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dense.go
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dense.go
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package base
import (
"bytes"
"fmt"
"github.com/sjwhitworth/golearn/base/edf"
"math"
"sync"
)
// DenseInstances stores each Attribute value explicitly
// in a large grid.
type DenseInstances struct {
storage *edf.EdfFile
agMap map[string]int
ags []AttributeGroup
lock sync.Mutex
fixed bool
classAttrs map[AttributeSpec]bool
maxRow int
attributes []Attribute
}
// NewDenseInstances generates a new DenseInstances set
// with an anonymous EDF mapping and default settings.
func NewDenseInstances() *DenseInstances {
storage, err := edf.EdfAnonMap()
if err != nil {
panic(err)
}
return &DenseInstances{
storage,
make(map[string]int),
make([]AttributeGroup, 0),
sync.Mutex{},
false,
make(map[AttributeSpec]bool),
0,
make([]Attribute, 0),
}
}
//
// AttributeGroup functions
//
// createAttributeGroup adds a new AttributeGroup to this set of Instances
// IMPORTANT: do not call unless you've acquired the lock
func (inst *DenseInstances) createAttributeGroup(name string, size int) {
var agAdd AttributeGroup
if inst.fixed {
panic("Can't add additional Attributes")
}
// Resolve or create thread
threads, err := inst.storage.GetThreads()
if err != nil {
panic(err)
}
ok := false
for i := range threads {
if threads[i] == name {
ok = true
break
}
}
if ok {
panic("Can't create AttributeGroup: thread already exists")
}
// Write the pool's thread into the file
thread := edf.NewThread(inst.storage, name)
err = inst.storage.WriteThread(thread)
if err != nil {
panic(fmt.Sprintf("Can't write thread: %s", err))
}
// Create the AttributeGroup information
if size != 0 {
ag := new(FixedAttributeGroup)
ag.threadNo = thread.GetId()
ag.parent = inst
ag.attributes = make([]Attribute, 0)
ag.size = size
ag.alloc = make([][]byte, 0)
agAdd = ag
} else {
ag := new(BinaryAttributeGroup)
ag.threadNo = thread.GetId()
ag.parent = inst
ag.attributes = make([]Attribute, 0)
ag.size = size
ag.alloc = make([][]byte, 0)
agAdd = ag
}
inst.agMap[name] = len(inst.ags)
inst.ags = append(inst.ags, agAdd)
}
// CreateAttributeGroup adds a new AttributeGroup to this set of instances
// with a given name. If the size is 0, a bit-ag is added
// if the size of not 0, then the size of each ag attribute
// is set to that number of bytes.
func (inst *DenseInstances) CreateAttributeGroup(name string, size int) (err error) {
defer func() {
if r := recover(); r != nil {
var ok bool
if err, ok = r.(error); !ok {
err = fmt.Errorf("CreateAttributeGroup: %v (not created)", r)
}
}
}()
inst.lock.Lock()
defer inst.lock.Unlock()
inst.createAttributeGroup(name, size)
return nil
}
// GetAttributeGroup returns a reference to a AttributeGroup of a given name /
func (inst *DenseInstances) GetAttributeGroup(name string) (AttributeGroup, error) {
inst.lock.Lock()
defer inst.lock.Unlock()
// Check if the ag exists
if id, ok := inst.agMap[name]; !ok {
return nil, fmt.Errorf("AttributeGroup '%s' doesn't exist", name)
} else {
// Return the ag
return inst.ags[id], nil
}
}
//
// Attribute creation and handling
//
// AddAttribute adds an Attribute to this set of DenseInstances
// Creates a default AttributeGroup for it if a suitable one doesn't exist.
// Returns an AttributeSpec for subsequent Set() calls.
//
// IMPORTANT: will panic if storage has been allocated via Extend.
func (inst *DenseInstances) AddAttribute(a Attribute) AttributeSpec {
inst.lock.Lock()
defer inst.lock.Unlock()
if inst.fixed {
panic("Can't add additional Attributes")
}
// Generate a default AttributeGroup name
ag := "FLOAT"
if _, ok := a.(*CategoricalAttribute); ok {
ag = "CAT"
} else if _, ok := a.(*FloatAttribute); ok {
ag = "FLOAT"
} else if _, ok := a.(*BinaryAttribute); ok {
ag = "BIN"
} else {
panic("Unrecognised Attribute type")
}
// Create the ag if it doesn't exist
if _, ok := inst.agMap[ag]; !ok {
if ag != "BIN" {
inst.createAttributeGroup(ag, 8)
} else {
inst.createAttributeGroup(ag, 0)
}
}
id := inst.agMap[ag]
p := inst.ags[id]
p.AddAttribute(a)
inst.attributes = append(inst.attributes, a)
return AttributeSpec{id, len(p.Attributes()) - 1, a}
}
// AddAttributeToAttributeGroup adds an Attribute to a given ag
func (inst *DenseInstances) AddAttributeToAttributeGroup(newAttribute Attribute, ag string) (AttributeSpec, error) {
inst.lock.Lock()
defer inst.lock.Unlock()
// Check if the ag exists
if _, ok := inst.agMap[ag]; !ok {
return AttributeSpec{-1, 0, nil}, fmt.Errorf("Pond '%s' doesn't exist. Call CreatePond() first", ag)
}
id := inst.agMap[ag]
p := inst.ags[id]
for i, a := range p.Attributes() {
if !a.Compatable(newAttribute) {
return AttributeSpec{-1, 0, nil}, fmt.Errorf("Attribute %s is not compatable with %s in pond '%s' (position %d)", newAttribute, a, ag, i)
}
}
p.AddAttribute(newAttribute)
inst.attributes = append(inst.attributes, newAttribute)
return AttributeSpec{id, len(p.Attributes()) - 1, newAttribute}, nil
}
// GetAttribute returns an Attribute equal to the argument.
//
// TODO: Write a function to pre-compute this once we've allocated
// TODO: Write a utility function which retrieves all AttributeSpecs for
// a given instance set.
func (inst *DenseInstances) GetAttribute(get Attribute) (AttributeSpec, error) {
inst.lock.Lock()
defer inst.lock.Unlock()
for i, p := range inst.ags {
for j, a := range p.Attributes() {
if a.Equals(get) {
return AttributeSpec{i, j, a}, nil
}
}
}
return AttributeSpec{-1, 0, nil}, fmt.Errorf("Couldn't resolve %s", get)
}
// AllAttributes returns a slice of all Attributes.
func (inst *DenseInstances) AllAttributes() []Attribute {
inst.lock.Lock()
defer inst.lock.Unlock()
ret := make([]Attribute, 0)
for _, p := range inst.ags {
for _, a := range p.Attributes() {
ret = append(ret, a)
}
}
return ret
}
// AddClassAttribute sets an Attribute to be a class Attribute.
func (inst *DenseInstances) AddClassAttribute(a Attribute) error {
as, err := inst.GetAttribute(a)
if err != nil {
return err
}
inst.lock.Lock()
defer inst.lock.Unlock()
inst.classAttrs[as] = true
return nil
}
// RemoveClassAttribute removes an Attribute from the set of class Attributes.
func (inst *DenseInstances) RemoveClassAttribute(a Attribute) error {
inst.lock.Lock()
defer inst.lock.Unlock()
as, err := inst.GetAttribute(a)
if err != nil {
return err
}
inst.lock.Lock()
defer inst.lock.Unlock()
inst.classAttrs[as] = false
return nil
}
// AllClassAttributes returns a slice of Attributes which have
// been designated class Attributes.
func (inst *DenseInstances) AllClassAttributes() []Attribute {
var ret []Attribute
inst.lock.Lock()
defer inst.lock.Unlock()
for a := range inst.classAttrs {
if inst.classAttrs[a] {
ret = append(ret, a.attr)
}
}
return ret
}
//
// Allocation functions
//
// Extend extends this set of Instances to store rows additional rows.
// It's recommended to set rows to something quite large.
//
// IMPORTANT: panics if the allocation fails
func (inst *DenseInstances) Extend(rows int) error {
inst.lock.Lock()
defer inst.lock.Unlock()
// Get the size of each page
pageSize := inst.storage.GetPageSize()
for _, p := range inst.ags {
// Compute ag row storage requirements
rowSize := p.RowSize()
// How many rows can we store per page?
rowsPerPage := float64(pageSize) / float64(rowSize)
// How many pages?
pagesNeeded := uint32(math.Ceil(float64(rows) / rowsPerPage))
// Allocate those pages
r, err := inst.storage.AllocPages(pagesNeeded, p.getThreadNo())
if err != nil {
panic(fmt.Sprintf("Allocation error: %s (rowSize %d, pageSize %d, rowsPerPage %.2f, tried to allocate %d page(s) and extend by %d row(s))", err, rowSize, pageSize, rowsPerPage, pagesNeeded, rows))
}
// Resolve and assign those pages
byteBlock := inst.storage.ResolveRange(r)
for _, block := range byteBlock {
p.addStorage(block)
}
}
inst.fixed = true
inst.maxRow += rows
return nil
}
// Set sets a particular Attribute (given as an AttributeSpec) on a particular
// row to a particular value.
//
// AttributeSpecs can be obtained using GetAttribute() or AddAttribute().
//
// IMPORTANT: Will panic() if the AttributeSpec isn't valid
//
// IMPORTANT: Will panic() if the row is too large
//
// IMPORTANT: Will panic() if the val is not the right length
func (inst *DenseInstances) Set(a AttributeSpec, row int, val []byte) {
inst.ags[a.pond].set(a.position, row, val)
}
// Get gets a particular Attribute (given as an AttributeSpec) on a particular
// row.
// AttributeSpecs can be obtained using GetAttribute() or AddAttribute()
func (inst *DenseInstances) Get(a AttributeSpec, row int) []byte {
return inst.ags[a.pond].get(a.position, row)
}
// RowString returns a string representation of a given row.
func (inst *DenseInstances) RowString(row int) string {
var buffer bytes.Buffer
first := true
for _, p := range inst.ags {
if first {
first = false
} else {
buffer.WriteString(" ")
}
p.appendToRowBuf(row, &buffer)
}
return buffer.String()
}
// MapOverRows passes each row map into a function.
// First argument is a list of AttributeSpec in the order
// they're needed in for the function. The second is the function
// to call on each row.
func (inst *DenseInstances) MapOverRows(asv []AttributeSpec, mapFunc func([][]byte, int) (bool, error)) error {
rowBuf := make([][]byte, len(asv))
for i := 0; i < inst.maxRow; i++ {
for j, as := range asv {
p := inst.ags[as.pond]
rowBuf[j] = p.get(as.position, i)
}
ok, err := mapFunc(rowBuf, i)
if err != nil {
return err
}
if !ok {
break
}
}
return nil
}
// Size returns the number of Attributes as the first return value
// and the maximum allocated row as the second value.
func (inst *DenseInstances) Size() (int, int) {
return len(inst.AllAttributes()), inst.maxRow
}
// swapRows swaps over rows i and j
func (inst *DenseInstances) swapRows(i, j int) {
as := ResolveAllAttributes(inst)
for _, a := range as {
v1 := inst.Get(a, i)
v2 := inst.Get(a, j)
v3 := make([]byte, len(v2))
copy(v3, v2)
inst.Set(a, j, v1)
inst.Set(a, i, v3)
}
}
// Equal checks whether a given Instance set is exactly the same
// as another: same size and same values (as determined by the Attributes)
//
// IMPORTANT: does not explicitly check if the Attributes are considered equal.
func (inst *DenseInstances) Equal(other DataGrid) bool {
_, rows := inst.Size()
for _, a := range inst.AllAttributes() {
as1, err := inst.GetAttribute(a)
if err != nil {
panic(err) // That indicates some kind of error
}
as2, err := inst.GetAttribute(a)
if err != nil {
return false // Obviously has different Attributes
}
for i := 0; i < rows; i++ {
b1 := inst.Get(as1, i)
b2 := inst.Get(as2, i)
if !byteSeqEqual(b1, b2) {
return false
}
}
}
return true
}
// String returns a human-readable summary of this dataset.
func (inst *DenseInstances) String() string {
var buffer bytes.Buffer
// Get all Attribute information
as := ResolveAllAttributes(inst)
// Print header
cols, rows := inst.Size()
buffer.WriteString("Instances with ")
buffer.WriteString(fmt.Sprintf("%d row(s) ", rows))
buffer.WriteString(fmt.Sprintf("%d attribute(s)\n", cols))
buffer.WriteString(fmt.Sprintf("Attributes: \n"))
for _, a := range as {
prefix := "\t"
if inst.classAttrs[a] {
prefix = "*\t"
}
buffer.WriteString(fmt.Sprintf("%s%s\n", prefix, a.attr))
}
buffer.WriteString("\nData:\n")
maxRows := 30
if rows < maxRows {
maxRows = rows
}
for i := 0; i < maxRows; i++ {
buffer.WriteString("\t")
for _, a := range as {
val := inst.Get(a, i)
buffer.WriteString(fmt.Sprintf("%s ", a.attr.GetStringFromSysVal(val)))
}
buffer.WriteString("\n")
}
missingRows := rows - maxRows
if missingRows != 0 {
buffer.WriteString(fmt.Sprintf("\t...\n%d row(s) undisplayed", missingRows))
} else {
buffer.WriteString("All rows displayed")
}
return buffer.String()
}