diff --git a/go.mod b/go.mod index 35313d7..cc32e7d 100644 --- a/go.mod +++ b/go.mod @@ -8,11 +8,4 @@ require ( golang.org/x/text v0.3.8 ) -require ( - github.com/davecgh/go-spew v1.1.1 // indirect - github.com/pmezard/go-difflib v1.0.0 // indirect - github.com/stretchr/objx v0.5.0 // indirect - github.com/stretchr/testify v1.8.4 // indirect - golang.org/x/xerrors v0.0.0-20191204190536-9bdfabe68543 // indirect - gopkg.in/yaml.v3 v3.0.1 // indirect -) +require golang.org/x/xerrors v0.0.0-20191204190536-9bdfabe68543 // indirect diff --git a/go.sum b/go.sum index f9de78b..6cf5601 100644 --- a/go.sum +++ b/go.sum @@ -1,20 +1,7 @@ -github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38= -github.com/davecgh/go-spew v1.1.1 h1:vj9j/u1bqnvCEfJOwUhtlOARqs3+rkHYY13jYWTU97c= -github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38= github.com/golang/mock v1.4.4 h1:l75CXGRSwbaYNpl/Z2X1XIIAMSCquvXgpVZDhwEIJsc= github.com/golang/mock v1.4.4/go.mod h1:l3mdAwkq5BuhzHwde/uurv3sEJeZMXNpwsxVWU71h+4= github.com/google/go-cmp v0.5.2 h1:X2ev0eStA3AbceY54o37/0PQ/UWqKEiiO2dKL5OPaFM= github.com/google/go-cmp v0.5.2/go.mod h1:v8dTdLbMG2kIc/vJvl+f65V22dbkXbowE6jgT/gNBxE= -github.com/pmezard/go-difflib v1.0.0 h1:4DBwDE0NGyQoBHbLQYPwSUPoCMWR5BEzIk/f1lZbAQM= -github.com/pmezard/go-difflib v1.0.0/go.mod h1:iKH77koFhYxTK1pcRnkKkqfTogsbg7gZNVY4sRDYZ/4= -github.com/stretchr/objx v0.1.0/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME= -github.com/stretchr/objx v0.4.0/go.mod h1:YvHI0jy2hoMjB+UWwv71VJQ9isScKT/TqJzVSSt89Yw= -github.com/stretchr/objx v0.5.0 h1:1zr/of2m5FGMsad5YfcqgdqdWrIhu+EBEJRhR1U7z/c= -github.com/stretchr/objx v0.5.0/go.mod h1:Yh+to48EsGEfYuaHDzXPcE3xhTkx73EhmCGUpEOglKo= -github.com/stretchr/testify v1.7.1/go.mod h1:6Fq8oRcR53rry900zMqJjRRixrwX3KX962/h/Wwjteg= -github.com/stretchr/testify v1.8.0/go.mod h1:yNjHg4UonilssWZ8iaSj1OCr/vHnekPRkoO+kdMU+MU= -github.com/stretchr/testify v1.8.4 h1:CcVxjf3Q8PM0mHUKJCdn+eZZtm5yQwehR5yeSVQQcUk= -github.com/stretchr/testify v1.8.4/go.mod h1:sz/lmYIOXD/1dqDmKjjqLyZ2RngseejIcXlSw2iwfAo= golang.org/x/crypto v0.0.0-20190308221718-c2843e01d9a2/go.mod h1:djNgcEr1/C05ACkg1iLfiJU5Ep61QUkGW8qpdssI0+w= golang.org/x/net v0.0.0-20190311183353-d8887717615a/go.mod h1:t9HGtf8HONx5eT2rtn7q6eTqICYqUVnKs3thJo3Qplg= golang.org/x/sync v0.0.0-20190423024810-112230192c58/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= @@ -25,7 +12,3 @@ golang.org/x/text v0.3.8/go.mod h1:E6s5w1FMmriuDzIBO73fBruAKo1PCIq6d2Q6DHfQ8WQ= golang.org/x/tools v0.0.0-20190425150028-36563e24a262/go.mod h1:RgjU9mgBXZiqYHBnxXauZ1Gv1EHHAz9KjViQ78xBX0Q= golang.org/x/xerrors v0.0.0-20191204190536-9bdfabe68543 h1:E7g+9GITq07hpfrRu66IVDexMakfv52eLZ2CXBWiKr4= golang.org/x/xerrors v0.0.0-20191204190536-9bdfabe68543/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0= -gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0= -gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM= -gopkg.in/yaml.v3 v3.0.1 h1:fxVm/GzAzEWqLHuvctI91KS9hhNmmWOoWu0XTYJS7CA= -gopkg.in/yaml.v3 v3.0.1/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM= diff --git a/pkg/frame/inplace/read.go b/pkg/frame/inplace/read.go index 6e6d40a..871ea4e 100644 --- a/pkg/frame/inplace/read.go +++ b/pkg/frame/inplace/read.go @@ -10,11 +10,11 @@ func ReadUnprocessedValueData(info *PixelDataMetadata, unprocessedValueData []by offset := frameIndex * pixelsPerFrame * info.SamplesPerPixel * bytesAllocated samplesPerPixel := info.SamplesPerPixel - re := make([][]int, pixelsPerFrame) - for i := 0; i < pixelsPerFrame; i++ { - re[i] = make([]int, samplesPerPixel) - for j := 0; j < samplesPerPixel; j++ { - pointOffset := offset + i*info.SamplesPerPixel*bytesAllocated + j*bytesAllocated + re := make([][]int, samplesPerPixel) + for i := 0; i < samplesPerPixel; i++ { + re[i] = make([]int, pixelsPerFrame) + for j := 0; j < pixelsPerFrame; j++ { + pointOffset := offset + j*info.SamplesPerPixel*bytesAllocated + i*bytesAllocated switch bytesAllocated { case 1: re[i][j] = int(unprocessedValueData[pointOffset]) diff --git a/pkg/frame/inplace/read_test.go b/pkg/frame/inplace/read_test.go index af729f2..1461047 100644 --- a/pkg/frame/inplace/read_test.go +++ b/pkg/frame/inplace/read_test.go @@ -2,11 +2,12 @@ package inplace import ( "bytes" + "fmt" "io" "testing" - "github.com/stretchr/testify/assert" - "github.com/stretchr/testify/require" + "github.com/google/go-cmp/cmp" + "github.com/google/go-cmp/cmp/cmpopts" "github.com/suyashkumar/dicom" "github.com/suyashkumar/dicom/pkg/frame" @@ -15,8 +16,11 @@ import ( ) func mustNewElement(t *testing.T, tag tag.Tag, data interface{}) *dicom.Element { + t.Helper() elem, err := dicom.NewElement(tag, data) - require.NoError(t, err) + if err != nil { + t.Errorf("dicom.NewElement: %v", err) + } return elem } @@ -189,31 +193,65 @@ func TestReadReadUnprocessedValueData(t *testing.T) { for _, tc := range cases { t.Run(tc.Name, func(t *testing.T) { var filesOut bytes.Buffer - require.NoError(t, dicom.Write(io.Writer(&filesOut), tc.existingData)) + var err error + if err = dicom.Write(io.Writer(&filesOut), tc.existingData); err != nil { + t.Errorf("Write DICOM obj to bytes: %v", err) + } rawData := filesOut.Bytes() dataset, err := dicom.Parse(bytes.NewReader(rawData), int64(len(rawData)), nil, dicom.SkipProcessingPixelDataValue()) - require.NoError(t, err) + if err != nil { + t.Errorf("dicom.Parse: %v", err) + } metadata, err := GetPixelDataMetadata(&dataset) - require.NoError(t, err) + if err != nil { + t.Errorf("GetPixelDataMetadata: %v", err) + } pixelElement, err := dataset.FindElementByTag(tag.PixelData) - require.NoError(t, err) + if err != nil { + t.Errorf("tag.PixelData not found: %v", err) + } pixelDataInfo := dicom.MustGetPixelDataInfo(pixelElement.Value) - assert.Equal(t, pixelDataInfo.IntentionallyUnprocessed, true) - assert.Equal(t, pixelDataInfo.IsEncapsulated, false) + if pixelDataInfo.IsEncapsulated || !pixelDataInfo.IntentionallyUnprocessed { + t.Errorf("pixelDataInfo should be IntentionallyUnprocessed: IsEncapsulated=%t IntentionallyUnprocessed%t", + pixelDataInfo.IsEncapsulated, pixelDataInfo.IntentionallyUnprocessed) + } - require.NoError(t, IsSafeForUnprocessedValueDataHandling(metadata, pixelDataInfo.UnprocessedValueData)) + if err = IsSafeForUnprocessedValueDataHandling(metadata, pixelDataInfo.UnprocessedValueData); err != nil { + t.Errorf("IsSafeForUnprocessedValueDataHandling(%v)", err) + } originPixelElement, err := tc.existingData.FindElementByTag(tag.PixelData) - require.NoError(t, err) + if err != nil { + t.Errorf("Find tag.PixelData(%v)", err) + } originPixelDataInfo := dicom.MustGetPixelDataInfo(originPixelElement.Value) for i := 0; i < metadata.Frames; i++ { originData := originPixelDataInfo.Frames[i].NativeData.Data inplaceData, err := ReadUnprocessedValueData(metadata, pixelDataInfo.UnprocessedValueData, i) - require.NoError(t, err) - assert.Equal(t, originData, inplaceData, "missing match value", i) + if err != nil { + t.Errorf("ReadUnprocessedValueData(%v)", err) + } + assertUnprocessedPixelData(t, originData, inplaceData, fmt.Sprint("frame:", i)) } }) } } + +func assertUnprocessedPixelData(t *testing.T, inplaceData [][]int, originData [][]int, msg string) { + if len(inplaceData[0]) != len(originData) || len(inplaceData) != len(originData[0]) { + t.Errorf("Mismatch data size: origin-data(%d-%d) inplace-data(%d-%d)", + len(originData), len(originData[0]), len(inplaceData), len(inplaceData[0])) + } + tmp := make([][]int, len(originData)) + for i := 0; i < len(tmp); i++ { + tmp[i] = make([]int, len(originData[0])) + for j := 0; j < len(originData[0]); j++ { + tmp[i][j] = inplaceData[j][i] + } + } + if diff := cmp.Diff(originData, tmp, cmpopts.EquateErrors()); diff != "" { + t.Errorf("assertUnprocessedPixelData(%v-%s): unexpected diff: %v", inplaceData, msg, diff) + } +} diff --git a/pkg/frame/inplace/write_test.go b/pkg/frame/inplace/write_test.go index 75d970a..6b81f40 100644 --- a/pkg/frame/inplace/write_test.go +++ b/pkg/frame/inplace/write_test.go @@ -5,8 +5,8 @@ import ( "io" "testing" - "github.com/stretchr/testify/assert" - "github.com/stretchr/testify/require" + "github.com/google/go-cmp/cmp" + "github.com/google/go-cmp/cmp/cmpopts" "github.com/suyashkumar/dicom" "github.com/suyashkumar/dicom/pkg/frame" @@ -52,7 +52,9 @@ func TestWriteUnprocessedValueData(t *testing.T) { }, } var buffer bytes.Buffer - require.NoError(t, dicom.Write(io.Writer(&buffer), originDataset)) + if err := dicom.Write(io.Writer(&buffer), originDataset); err != nil { + t.Errorf("write from dataset to DICOM bytes: %v", err) + } rawData := buffer.Bytes() for _, tc := range []struct { @@ -96,21 +98,17 @@ func TestWriteUnprocessedValueData(t *testing.T) { }, }, } { - dataset, err := dicom.Parse(bytes.NewReader(rawData), int64(len(rawData)), nil, dicom.SkipProcessingPixelDataValue()) - require.NoError(t, err) - metadata, err := GetPixelDataMetadata(&dataset) - require.NoError(t, err) - pixelElement, err := dataset.FindElementByTag(tag.PixelData) - require.NoError(t, err) - pixelDataInfo := dicom.MustGetPixelDataInfo(pixelElement.Value) - assert.Equal(t, pixelDataInfo.IntentionallyUnprocessed, true) - assert.Equal(t, pixelDataInfo.IsEncapsulated, false) - // Sanity check if the dataset is suitable for in-place read-write - require.NoError(t, IsSafeForUnprocessedValueDataHandling(metadata, pixelDataInfo.UnprocessedValueData)) + var err error + dataset, metadata, pixelDataInfo := setupUnprocessedPixelData(t, rawData) // in-place write then converts to bytes - require.NoError(t, WriteUnprocessedValueData(metadata, pixelDataInfo.UnprocessedValueData, tc.rowIndex, tc.colIndex, tc.frameIndex, tc.sampleIndex, 100)) + if err = WriteUnprocessedValueData(metadata, pixelDataInfo.UnprocessedValueData, + tc.rowIndex, tc.colIndex, tc.frameIndex, tc.sampleIndex, 100); err != nil { + t.Errorf("WriteUnprocessedValueData: %v", err) + } var buffer2 bytes.Buffer - require.NoError(t, dicom.Write(io.Writer(&buffer2), dataset)) + if err = dicom.Write(io.Writer(&buffer2), dataset); err != nil { + t.Errorf("Write new DICOM obj to file: %v", err) + } outputBytes := buffer2.Bytes() assertPixelDataInfo(t, outputBytes, tc.expectedPixelInfo) } @@ -154,7 +152,9 @@ func TestWriteUnprocessedValueData_BigEndian(t *testing.T) { }, } var buffer bytes.Buffer - require.NoError(t, dicom.Write(io.Writer(&buffer), originDataset)) + if err := dicom.Write(io.Writer(&buffer), originDataset); err != nil { + t.Errorf("write from dataset to DICOM bytes: %v", err) + } rawData := buffer.Bytes() for _, tc := range []struct { @@ -198,31 +198,58 @@ func TestWriteUnprocessedValueData_BigEndian(t *testing.T) { }, }, } { - dataset, err := dicom.Parse(bytes.NewReader(rawData), int64(len(rawData)), nil, dicom.SkipProcessingPixelDataValue()) - require.NoError(t, err) - metadata, err := GetPixelDataMetadata(&dataset) - require.NoError(t, err) - pixelElement, err := dataset.FindElementByTag(tag.PixelData) - require.NoError(t, err) - pixelDataInfo := dicom.MustGetPixelDataInfo(pixelElement.Value) - assert.Equal(t, pixelDataInfo.IntentionallyUnprocessed, true) - assert.Equal(t, pixelDataInfo.IsEncapsulated, false) - // Sanity check if the dataset is suitable for in-place read-write - require.NoError(t, IsSafeForUnprocessedValueDataHandling(metadata, pixelDataInfo.UnprocessedValueData)) + dataset, metadata, pixelDataInfo := setupUnprocessedPixelData(t, rawData) + var err error // in-place write then converts to bytes - require.NoError(t, WriteUnprocessedValueData(metadata, pixelDataInfo.UnprocessedValueData, tc.rowIndex, tc.colIndex, tc.frameIndex, tc.sampleIndex, 100)) + if err = WriteUnprocessedValueData(metadata, pixelDataInfo.UnprocessedValueData, + tc.rowIndex, tc.colIndex, tc.frameIndex, tc.sampleIndex, 100); err != nil { + t.Errorf("WriteUnprocessedValueData: %v", err) + } var buffer2 bytes.Buffer - require.NoError(t, dicom.Write(io.Writer(&buffer2), dataset)) + if err = dicom.Write(io.Writer(&buffer2), dataset); err != nil { + t.Errorf("Write new DICOM obj to file: %v", err) + } outputBytes := buffer2.Bytes() assertPixelDataInfo(t, outputBytes, tc.expectedPixelInfo) } } +func setupUnprocessedPixelData(t testing.TB, rawData []byte) (dicom.Dataset, *PixelDataMetadata, dicom.PixelDataInfo) { + dataset, err := dicom.Parse(bytes.NewReader(rawData), int64(len(rawData)), nil, dicom.SkipProcessingPixelDataValue()) + if err != nil { + t.Errorf("dicom.Parse: %v", err) + } + metadata, err := GetPixelDataMetadata(&dataset) + if err != nil { + t.Errorf("GetPixelDataMetadata: %v", err) + } + pixelElement, err := dataset.FindElementByTag(tag.PixelData) + if err != nil { + t.Errorf("tag.PixelData not found: %v", err) + } + pixelDataInfo := dicom.MustGetPixelDataInfo(pixelElement.Value) + if !pixelDataInfo.IntentionallyUnprocessed || pixelDataInfo.IsEncapsulated { + t.Errorf("unexpected pixelDataInfo: IntentionallyUnprocessed=%t IsEncapsulated=%t", + pixelDataInfo.IntentionallyUnprocessed, pixelDataInfo.IsEncapsulated) + } + // Sanity check if the dataset is suitable for in-place read-write + if err = IsSafeForUnprocessedValueDataHandling(metadata, pixelDataInfo.UnprocessedValueData); err != nil { + t.Errorf("IsSafeForUnprocessedValueDataHandling(%v)", err) + } + return dataset, metadata, pixelDataInfo +} + func assertPixelDataInfo(t testing.TB, rawData []byte, expectedPixelDataInfo dicom.PixelDataInfo) { dataset2, err := dicom.Parse(bytes.NewReader(rawData), int64(len(rawData)), nil) - require.NoError(t, err) + if err != nil { + t.Errorf("read new create dcm file: %v", err) + } pixelElement, err := dataset2.FindElementByTag(tag.PixelData) - require.NoError(t, err) + if err != nil { + t.Errorf("pixel data not found: %v", err) + } pixelDataInfo := dicom.MustGetPixelDataInfo(pixelElement.Value) - require.Equal(t, pixelDataInfo, expectedPixelDataInfo) + if diff := cmp.Diff(pixelDataInfo, expectedPixelDataInfo, cmpopts.EquateErrors()); diff != "" { + t.Errorf("assert pixelDataInfo in dicom file(%v): unexpected diff: %v", pixelDataInfo, diff) + } }