func main() {
fm := flag.String("fm", "featurematrix.afm", "AFM formated feature matrix to use.")
rf := flag.String("rfpred", "rface.sf", "A predictor forest as outputed by rf-ace")
outf := flag.String("leaves", "leaves.tsv", "a case by case sparse matrix of leaf cooccurance in tsv format")
boutf := flag.String("branches", "branches.tsv", "a case by feature sparse matrix of leaf cooccurance in tsv format")
flag.Parse()
datafile, err := os.Open(*fm) // For read access.
if err != nil {
log.Fatal(err)
}
defer datafile.Close()
data := CloudForest.ParseAFM(datafile)
log.Print("Data file ", len(data.Data), " by ", len(data.Data[0].Data))
forestfile, err := os.Open(*rf) // For read access.
if err != nil {
log.Fatal(err)
}
defer forestfile.Close()
forest := CloudForest.ParseRfAcePredictor(forestfile)
log.Print("Forest has ", len(forest.Trees), " trees ")
counts := new(CloudForest.SparseCounter)
caseFeatureCounts := new(CloudForest.SparseCounter)
for i := 0; i < len(forest.Trees); i++ {
leaves := forest.Trees[i].GetLeaves(data, caseFeatureCounts)
for _, leaf := range leaves {
for j := 0; j < len(leaf.Cases); j++ {
for k := 0; k < len(leaf.Cases); k++ {
counts.Add(leaf.Cases[j], leaf.Cases[k], 1)
}
}
}
}
log.Print("Outputing Case Case Cocurance Counts")
outfile, err := os.Create(*outf) // For read access.
if err != nil {
log.Fatal(err)
}
defer outfile.Close()
counts.WriteTsv(outfile)
log.Print("Outputing Case Feature Cocurance Counts")
boutfile, err := os.Create(*boutf) // For read access.
if err != nil {
log.Fatal(err)
}
defer boutfile.Close()
caseFeatureCounts.WriteTsv(boutfile)
}
func main() {
fm := flag.String("fm", "featurematrix.afm", "AFM formated feature matrix to use.")
rf := flag.String("rfpred", "rface.sf", "A predictor forest.")
outf := flag.String("leaves", "leaves.tsv", "a case by case sparse matrix of leaf co-occurrence in tsv format")
boutf := flag.String("branches", "", "a case by feature sparse matrix of leaf co-occurrence in tsv format")
soutf := flag.String("splits", "", "a file to write a json record of splite per feature")
var threads int
flag.IntVar(&threads, "threads", 1, "Parse seperate forests in n seperate threads.")
flag.Parse()
splits := make(map[string][]string)
//Parse Data
data, err := CloudForest.LoadAFM(*fm)
if err != nil {
log.Fatal(err)
}
log.Print("Data file ", len(data.Data), " by ", data.Data[0].Length())
counts := new(CloudForest.SparseCounter)
var caseFeatureCounts *CloudForest.SparseCounter
if *boutf != "" {
caseFeatureCounts = new(CloudForest.SparseCounter)
}
files := strings.Split(*rf, ",")
runtime.GOMAXPROCS(threads)
fileChan := make(chan string, 0)
doneChan := make(chan int, 0)
go func() {
for _, fn := range files {
fileChan <- fn
}
}()
for i := 0; i < threads; i++ {
go func() {
for {
fn := <-fileChan
forestfile, err := os.Open(fn) // For read access.
if err != nil {
log.Fatal(err)
}
defer forestfile.Close()
forestreader := CloudForest.NewForestReader(forestfile)
forest, err := forestreader.ReadForest()
if err != nil {
log.Fatal(err)
}
log.Print("Forest has ", len(forest.Trees), " trees ")
for i := 0; i < len(forest.Trees); i++ {
fmt.Print(".")
leaves := forest.Trees[i].GetLeaves(data, caseFeatureCounts)
for _, leaf := range leaves {
for j := 0; j < len(leaf.Cases); j++ {
for k := 0; k < len(leaf.Cases); k++ {
counts.Add(leaf.Cases[j], leaf.Cases[k], 1)
}
}
}
if *soutf != "" {
forest.Trees[i].Root.Climb(func(n *CloudForest.Node) {
if n.Splitter != nil {
name := n.Splitter.Feature
_, ok := splits[name]
if !ok {
splits[name] = make([]string, 0, 10)
}
split := ""
switch n.Splitter.Numerical {
case true:
split = fmt.Sprintf("%v", n.Splitter.Value)
case false:
keys := make([]string, 0, len(n.Splitter.Left))
for k := range n.Splitter.Left {
keys = append(keys, k)
}
split = strings.Join(keys, ",")
}
splits[name] = append(splits[name], split)
}
})
}
}
doneChan <- 1
}
}()
}
for i := 0; i < len(files); i++ {
<-doneChan
}
log.Print("Outputting Case Case Co-Occurrence Counts")
outfile, err := os.Create(*outf)
if err != nil {
log.Fatal(err)
}
defer outfile.Close()
counts.WriteTsv(outfile)
if *boutf != "" {
log.Print("Outputting Case Feature Co-Occurrence Counts")
boutfile, err := os.Create(*boutf)
if err != nil {
log.Fatal(err)
}
defer boutfile.Close()
caseFeatureCounts.WriteTsv(boutfile)
}
if *soutf != "" {
soutfile, err := os.Create(*soutf)
if err != nil {
log.Fatal(err)
}
defer soutfile.Close()
encoder := json.NewEncoder(soutfile)
encoder.Encode(splits)
}
}
func main() {
fm := flag.String("fm", "featurematrix.afm", "AFM formated feature matrix to use.")
rf := flag.String("rfpred", "rface.sf", "A predictor forest.")
outf := flag.String("leaves", "leaves.tsv", "a case by case sparse matrix of leaf co-occurrence in tsv format")
boutf := flag.String("branches", "", "a case by feature sparse matrix of leaf co-occurrence in tsv format")
var threads int
flag.IntVar(&threads, "threads", 1, "Parse seperate forests in n seperate threads.")
flag.Parse()
//Parse Data
data, err := CloudForest.LoadAFM(*fm)
if err != nil {
log.Fatal(err)
}
log.Print("Data file ", len(data.Data), " by ", data.Data[0].Length())
counts := new(CloudForest.SparseCounter)
var caseFeatureCounts *CloudForest.SparseCounter
if *boutf != "" {
caseFeatureCounts = new(CloudForest.SparseCounter)
}
files := strings.Split(*rf, ",")
runtime.GOMAXPROCS(threads)
fileChan := make(chan string, 0)
doneChan := make(chan int, 0)
go func() {
for _, fn := range files {
fileChan <- fn
}
}()
for i := 0; i < threads; i++ {
go func() {
for {
fn := <-fileChan
forestfile, err := os.Open(fn) // For read access.
if err != nil {
log.Fatal(err)
}
defer forestfile.Close()
forestreader := CloudForest.NewForestReader(forestfile)
forest, err := forestreader.ReadForest()
if err != nil {
log.Fatal(err)
}
log.Print("Forest has ", len(forest.Trees), " trees ")
for i := 0; i < len(forest.Trees); i++ {
leaves := forest.Trees[i].GetLeaves(data, caseFeatureCounts)
for _, leaf := range leaves {
for j := 0; j < len(leaf.Cases); j++ {
for k := 0; k < len(leaf.Cases); k++ {
counts.Add(leaf.Cases[j], leaf.Cases[k], 1)
}
}
}
}
doneChan <- 1
}
}()
}
for i := 0; i < len(files); i++ {
<-doneChan
}
log.Print("Outputting Case Case Co-Occurrence Counts")
outfile, err := os.Create(*outf) // For read access.
if err != nil {
log.Fatal(err)
}
defer outfile.Close()
counts.WriteTsv(outfile)
if *boutf != "" {
log.Print("Outputting Case Feature Co-Occurrence Counts")
boutfile, err := os.Create(*boutf) // For read access.
if err != nil {
log.Fatal(err)
}
defer boutfile.Close()
caseFeatureCounts.WriteTsv(boutfile)
}
}