mirror of
https://github.com/sjwhitworth/golearn.git
synced 2025-04-25 13:48:49 +08:00
356 lines
9.2 KiB
Go
356 lines
9.2 KiB
Go
package base
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import (
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"archive/tar"
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"compress/gzip"
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"encoding/csv"
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"fmt"
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"io"
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"os"
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"reflect"
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"runtime"
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)
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func SerializeInstancesToFile(inst FixedDataGrid, path string) error {
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f, err := os.OpenFile(path, os.O_RDWR, 0600)
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if err != nil {
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return err
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}
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err = SerializeInstances(inst, f)
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if err != nil {
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return err
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}
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err = f.Sync()
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if err != nil {
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return fmt.Errorf("Couldn't flush file: %s", err)
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}
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f.Close()
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return nil
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}
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// SerializesInstancesToCSV converts a FixedDataGrid into a CSV file format.
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func SerializeInstancesToCSV(inst FixedDataGrid, path string) error {
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f, err := os.OpenFile(path, os.O_RDWR, 0600)
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if err != nil {
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return err
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}
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defer func() {
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f.Sync()
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f.Close()
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}()
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return SerializeInstancesToCSVStream(inst, f)
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}
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// SerializeInstancesToCSVStream outputs a FixedDataGrid into a CSV file format, via the io.Writer stream.
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func SerializeInstancesToCSVStream(inst FixedDataGrid, f io.Writer) error {
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// Create the CSV writer
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w := csv.NewWriter(f)
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colCount, _ := inst.Size()
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// Write out Attribute headers
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// Start with the regular Attributes
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normalAttrs := NonClassAttributes(inst)
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classAttrs := inst.AllClassAttributes()
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allAttrs := make([]Attribute, colCount)
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n := copy(allAttrs, normalAttrs)
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copy(allAttrs[n:], classAttrs)
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headerRow := make([]string, colCount)
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for i, v := range allAttrs {
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headerRow[i] = v.GetName()
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}
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w.Write(headerRow)
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specs := ResolveAttributes(inst, allAttrs)
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curRow := make([]string, colCount)
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inst.MapOverRows(specs, func(row [][]byte, rowNo int) (bool, error) {
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for i, v := range row {
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attr := allAttrs[i]
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curRow[i] = attr.GetStringFromSysVal(v)
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}
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w.Write(curRow)
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return true, nil
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})
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w.Flush()
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return nil
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}
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// DeserializeInstancesFromTarReader returns DenseInstances from a FunctionalTarReader with the name prefix.
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func DeserializeInstancesFromTarReader(tr *FunctionalTarReader, prefix string) (ret *DenseInstances, err error) {
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p := func(n string) string {
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return fmt.Sprintf("%s%s", prefix, n)
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}
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// Retrieve the MANIFEST and verify
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manifestBytes, err := tr.GetNamedFile(p("MANIFEST"))
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if err != nil {
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return nil, err
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}
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if !reflect.DeepEqual(manifestBytes, []byte(SerializationFormatVersion)) {
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return nil, fmt.Errorf("Unsupported MANIFEST: %s", string(manifestBytes))
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}
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// Get the size
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sizeBytes, err := tr.GetNamedFile(p("DIMS"))
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if err != nil {
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return nil, WrapError(fmt.Errorf("Unable to read DIMS: %v", err))
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}
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if len(sizeBytes) < 16 {
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return nil, WrapError(fmt.Errorf("DIMS: must be 16 bytes"))
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}
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attrCount := int(UnpackBytesToU64(sizeBytes[0:8]))
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rowCount := int(UnpackBytesToU64(sizeBytes[8:]))
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// Unmarshal the Attributes
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attrBytes, err := tr.GetNamedFile(p("CATTRS"))
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if err != nil {
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return nil, DescribeError("Unable to read CATTRS", err)
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}
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cAttrs, err := DeserializeAttributes(attrBytes)
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if err != nil {
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return nil, DescribeError("Class Attribute deserialization error", err)
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}
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attrBytes, err = tr.GetNamedFile(p("ATTRS"))
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if err != nil {
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return nil, DescribeError("Unable to read ATTRS", err)
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}
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normalAttrs, err := DeserializeAttributes(attrBytes)
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if err != nil {
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return nil, DescribeError("Unable to deserialize normal attributes", err)
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}
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// Create the return instances
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ret = NewDenseInstances()
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// Normal Attributes first, class Attributes on the end
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allAttributes := make([]Attribute, attrCount)
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for i, v := range normalAttrs {
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ret.AddAttribute(v)
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allAttributes[i] = v
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}
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for i, v := range cAttrs {
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ret.AddAttribute(v)
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err = ret.AddClassAttribute(v)
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if err != nil {
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return nil, DescribeError(fmt.Sprintf("Could not set Attribute '%s' as a class Attribute", v), err)
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}
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allAttributes[i+len(normalAttrs)] = v
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}
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// Allocate memory
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err = ret.Extend(int(rowCount))
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if err != nil {
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return nil, WrapError(fmt.Errorf("Could not allocate memory"))
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}
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// Seek through the TAR file until we get to the DATA section
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reader := tr.Regenerate()
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for {
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hdr, err := reader.Next()
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if err == io.EOF {
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return nil, WrapError(fmt.Errorf("DATA section missing!"))
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} else if err != nil {
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return nil, WrapError(fmt.Errorf("Error seeking to DATA section: %s", err))
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}
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if hdr.Name == p("DATA") {
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break
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}
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}
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// Resolve AttributeSpecs
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specs := ResolveAttributes(ret, allAttributes)
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// Finally, read the values out of the data section
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for i := 0; i < rowCount; i++ {
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for j, s := range specs {
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r := ret.Get(s, i)
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n, err := reader.Read(r)
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if n != len(r) {
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return nil, WrapError(fmt.Errorf("Expected %d bytes (read %d) on row %d", len(r), n, i))
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}
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ret.Set(s, i, r)
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if err != nil {
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if i == rowCount-1 && j == len(specs)-1 && err == io.EOF {
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break
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}
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return nil, WrapError(fmt.Errorf("Read error in data section (at row %d from %d, attr %d from %d): %s", i, rowCount, j, len(specs), err))
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}
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}
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}
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return ret, nil
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}
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// DeserializeInstances returns a DenseInstances using a given io.Reader.
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func DeserializeInstances(f io.ReadSeeker) (ret *DenseInstances, err error) {
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// Recovery function
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defer func() {
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if r := recover(); r != nil {
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if _, ok := r.(runtime.Error); ok {
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panic(r)
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}
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err = r.(error)
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}
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}()
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// Open the .gz layer
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gzReader, err := gzip.NewReader(f)
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if err != nil {
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panic(WrapError(err))
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}
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regenerateTarReader := func() *tar.Reader {
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f.Seek(0, os.SEEK_SET)
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gzReader.Reset(f)
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tr := tar.NewReader(gzReader)
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return tr
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}
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tr := NewFunctionalTarReader(regenerateTarReader)
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ret, deSerializeErr := DeserializeInstancesFromTarReader(tr, "")
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if err = gzReader.Close(); err != nil {
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return ret, fmt.Errorf("Error closing gzip stream: %s", err)
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}
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return ret, deSerializeErr
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}
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// SerializeInstances stores a FixedDataGrid into an efficient format to the given io.Writer stream.
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func SerializeInstances(inst FixedDataGrid, f io.Writer) error {
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// Create a .tar.gz container
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gzWriter := gzip.NewWriter(f)
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tw := tar.NewWriter(gzWriter)
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serializeErr := SerializeInstancesToTarWriter(inst, tw, "", true)
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// Finally, close and flush the various levels
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if err := tw.Flush(); err != nil {
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return fmt.Errorf("Could not flush tar: %s", err)
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}
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if err := tw.Close(); err != nil {
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return fmt.Errorf("Could not close tar: %s", err)
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}
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if err := gzWriter.Flush(); err != nil {
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return fmt.Errorf("Could not flush gz: %s", err)
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}
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if err := gzWriter.Close(); err != nil {
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return fmt.Errorf("Could not close gz: %s", err)
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}
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return serializeErr
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}
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// SerializeInstancesToTarWriter stores a FixedDataGrid into an efficient form given a tar.Writer.
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func SerializeInstancesToTarWriter(inst FixedDataGrid, tw *tar.Writer, prefix string, includeData bool) error {
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var hdr *tar.Header
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p := func(n string) string {
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return fmt.Sprintf("%s%s", prefix, n)
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}
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// Write the MANIFEST entry
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hdr = &tar.Header{
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Name: p("MANIFEST"),
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Size: int64(len(SerializationFormatVersion)),
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}
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if err := tw.WriteHeader(hdr); err != nil {
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return fmt.Errorf("Could not write MANIFEST header: %s", err)
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}
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if _, err := tw.Write([]byte(SerializationFormatVersion)); err != nil {
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return fmt.Errorf("Could not write MANIFEST contents: %s", err)
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}
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tw.Flush()
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// Now write the dimensions of the dataset
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attrCount, rowCount := inst.Size()
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hdr = &tar.Header{
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Name: p("DIMS"),
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Size: 16,
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}
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if err := tw.WriteHeader(hdr); err != nil {
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return fmt.Errorf("Could not write DIMS header: %s", err)
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}
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if _, err := tw.Write(PackU64ToBytes(uint64(attrCount))); err != nil {
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return fmt.Errorf("Could not write DIMS (attrCount): %s", err)
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}
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if _, err := tw.Write(PackU64ToBytes(uint64(rowCount))); err != nil {
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return fmt.Errorf("Could not write DIMS (rowCount): %s", err)
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}
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// Write the ATTRIBUTES files
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classAttrs := inst.AllClassAttributes()
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normalAttrs := NonClassAttributes(inst)
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if err := writeAttributesToFilePart(classAttrs, tw, p("CATTRS")); err != nil {
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return fmt.Errorf("Could not write CATTRS: %s", err)
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}
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if err := writeAttributesToFilePart(normalAttrs, tw, p("ATTRS")); err != nil {
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return fmt.Errorf("Could not write ATTRS: %s", err)
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}
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// Data must be written out in the same order as the Attributes
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allAttrs := make([]Attribute, attrCount)
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normCount := copy(allAttrs, normalAttrs)
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for i, v := range classAttrs {
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allAttrs[normCount+i] = v
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}
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allSpecs := ResolveAttributes(inst, allAttrs)
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if len(allSpecs) != len(allAttrs) {
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return WrapError(fmt.Errorf("Error resolving all Attributes: resolved %d, expected %d", len(allSpecs), len(allAttrs)))
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}
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// First, estimate the amount of data we'll need...
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dataLength := int64(0)
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inst.MapOverRows(allSpecs, func(val [][]byte, row int) (bool, error) {
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for _, v := range val {
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dataLength += int64(len(v))
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}
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return true, nil
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})
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// Then write the header
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hdr = &tar.Header{
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Name: p("DATA"),
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Size: dataLength,
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}
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if err := tw.WriteHeader(hdr); err != nil {
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return fmt.Errorf("Could not write DATA: %s", err)
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}
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tw.Flush()
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if !includeData {
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return nil
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}
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// Then write the actual data
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writtenLength := int64(0)
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if err := inst.MapOverRows(allSpecs, func(val [][]byte, row int) (bool, error) {
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for _, v := range val {
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wl, err := tw.Write(v)
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writtenLength += int64(wl)
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if err != nil {
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return false, err
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}
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}
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return true, nil
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}); err != nil {
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return err
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}
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if writtenLength != dataLength {
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return fmt.Errorf("Could not write DATA: changed size from %v to %v", dataLength, writtenLength)
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}
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tw.Flush()
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return nil
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}
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