Merge pull request #13 from okieraised/hotfix/get-slice-index

Hotfix/get slice index
okieraised · Apr 3, 2023 · fa087bb · fa087bb
2 parents f3f14a6 + f9cdf50
commit fa087bb
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Showing 2 changed files with 52 additions and 4 deletions.
diff --git a/annotation_test.go b/annotation_test.go
@@ -7,6 +7,7 @@ import (
 	"github.com/stretchr/testify/assert"
 	"io/ioutil"
 	"os"
+	"strings"
 	"testing"
 )
 
@@ -190,3 +191,48 @@ func TestSegmentation_Annotation2(t *testing.T) {
 
 	fmt.Println(len(b))
 }
+
+func TestSegmentation_Annotation3(t *testing.T) {
+
+	y := []float64{1, 3, 4, 6, 8, 2, 532, 6234, 5, 75, 75, 656}
+	var res string
+	for _, e := range y {
+		res += fmt.Sprintf("%d ", int(e))
+	}
+
+	fmt.Println("res", strings.TrimSpace(res))
+}
+
+func TestSegmentation_Annotation4(t *testing.T) {
+	assert := assert.New(t)
+
+	filePath := "/home/tripg/Downloads/annot_import/CT_Abdo.1680080052.TSK-7.seg.nii.gz"
+	rd, err := NewNiiReader(WithReadImageFile(filePath), WithReadRetainHeader(true))
+	assert.NoError(err)
+	err = rd.Parse()
+	assert.NoError(err)
+
+	voxels := rd.GetNiiData().GetVoxels()
+	//voxels.FlipX()
+	//voxels.FlipY()
+	//voxels.FlipZ()
+	err = rd.GetNiiData().SetVoxelToRawVolume(voxels)
+	assert.NoError(err)
+
+	segments, err := rd.GetNiiData().GetVoxels().ImportAsRLE()
+	assert.NoError(err)
+
+	voxels, err = rd.GetNiiData().GetVoxels().ExportSingleFromRLE(segments)
+	assert.NoError(err)
+
+	err = rd.GetNiiData().SetVoxelToRawVolume(voxels)
+	assert.NoError(err)
+
+	writer, err := NewNiiWriter("/home/tripg/Downloads/reexport.nii.gz",
+		WithWriteNIfTIData(rd.GetNiiData()),
+		WithWriteCompression(true),
+	)
+	err = writer.WriteToFile()
+	assert.NoError(err)
+
+}
diff --git a/pkg/nifti/voxel.go b/pkg/nifti/voxel.go
@@ -26,7 +26,7 @@ func NewVoxels(dimX, dimY, dimZ, dimT int64, datatype int32) *Voxels {
 }
 
 // Flip flips the image along the specified axes
-func (v *Voxels) Flip(flipX, flipY, flipZ bool) {
+func (v *Voxels) Flip(flipX, flipY, flipZ bool) *Voxels {
 	if flipX {
 		v.FlipX()
 	}
@@ -36,6 +36,8 @@ func (v *Voxels) Flip(flipX, flipY, flipZ bool) {
 	if flipZ {
 		v.FlipZ()
 	}
+
+	return v
 }
 
 // FlipSagittal flips the image along Sagittal-axis (Y-Z)
@@ -141,10 +143,10 @@ func (v *Voxels) GetDimT() int64 {
 
 // GetSlice returns the values of voxel as a 1-D slice of float64 calculated from z, t input
 func (v *Voxels) GetSlice(z, t int64) []float64 {
-	res := make([]float64, 0)
+	res := make([]float64, v.dimX*v.dimY)
 	for x := int64(0); x < v.dimX; x++ {
 		for y := int64(0); y < v.dimY; y++ {
-			res = append(res, v.Get(x, y, z, t))
+			res[y*v.dimX+x] = v.Get(x, y, z, t)
 		}
 	}
 	return res
@@ -196,7 +198,6 @@ func (v *Voxels) Histogram(bins int) (utils.Histogram, error) {
 
 // RLEEncode encodes the 1-D float64 array using the RLE encoding
 func (v *Voxels) RLEEncode() ([]float64, error) {
-	//v.voxel = []float64{1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1}
 	return RLEEncode(v.voxel)
 }
 
@@ -222,6 +223,7 @@ func (v *Voxels) ImportAsRLE() ([]SegmentRLE, error) {
 					continue
 				}
 				keyArr := make([]float64, len(sliceData))
+
 				for idx, voxVal := range sliceData {
 					if voxVal == key {
 						keyArr[idx] = key