
@@ -0,0 +1,57 @@
+#include <fstream>
+#include <sstream>
+#include "utilities/log.h"
+
+/** AvidaOrganismDetail */
+
+AvidaOrganismDetail::
+AvidaOrganismDetail(std::string line)
+{
+ std::stringstream linestream(line);
+ linestream >> id_ >> parent_id_ >> parent_distance_;
+ linestream >> num_organisms_alive_ >> num_organisms_ever_;
+ linestream >> genome_length_;
+ linestream >> merit_ >> gestation_time_;
+ linestream >> fitness_;
+ linestream >> update_born_ >> update_deactivated_ >> depth_phylogenetic_tree_;
+ linestream >> genome_;
+
+ AssertMsg(genome_length_ == genome_.size(), "Genome must be of given length");
+}
+
+AvidaOrganismDetail::DistanceType
+AvidaOrganismDetail::
+genome_distance(const AvidaOrganismDetail& other) const
+{
+ AssertMsg(genome_.size() == other.genome_.size(), "Currently genome sizes must be the same for distance computation");
+ AssertMsg(genome_length_ == genome_.size(), "Genome length value must match the length of the genome string");
+ AssertMsg(other.genome_length_ == other.genome_.size(), "Genome length value must match the length of the genome string");
+
+ CountType count = 0;
+ for (CountType i = 0; i < genome_.size(); ++i)
+ if (genome_[i] != other.genome_[i])
+ ++count;
+
+ return count;
+}
+
+
+/** AvidaPopulationDetail */
+AvidaPopulationDetail::
+AvidaPopulationDetail(std::string filename)
+{
+ std::ifstream infile(filename.c_str());
+ while(infile)
+ {
+ std::string line;
+ std::getline(infile, line);
+
+ // Skip comments and empty lines
+ char c = '#';
+ std::istringstream linestream(line);
+ linestream >> c;
+ if (c == '#') continue;
+
+ organisms_.push_back(AvidaOrganismDetail(line));
+ }
+}
--- a/include/topology/simplex.h Sun Feb 17 08:47:20 2008 -0500
+++ b/include/topology/simplex.h Sun Feb 17 09:16:30 2008 -0500
@@ -165,6 +165,21 @@
void serialize(Archive& ar, version_type );
};
+template<class Simplex_>
+class DimensionValueComparison
+{
+ public:
+ typedef Simplex_ Simplex;
+
+ bool operator()(const Simplex& s1, const Simplex& s2) const
+ {
+ if (s1.dimension() == s2.dimension())
+ return s1.get_value() < s2.get_value();
+ else
+ return s1.dimension() < s2.dimension();
+ }
+};
+
#include "simplex.hpp"
#endif // __SIMPLEX_H__