forked from yaricom/goNEAT
/
genome_writer.go
264 lines (234 loc) · 6.46 KB
/
genome_writer.go
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package genetics
import (
"io"
"bufio"
"fmt"
"gopkg.in/yaml.v2"
"github.com/spf13/cast"
"github.com/elmware/goNEAT/neat"
"github.com/elmware/goNEAT/neat/network"
"github.com/elmware/goNEAT/neat/utils"
)
// The interface to define genome writer
type GenomeWriter interface {
// Writes Genome record
WriteGenome(genome *Genome) error
}
// Creates genome writer with specified data encoding format
func NewGenomeWriter(w io.Writer, encoding GenomeEncoding) (GenomeWriter, error) {
switch encoding {
case PlainGenomeEncoding:
return &plainGenomeWriter{w:bufio.NewWriter(w)}, nil
case YAMLGenomeEncoding:
return &yamlGenomeWriter{w:bufio.NewWriter(w)}, nil
default:
return nil, ErrUnsupportedGenomeEncoding
}
}
// The plain text encoded genome writer
type plainGenomeWriter struct {
w *bufio.Writer
}
// Writes genome in Plain Text format
func (wr *plainGenomeWriter) WriteGenome(g *Genome) error {
_, err := fmt.Fprintf(wr.w, "genomestart %d\n", g.Id)
if err != nil {
return err
}
for _, tr := range g.Traits {
fmt.Fprint(wr.w, "trait ")
err := wr.writeTrait(tr)
if err != nil {
return err
}
fmt.Fprintln(wr.w, "")
}
for _, nd := range g.Nodes {
fmt.Fprint(wr.w, "node ")
err := wr.writeNetworkNode(nd)
if err != nil {
return err
}
fmt.Fprintln(wr.w, "")
}
for _, gn := range g.Genes {
fmt.Fprint(wr.w, "gene ")
err := wr.writeConnectionGene(gn)
if err != nil {
return err
}
fmt.Fprintln(wr.w, "")
}
_, err = fmt.Fprintf(wr.w, "genomeend %d\n", g.Id)
// flush buffer
err = wr.w.Flush()
return err
}
// Dump trait in plain text format
func (wr *plainGenomeWriter) writeTrait(t *neat.Trait) error {
_, err := fmt.Fprintf(wr.w, "%d ", t.Id)
if err == nil {
for i, p := range t.Params {
if i < len(t.Params) - 1 {
_, err = fmt.Fprintf(wr.w, "%g ", p)
} else {
_, err = fmt.Fprintf(wr.w, "%g", p)
}
if err != nil {
return err
}
}
}
return err
}
// Dump network node in plain text format
func (wr *plainGenomeWriter) writeNetworkNode(n *network.NNode) error {
trait_id := 0
if n.Trait != nil {
trait_id = n.Trait.Id
}
act_str, err := utils.NodeActivators.ActivationNameFromType(n.ActivationType)
if err == nil {
_, err = fmt.Fprintf(wr.w, "%d %d %d %d %s", n.Id, trait_id, n.NodeType(),
n.NeuronType, act_str)
}
return err
}
// Dump connection gene in plain text format
func (wr *plainGenomeWriter) writeConnectionGene(g *Gene) error {
link := g.Link
traitId := 0
if link.Trait != nil {
traitId = link.Trait.Id
}
inNodeId := link.InNode.Id
outNodeId := link.OutNode.Id
weight := link.Weight
recurrent := link.IsRecurrent
innov_num := g.InnovationNum
mut_num := g.MutationNum
enabled := g.IsEnabled
_, err := fmt.Fprintf(wr.w, "%d %d %d %g %t %d %g %t",
traitId, inNodeId, outNodeId, weight, recurrent, innov_num, mut_num, enabled)
return err
}
// The YAML encoded genome writer
type yamlGenomeWriter struct {
w *bufio.Writer
}
func (wr *yamlGenomeWriter) WriteGenome(g *Genome) (err error) {
g_map := make(map[string]interface{})
g_map["id"] = g.Id
// encode traits
traits := make([]map[string]interface{}, len(g.Traits))
for i, t := range g.Traits {
traits[i] = wr.encodeGenomeTrait(t)
}
g_map["traits"] = traits
// encode network nodes
nodes := make([]map[string]interface{}, len(g.Nodes))
for i, n := range g.Nodes {
nodes[i], err = wr.encodeNetworkNode(n)
if err != nil {
return err
}
}
g_map["nodes"] = nodes
// encode connection genes
genes := make([]map[string]interface{}, len(g.Genes))
for i, gn := range g.Genes {
genes[i] = wr.encodeConnectionGene(gn)
}
g_map["genes"] = genes
// encode control genes if any
if len(g.ControlGenes) > 0 {
modules := make([]map[string]interface{}, len(g.ControlGenes))
for i, cg := range g.ControlGenes {
modules[i], err = wr.encodeControlGene(cg)
if err != nil {
return err
}
}
g_map["modules"] = modules
}
// store genome map
r_map := make(map[string]interface{})
r_map["genome"] = g_map
// encode everything as YAML
enc := yaml.NewEncoder(wr.w)
err = enc.Encode(r_map)
if err == nil {
// flush stream
err = wr.w.Flush()
}
return err
}
func (wr *yamlGenomeWriter) encodeControlGene(gene *MIMOControlGene) (g_map map[string]interface{}, err error) {
g_map = make(map[string]interface{})
g_map["id"] = gene.ControlNode.Id
if gene.ControlNode.Trait != nil {
g_map["trait_id"] = gene.ControlNode.Trait.Id
} else {
g_map["trait_id"] = 0
}
g_map["innov_num"] = gene.InnovationNum
g_map["mut_num"] = gene.MutationNum
g_map["enabled"] = gene.IsEnabled
g_map["activation"], err = utils.NodeActivators.ActivationNameFromType(gene.ControlNode.ActivationType)
if err != nil {
return nil, err
}
// store inputs
inputs := make([]map[string]interface{}, len(gene.ControlNode.Incoming))
for i, in := range gene.ControlNode.Incoming {
inputs[i] = wr.encodeModuleLink(in.InNode.Id, i)
}
g_map["inputs"] = inputs
// store outputs
outputs := make([]map[string]interface{}, len(gene.ControlNode.Outgoing))
for i, out := range gene.ControlNode.Outgoing {
outputs[i] = wr.encodeModuleLink(out.OutNode.Id, i)
}
g_map["outputs"] = outputs
return g_map, err
}
func (wr *yamlGenomeWriter) encodeModuleLink(id, order int) map[string]interface{} {
l_map := make(map[string]interface{})
l_map["id"] = id
l_map["order"] = order
return l_map
}
func (wr *yamlGenomeWriter) encodeConnectionGene(gene *Gene) map[string]interface{} {
g_map := make(map[string]interface{})
if gene.Link.Trait != nil {
g_map["trait_id"] = gene.Link.Trait.Id
} else {
g_map["trait_id"] = 0
}
g_map["src_id"] = gene.Link.InNode.Id
g_map["tgt_id"] = gene.Link.OutNode.Id
g_map["innov_num"] = gene.InnovationNum
g_map["weight"] = gene.Link.Weight
g_map["mut_num"] = gene.MutationNum
g_map["recurrent"] = cast.ToString(gene.Link.IsRecurrent)
g_map["enabled"] = cast.ToString(gene.IsEnabled)
return g_map
}
func (wr *yamlGenomeWriter) encodeNetworkNode(node *network.NNode) (n_map map[string]interface{}, err error) {
n_map = make(map[string]interface{})
n_map["id"] = node.Id
if node.Trait != nil {
n_map["trait_id"] = node.Trait.Id
} else {
n_map["trait_id"] = 0
}
n_map["type"] = network.NeuronTypeName(node.NeuronType)
n_map["activation"], err = utils.NodeActivators.ActivationNameFromType(node.ActivationType)
return n_map, err
}
func (wr *yamlGenomeWriter) encodeGenomeTrait(trait *neat.Trait) map[string]interface{} {
tr_map := make(map[string]interface{})
tr_map["id"] = trait.Id
tr_map["params"] = trait.Params
return tr_map
}