Merge pull request #4 from okieraised/dev

Fixed bug with bytes.Reader

io.go

@@ -63,6 +63,9 @@ func WithReadHeaderFile(headerFile string) func(*nifti.NiiReader) error {
 		}
 		// Check the content type to see if the file is gzipped. Do not depend on just the extensions of the file
 		bData, err = deflateFileContent(bData)
+		if err != nil {
+			return err
+		}
 		w.SetHdrReader(bytes.NewReader(bData))
 		return nil
 	}
@@ -77,22 +80,45 @@ func WithReadImageFile(niiFile string) func(*nifti.NiiReader) error {
 		}
 		// Check the content type to see if the file is gzipped. Do not depend on just the extensions of the file
 		bData, err = deflateFileContent(bData)
+		if err != nil {
+			return err
+		}
 		w.SetReader(bytes.NewReader(bData))
 		return nil
 	}
 }
 
 // WithReadImageReader allows option for users to specify the NIfTI bytes reader (.nii.gz or .nii)
-func WithReadImageReader(r *bytes.Reader) func(*nifti.NiiReader) {
-	return func(w *nifti.NiiReader) {
-		w.SetReader(r)
+func WithReadImageReader(r *bytes.Reader) func(*nifti.NiiReader) error {
+	return func(w *nifti.NiiReader) error {
+		bArr := make([]byte, r.Len())
+		_, err := r.Read(bArr)
+		if err != nil {
+			return err
+		}
+		bArr, err = deflateFileContent(bArr)
+		if err != nil {
+			return err
+		}
+		w.SetReader(bytes.NewReader(bArr))
+		return nil
 	}
 }
 
 // WithReadHeaderReader allows option for users to specify the separate header file reader in case of NIfTI pair .hdr/.img
-func WithReadHeaderReader(r *bytes.Reader) func(*nifti.NiiReader) {
-	return func(w *nifti.NiiReader) {
+func WithReadHeaderReader(r *bytes.Reader) func(*nifti.NiiReader) error {
+	return func(w *nifti.NiiReader) error {
+		bArr := make([]byte, r.Len())
+		_, err := r.Read(bArr)
+		if err != nil {
+			return err
+		}
+		bArr, err = deflateFileContent(bArr)
+		if err != nil {
+			return err
+		}
 		w.SetHdrReader(r)
+		return nil
 	}
 }
 

io_test.go

@@ -1,11 +1,13 @@
 package gonii
 
 import (
+	"bytes"
 	"encoding/binary"
 	"fmt"
 	"github.com/okieraised/gonii/pkg/matrix"
 	"github.com/okieraised/gonii/pkg/nifti"
 	"github.com/stretchr/testify/assert"
+	"os"
 	"testing"
 )
 
@@ -280,3 +282,30 @@ func TestNewNiiWriter_90MB(t *testing.T) {
 	err = rd.Parse()
 	assert.NoError(err)
 }
+
+func TestNewNiiWriter_Nii2_BytesReader(t *testing.T) {
+	assert := assert.New(t)
+
+	filePath := "./test_data/int16.nii.gz"
+
+	bContent, err := os.ReadFile(filePath)
+	assert.NoError(err)
+
+	rd, err := NewNiiReader(WithReadImageReader(bytes.NewReader(bContent)))
+	assert.NoError(err)
+	err = rd.Parse()
+	assert.NoError(err)
+
+	voxels := rd.GetNiiData().GetVoxels()
+
+	err = rd.GetNiiData().SetVoxelToRawVolume(voxels)
+	assert.NoError(err)
+
+	writer, err := NewNiiWriter("./test_data/int16_nii2.nii.gz",
+		WithWriteNIfTIData(rd.GetNiiData()),
+		WithWriteCompression(true),
+		WithWriteVersion(2),
+	)
+	err = writer.WriteToFile()
+	assert.NoError(err)
+}