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read_test.go
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read_test.go
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package dicom
import (
"bufio"
"bytes"
"encoding/binary"
"errors"
"io"
"math/rand"
"strconv"
"testing"
"github.com/google/go-cmp/cmp/cmpopts"
"github.com/suyashkumar/dicom/pkg/vrraw"
"github.com/suyashkumar/dicom/pkg/dicomio"
"github.com/suyashkumar/dicom/pkg/frame"
"github.com/google/go-cmp/cmp"
"github.com/suyashkumar/dicom/pkg/tag"
)
func TestReadTag(t *testing.T) {
cases := []struct {
name string
data []byte
wantTag tag.Tag
wantErr error
}{
{
name: "basic",
data: buildTagData(t, tag.Rows),
wantTag: tag.Rows,
wantErr: nil,
},
{
name: "custom",
data: buildTagData(t, tag.Tag{0x0011, 0x0010}),
wantTag: tag.Tag{0x0011, 0x0010},
wantErr: nil,
},
{
name: "expected EOF on group read",
data: []byte{0x1},
wantErr: io.EOF,
},
{
name: "expected EOF on element read",
data: []byte{0x1, 0x2},
wantErr: io.EOF,
},
}
for _, tc := range cases {
t.Run(tc.name, func(t *testing.T) {
data := bytes.NewBuffer(tc.data)
r := &reader{
rawReader: dicomio.NewReader(bufio.NewReader(data), binary.LittleEndian, int64(data.Len())),
}
gotTag, err := r.readTag()
if !errors.Is(err, tc.wantErr) {
t.Errorf("TestReadTag: unexpected err. got: %v, want: %v", err, tc.wantErr)
}
if gotTag != nil && !gotTag.Equals(tc.wantTag) {
t.Errorf("TestReadTag: unexpected output. got: %v, want: %v", gotTag, tc.wantTag)
}
})
}
}
func TestReadFloat_float64(t *testing.T) {
cases := []struct {
name string
floats []float64
VR string
want Value
expectedErr error
}{
{
name: "float64",
floats: []float64{20.1, 32.22},
VR: vrraw.FloatingPointDouble,
want: &floatsValue{value: []float64{20.1, 32.22}},
expectedErr: nil,
},
{
name: "float64 with wrong VR",
floats: []float64{20.1, 32.22},
VR: "XX",
want: nil,
expectedErr: errorUnableToParseFloat,
},
}
for _, tc := range cases {
t.Run(tc.name, func(t *testing.T) {
data := bytes.Buffer{}
for _, fl := range tc.floats {
if err := binary.Write(&data, binary.LittleEndian, fl); err != nil {
t.Errorf("TestReadFloat: Unable to setup test buffer")
}
}
r := &reader{
rawReader: dicomio.NewReader(bufio.NewReader(&data), binary.LittleEndian, int64(data.Len())),
}
got, err := r.readFloat(tag.Tag{}, tc.VR, uint32(data.Len()))
if !errors.Is(err, tc.expectedErr) {
t.Fatalf("readFloat(r, tg, %s, %d) got unexpected error: got: %v, want: %v", tc.VR, data.Len(), err, tc.expectedErr)
}
if diff := cmp.Diff(got, tc.want, cmp.AllowUnexported(floatsValue{})); diff != "" {
t.Errorf("readFloat(r, tg, %s, %d) unexpected diff: %s", tc.VR, data.Len(), diff)
}
})
}
}
func TestReadFloat_float32(t *testing.T) {
cases := []struct {
name string
floats []float32
VR string
want Value
expectedErr error
}{
{
name: "float32",
floats: []float32{20.1001, 32.22},
VR: vrraw.FloatingPointSingle,
want: &floatsValue{value: []float64{20.1001, 32.22}},
expectedErr: nil,
},
{
name: "float32 with wrong VR",
floats: []float32{20.1001, 32.22},
VR: "XX",
want: nil,
expectedErr: errorUnableToParseFloat,
},
}
for _, tc := range cases {
t.Run(tc.name, func(t *testing.T) {
data := bytes.Buffer{}
for _, fl := range tc.floats {
if err := binary.Write(&data, binary.LittleEndian, fl); err != nil {
t.Errorf("TestReadFloat: Unable to setup test buffer")
}
}
r := &reader{
rawReader: dicomio.NewReader(bufio.NewReader(&data), binary.LittleEndian, int64(data.Len())),
}
got, err := r.readFloat(tag.Tag{}, tc.VR, uint32(data.Len()))
if !errors.Is(err, tc.expectedErr) {
t.Fatalf("readFloat(r, tg, %s, %d) got unexpected error: got: %v, want: %v", tc.VR, data.Len(), err, tc.expectedErr)
}
if diff := cmp.Diff(got, tc.want, cmp.AllowUnexported(floatsValue{})); diff != "" {
t.Errorf("readFloat(r, tg, %s, %d) unexpected diff: %s", tc.VR, data.Len(), diff)
}
})
}
}
func TestReadOWBytes(t *testing.T) {
cases := []struct {
name string
bytes []byte
VR string
want Value
expectedErr error
}{
{
name: "OW VR with even-number bytes",
bytes: []byte{0x1, 0x2, 0x3, 0x4},
VR: vrraw.OtherWord,
want: &bytesValue{value: []byte{0x1, 0x2, 0x3, 0x4}},
expectedErr: nil,
},
{
name: "UN VR even-number bytes",
bytes: []byte{0x1, 0x2, 0x3, 0x4},
VR: vrraw.Unknown,
want: &bytesValue{value: []byte{0x1, 0x2, 0x3, 0x4}},
expectedErr: nil,
},
{
name: "error on odd-number bytes",
bytes: []byte{0x1, 0x2, 0x3},
VR: vrraw.OtherWord,
want: nil,
expectedErr: ErrorOWRequiresEvenVL,
},
}
for _, tc := range cases {
t.Run(tc.name, func(t *testing.T) {
data := bytes.Buffer{}
if err := binary.Write(&data, binary.LittleEndian, tc.bytes); err != nil {
t.Errorf("TestReadOWBytes: Unable to setup test buffer")
}
r := &reader{rawReader: dicomio.NewReader(bufio.NewReader(&data), binary.LittleEndian, int64(data.Len()))}
got, err := r.readBytes(tag.Tag{}, tc.VR, uint32(data.Len()))
if !errors.Is(err, tc.expectedErr) {
t.Fatalf("readBytes(r, tg, %s, %d) got unexpected error: got: %v, want: %v", tc.VR, data.Len(), err, tc.expectedErr)
}
if diff := cmp.Diff(got, tc.want, cmp.AllowUnexported(bytesValue{})); diff != "" {
t.Errorf("readBytes(r, tg, %s, %d) unexpected diff: %s", tc.VR, data.Len(), diff)
}
})
}
}
func TestReadNativeFrames(t *testing.T) {
cases := []struct {
Name string
existingData Dataset
uint16Data []uint16
dataBytes []byte
uint32Data []uint32
expectedPixelData *PixelDataInfo
expectedError error
pixelVLOverride uint32
parseOptSet parseOptSet
}{
{
Name: "5x5, 1 frame, 1 samples/pixel, bitsAllocated=16",
existingData: Dataset{Elements: []*Element{
mustNewElement(tag.Rows, []int{5}),
mustNewElement(tag.Columns, []int{5}),
mustNewElement(tag.NumberOfFrames, []string{"1"}),
mustNewElement(tag.BitsAllocated, []int{16}),
mustNewElement(tag.SamplesPerPixel, []int{1}),
}},
uint16Data: []uint16{1, 2, 3, 4, 5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
expectedPixelData: &PixelDataInfo{
IsEncapsulated: false,
Frames: []*frame.Frame{
{
Encapsulated: false,
NativeData: &frame.NativeFrame[uint16]{
InternalBitsPerSample: 16,
InternalRows: 5,
InternalCols: 5,
InternalSamplesPerPixel: 1,
RawData: []uint16{1, 2, 3, 4, 5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
},
},
},
},
expectedError: nil,
},
{
Name: "2x2, 3 frames, 1 samples/pixel, bitsAllocated=16",
existingData: Dataset{Elements: []*Element{
mustNewElement(tag.Rows, []int{2}),
mustNewElement(tag.Columns, []int{2}),
mustNewElement(tag.NumberOfFrames, []string{"3"}),
mustNewElement(tag.BitsAllocated, []int{16}),
mustNewElement(tag.SamplesPerPixel, []int{1}),
}},
uint16Data: []uint16{1, 2, 3, 2, 1, 2, 3, 2, 1, 2, 3, 0},
expectedPixelData: &PixelDataInfo{
IsEncapsulated: false,
Frames: []*frame.Frame{
{
Encapsulated: false,
NativeData: &frame.NativeFrame[uint16]{
InternalBitsPerSample: 16,
InternalRows: 2,
InternalCols: 2,
InternalSamplesPerPixel: 1,
RawData: []uint16{1, 2, 3, 2},
},
},
{
Encapsulated: false,
NativeData: &frame.NativeFrame[uint16]{
InternalBitsPerSample: 16,
InternalRows: 2,
InternalCols: 2,
InternalSamplesPerPixel: 1,
RawData: []uint16{1, 2, 3, 2},
},
},
{
Encapsulated: false,
NativeData: &frame.NativeFrame[uint16]{
InternalBitsPerSample: 16,
InternalRows: 2,
InternalCols: 2,
InternalSamplesPerPixel: 1,
RawData: []uint16{1, 2, 3, 0},
},
},
},
},
expectedError: nil,
},
{
Name: "2x2, 2 frames, 2 samples/pixel, bitsAllocated=16",
existingData: Dataset{Elements: []*Element{
mustNewElement(tag.Rows, []int{2}),
mustNewElement(tag.Columns, []int{2}),
mustNewElement(tag.NumberOfFrames, []string{"2"}),
mustNewElement(tag.BitsAllocated, []int{16}),
mustNewElement(tag.SamplesPerPixel, []int{2}),
}},
uint16Data: []uint16{1, 2, 3, 2, 1, 2, 3, 2, 1, 2, 3, 2, 1, 2, 3, 5},
expectedPixelData: &PixelDataInfo{
IsEncapsulated: false,
Frames: []*frame.Frame{
{
Encapsulated: false,
NativeData: &frame.NativeFrame[uint16]{
InternalBitsPerSample: 16,
InternalRows: 2,
InternalCols: 2,
InternalSamplesPerPixel: 2,
RawData: []uint16{1, 2, 3, 2, 1, 2, 3, 2},
},
},
{
Encapsulated: false,
NativeData: &frame.NativeFrame[uint16]{
InternalBitsPerSample: 16,
InternalRows: 2,
InternalCols: 2,
InternalSamplesPerPixel: 2,
RawData: []uint16{1, 2, 3, 2, 1, 2, 3, 5},
},
},
},
},
expectedError: nil,
},
{
Name: "bitsAllocated=32",
existingData: Dataset{Elements: []*Element{
mustNewElement(tag.Rows, []int{5}),
mustNewElement(tag.Columns, []int{5}),
mustNewElement(tag.NumberOfFrames, []string{"1"}),
mustNewElement(tag.BitsAllocated, []int{32}),
mustNewElement(tag.SamplesPerPixel, []int{1}),
}},
uint32Data: []uint32{1, 2, 3, 4, 5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
expectedPixelData: &PixelDataInfo{
IsEncapsulated: false,
Frames: []*frame.Frame{
{
Encapsulated: false,
NativeData: &frame.NativeFrame[uint32]{
InternalBitsPerSample: 32,
InternalRows: 5,
InternalCols: 5,
InternalSamplesPerPixel: 1,
RawData: []uint32{1, 2, 3, 4, 5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
},
},
},
},
expectedError: nil,
},
{
Name: "insufficient bytes, uint32",
existingData: Dataset{Elements: []*Element{
mustNewElement(tag.Rows, []int{2}),
mustNewElement(tag.Columns, []int{2}),
mustNewElement(tag.NumberOfFrames, []string{"2"}),
mustNewElement(tag.BitsAllocated, []int{32}),
mustNewElement(tag.SamplesPerPixel, []int{2}),
}},
uint16Data: []uint16{1, 2, 3, 2, 1, 2, 3, 2, 1, 2, 3, 2, 1, 2, 3},
expectedPixelData: nil,
expectedError: ErrorMismatchPixelDataLength,
},
{
Name: "redundant bytes, uint32",
existingData: Dataset{Elements: []*Element{
mustNewElement(tag.Rows, []int{2}),
mustNewElement(tag.Columns, []int{2}),
mustNewElement(tag.NumberOfFrames, []string{"1"}),
mustNewElement(tag.BitsAllocated, []int{32}),
mustNewElement(tag.SamplesPerPixel, []int{2}),
}},
uint16Data: []uint16{1, 2, 3, 2, 1, 2, 3, 2, 1, 2, 3, 2, 1, 2, 3, 2, 2},
expectedPixelData: nil,
expectedError: ErrorMismatchPixelDataLength,
},
{
Name: "redundant bytes, uint32 with allowing mismatch length",
existingData: Dataset{Elements: []*Element{
mustNewElement(tag.Rows, []int{2}),
mustNewElement(tag.Columns, []int{2}),
mustNewElement(tag.NumberOfFrames, []string{"1"}),
mustNewElement(tag.BitsAllocated, []int{32}),
mustNewElement(tag.SamplesPerPixel, []int{2}),
}},
uint16Data: []uint16{1, 2, 3, 2, 1, 2, 3, 2, 1, 2, 3, 2, 1, 2, 3, 2, 2},
expectedPixelData: &PixelDataInfo{
ParseErr: ErrorMismatchPixelDataLength,
Frames: []*frame.Frame{
{
EncapsulatedData: frame.EncapsulatedFrame{
Data: []byte{1, 0, 2, 0, 3, 0, 2, 0, 1, 0, 2, 0, 3, 0, 2, 0, 1, 0, 2, 0, 3, 0, 2, 0, 1, 0, 2, 0, 3, 0, 2, 0, 2, 0},
},
},
},
},
parseOptSet: parseOptSet{allowMismatchPixelDataLength: true},
expectedError: nil,
},
{
Name: "missing Columns",
existingData: Dataset{Elements: []*Element{
mustNewElement(tag.Rows, []int{5}),
mustNewElement(tag.NumberOfFrames, []string{"1"}),
mustNewElement(tag.BitsAllocated, []int{16}),
mustNewElement(tag.SamplesPerPixel, []int{1}),
}},
uint16Data: []uint16{1, 2, 3, 4, 5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
expectedPixelData: nil,
expectedError: ErrorElementNotFound,
},
{
Name: "unsupported BitsAllocated",
existingData: Dataset{Elements: []*Element{
mustNewElement(tag.Rows, []int{5}),
mustNewElement(tag.Columns, []int{2}),
mustNewElement(tag.NumberOfFrames, []string{"1"}),
mustNewElement(tag.BitsAllocated, []int{24}),
mustNewElement(tag.SamplesPerPixel, []int{1}),
}},
uint16Data: []uint16{1, 2, 3, 4, 5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
expectedPixelData: nil,
expectedError: ErrorUnsupportedBitsAllocated,
},
{
Name: "3x3, 3 frames, 1 samples/pixel, bytes data (uint8) with padded 0",
existingData: Dataset{Elements: []*Element{
mustNewElement(tag.Rows, []int{3}),
mustNewElement(tag.Columns, []int{3}),
mustNewElement(tag.NumberOfFrames, []string{"3"}),
mustNewElement(tag.BitsAllocated, []int{8}),
mustNewElement(tag.SamplesPerPixel, []int{1}),
}},
dataBytes: []byte{11, 12, 13, 21, 22, 23, 31, 32, 33, 11, 12, 13, 21, 22, 23, 31, 32, 33, 11, 12, 13, 21, 22, 23, 31, 32, 33, 0}, // there is a 28th byte to make total value length even, as required by DICOM spec
expectedPixelData: &PixelDataInfo{
IsEncapsulated: false,
Frames: []*frame.Frame{
{
Encapsulated: false,
NativeData: &frame.NativeFrame[uint8]{
InternalBitsPerSample: 8,
InternalRows: 3,
InternalCols: 3,
InternalSamplesPerPixel: 1,
RawData: []uint8{11, 12, 13, 21, 22, 23, 31, 32, 33},
},
},
{
Encapsulated: false,
NativeData: &frame.NativeFrame[uint8]{
InternalBitsPerSample: 8,
InternalRows: 3,
InternalCols: 3,
InternalSamplesPerPixel: 1,
RawData: []uint8{11, 12, 13, 21, 22, 23, 31, 32, 33},
},
},
{
Encapsulated: false,
NativeData: &frame.NativeFrame[uint8]{
InternalBitsPerSample: 8,
InternalRows: 3,
InternalCols: 3,
InternalSamplesPerPixel: 1,
RawData: []uint8{11, 12, 13, 21, 22, 23, 31, 32, 33},
},
},
},
},
expectedError: nil,
},
{
Name: "1x1, 3 frames, 3 samples/pixel, bytes data (uint8) with padded 0",
existingData: Dataset{Elements: []*Element{
mustNewElement(tag.Rows, []int{1}),
mustNewElement(tag.Columns, []int{1}),
mustNewElement(tag.NumberOfFrames, []string{"3"}),
mustNewElement(tag.BitsAllocated, []int{8}),
mustNewElement(tag.SamplesPerPixel, []int{3}),
}},
dataBytes: []byte{1, 2, 3, 1, 2, 3, 1, 2, 3, 0}, // 10th byte to make total value length even
expectedPixelData: &PixelDataInfo{
IsEncapsulated: false,
Frames: []*frame.Frame{
{
Encapsulated: false,
NativeData: &frame.NativeFrame[uint8]{
InternalBitsPerSample: 8,
InternalRows: 1,
InternalCols: 1,
InternalSamplesPerPixel: 3,
RawData: []uint8{1, 2, 3},
},
},
{
Encapsulated: false,
NativeData: &frame.NativeFrame[uint8]{
InternalBitsPerSample: 8,
InternalRows: 1,
InternalCols: 1,
InternalSamplesPerPixel: 3,
RawData: []uint8{1, 2, 3},
},
},
{
Encapsulated: false,
NativeData: &frame.NativeFrame[uint8]{
InternalBitsPerSample: 8,
InternalRows: 1,
InternalCols: 1,
InternalSamplesPerPixel: 3,
RawData: []uint8{1, 2, 3},
},
},
},
},
expectedError: nil,
},
{
Name: "1x1, 2 frames, 3 samples/pixel, bad pixel length",
existingData: Dataset{Elements: []*Element{
mustNewElement(tag.Rows, []int{1}),
mustNewElement(tag.Columns, []int{1}),
mustNewElement(tag.NumberOfFrames, []string{"2"}),
mustNewElement(tag.BitsAllocated, []int{8}),
mustNewElement(tag.SamplesPerPixel, []int{3}),
}},
dataBytes: []byte{1, 2, 3, 1, 2, 3},
expectedPixelData: nil,
pixelVLOverride: 7,
expectedError: ErrorExpectedEvenLength,
},
}
for _, tc := range cases {
tc := tc
t.Run(tc.Name, func(t *testing.T) {
dcmdata := bytes.Buffer{}
var expectedBytes int
if len(tc.dataBytes) != 0 {
// writing byte-by-byte
expectedBytes = len(tc.dataBytes)
for _, item := range tc.dataBytes {
if err := binary.Write(&dcmdata, binary.LittleEndian, item); err != nil {
t.Errorf("TestReadNativeFrames: Unable to setup test buffer")
}
}
} else if len(tc.uint16Data) != 0 {
// writing 2 bytes (uint16) at a time
expectedBytes = len(tc.uint16Data) * 2
for _, item := range tc.uint16Data {
if err := binary.Write(&dcmdata, binary.LittleEndian, item); err != nil {
t.Errorf("TestReadNativeFrames: Unable to setup test buffer")
}
}
} else if len(tc.uint32Data) != 0 {
expectedBytes = len(tc.uint32Data) * 4
for _, item := range tc.uint32Data {
if err := binary.Write(&dcmdata, binary.LittleEndian, item); err != nil {
t.Errorf("TestReadNativeFrames: Unable to setup test buffer")
}
}
}
var vl uint32
if tc.pixelVLOverride > 0 {
vl = tc.pixelVLOverride
} else {
vl = uint32(dcmdata.Len())
}
r := &reader{
rawReader: dicomio.NewReader(bufio.NewReader(&dcmdata), binary.LittleEndian, int64(dcmdata.Len())),
opts: tc.parseOptSet,
}
pixelData, bytesRead, err := r.readNativeFrames(&tc.existingData, nil, vl)
if !errors.Is(err, tc.expectedError) {
t.Errorf("TestReadNativeFrames(%+v): did not get expected error. got: %v, want: %v", tc, err, tc.expectedError)
}
if err == nil && bytesRead != expectedBytes {
t.Errorf("TestReadNativeFrames(%+v): did not read expected number of bytes. got: %d, want: %d", tc, bytesRead, expectedBytes)
}
if diff := cmp.Diff(tc.expectedPixelData, pixelData, cmpopts.EquateErrors()); diff != "" {
t.Errorf("TestReadNativeFrames(%+v): unexpected diff: %v", tc, diff)
}
})
}
}
func TestReadPixelData_SkipPixelData(t *testing.T) {
cases := []struct {
name string
vl uint32
data []byte
}{
{
name: "NativePixelData",
vl: 6,
data: []byte{1, 2, 3, 4, 5, 6},
},
{
name: "EncapsulatedPixelData",
vl: tag.VLUndefinedLength,
data: makeEncapsulatedSequence(t),
},
}
for _, tc := range cases {
tc := tc
t.Run(tc.name, func(t *testing.T) {
opts := parseOptSet{skipPixelData: true}
dcmdata := bytes.NewBuffer(tc.data)
r := &reader{
rawReader: dicomio.NewReader(bufio.NewReader(dcmdata), binary.LittleEndian, int64(dcmdata.Len())),
opts: opts,
}
val, err := r.readPixelData(tc.vl, &Dataset{}, nil)
if err != nil {
t.Errorf("unexpected error in readPixelData: %v", err)
}
pixelVal, ok := val.GetValue().(PixelDataInfo)
if !ok {
t.Errorf("Expected value to be of type PixelDataInfo")
}
if !pixelVal.IntentionallySkipped {
t.Errorf("Expected PixelDataInfo to have IntentionallySkipped=true")
}
})
}
}
// Used to encode the data from the generated headers.
type headerData struct {
// The byte encoded header data.
HeaderBytes *bytes.Buffer
// The decoded elements conforming the header.
Elements []*Element
}
// Write a collection of elements and return them as an encoded buffer of bytes.
func writeElements(elements []*Element) ([]byte, error) {
buff := bytes.Buffer{}
dcmWriter, err := NewWriter(&buff)
if err != nil {
return []byte{}, err
}
dcmWriter.SetTransferSyntax(binary.LittleEndian, true)
for _, e := range elements {
err := dcmWriter.WriteElement(e)
if err != nil {
return nil, err
}
}
data := buff.Bytes()
return data, nil
}
// Returns a fake DICOM group 2 header with the FileMetaInformationGroupLength tag missing (0x0002,0x0000).
func headerWithNoFileMetaInformationGroupLength() (*headerData, error) {
headerData := new(headerData)
elements := []*Element{
mustNewElement(tag.MediaStorageSOPClassUID, []string{"SecondaryCapture"}),
mustNewElement(tag.MediaStorageSOPInstanceUID, []string{"1.3.6.1.4.1.35190.4.1.20210608.607733549593"}),
mustNewElement(tag.TransferSyntaxUID, []string{"=RLELossless"}),
mustNewElement(tag.ImplementationClassUID, []string{"1.6.6.1.4.1.9590.100.1.0.100.4.0"}),
mustNewElement(tag.SOPInstanceUID, []string{"1.3.6.1.4.1.35190.4.1.20210608.607733549593"}),
}
data, err := writeElements(elements)
if err != nil {
return nil, err
}
// Construct valid DICOM header preamble.
magicWord := []byte("DICM")
preamble := make([]byte, 128)
preamble = append(preamble, magicWord...)
headerBytes := append(preamble, data...)
headerData.HeaderBytes = bytes.NewBuffer(headerBytes)
headerData.Elements = elements[0 : len(elements)-1]
return headerData, nil
}
// Returns a fake DICOM group 2 header with a FileMetaInformationGroupLength tag (0x0002,0x0000).
func headerWithFileMetaInformationGroupLength() (*headerData, error) {
headerData := new(headerData)
sopInstanceUidElement := mustNewElement(tag.SOPInstanceUID, []string{"1.3.6.1.4.1.35190.4.1.20210608.607733549593"})
elements := []*Element{
mustNewElement(tag.FileMetaInformationVersion, []byte{0x00, 0x01}),
mustNewElement(tag.MediaStorageSOPClassUID, []string{"1.2.276.0.7230010.3.1.0.1"}),
mustNewElement(tag.MediaStorageSOPInstanceUID, []string{"1.3.6.1.4.1.35190.4.1.20210608.607733549593"}),
mustNewElement(tag.TransferSyntaxUID, []string{"=RLELossless"}),
mustNewElement(tag.ImplementationClassUID, []string{"1.2.276.0.7230010.3.0.3.6.7"}),
mustNewElement(tag.ImplementationVersionName, []string{"OFFIS_DCMTK_367"}),
}
dataHeader, err := writeElements(elements)
if err != nil {
return nil, err
}
fileMetaInfoElement := mustNewElement(tag.FileMetaInformationGroupLength, []int{len(dataHeader)})
dataFileMetaInfo, err := writeElements([]*Element{fileMetaInfoElement})
if err != nil {
return nil, err
}
dataSopInstanceUid, err := writeElements([]*Element{sopInstanceUidElement})
if err != nil {
return nil, err
}
data := append(dataFileMetaInfo, dataHeader...)
data = append(data, dataSopInstanceUid...)
// Construct valid DICOM header preamble.
magicWord := []byte("DICM")
preamble := make([]byte, 128)
preamble = append(preamble, magicWord...)
headerBytes := append(preamble, data...)
headerData.HeaderBytes = bytes.NewBuffer(headerBytes)
headerData.Elements = append([]*Element{fileMetaInfoElement}, elements...)
return headerData, nil
}
func TestReadHeader_TryAllowErrorMetaElementGroupLength(t *testing.T) {
opts := parseOptSet{allowMissingMetaElementGroupLength: true}
t.Run("NoFileMetaInformationGroupLength", func(t *testing.T) {
dcmheaderNoInfoGrpLen, err := headerWithNoFileMetaInformationGroupLength()
if err != nil {
t.Fatalf("unsuccessful generation of fake header data")
} else {
r := &reader{
rawReader: dicomio.NewReader(bufio.NewReader(dcmheaderNoInfoGrpLen.HeaderBytes), binary.LittleEndian, int64(dcmheaderNoInfoGrpLen.HeaderBytes.Len())),
opts: opts,
}
r.rawReader.SetTransferSyntax(binary.LittleEndian, true)
wantElements, err := r.readHeader()
if err != nil {
t.Errorf("unsuccessful readHeader when parse option %v is turned on and header has no MetaElementGroupLength tag", opts.allowMissingMetaElementGroupLength)
}
// Ensure dataset read from readHeader and the test header are the same except for the ValueLength field.
if diff := cmp.Diff(wantElements, dcmheaderNoInfoGrpLen.Elements, cmp.AllowUnexported(allValues...), cmpopts.IgnoreFields(Element{}, "ValueLength")); diff != "" {
t.Errorf("Elements parsed from test header do not match: %v", diff)
}
}
})
t.Run("WithFileMetaInformationGroupLength", func(t *testing.T) {
dcmHeaderInfoGrpLen, err := headerWithFileMetaInformationGroupLength()
if err != nil {
t.Fatalf("unsuccessful generation of fake header data with FileMetaInformationGroupLength")
} else {
r := &reader{
rawReader: dicomio.NewReader(bufio.NewReader(dcmHeaderInfoGrpLen.HeaderBytes), binary.LittleEndian, int64(dcmHeaderInfoGrpLen.HeaderBytes.Len())),
opts: opts,
}
r.rawReader.SetTransferSyntax(binary.LittleEndian, true)
wantElements, err := r.readHeader()
if err != nil {
t.Errorf("unsuccessful readHeader when parse option %v is turned on and header has no MetaElementGroupLength tag", opts.allowMissingMetaElementGroupLength)
}
// Ensure dataset read from readHeader and the test header are the same except for the ValueLength field.
if diff := cmp.Diff(wantElements, dcmHeaderInfoGrpLen.Elements, cmp.AllowUnexported(allValues...), cmpopts.IgnoreFields(Element{}, "ValueLength")); diff != "" {
t.Errorf("Elements parsed from test header do not match: %v", diff)
}
}
})
}
func TestReadPixelData_TrySkipProcessingPixelDataValue(t *testing.T) {
opts := parseOptSet{skipProcessingPixelDataValue: true}
valueBytes := []byte{1, 2, 3, 4, 5, 6}
dcmdata := bytes.NewBuffer(valueBytes)
r := &reader{
rawReader: dicomio.NewReader(bufio.NewReader(dcmdata), binary.LittleEndian, int64(dcmdata.Len())),
opts: opts,
}
val, err := r.readPixelData(6, &Dataset{}, nil)
if err != nil {
t.Errorf("unexpected error in readPixelData: %v", err)
}
pixelVal, ok := val.GetValue().(PixelDataInfo)
if !ok {
t.Errorf("Expected value to be of type PixelDataInfo")
}
if !pixelVal.IntentionallyUnprocessed {
t.Errorf("Expected PixelDataInfo to have IntentionallyUnprocessed=true")
}
if !cmp.Equal(pixelVal.UnprocessedValueData, valueBytes) {
t.Errorf("expected UnprocessedValueData to match valueBytes. got: %v, want: %v", pixelVal.UnprocessedValueData, valueBytes)
}
}
func makeEncapsulatedSequence(t *testing.T) []byte {
t.Helper()
buf := &bytes.Buffer{}
w := dicomio.NewWriter(buf, binary.LittleEndian, true)
writePixelData(w, tag.PixelData, &pixelDataValue{PixelDataInfo{IsEncapsulated: true, Frames: []*frame.Frame{
{
Encapsulated: true,
EncapsulatedData: frame.EncapsulatedFrame{
Data: []byte{1, 2, 3, 4},
},
},
}}}, "", tag.VLUndefinedLength)
return buf.Bytes()
}
func TestReadNativeFrames_OneBitAllocated(t *testing.T) {
cases := []struct {
Name string
existingData Dataset
data []byte
expectedPixelData *PixelDataInfo
expectedError error
byteOrder binary.ByteOrder
}{
{
Name: "LittleEndian, 4x4, 1 frames, 1 samples/pixel",
existingData: Dataset{Elements: []*Element{
mustNewElement(tag.Rows, []int{4}),
mustNewElement(tag.Columns, []int{4}),
mustNewElement(tag.NumberOfFrames, []string{"1"}),
mustNewElement(tag.BitsAllocated, []int{1}),
mustNewElement(tag.SamplesPerPixel, []int{1}),
}},
data: []byte{0b00010111, 0b10010111},
expectedPixelData: &PixelDataInfo{
IsEncapsulated: false,
Frames: []*frame.Frame{
{
Encapsulated: false,
NativeData: &frame.NativeFrame[int]{
InternalBitsPerSample: 1,
InternalRows: 4,
InternalCols: 4,
InternalSamplesPerPixel: 1,
RawData: []int{0, 0, 0, 1, 0, 1, 1, 1, 1, 0, 0, 1, 0, 1, 1, 1},
},
},
},
},
expectedError: nil,
byteOrder: binary.LittleEndian,
},
{
Name: "\"BigEndian\" (maybe), 4x4, 1 frames, 1 samples/pixel",
existingData: Dataset{Elements: []*Element{
mustNewElement(tag.Rows, []int{4}),
mustNewElement(tag.Columns, []int{4}),
mustNewElement(tag.NumberOfFrames, []string{"1"}),
mustNewElement(tag.BitsAllocated, []int{1}),
mustNewElement(tag.SamplesPerPixel, []int{1}),
}},
data: []byte{0b00010111, 0b10010111},
expectedPixelData: &PixelDataInfo{
IsEncapsulated: false,
Frames: []*frame.Frame{
{
Encapsulated: false,
NativeData: &frame.NativeFrame[int]{
InternalBitsPerSample: 1,
InternalRows: 4,
InternalCols: 4,
InternalSamplesPerPixel: 1,
RawData: []int{0, 0, 0, 1, 0, 1, 1, 1, 1, 0, 0, 1, 0, 1, 1, 1},
},
},
},
},
expectedError: nil,
// For some reason, this doesn't make a difference, even though we
// don't change the order in which we read the bits in the
// implementation. For some reason, binary.Write isn't changing the
// order of the bits (or it is, and we somehow always read it back
// in the correct order).
byteOrder: binary.BigEndian,
},
}
for _, tc := range cases {
t.Run(tc.Name, func(t *testing.T) {
dcmdata := bytes.Buffer{}
for _, item := range tc.data {
if err := binary.Write(&dcmdata, tc.byteOrder, item); err != nil {
t.Errorf("TestReadNativeFrames: Unable to setup test buffer")
}
}
r := &reader{rawReader: dicomio.NewReader(bufio.NewReader(&dcmdata), tc.byteOrder, int64(dcmdata.Len()))}
pixelData, _, err := r.readNativeFrames(&tc.existingData, nil, uint32(dcmdata.Len()))
if !errors.Is(err, tc.expectedError) {
t.Errorf("TestReadNativeFrames(%v): did not get expected error. got: %v, want: %v", tc.data, err, tc.expectedError)
}
if diff := cmp.Diff(tc.expectedPixelData, pixelData); diff != "" {
t.Errorf("TestReadNativeFrames(%v): unexpected diff: %v\ndata:%v", tc.data, diff, pixelData)
}
})
}
}
func BenchmarkReadNativeFrames(b *testing.B) {
cases := []struct {
Name string
Rows int
Cols int
NumFrames int
SamplesPerPixel int
}{
{
Name: "10x10, 10 frames, 1 sample/pixel",
Rows: 10,
Cols: 10,
NumFrames: 10,
SamplesPerPixel: 1,
},
{
Name: "100x100, 10 frames, 1 sample/pixel",
Rows: 100,
Cols: 100,
NumFrames: 10,
SamplesPerPixel: 1,
},
{
Name: "512x512, 10 frames, 1 sample/pixel",
Rows: 512,
Cols: 512,
NumFrames: 10,
SamplesPerPixel: 1,
},
{
Name: "512x512, 10 frames, 5 sample/pixel",
Rows: 512,
Cols: 512,
NumFrames: 10,
SamplesPerPixel: 5,
},
}
for _, c := range cases {
b.Run(c.Name, func(b *testing.B) {
dataset, rawReader := buildReadNativeFramesInput(c.Rows, c.Cols, c.NumFrames, c.SamplesPerPixel, b)
r := &reader{rawReader: rawReader}
b.ResetTimer()
for i := 0; i < b.N; i++ {
_, _, _ = r.readNativeFrames(dataset, nil, uint32(c.Rows*c.Cols*c.NumFrames))
}
})
}
}
func buildReadNativeFramesInput(rows, cols, numFrames, samplesPerPixel int, b *testing.B) (*Dataset, *dicomio.Reader) {
b.Helper()
dataset := Dataset{
Elements: []*Element{
mustNewElement(tag.Rows, []int{rows}),
mustNewElement(tag.Columns, []int{cols}),
mustNewElement(tag.NumberOfFrames, []string{strconv.Itoa(numFrames)}),
mustNewElement(tag.BitsAllocated, []int{16}),
mustNewElement(tag.SamplesPerPixel, []int{samplesPerPixel}),
},
}
dcmdata := bytes.Buffer{}
dcmdata.Grow(2 * numFrames * rows * cols * samplesPerPixel)
for fr := 0; fr < numFrames; fr++ {
for r := 0; r < rows; r++ {
for c := 0; c < cols; c++ {
for pxs := 0; pxs < samplesPerPixel; pxs++ {
if err := binary.Write(&dcmdata, binary.LittleEndian, uint16(rand.Intn(100))); err != nil {
b.Fatalf("TestReadNativeFrames: Unable to setup test buffer")
}