public void populate(EvolutionState state, int thread) {
// should we load individuals from a file? -- duplicates are permitted
if (loadInds != null) {
try {
readSubpopulation(state, new LineNumberReader(new FileReader(loadInds)));
} catch (IOException e) {
state.output.fatal(
"An IOException occurred when trying to read from the file "
+ loadInds
+ ". The IOException was: \n"
+ e);
}
} else {
Hashtable h = null;
if (numDuplicateRetries >= 1) h = new Hashtable(individuals.length / 2); // seems reasonable
for (int x = 0; x < individuals.length; x++) {
for (int tries = 0; tries <= /* Yes, I see that*/ numDuplicateRetries; tries++) {
individuals[x] = species.newIndividual(state, thread);
if (numDuplicateRetries >= 1) {
// check for duplicates
Object o = h.get(individuals[x]);
if (o == null) // found nothing, we're safe
// hash it and go
{
h.put(individuals[x], individuals[x]);
break;
}
}
} // oh well, we tried to cut down the duplicates
}
}
}
public void setup(final EvolutionState state, final Parameter base) {
Parameter def = defaultBase();
int size;
// do we load from a file?
loadInds = state.parameters.getFile(base.push(P_FILE), null);
// what species do we use?
species =
(Species)
state.parameters.getInstanceForParameter(
base.push(P_SPECIES), def.push(P_SPECIES), Species.class);
species.setup(state, base.push(P_SPECIES));
// how big should our subpopulation be?
size = state.parameters.getInt(base.push(P_SUBPOPSIZE), def.push(P_SUBPOPSIZE), 1);
if (size <= 0)
state.output.fatal(
"Subpopulation size must be an integer >= 1.\n",
base.push(P_SUBPOPSIZE),
def.push(P_SUBPOPSIZE));
// How often do we retry if we find a duplicate?
numDuplicateRetries = state.parameters.getInt(base.push(P_RETRIES), def.push(P_RETRIES), 0);
if (numDuplicateRetries < 0)
state.output.fatal(
"The number of retries for duplicates must be an integer >= 0.\n",
base.push(P_RETRIES),
def.push(P_RETRIES));
individuals = new Individual[size];
}
/**
* Reads a subpopulation in binary form, from the format generated by writeSubpopulation(...). If
* the number of individuals is not identical, the individuals array will be deleted and replaced
* with a new array, and a warning will be generated as individuals will have to be created using
* newIndividual(...) rather than readIndividual(...)
*/
public void readSubpopulation(final EvolutionState state, final DataInput dataInput)
throws IOException {
int numIndividuals = dataInput.readInt();
if (numIndividuals != individuals.length) {
state.output.warnOnce(
"On reading subpopulation from binary stream, the subpopulation size was incorrect.\n"
+ "Had to resize and use newIndividual() instead of readIndividual().");
individuals = new Individual[numIndividuals];
for (int i = 0; i < individuals.length; i++)
individuals[i] = species.newIndividual(state, dataInput);
} else
for (int i = 0; i < individuals.length; i++) individuals[i].readIndividual(state, dataInput);
}
/**
* Reads a subpopulation from the format generated by printSubpopulation(....). If the number of
* individuals is not identical, the individuals array will be deleted and replaced with a new
* array, and a warning will be generated as individuals will have to be created using
* newIndividual(...) rather than readIndividual(...).
*/
public void readSubpopulation(final EvolutionState state, final LineNumberReader reader)
throws IOException {
// read in number of individuals and check to see if this appears to be a valid subpopulation
int numIndividuals = Code.readIntegerWithPreamble(NUM_INDIVIDUALS_PREAMBLE, state, reader);
// read in individuals
if (numIndividuals != individuals.length) {
state.output.warnOnce(
"On reading subpopulation from text stream, the subpopulation size didn't match.\n"
+ "Had to resize and use newIndividual() instead of readIndividual().");
individuals = new Individual[numIndividuals];
for (int i = 0; i < individuals.length; i++) {
int j = Code.readIntegerWithPreamble(INDIVIDUAL_INDEX_PREAMBLE, state, reader);
// sanity check
if (j != i)
state.output.warnOnce(
"On reading subpopulation from text stream, some individual indexes in the subpopulation did not match.");
individuals[i] = species.newIndividual(state, reader);
}
} else
for (int i = 0; i < individuals.length; i++) {
int j = Code.readIntegerWithPreamble(INDIVIDUAL_INDEX_PREAMBLE, state, reader);
// sanity check
if (j != i)
state.output.warnOnce(
"On reading subpopulation from text stream, some individual indexes in the subpopulation did not match.");
if (individuals[i] != null) individuals[i].readIndividual(state, reader);
else {
state.output.warnOnce(
"On reading subpopulation from text stream, some of the preexisting subpopulation's slots were null.\n"
+ "Had to use newIndividual() instead of readIndividual(). If you're starting an evolutionary run by reading an\n"
+ "existing population from a file, this is expected -- ignore this message.");
individuals[i] = species.newIndividual(state, reader);
}
}
}