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

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, 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])
+			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
+}