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annotation.go
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annotation.go
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package gonii
import (
"bytes"
"encoding/binary"
"encoding/json"
"errors"
"github.com/okieraised/gonii/internal/system"
"github.com/okieraised/gonii/pkg/nifti"
"os"
)
type Segmentation struct {
nii1Hdr *nifti.Nii1Header
nii2Hdr *nifti.Nii2Header
img *nifti.Nii
outFile string
compression bool
annotations []SegmentCoordinate
annotationRLE []nifti.SegmentRLE
}
// SegmentCoordinate defines the structure for segmentation coordinate
type SegmentCoordinate struct {
Value any `json:"value"`
X int64 `json:"x"`
Y int64 `json:"y"`
Z int64 `json:"z"`
T int64 `json:"t"`
}
func NewSegmentation(opts ...SegmentationOption) *Segmentation {
seg := &Segmentation{
compression: true,
}
for _, opt := range opts {
opt(seg)
}
return seg
}
type SegmentationOption func(s *Segmentation)
// WithSegCompression allows user to write the segmentation as compressed NIfTI file
func WithSegCompression(compression bool) SegmentationOption {
return func(s *Segmentation) {
s.compression = compression
}
}
// WithOutFile allows user to specify the location to write the segmentation data to file
func WithOutFile(outFile string) SegmentationOption {
return func(s *Segmentation) {
s.outFile = outFile
}
}
// WithNii1Hdr allows users to specify NIfTI-1 header to write the annotation file to
//
// If both NIfTI-1 and NIfTI-2 header are specified. NIfTI-2 header takes precedence
func WithNii1Hdr(hdr *nifti.Nii1Header) SegmentationOption {
return func(s *Segmentation) {
s.nii1Hdr = hdr
}
}
// WithNii2Hdr allows users to specify NIfTI-1 header to write the annotation file to
//
// If both NIfTI-1 and NIfTI-2 header are specified. NIfTI-2 header takes precedence
func WithNii2Hdr(hdr *nifti.Nii2Header) SegmentationOption {
return func(s *Segmentation) {
s.nii2Hdr = hdr
}
}
// WithAnnotations allows users to specify the annotation coordinates to convert to NIfTI file
func WithAnnotations(annotations []SegmentCoordinate) SegmentationOption {
return func(s *Segmentation) {
s.annotations = annotations
}
}
// WithSegmentRLE allows users to specify the annotation as RLE-encoded array to convert to NIfTI file
func WithSegmentRLE(segments []nifti.SegmentRLE) SegmentationOption {
return func(s *Segmentation) {
s.annotationRLE = segments
}
}
// WithImage allows users to specify the NIfTI image structure to convert to (x,y,z,t) coordinate array
func WithImage(image *nifti.Nii) SegmentationOption {
return func(s *Segmentation) {
s.img = image
}
}
// AnnotationNiiToJson converts the NIfTI file to a corresponding annotation coordinates (x,y,z,t) array
func (s *Segmentation) AnnotationNiiToJson() error {
voxels := s.img.GetVoxels()
var res []SegmentCoordinate
for x := int64(0); x < s.img.Nx; x++ {
for y := int64(0); y < s.img.Ny; y++ {
for z := int64(0); z < s.img.Nz; z++ {
for t := int64(0); t < s.img.Nt; t++ {
val := voxels.Get(x, y, z, t)
if val != 0 {
coord := SegmentCoordinate{
X: x,
Y: y,
Z: z,
T: t,
Value: int64(val),
}
res = append(res, coord)
}
}
}
}
}
if s.outFile != "" {
file, err := os.Create(s.outFile)
if err != nil {
return err
}
defer file.Close()
dataset, err := json.MarshalIndent(res, "", "\t")
_, err = file.Write(dataset)
if err != nil {
return err
}
}
return nil
}
// AnnotationJsonToNii converts the annotation coordinates (x,y,z,t) array to a corresponding NIfTI file
func (s *Segmentation) AnnotationJsonToNii() error {
if s.annotations == nil {
return errors.New("no input annotations is specified")
}
if s.nii1Hdr == nil && s.nii2Hdr == nil {
return errors.New("at least one header structure must be specified")
}
if (s.nii1Hdr != nil && s.nii2Hdr != nil) || (s.nii1Hdr == nil && s.nii2Hdr != nil) {
err := s.convertSegmentationToNii2()
if err != nil {
return err
}
} else {
err := s.convertSegmentationToNii1()
if err != nil {
return err
}
}
return nil
}
// convertSegmentationToNii1 converts the voxel and the header to a NIfTI-1 file
func (s *Segmentation) convertSegmentationToNii1() error {
// Check and fix bad value in header
for index, _ := range s.nii1Hdr.Dim {
if index > 0 {
if s.nii1Hdr.Dim[index] <= 0 {
s.nii1Hdr.Dim[index] = 1
}
}
}
// If bitpix is zero then just return error
if s.nii1Hdr.Bitpix <= 0 {
return errors.New("bitpix value must be larger than 0")
}
nx, ny, nz, nt := int64(s.nii1Hdr.Dim[1]), int64(s.nii1Hdr.Dim[2]), int64(s.nii1Hdr.Dim[3]), int64(s.nii1Hdr.Dim[4])
datatype := int32(s.nii1Hdr.Datatype)
vox := nifti.NewVoxels(nx, ny, nz, nt, datatype)
valMapper := map[any]float64{}
// NIfTI can have multiple annotations on the same file,
// so we have to assign the same pixel value for coordinates with same value
for _, coord := range s.annotations {
var byteCode float64 = 1
_, ok := valMapper[coord.Value]
if !ok {
valMapper[coord.Value] = byteCode
byteCode++
} else {
vox.Set(coord.X, coord.Y, coord.Z, coord.T, valMapper[coord.Value])
}
}
// Create a zero-filled voxel slice then we convert the voxel at each index from float64 to []byte
nByPer, _ := nifti.AssignDatatypeSize(datatype)
rawImg := make([]byte, vox.GetRawByteSize(), vox.GetRawByteSize())
for index, voxel := range vox.GetDataset() {
bVal, err := nifti.ConvertVoxelToBytes(
voxel,
float64(s.nii1Hdr.SclSlope),
float64(s.nii1Hdr.SclInter),
int32(s.nii1Hdr.Datatype),
system.NativeEndian,
int32(nByPer),
)
if err != nil {
return err
}
copy(rawImg[index*int(nByPer):(index+1)*int(nByPer)], bVal)
}
// Export segmentation to file
hdrBuf := &bytes.Buffer{}
err := binary.Write(hdrBuf, system.NativeEndian, s.nii1Hdr)
if err != nil {
return err
}
if s.outFile != "" {
wr, err := NewNiiWriter(s.outFile,
WithWriteCompression(s.compression),
WithWriteVersion(nifti.NIIVersion1),
WithWriteNii1Header(s.nii1Hdr),
WithWriteNIfTIData(&nifti.Nii{Volume: rawImg}),
)
if err != nil {
return err
}
err = wr.WriteToFile()
if err != nil {
return err
}
}
return nil
}
// convertSegmentationToNii2 converts the voxel and the header to a NIfTI-2 file
func (s *Segmentation) convertSegmentationToNii2() error {
// Check and fix bad value in header
for index, _ := range s.nii2Hdr.Dim {
if index > 0 {
if s.nii2Hdr.Dim[index] <= 0 {
s.nii2Hdr.Dim[index] = 1
}
}
}
// If bitpix is zero then just return error
if s.nii2Hdr.Bitpix <= 0 {
return errors.New("bitpix value must be larger than 0")
}
nx, ny, nz, nt := s.nii2Hdr.Dim[1], s.nii2Hdr.Dim[2], s.nii2Hdr.Dim[3], s.nii2Hdr.Dim[4]
datatype := int32(s.nii1Hdr.Datatype)
vox := nifti.NewVoxels(nx, ny, nz, nt, datatype)
valMapper := map[any]float64{}
// NIfTI can have multiple annotations on the same file,
// so we have to assign the same pixel value for coordinates with same value
for _, coord := range s.annotations {
var byteCode float64 = 1
_, ok := valMapper[coord.Value]
if !ok {
valMapper[coord.Value] = byteCode
byteCode++
} else {
vox.Set(coord.X, coord.Y, coord.Z, coord.T, valMapper[coord.Value])
}
}
// Create a zero-filled voxel slice then we convert the voxel at each index from float64 to []byte
nByPer, _ := nifti.AssignDatatypeSize(datatype)
rawImg := make([]byte, vox.GetRawByteSize(), vox.GetRawByteSize())
for index, voxel := range vox.GetDataset() {
bVal, err := nifti.ConvertVoxelToBytes(
voxel,
s.nii2Hdr.SclSlope,
s.nii2Hdr.SclInter,
int32(s.nii2Hdr.Datatype),
system.NativeEndian,
int32(nByPer),
)
if err != nil {
return err
}
copy(rawImg[index*int(nByPer):(index+1)*int(nByPer)], bVal)
}
// Export segmentation to file
hdrBuf := &bytes.Buffer{}
err := binary.Write(hdrBuf, system.NativeEndian, s.nii2Hdr)
if err != nil {
return err
}
if s.outFile != "" {
wr, err := NewNiiWriter(s.outFile,
WithWriteCompression(s.compression),
WithWriteVersion(nifti.NIIVersion2),
WithWriteNii2Header(s.nii2Hdr),
WithWriteNIfTIData(&nifti.Nii{Volume: rawImg}),
)
if err != nil {
return err
}
err = wr.WriteToFile()
if err != nil {
return err
}
}
return nil
}