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Merge pull request #42 from yaricom/experiment-utils
Extracted common genome write functions used by examples into utils.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,74 @@ | ||
| // Package utils provides common utilities to be used by experiments. | ||
| package utils | ||
|
|
||
| import ( | ||
| "fmt" | ||
| "github.com/yaricom/goNEAT/v2/experiment" | ||
| "github.com/yaricom/goNEAT/v2/neat/genetics" | ||
| "github.com/yaricom/goNEAT/v2/neat/network/formats" | ||
| "log" | ||
| "os" | ||
| ) | ||
|
|
||
| // WriteGenomePlain is to write genome of the organism to the genomeFile in the outDir directory using plain encoding. | ||
| // The method return path to the file if successful or error if failed. | ||
| func WriteGenomePlain(genomeFile, outDir string, org *genetics.Organism, epoch *experiment.Generation) (string, error) { | ||
| orgPath := fmt.Sprintf("%s/%s_%d-%d", createOutDirForTrial(outDir, epoch.TrialId), | ||
| genomeFile, org.Phenotype.NodeCount(), org.Phenotype.LinkCount()) | ||
| if file, err := os.Create(orgPath); err != nil { | ||
| return "", err | ||
| } else if err = org.Genotype.Write(file); err != nil { | ||
| return "", err | ||
| } | ||
| return orgPath, nil | ||
| } | ||
|
|
||
| // WriteGenomeDOT is to write genome of the organism to the genomeFile in the outDir directory using DOT encoding. | ||
| // The method return path to the file if successful or error if failed. | ||
| func WriteGenomeDOT(genomeFile, outDir string, org *genetics.Organism, epoch *experiment.Generation) (string, error) { | ||
| orgPath := fmt.Sprintf("%s/%s_%d-%d.dot", createOutDirForTrial(outDir, epoch.TrialId), | ||
| genomeFile, org.Phenotype.NodeCount(), org.Phenotype.LinkCount()) | ||
| if file, err := os.Create(orgPath); err != nil { | ||
| return "", err | ||
| } else if err = formats.WriteDOT(file, org.Phenotype); err != nil { | ||
| return "", err | ||
| } | ||
| return orgPath, nil | ||
| } | ||
|
|
||
| // WriteGenomeCytoscapeJSON is to write genome of the organism to the genomeFile in the outDir directory using Cytoscape JSON encoding. | ||
| // The method return path to the file if successful or error if failed. | ||
| func WriteGenomeCytoscapeJSON(genomeFile, outDir string, org *genetics.Organism, epoch *experiment.Generation) (string, error) { | ||
| orgPath := fmt.Sprintf("%s/%s_%d-%d.cyjs", createOutDirForTrial(outDir, epoch.TrialId), | ||
| genomeFile, org.Phenotype.NodeCount(), org.Phenotype.LinkCount()) | ||
| if file, err := os.Create(orgPath); err != nil { | ||
| return "", err | ||
| } else if err = formats.WriteCytoscapeJSON(file, org.Phenotype); err != nil { | ||
| return "", err | ||
| } | ||
| return orgPath, nil | ||
| } | ||
|
|
||
| // WritePopulationPlain is to write genomes of the entire population using plain encoding in the outDir directory. | ||
| // The methods return path to the file if successful or error if failed. | ||
| func WritePopulationPlain(outDir string, pop *genetics.Population, epoch *experiment.Generation) (string, error) { | ||
| popPath := fmt.Sprintf("%s/gen_%d", createOutDirForTrial(outDir, epoch.TrialId), epoch.Id) | ||
| if file, err := os.Create(popPath); err != nil { | ||
| return "", err | ||
| } else if err = pop.WriteBySpecies(file); err != nil { | ||
| return "", err | ||
| } | ||
| return popPath, nil | ||
| } | ||
|
|
||
| // createOutDirForTrial allows creating the output directory for specific trial using standard name. | ||
| func createOutDirForTrial(outDir string, trialID int) string { | ||
| dir := fmt.Sprintf("%s/%d", outDir, trialID) | ||
| if _, err := os.Stat(dir); err != nil { | ||
| // create output dir | ||
| if err = os.MkdirAll(dir, os.ModePerm); err != nil { | ||
| log.Fatal("Failed to create output directory: ", err) | ||
| } | ||
| } | ||
| return dir | ||
| } |