Utils function for read/write value from unprocessed data

dataset.go

@@ -36,7 +36,7 @@ func (d *Dataset) FindElementByTag(tag tag.Tag) (*Element, error) {
 	return nil, ErrorElementNotFound
 }
 
-func (d *Dataset) transferSyntax() (binary.ByteOrder, bool, error) {
+func (d *Dataset) TransferSyntax() (binary.ByteOrder, bool, error) {
 	elem, err := d.FindElementByTag(tag.TransferSyntaxUID)
 	if err != nil {
 		return nil, false, err

go.mod

@@ -8,4 +8,11 @@ require (
 	golang.org/x/text v0.3.8
 )
 
-require golang.org/x/xerrors v0.0.0-20191204190536-9bdfabe68543 // indirect
+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
+)

go.sum

@@ -1,7 +1,20 @@
+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=
@@ -12,3 +25,7 @@ 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=

pkg/frame/inplace/pixeldata_info.go

@@ -0,0 +1,143 @@
+package inplace
+
+import (
+	"encoding/binary"
+	"errors"
+	"fmt"
+	"strconv"
+
+	"github.com/suyashkumar/dicom"
+	"github.com/suyashkumar/dicom/pkg/tag"
+)
+
+// GetIntFromValue is similar to dicom.MustGetInts but without panic
+func GetIntFromValue(v dicom.Value) (int, error) {
+	if v.ValueType() != dicom.Ints {
+		return 0, errors.New("value is not ints")
+	}
+	arr, ok := v.GetValue().([]int)
+	if !ok {
+		return 0, errors.New("actual value is not ints")
+	}
+	if len(arr) == 0 {
+		return 0, errors.New("empty ints value")
+	}
+	return arr[0], nil
+}
+
+// GetStringFromValue is similar to dicom.MustGetStrings but without panic
+func GetStringFromValue(v dicom.Value) (string, error) {
+	if v.ValueType() != dicom.Strings {
+		return "", errors.New("value is not ints")
+	}
+	arr, ok := v.GetValue().([]string)
+	if !ok {
+		return "", errors.New("actual value is not ints")
+	}
+	if len(arr) == 0 {
+		return "", errors.New("empty ints value")
+	}
+	return arr[0], nil
+}
+
+// PixelDataMetadata is the metadata for tag.PixelData
+type PixelDataMetadata struct {
+	Rows                int
+	Cols                int
+	Frames              int
+	SamplesPerPixel     int
+	BitsAllocated       int
+	PlanarConfiguration int
+	Bo                  binary.ByteOrder
+}
+
+// GetPixelDataMetadata returns the pixel data metadata.
+func GetPixelDataMetadata(ds *dicom.Dataset) (*PixelDataMetadata, error) {
+	re := &PixelDataMetadata{}
+	rows, err := ds.FindElementByTag(tag.Rows)
+	if err != nil {
+		return nil, fmt.Errorf("get Rows element: %w", err)
+	}
+	if re.Rows, err = GetIntFromValue(rows.Value); err != nil {
+		return nil, fmt.Errorf("convert Rows element to int: %w", err)
+	}
+
+	cols, err := ds.FindElementByTag(tag.Columns)
+	if err != nil {
+		return nil, fmt.Errorf("get Columns element: %w", err)
+	}
+	if re.Cols, err = GetIntFromValue(cols.Value); err != nil {
+		return nil, fmt.Errorf("convert Columns element to int: %w", err)
+	}
+
+	numberOfFrames, err := ds.FindElementByTag(tag.NumberOfFrames)
+	if err != nil {
+		re.Frames = 1
+	} else {
+		var framesStr string
+		framesStr, err = GetStringFromValue(numberOfFrames.Value)
+		if err != nil {
+			return nil, fmt.Errorf("convert NumberOfFrames element to str: %w", err)
+		}
+		if re.Frames, err = strconv.Atoi(framesStr); err != nil {
+			return nil, fmt.Errorf("convert NumberOfFrames to int: %w", err)
+		}
+	}
+
+	samplesPerPixel, err := ds.FindElementByTag(tag.SamplesPerPixel)
+	if err != nil {
+		return nil, fmt.Errorf("get SamplesPerPixel element: %w", err)
+	}
+	if re.SamplesPerPixel, err = GetIntFromValue(samplesPerPixel.Value); err != nil {
+		return nil, fmt.Errorf("convert SamplesPerPixel element to int: %w", err)
+	}
+	bitsAllocated, err := ds.FindElementByTag(tag.BitsAllocated)
+	if err != nil {
+		return nil, fmt.Errorf("get BitsAllocated element: %w", err)
+	}
+	if re.BitsAllocated, err = GetIntFromValue(bitsAllocated.Value); err != nil {
+		return nil, fmt.Errorf("convert BitsAllocated element to int: %w", err)
+	}
+	re.Bo, _, err = ds.TransferSyntax()
+	if err != nil {
+		return nil, fmt.Errorf("get byteOrder: %w", err)
+	}
+
+	planarConfElement, err := ds.FindElementByTag(tag.PlanarConfiguration)
+	if err != nil {
+		re.PlanarConfiguration = 0
+	} else {
+		if re.PlanarConfiguration, err = GetIntFromValue(planarConfElement.Value); err != nil {
+			return nil, fmt.Errorf("convert Rows element to int: %w", err)
+		}
+	}
+
+	return re, nil
+}
+
+// IsSafeForUnprocessedValueDataHandling check if we can support in-place read-write
+// from Pixeldata.UnprocessedValueData
+// This avoids the case that we can not handle it, yet.
+func IsSafeForUnprocessedValueDataHandling(info *PixelDataMetadata, unprocessedValueData []byte) error {
+	// https://dicom.innolitics.com/ciods/enhanced-mr-image/enhanced-mr-image/00280006
+	if info.PlanarConfiguration == 1 {
+		return fmt.Errorf("unsupported PlanarConfiguration: %d", info.PlanarConfiguration)
+	}
+	// TODO: support for BitsAllocated == 1
+	switch info.BitsAllocated {
+	case 8, 16, 32:
+	default: // bitsAllocated = 1 and other cases
+		return fmt.Errorf("unsupported bit allocated: %d", info.BitsAllocated)
+	}
+	pixelsPerFrame := info.Rows * info.Cols
+	bytesAllocated := info.BitsAllocated / 8
+	expectedBytes := bytesAllocated * info.SamplesPerPixel * info.Frames * pixelsPerFrame
+	// odd number of bytes.
+	if expectedBytes%2 == 1 {
+		expectedBytes += 1
+	}
+	if len(unprocessedValueData) != expectedBytes {
+		return errors.New("mismatch data size")
+	}
+	return nil
+}

pkg/frame/inplace/read.go

@@ -0,0 +1,29 @@
+// Package inplace contains code for handling UnprocessedValueData
+package inplace
+
+// ReadUnprocessedValueData read the value of Dicom image directly
+// from the byte array of PixelData.UnprocessedValueData with given frame ID.
+// This ease the memory usage of reading DICOM image.
+func ReadUnprocessedValueData(info *PixelDataMetadata, unprocessedValueData []byte, frameIndex int) ([][]int, error) {
+	pixelsPerFrame := info.Rows * info.Cols
+	bytesAllocated := info.BitsAllocated / 8
+	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
+			switch bytesAllocated {
+			case 1:
+				re[i][j] = int(unprocessedValueData[pointOffset])
+			case 2:
+				re[i][j] = int(info.Bo.Uint16(unprocessedValueData[pointOffset : pointOffset+bytesAllocated]))
+			case 4:
+				re[i][j] = int(info.Bo.Uint32(unprocessedValueData[pointOffset : pointOffset+bytesAllocated]))
+			}
+		}
+	}
+	return re, nil
+}