[Avida-SVN] r1597 - in development: documentation source/actions source/tools
matt at myxo.css.msu.edu
matt at myxo.css.msu.edu
Wed May 23 11:45:49 PDT 2007
Author: matt
Date: 2007-05-23 14:45:49 -0400 (Wed, 23 May 2007)
New Revision: 1597
Modified:
development/documentation/actions.html
development/source/actions/PrintActions.cc
development/source/tools/tArray.h
Log:
Added cclade print actions along with some generic fitness histogram functions.
Modified: development/documentation/actions.html
===================================================================
--- development/documentation/actions.html 2007-05-23 18:16:59 UTC (rev 1596)
+++ development/documentation/actions.html 2007-05-23 18:45:49 UTC (rev 1597)
@@ -1210,8 +1210,9 @@
</pre></p>
<li><p>Define the private data members, constructor, description string in GetDescription, and the Process function. Any arguments that you specify after the action name in the events configuration will be passed to your new class via the args argument in the constructor.</p></li>
- <li><p>Register the new action with the action library. At the bottom of each action definitions file, there are the commands that register the individual actions with the action library. To register our example action "MyAction", we'd write<p>
-<p><pre>action_lib->Register<cActionMyAction>("MyAction");</pre><p>
+ <li><p>Register the new action with the action library. At the bottom of each action definitions file, there are the commands that register the individual actions with the action library. In the PrintActions.cc file, for instance, this function is called RegisterPrintActions.
+ <p> To register our example action "MyAction", we'd write:<p>
+<p><pre>action_lib->Register<cActionMyAction>("MyAction");</pre><p>
<li><p>Test your action.</p></li>
</ol>
</p>
Modified: development/source/actions/PrintActions.cc
===================================================================
--- development/source/actions/PrintActions.cc 2007-05-23 18:16:59 UTC (rev 1596)
+++ development/source/actions/PrintActions.cc 2007-05-23 18:45:49 UTC (rev 1597)
@@ -49,6 +49,7 @@
#include "tVector.h"
#include <cmath>
#include <cerrno>
+#include <map>
#define STATS_OUT_FILE(METHOD, DEFAULT) /* 1 */ \
@@ -771,7 +772,7 @@
/*
- @MRR March 2007
+ @MRR May 2007 [UNTESTED]
This function prints out fitness data. The main point is that it
calculates the average fitness from info from the testCPU + the actual
merit of the organisms, and assigns zero fitness to those organisms
@@ -782,12 +783,15 @@
This version of the DetailedFitnessData prints the information as a log histogram.
+ THIS FUNCTION CONTAINS STATIC METHODS USED IN OTHER PRINT ACTION CLASSES.
+ MOVEMENT OF THIS FUNCTION TO A LOWER POINT IN THE FILE MAY CAUSE CONFLICTS.
+
Parameters:
filename (cString) Where the fitness histogram should be written.
fit_mode (cString) Either {Current, Actual, TestCPU}, where
- Current is the current value in the grid. [Default]
- Actual uses the current merit, but the true gestation time.
- TestCPU determined.
+ Current is the current value in the grid. [Default]
+ Actual uses the current merit, but the true gestation time.
+ TestCPU determined.
hist_fmin (double) The minimum fitness value for the fitness histogram. [Default: -3]
hist_fmax (double) The maximum fitness value for the fitness histogram. [Default: 12]
hist_fstep (double) The width of the individual bins in the histogram. [Default: 0.5]
@@ -795,11 +799,11 @@
class cActionPrintLogFitnessHistogram : public cAction
{
private:
-
+
double m_hist_fmin;
double m_hist_fstep;
double m_hist_fmax;
- string m_mode;
+ cString m_mode;
cString m_filename;
public:
@@ -814,14 +818,93 @@
m_hist_fmax = (largs.GetSize()) ? largs.PopWord().AsDouble(): 12;
}
- static const cString GetDescription() { return "Parameters:\n\tfilename (cString) [fitness_log_hist.dat] Where the fitness histogram should be written.\n\tfit_mode (cString) Either {Current, Actual, TestCPU}, where\n\t\t Current is the current value in the grid. [Default]\n\tActual uses the current merit, but the true gestation time.\n\tTestCPU determined.\n\thist_fmin (double) The minimum fitness value for the fitness histogram. [Default: -3]\n\thist_fmax (double) The maximum fitness value for the fitness histogram. [Default: 12]\n\thist_fstep (double) The width of the individual bins in the histogram. [Default: 0.5]\n\n";}
+ static const cString GetDescription() { return "Parameters: <filename> <mode> <min> <step> <max>";}
+ //Given a min:step:max and bin number, return a string reprsenting the range of fitness values.
+ //This function may be called from other classes.
+ static cString GetHistogramBinLabel(int k, double min, double step, double max)
+ {
+ int num_bins = static_cast<int>(ceil( (max - min) / step)) + 3;
+ cString retval;
+
+ if (k == 0)
+ retval = "Inviable";
+ else if (k == 1)
+ retval = cString("[<") + cStringUtil::Convert(min) + ", " + cStringUtil::Convert(min) + cString(")");
+ else if (k < num_bins - 1)
+ retval = cString("(") + cStringUtil::Convert(min+step*(k-2))
+ + cString(", ") + cStringUtil::Convert(min+step*(k-1)) +
+ + cString("]");
+ else
+ retval = cString("[>") + cStringUtil::Convert(max) + cString("]");
+ return retval;
+ }
+
+
+ //This function may get called by outside classes to generate a histogram of log10 fitnesses;
+ //max may be updated by this function if the range is not evenly divisible by the step
+ static tArray<int> MakeHistogram(const tArray<cOrganism*>& orgs, const tArray<cGenotype*>& gens,
+ double min, double step, double& max, const cString& mode, cWorld* world,
+ cAvidaContext& ctx)
+ {
+ //Set up histogram; extra columns prepended (non-viable, < m_hist_fmin) and appended ( > f_hist_fmax)
+ //If the bin size is not a multiple of the step size, the last bin is expanded to make it a multiple.
+ //All bins are [min, max)
+ tArray<int> histogram;
+ int num_bins = static_cast<int>(ceil( (max - min) / step)) + 3;
+ max = min + (num_bins - 3) * step;
+ histogram.Resize(num_bins, 0);
+ cTestCPU* testcpu = world->GetHardwareManager().CreateTestCPU();
+
+
+ // We calculate the fitness based on the current merit,
+ // but with the true gestation time. Also, we set the fitness
+ // to zero if the creature is not viable.
+ tArray<cGenotype*>::const_iterator git;
+ tArray<cOrganism*>::const_iterator oit;
+ for (git = gens.begin(), oit = orgs.begin(); git != gens.end(); git++, oit++){
+ cCPUTestInfo test_info;
+ double fitness = 0.0;
+ if (mode == "TEST_CPU" || mode == "ACTUAL"){
+ testcpu->TestGenome(ctx, test_info, (*git)->GetGenome());
+ }
+
+ if (mode == "TEST_CPU"){
+ fitness = test_info.GetColonyFitness();
+ }
+ else if (mode == "CURRENT"){
+ fitness = (*oit)->GetPhenotype().GetFitness();
+ }
+ else if (mode == "ACTUAL"){
+ fitness = (test_info.IsViable()) ?
+ (*oit)->GetPhenotype().GetMerit().CalcFitness(test_info.GetTestPhenotype().GetGestationTime()) : 0.0;
+ }
+ else
+ world->GetDriver().RaiseFatalException(1, "PrintLogFitnessHistogram::MakeHistogram: Invalid fitness mode requested.");
+
+ //Update the histogram
+ const double log_fitness = log10(fitness);
+ int update_bin = (errno == ERANGE) ? 0 : //If we have a log of zero, this will be true.
+ static_cast<int>((log_fitness - min) / step);
+
+ if (update_bin < 0) //Non-zero bins
+ update_bin = 1; //Below range
+ else if (update_bin >= num_bins - 3)
+ update_bin = num_bins - 1; //Above range
+ else
+ update_bin = update_bin + 2; //Within range
+
+ histogram[update_bin]++;
+ }
+ delete testcpu;
+ return histogram;
+ }
+
void Process(cAvidaContext& ctx)
{
-
//Verify input parameters
if ( (m_mode != "ACTUAL" && m_mode != "CURRENT" && m_mode != "TESTCPU") ||
- m_hist_fmin > m_hist_fmax)
+ m_hist_fmin > m_hist_fmax)
{
cerr << "cActionPrintFitnessHistogram: Please check arguments. Abort.\n";
cerr << "Parameters: " << m_filename << ", " << m_mode << ", " << m_hist_fmin << ":" << m_hist_fstep << ":" << m_hist_fmax << endl;
@@ -832,72 +915,28 @@
cPopulation& pop = m_world->GetPopulation();
const int update = m_world->GetStats().GetUpdate();
const double generation = m_world->GetStats().SumGeneration().Average();
-
- //Set up histogram; extra columns prepended (non-viable, < m_hist_fmin) and appended ( > f_hist_fmax)
- //If the bin size is not a multiple of the step size, the last bin is expanded to make it a multiple.
- //All bins are [min, max)
- tArray<int> histogram;
- int num_bins = static_cast<int>(ceil( (m_hist_fmax - m_hist_fmin) / m_hist_fstep)) + 3;
- m_hist_fmax = m_hist_fmin + (num_bins - 3) * m_hist_fstep;
- histogram.Resize(num_bins, 0);
+ tArray<cOrganism*> orgs;
+ tArray<cGenotype*> gens;
-
- cTestCPU* testcpu = m_world->GetHardwareManager().CreateTestCPU();
-
for (int i = 0; i < pop.GetSize(); i++)
{
if (pop.GetCell(i).IsOccupied() == false) continue; //Skip unoccupied cells
-
cOrganism* organism = pop.GetCell(i).GetOrganism();
cGenotype* genotype = organism->GetGenotype();
-
- cCPUTestInfo test_info;
- testcpu->TestGenome(ctx, test_info, genotype->GetGenome());
-
- // We calculate the fitness based on the current merit,
- // but with the true gestation time. Also, we set the fitness
- // to zero if the creature is not viable.
- const double fitness = (m_mode == "CURRENT") ? organism->GetPhenotype().GetFitness() :
- (m_mode == "ACUTAL") ?
- ((test_info.IsViable()) ?
- organism->GetPhenotype().GetMerit().CalcFitness(test_info.GetTestPhenotype().GetGestationTime()) : 0.0) :
- test_info.GetColonyFitness();
+ orgs.Push(organism);
+ gens.Push(genotype);
+ }
- //Update the histogram
- const double log_fitness = log10(fitness);
-
- int update_bin = (errno == ERANGE) ? 0 : //If we have a log of zero, this will be true.
- static_cast<int>((log_fitness - m_hist_fmin) / m_hist_fstep);
- if (update_bin < 0)
- update_bin = 1;
- else if (update_bin >= num_bins - 3)
- update_bin = num_bins - 1;
- else
- update_bin = update_bin + 2;
+ tArray<int> histogram = MakeHistogram(orgs, gens, m_hist_fmin, m_hist_fstep, m_hist_fstep, m_mode, m_world, ctx);
- histogram[update_bin]++;
- }
-
- delete testcpu;
-
+
//Output histogram
cDataFile& hdf = m_world->GetDataFile(m_filename);
hdf.Write(update, "Update");
hdf.Write(generation, "Generation");
for (int k = 0; k < histogram.GetSize(); k++)
- {
- if (k == 0)
- hdf.Write(histogram[k], "Inviable");
- else if (k == 1)
- hdf.Write(histogram[k], cString("< ") + cStringUtil::Convert(m_hist_fmin));
- else if (k < histogram.GetSize() - 1)
- hdf.Write(histogram[k], cString("(") + cStringUtil::Convert(m_hist_fmin+m_hist_fstep*(k-2))
- + cString(", ") + cStringUtil::Convert(m_hist_fmin+m_hist_fstep*(k-1)) +
- + cString("]"));
- else
- hdf.Write(histogram[k], cString("> ") + cStringUtil::Convert(m_hist_fmax));
- }
+ hdf.Write(histogram[k], GetHistogramBinLabel(k, m_hist_fmin, m_hist_fstep, m_hist_fmax));
hdf.Endl();
}
};
@@ -905,7 +944,386 @@
/*
- @MRR March 2007
+ @MRR May 2007 [INCOMPLETE]
+
+ This function requires Avida be in run mode.
+
+ This function will print histograms of the relative fitness of
+ organisms as compared to the parent.
+
+ STATIC METHODS IN THIS CLASS ARE CALLED BY OTHER ACTIONS.
+ MOVING THIS CLASS MAY BREAK DEPENDENCIES.
+
+ Parameters:
+ filename (cString) Name of the output file
+ fit_mode (cString) Either {Current, Actual, TestCPU}, where
+ Current is the current value in the grid. [Default]
+ Actual uses the current merit, but the true gestation time.
+ that have reproduced.
+ TestCPU determined.
+ hist_fmin (double) The minimum fitness value for the fitness histogram. [Default: 0.50]
+ hist_fmax (double) The maximum fitness value for the fitness histogram. [Default: 0.02]
+ hist_fstep (double) The width of the individual bins in the histogram. [Default: 1.50]
+
+ The file will be formatted:
+ <update> [ <min, min, min+step, ..., max-step, max, >max], each bin [min,max)
+*/
+class cActionPrintRelativeFitnessHistogram : public cAction
+{
+private:
+ double m_hist_fmin;
+ double m_hist_fstep;
+ double m_hist_fmax;
+ cString m_mode;
+ cString m_filename;
+ bool first_run;
+
+public:
+ cActionPrintRelativeFitnessHistogram(cWorld* world, const cString& args) : cAction(world, args)
+ {
+ cString largs(args);
+ m_filename = (largs.GetSize()) ? largs.PopWord() : "rel_fitness.dat";
+ m_mode = (largs.GetSize()) ? largs.PopWord().ToUpper() : "CURRENT";
+ m_hist_fmin = (largs.GetSize()) ? largs.PopWord().AsDouble(): 0;
+ m_hist_fstep = (largs.GetSize()) ? largs.PopWord().AsDouble(): 0.1;
+ m_hist_fmax = (largs.GetSize()) ? largs.PopWord().AsDouble(): 2;
+ }
+
+ static const cString GetDescription() { return "Arguments: [filename] [fit_mode] [hist_min] [hist_step] [hist_max]"; }
+
+
+ static cString GetHistogramBinLabel(int k, double min, double step, double max)
+ {
+ int num_bins = static_cast<int>(ceil( (max - min) / step)) + 2;
+ cString retval;
+
+ if (k == 0)
+ retval = "Inviable";
+ else if (k == 1)
+ retval = cString("[<") + cStringUtil::Convert(min) + ", " + cStringUtil::Convert(min) + cString(")");
+ else if (k < num_bins - 1)
+ retval = cString("(") + cStringUtil::Convert(min+step*(k-2))
+ + cString(", ") + cStringUtil::Convert(min+step*(k-1)) +
+ + cString("]");
+ else
+ retval = cString("[>") + cStringUtil::Convert(max) + cString("]");
+
+ return retval;
+ }
+
+ static tArray<int> MakeHistogram(const tArray<cOrganism*>& orgs, const tArray<cGenotype*>& gens,
+ double min, double step, double& max, const cString& mode, cWorld* world,
+ cAvidaContext& ctx)
+ {
+ //Set up histogram; extra columns prepended (non-viable, < m_hist_fmin) and appended ( > f_hist_fmax)
+ //If the bin size is not a multiple of the step size, the last bin is expanded to make it a multiple.
+ //All bins are [min, max)
+ tArray<int> histogram;
+ int num_bins = static_cast<int>(ceil( (max - min) / step)) + 3;
+ max = min + (num_bins - 3) * step;
+ histogram.Resize(num_bins, 0);
+ cTestCPU* testcpu = world->GetHardwareManager().CreateTestCPU();
+
+
+ // We calculate the fitness based on the current merit,
+ // but with the true gestation time. Also, we set the fitness
+ // to zero if the creature is not viable.
+ tArray<cGenotype*>::const_iterator git;
+ tArray<cOrganism*>::const_iterator oit;
+ for (git = gens.begin(), oit = orgs.begin(); git != gens.end(); git++, oit++){
+ cCPUTestInfo test_info;
+ double fitness = 0.0;
+ double parent_fitness = (*git)->GetParentGenotype()->GetFitness();
+ if (mode == "TEST_CPU" || mode == "ACTUAL"){
+ testcpu->TestGenome(ctx, test_info, (*git)->GetGenome());
+ }
+
+ if (mode == "TEST_CPU"){
+ fitness = test_info.GetColonyFitness();
+ }
+ else if (mode == "CURRENT"){
+ fitness = (*oit)->GetPhenotype().GetFitness();
+ }
+ else if (mode == "ACTUAL"){
+ fitness = (test_info.IsViable()) ?
+ (*oit)->GetPhenotype().GetMerit().CalcFitness(test_info.GetTestPhenotype().GetGestationTime()) : 0.0;
+ }
+ else
+ world->GetDriver().RaiseFatalException(1, "MakeHistogram: Invalid fitness mode requested.");
+
+ //Update the histogram
+ if (parent_fitness <= 0.0)
+ world->GetDriver().RaiseFatalException(1, "PrintRelativeFitness::MakeHistogram: Parent fitness is zero.");
+
+ double rfitness = fitness/parent_fitness;
+ int update_bin = (rfitness == 0) ? 0 :
+ static_cast<int>( ((fitness/parent_fitness) - min) / step);
+
+ if (update_bin < 0 && fitness > 0) //Non-zero bins
+ update_bin = 1; //Below range
+ else if (update_bin >= num_bins - 3)
+ update_bin = num_bins - 1; //Above range
+ else
+ update_bin = update_bin + 2; //Within range
+
+ histogram[update_bin]++;
+ }
+ delete testcpu;
+ return histogram;
+ }
+
+
+
+ void Process(cAvidaContext& ctx)
+ {
+ //Handle possible errors
+ if (ctx.GetAnalyzeMode())
+ m_world->GetDriver().RaiseFatalException(1, "PrintRelativeFitnessHistogram requires avida to be in run mode.");
+ }
+};
+
+
+
+/*
+ @MRR May 2007 [UNTESTED]
+ This function requires CCLADE_TRACKING to be enabled and avida
+ operating non-analyze mode.
+
+ This function will print histograms of log10 fitness of each of the
+ tagged clades.
+
+ Parameters:
+ filename (cString) Name of the output file
+ fit_mode (cString) Either {Current, Actual, ActualRepro, TestCPU}, where
+ Current is the current value in the grid. [Default]
+ Actual uses the current merit, but the true gestation time.
+ CurrentRepro is the same as current, but counts only those orgs
+ that have reproduced.
+ TestCPU determined.
+ hist_fmin (double) The minimum fitness value for the fitness histogram. [Default: -3]
+ hist_fmax (double) The maximum fitness value for the fitness histogram. [Default: 12]
+ hist_fstep (double) The width of the individual bins in the histogram. [Default: 0.5]
+
+ The file will be formatted:
+ <update> <cclade_count> <cclade_id> [...] <cclade_id> [...] ...
+ where [...] will be [ <min, min, min+step, ..., max-step, max, > max], each bin (min,max]
+ */
+class cActionPrintCCladeFitnessHistogram : public cAction
+{
+ private:
+ double m_hist_fmin;
+ double m_hist_fstep;
+ double m_hist_fmax;
+ cString m_mode;
+ cString m_filename;
+ bool first_run;
+
+ public:
+ cActionPrintCCladeFitnessHistogram(cWorld* world, const cString& args) : cAction(world, args)
+ {
+ cString largs(args);
+ m_filename = (largs.GetSize()) ? largs.PopWord() : "cclade_fitness.dat";
+ m_mode = (largs.GetSize()) ? largs.PopWord().ToUpper() : "CURRENT";
+ m_hist_fmin = (largs.GetSize()) ? largs.PopWord().AsDouble(): -3.0;
+ m_hist_fstep = (largs.GetSize()) ? largs.PopWord().AsDouble(): 0.5;
+ m_hist_fmax = (largs.GetSize()) ? largs.PopWord().AsDouble(): 12;
+ first_run = true;
+ }
+
+ static const cString GetDescription() { return "Arguments: [filename] [fit_mode] [hist_min] [hist_step] [hist_max]"; }
+
+ void Process(cAvidaContext& ctx)
+ {
+ //Handle possible errors
+ if (ctx.GetAnalyzeMode())
+ m_world->GetDriver().RaiseFatalException(1, "PrintCCladeFitnessHistogram requires avida to be in run mode.");
+
+ if (m_world->GetConfig().TRACK_CCLADES.Get() == 0)
+ m_world->GetDriver().RaiseFatalException(1, "PrintCCladeFitnessHistogram requires coalescence clade tracking to be enabled.");
+
+ //Verify input parameters
+ if ( (m_mode != "ACTUAL" && m_mode != "CURRENT" && m_mode != "TESTCPU") ||
+ m_hist_fmin > m_hist_fmax)
+ m_world->GetDriver().RaiseFatalException(1, "PrintCCladeFitnessHistogram: Check parameters.");
+
+ //Gather data objects
+ cPopulation& pop = m_world->GetPopulation();
+ const int update = m_world->GetStats().GetUpdate();
+ const double generation = m_world->GetStats().SumGeneration().Average();
+ map< int, tArray<cOrganism*> > org_map; //Map of ccladeID to array of organism IDs
+ map< int, tArray<cGenotype*> > gen_map; //Map of ccladeID to array of genotype IDs
+
+ //Collect clade information
+ for (int i = 0; i < pop.GetSize(); i++){
+ if (pop.GetCell(i).IsOccupied() == false) continue; //Skip unoccupied cells
+ cOrganism* organism = pop.GetCell(i).GetOrganism();
+ cGenotype* genotype = organism->GetGenotype();
+ int cladeID = organism->GetCCladeLabel();
+
+ map< int, tArray<cOrganism*> >::iterator oit = org_map.find(cladeID);
+ map< int, tArray<cGenotype*> >::iterator git = gen_map.find(cladeID);
+ if (oit == org_map.end()){ //The clade is new
+ org_map[cladeID] = tArray<cOrganism*>(1, organism);
+ gen_map[cladeID] = tArray<cGenotype*>(1, genotype);
+ }
+ else{ //The clade is known
+ oit->second.Push(organism);
+ git->second.Push(genotype);
+ }
+ }
+
+ //Create and print the histograms; this calls a static method in another action
+ ofstream& fp = m_world->GetDataFileManager().GetOFStream(m_filename);
+ if (!fp.is_open())
+ m_world->GetDriver().RaiseFatalException(1, "PrintCCladeFitnessHistogram: Unable to open output file.");
+ map< int, tArray<cOrganism*> >::iterator oit = org_map.begin();
+ map< int, tArray<cGenotype*> >::iterator git = gen_map.begin();
+ for(; oit != org_map.end(); oit++, git++){
+ tArray<int> hist = cActionPrintLogFitnessHistogram::MakeHistogram( (oit->second), (git->second),
+ m_hist_fmin, m_hist_fstep, m_hist_fmax,
+ m_mode, m_world, ctx );
+ if (first_run){ //Print header information if first time through
+ first_run = false;
+ fp << "# PrintCCladeFitnessHistogram" << endl << "# Bins: ";
+ for (int k = 0; k < hist.GetSize(); k++)
+ fp << " " << cActionPrintLogFitnessHistogram::GetHistogramBinLabel(k, m_hist_fmin, m_hist_fstep, m_hist_fmax);
+ fp << endl << endl;
+ }
+ if (oit == org_map.begin()) //Print update and clade count if first clade
+ fp << update << " " << org_map.size();
+ fp << oit->first << " [";
+ for (int k = 0; k < hist.GetSize(); k++)
+ fp << " " << hist[k];
+ fp << " ]" << endl;
+ }
+ }
+};
+
+
+
+/*
+ @MRR May 2007 [INCOMPLETE]
+ This function requires CCLADE_TRACKING to be enabled and Avida
+ operating non-analyze mode.
+
+ This function will print histograms of the relative fitness of
+ clade members as compared to the parent.
+
+ Parameters:
+ filename (cString) Name of the output file
+ fit_mode (cString) Either {Current, Actual, ActualRepro, TestCPU}, where
+ Current is the current value in the grid. [Default]
+ Actual uses the current merit, but the true gestation time.
+ CurrentRepro is the same as current, but counts only those orgs
+ that have reproduced.
+ TestCPU determined.
+ hist_fmin (double) The minimum fitness value for the fitness histogram. [Default: 0.50]
+ hist_fmax (double) The maximum fitness value for the fitness histogram. [Default: 0.02]
+ hist_fstep (double) The width of the individual bins in the histogram. [Default: 1.50]
+
+ The file will be formatted:
+ <update> <cclade_count> <cclade_id> [...] <cclade_id> [...] ...
+ where [...] will be [ <min, min, min+step, ..., max-step, max, >max], each bin [min,max}
+ */
+class cActionPrintCCladeRelativeFitnessHistogram : public cAction
+{
+private:
+ double m_hist_fmin;
+ double m_hist_fstep;
+ double m_hist_fmax;
+ cString m_mode;
+ cString m_filename;
+ bool first_run;
+
+public:
+ cActionPrintCCladeRelativeFitnessHistogram(cWorld* world, const cString& args) : cAction(world, args)
+ {
+ cString largs(args);
+ m_filename = (largs.GetSize()) ? largs.PopWord() : "cclade_rel_fitness.dat";
+ m_mode = (largs.GetSize()) ? largs.PopWord().ToUpper() : "CURRENT";
+ m_hist_fmin = (largs.GetSize()) ? largs.PopWord().AsDouble(): 0;
+ m_hist_fstep = (largs.GetSize()) ? largs.PopWord().AsDouble(): 0.2;
+ m_hist_fmax = (largs.GetSize()) ? largs.PopWord().AsDouble(): 2.0;
+ first_run = true;
+ }
+
+ static const cString GetDescription() { return "Arguments: [filename] [fit_mode] [hist_min] [hist_step] [hist_max]"; }
+
+ void Process(cAvidaContext& ctx)
+ {
+ //Handle possible errors
+ if (ctx.GetAnalyzeMode())
+ m_world->GetDriver().RaiseFatalException(1, "PrintCCladeRelativeFitnessHistogram requires avida to be in run mode.");
+
+ if (m_world->GetConfig().TRACK_CCLADES.Get() == 0)
+ m_world->GetDriver().RaiseFatalException(1, "PrintCCladeRelativeFitnessHistogram requires coalescence clade tracking to be enabled.");
+
+ //Verify input parameters
+ if ( (m_mode != "ACTUAL" && m_mode != "CURRENT" && m_mode != "TESTCPU") ||
+ m_hist_fmin > m_hist_fmax)
+ m_world->GetDriver().RaiseFatalException(1, "PrintCCladeRelativeFitness: check parameters");
+
+ ///Gather data objects
+ cPopulation& pop = m_world->GetPopulation();
+ const int update = m_world->GetStats().GetUpdate();
+ const double generation = m_world->GetStats().SumGeneration().Average();
+ map< int, tArray<cOrganism*> > org_map; //Map of ccladeID to array of organism IDs
+ map< int, tArray<cGenotype*> > gen_map; //Map of ccladeID to array of genotype IDs
+
+ //Collect clade information
+ for (int i = 0; i < pop.GetSize(); i++){
+ if (pop.GetCell(i).IsOccupied() == false) continue; //Skip unoccupied cells
+ cOrganism* organism = pop.GetCell(i).GetOrganism();
+ cGenotype* genotype = organism->GetGenotype();
+ int cladeID = organism->GetCCladeLabel();
+
+ map< int, tArray<cOrganism*> >::iterator oit = org_map.find(cladeID);
+ map< int, tArray<cGenotype*> >::iterator git = gen_map.find(cladeID);
+ if (oit == org_map.end()){ //The clade is new
+ org_map[cladeID] = tArray<cOrganism*>(1, organism);
+ gen_map[cladeID] = tArray<cGenotype*>(1, genotype);
+ }
+ else{ //The clade is known
+ oit->second.Push(organism);
+ git->second.Push(genotype);
+ }
+ }
+
+ //Create and print the histograms; this calls a static method in another action
+ ofstream& fp = m_world->GetDataFileManager().GetOFStream(m_filename);
+ if (!fp.is_open())
+ m_world->GetDriver().RaiseFatalException(1, "PrintCCladeRelativeFitnessHistogram: Unable to open output file.");
+ map< int, tArray<cOrganism*> >::iterator oit = org_map.begin();
+ map< int, tArray<cGenotype*> >::iterator git = gen_map.begin();
+ for(; oit != org_map.end(); oit++, git++){
+ tArray<int> hist = cActionPrintRelativeFitnessHistogram::MakeHistogram( (oit->second), (git->second),
+ m_hist_fmin, m_hist_fstep, m_hist_fmax,
+ m_mode, m_world, ctx );
+ if (first_run){ //Print header information if first time through
+ first_run = false;
+ fp << "# PrintCCladeFitnessHistogram" << endl << "# Bins: ";
+ for (int k = 0; k < hist.GetSize(); k++)
+ fp << " " << cActionPrintRelativeFitnessHistogram::GetHistogramBinLabel(k, m_hist_fmin, m_hist_fstep, m_hist_fmax);
+ fp << endl << endl;
+ }
+ if (oit == org_map.begin()) //Print update and clade count if first clade
+ fp << update << " " << org_map.size();
+ fp << oit->first << " [";
+ for (int k = 0; k < hist.GetSize(); k++)
+ fp << " " << hist[k];
+ fp << " ]" << endl;
+ }
+
+ }
+};
+
+
+
+
+
+
+/*
+ @MRR March 2007 [UNTESTED]
This function will take the initial genotype for each organism in the
population/batch, align them, and calculate the per-site entropy of the
aligned sequences. Please note that there may be a variable number
@@ -921,17 +1339,14 @@
bool m_use_gap;
public:
- cActionPrintGenomicSiteEntropy(cWorld* world, const cString& args) : cAction(world, args)
- {
+ cActionPrintGenomicSiteEntropy(cWorld* world, const cString& args) : cAction(world, args){
cString largs = args;
m_filename = (largs.GetSize()) ? largs.PopWord() : "GenomicSiteEntropy.dat";
}
static const cString GetDescription() { return "Arguments: [filename = \"GenomicSiteEntropyData\"] [use_gap = false]";}
- void Process(cAvidaContext& ctx)
- {
-
+ void Process(cAvidaContext& ctx){
const int update = m_world->GetStats().GetUpdate();
const double generation = m_world->GetStats().SumGeneration().Average();
const int num_insts = m_world->GetNumInstructions();
@@ -1894,8 +2309,12 @@
action_lib->Register<cActionPrintPhenotypeData>("PrintPhenotypeData");
action_lib->Register<cActionPrintPhenotypeStatus>("PrintPhenotypeStatus");
action_lib->Register<cActionPrintDemeStats>("PrintDemeStats");
+
+ //Coalescence Clade Actions
action_lib->Register<cActionPrintCCladeCounts>("PrintCCladeCounts");
-
+ action_lib->Register<cActionPrintCCladeFitnessHistogram>("PrintCCladeFitnessHistogram");
+ action_lib->Register<cActionPrintCCladeRelativeFitnessHistogram>("PrintCCladeRelativeFitnessHistogram");
+
// Processed Data
action_lib->Register<cActionPrintData>("PrintData");
@@ -1910,6 +2329,7 @@
action_lib->Register<cActionPrintDominantParasiteGenotype>("PrintDominantParasiteGenotype");
action_lib->Register<cActionPrintDetailedFitnessData>("PrintDetailedFitnessData");
action_lib->Register<cActionPrintLogFitnessHistogram>("PrintLogFitnessHistogram");
+ action_lib->Register<cActionPrintRelativeFitnessHistogram>("PrintRelativeFitnessHistogram");
action_lib->Register<cActionPrintGeneticDistanceData>("PrintGeneticDistanceData");
action_lib->Register<cActionPrintPopulationDistanceData>("PrintPopulationDistanceData");
action_lib->Register<cActionPrintDebug>("PrintDebug");
Modified: development/source/tools/tArray.h
===================================================================
--- development/source/tools/tArray.h 2007-05-23 18:16:59 UTC (rev 1596)
+++ development/source/tools/tArray.h 2007-05-23 18:45:49 UTC (rev 1597)
@@ -52,7 +52,7 @@
typedef const T* const_iterator; //!< STL-compatible const_iterator.
explicit tArray(const int size = 0) : m_data(NULL), m_size(0) { ResizeClear(size); }
- //explicit tArray(const int size = 0, const T& init_val) : m_data(NULL), m_size(0) { Resize(size, init_val); }
+ tArray(const int size, const T& init_val) : m_data(NULL), m_size(0) { Resize(size, init_val); }
tArray(const tArray& rhs) : m_data(NULL), m_size(0) { this->operator=(rhs); }
~tArray() { delete [] m_data; }
More information about the Avida-cvs
mailing list