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write: fix/support BigEndian PixelData writes, pad odd byte lengths w…
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…ith extra byte (#302)


---------

Co-authored-by: quang18 <quang@segmed.ai>
Co-authored-by: Suyash Kumar <suyashkumar2003@gmail.com>
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@ducquangkstn @suyashkumar
3 people committed Mar 9, 2024
1 parent 8f1f151 commit 82da819
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Showing 2 changed files with 107 additions and 33 deletions.
14 changes: 11 additions & 3 deletions write.go
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Original file line number Diff line number Diff line change
Expand Up @@ -580,21 +580,22 @@ func writePixelData(w dicomio.Writer, t tag.Tag, value Value, vr string, vl uint

buf := &bytes.Buffer{}
buf.Grow(length)
bo, _ := w.GetTransferSyntax()
for frame := 0; frame < numFrames; frame++ {
for pixel := 0; pixel < numPixels; pixel++ {
for value := 0; value < numValues; value++ {
pixelValue := image.Frames[frame].NativeData.Data[pixel][value]
switch image.Frames[frame].NativeData.BitsPerSample {
case 8:
if err := binary.Write(buf, binary.LittleEndian, uint8(pixelValue)); err != nil {
if err := binary.Write(buf, bo, uint8(pixelValue)); err != nil {
return err
}
case 16:
if err := binary.Write(buf, binary.LittleEndian, uint16(pixelValue)); err != nil {
if err := binary.Write(buf, bo, uint16(pixelValue)); err != nil {
return err
}
case 32:
if err := binary.Write(buf, binary.LittleEndian, uint32(pixelValue)); err != nil {
if err := binary.Write(buf, bo, uint32(pixelValue)); err != nil {
return err
}
default:
Expand All @@ -603,6 +604,13 @@ func writePixelData(w dicomio.Writer, t tag.Tag, value Value, vr string, vl uint
}
}
}
// If the byte length is not even, append 1 padding byte to make it even.
// https://dicom.nema.org/medical/dicom/current/output/html/part05.html#sect_8.1.1
if buf.Len()%2 != 0 {
if err := buf.WriteByte(0); err != nil {
return err
}
}
if err := w.WriteBytes(buf.Bytes()); err != nil {
return err
}
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126 changes: 96 additions & 30 deletions write_test.go
View file
Original file line number Diff line number Diff line change
Expand Up @@ -442,6 +442,71 @@ func TestWrite(t *testing.T) {
}},
expectedError: nil,
},
{
name: "native_PixelData_2samples_2frames_BigEndian",
dataset: Dataset{Elements: []*Element{
mustNewElement(tag.MediaStorageSOPClassUID, []string{"1.2.840.10008.5.1.4.1.1.1.2"}),
mustNewElement(tag.MediaStorageSOPInstanceUID, []string{"1.2.3.4.5.6.7"}),
mustNewElement(tag.TransferSyntaxUID, []string{uid.ExplicitVRBigEndian}),
mustNewElement(tag.Rows, []int{2}),
mustNewElement(tag.Columns, []int{2}),
mustNewElement(tag.BitsAllocated, []int{32}),
mustNewElement(tag.NumberOfFrames, []string{"2"}),
mustNewElement(tag.SamplesPerPixel, []int{2}),
mustNewElement(tag.PixelData, PixelDataInfo{
IsEncapsulated: false,
Frames: []*frame.Frame{
{
Encapsulated: false,
NativeData: frame.NativeFrame{
BitsPerSample: 32,
Rows: 2,
Cols: 2,
Data: [][]int{{1, 1}, {2, 2}, {3, 3}, {4, 4}},
},
},
{
Encapsulated: false,
NativeData: frame.NativeFrame{
BitsPerSample: 32,
Rows: 2,
Cols: 2,
Data: [][]int{{5, 1}, {2, 2}, {3, 3}, {4, 5}},
},
},
},
}),
}},
expectedError: nil,
},
{
name: "native_PixelData_odd_bytes",
dataset: Dataset{Elements: []*Element{
mustNewElement(tag.MediaStorageSOPClassUID, []string{"1.2.840.10008.5.1.4.1.1.1.2"}),
mustNewElement(tag.MediaStorageSOPInstanceUID, []string{"1.2.3.4.5.6.7"}),
mustNewElement(tag.TransferSyntaxUID, []string{uid.ImplicitVRLittleEndian}),
mustNewElement(tag.Rows, []int{1}),
mustNewElement(tag.Columns, []int{3}),
mustNewElement(tag.BitsAllocated, []int{8}),
mustNewElement(tag.NumberOfFrames, []string{"1"}),
mustNewElement(tag.SamplesPerPixel, []int{1}),
mustNewElement(tag.PixelData, PixelDataInfo{
IsEncapsulated: false,
Frames: []*frame.Frame{
{
Encapsulated: false,
NativeData: frame.NativeFrame{
BitsPerSample: 8,
Rows: 1,
Cols: 3,
Data: [][]int{{1}, {2}, {3}},
},
},
},
}),
}},
expectedError: nil,
},
{
name: "PixelData with IntentionallyUnprocessed=true",
dataset: Dataset{Elements: []*Element{
Expand Down Expand Up @@ -500,43 +565,44 @@ func TestWrite(t *testing.T) {
t.Fatalf("Unexpected error when creating tempfile: %v", err)
}
if err = Write(file, tc.dataset, tc.opts...); err != tc.expectedError {
t.Errorf("Write(%v): unexpected error. got: %v, want: %v", tc.dataset, err, tc.expectedError)
t.Fatalf("Write(%v): unexpected error. got: %v, want: %v", tc.dataset, err, tc.expectedError)
}
file.Close()

// If we expect an error, we do not need to continue to check the value of the written data, so we continue to the next test case.
if tc.expectedError != nil {
return
}
// Read the data back in and check for equality to the tc.dataset:
if tc.expectedError == nil {
f, err := os.Open(file.Name())
if err != nil {
t.Fatalf("Unexpected error opening file %s: %v", file.Name(), err)
}
info, err := f.Stat()
if err != nil {
t.Fatalf("Unexpected error state file: %s: %v", file.Name(), err)
}
f, err := os.Open(file.Name())
if err != nil {
t.Fatalf("Unexpected error opening file %s: %v", file.Name(), err)
}
info, err := f.Stat()
if err != nil {
t.Fatalf("Unexpected error state file: %s: %v", file.Name(), err)
}

readDS, err := Parse(f, info.Size(), nil, tc.parseOpts...)
if err != nil {
t.Errorf("Parse of written file, unexpected error: %v", err)
}
readDS, err := Parse(f, info.Size(), nil, tc.parseOpts...)
if err != nil {
t.Errorf("Parse of written file, unexpected error: %v", err)
}

wantElems := append(tc.dataset.Elements, tc.extraElems...)
wantElems := append(tc.dataset.Elements, tc.extraElems...)

cmpOpts := []cmp.Option{
cmp.AllowUnexported(allValues...),
cmpopts.IgnoreFields(Element{}, "ValueLength"),
cmpopts.IgnoreSliceElements(func(e *Element) bool { return e.Tag == tag.FileMetaInformationGroupLength }),
cmpopts.SortSlices(func(x, y *Element) bool { return x.Tag.Compare(y.Tag) == 1 }),
}
cmpOpts = append(cmpOpts, tc.cmpOpts...)
cmpOpts := []cmp.Option{
cmp.AllowUnexported(allValues...),
cmpopts.IgnoreFields(Element{}, "ValueLength"),
cmpopts.IgnoreSliceElements(func(e *Element) bool { return e.Tag == tag.FileMetaInformationGroupLength }),
cmpopts.SortSlices(func(x, y *Element) bool { return x.Tag.Compare(y.Tag) == 1 }),
}
cmpOpts = append(cmpOpts, tc.cmpOpts...)

if diff := cmp.Diff(
wantElems,
readDS.Elements,
cmpOpts...,
); diff != "" {
t.Errorf("Reading back written dataset led to unexpected diff from source data: %s", diff)
}
if diff := cmp.Diff(
wantElems,
readDS.Elements,
cmpOpts...,
); diff != "" {
t.Errorf("Reading back written dataset led to unexpected diff from source data: %s", diff)
}
})
}
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