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⚡ Bolt: Optimize native frame reading #372

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⚡ Bolt: Optimize native frame reading #372

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39 changes: 26 additions & 13 deletions read.go
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Original file line number Diff line number Diff line change
Expand Up @@ -461,6 +461,9 @@ func (r *reader) readNativeFrames(parsedData *Dataset, fc chan<- *frame.Frame, v
bytesToRead = pixelsPerFrame * samplesPerPixel / 8 * nFrames
}

// Used to read whole frames at a time in readNativeFrame.
bytesPerFrame := bytesAllocated * samplesPerPixel * pixelsPerFrame

skipFinalPaddingByte := false
if uint32(bytesToRead) != vl {
switch {
Expand All @@ -487,7 +490,9 @@ func (r *reader) readNativeFrames(parsedData *Dataset, fc chan<- *frame.Frame, v
}
image.Frames = make([]*frame.Frame, nFrames)
bo := r.rawReader.ByteOrder()
pixelBuf := make([]byte, bytesAllocated)
// Allocating a buffer to hold a whole frame allows us to read the frame in one large chunk
// which significantly improves performance compared to reading pixel by pixel.
frameBuf := make([]byte, bytesPerFrame)
for frameIdx := 0; frameIdx < nFrames; frameIdx++ {
// Init current frame
currentFrame := frame.Frame{
Expand All @@ -509,11 +514,11 @@ func (r *reader) readNativeFrames(parsedData *Dataset, fc chan<- *frame.Frame, v
} else {
switch bitsAllocated {
case 8:
currentFrame, _, err = readNativeFrame[uint8](bitsAllocated, MustGetInts(rows.Value)[0], MustGetInts(cols.Value)[0], bytesToRead, samplesPerPixel, pixelsPerFrame, pixelBuf, r.rawReader)
currentFrame, _, err = readNativeFrame[uint8](bitsAllocated, MustGetInts(rows.Value)[0], MustGetInts(cols.Value)[0], bytesToRead, samplesPerPixel, pixelsPerFrame, frameBuf, r.rawReader)
case 16:
currentFrame, _, err = readNativeFrame[uint16](bitsAllocated, MustGetInts(rows.Value)[0], MustGetInts(cols.Value)[0], bytesToRead, samplesPerPixel, pixelsPerFrame, pixelBuf, r.rawReader)
currentFrame, _, err = readNativeFrame[uint16](bitsAllocated, MustGetInts(rows.Value)[0], MustGetInts(cols.Value)[0], bytesToRead, samplesPerPixel, pixelsPerFrame, frameBuf, r.rawReader)
case 32:
currentFrame, _, err = readNativeFrame[uint32](bitsAllocated, MustGetInts(rows.Value)[0], MustGetInts(cols.Value)[0], bytesToRead, samplesPerPixel, pixelsPerFrame, pixelBuf, r.rawReader)
currentFrame, _, err = readNativeFrame[uint32](bitsAllocated, MustGetInts(rows.Value)[0], MustGetInts(cols.Value)[0], bytesToRead, samplesPerPixel, pixelsPerFrame, frameBuf, r.rawReader)
default:
return nil, bytesToRead, fmt.Errorf("unsupported bitsAllocated, got: %v, %w", bitsAllocated, ErrorUnsupportedBitsAllocated)
}
Expand All @@ -538,40 +543,48 @@ func (r *reader) readNativeFrames(parsedData *Dataset, fc chan<- *frame.Frame, v

// readNativeFrame builds and reads a single NativeFrame[I] from the rawReader.
// TODO(suyashkumar): refactor args to an options struct, or something more compact and readable.
func readNativeFrame[I constraints.Integer](bitsAllocated, rows, cols, bytesToRead, samplesPerPixel, pixelsPerFrame int, pixelBuf []byte, rawReader *dicomio.Reader) (frame.Frame, int, error) {
func readNativeFrame[I constraints.Integer](bitsAllocated, rows, cols, bytesToRead, samplesPerPixel, pixelsPerFrame int, buf []byte, rawReader *dicomio.Reader) (frame.Frame, int, error) {
nativeFrame := frame.NewNativeFrame[I](bitsAllocated, rows, cols, pixelsPerFrame, samplesPerPixel)
currentFrame := frame.Frame{
Encapsulated: false,
NativeData: nativeFrame,
}

// Read the whole frame at once
_, err := io.ReadFull(rawReader, buf)
if err != nil {
return frame.Frame{}, bytesToRead,
fmt.Errorf("could not read uint%d from input: %w", bitsAllocated, err)
}

bo := rawReader.ByteOrder()
// bytesAllocated is not needed as we use constants in switch
bufIdx := 0

for pixel := 0; pixel < pixelsPerFrame; pixel++ {
for value := 0; value < samplesPerPixel; value++ {
_, err := io.ReadFull(rawReader, pixelBuf)
if err != nil {
return frame.Frame{}, bytesToRead,
fmt.Errorf("could not read uint%d from input: %w", bitsAllocated, err)
}
switch bitsAllocated {
case 8:
v, ok := any(pixelBuf[0]).(I)
v, ok := any(buf[bufIdx]).(I)
if !ok {
return frame.Frame{}, bytesToRead, fmt.Errorf("internal error - readNativeFrame unexpectedly unable to type cast pixel buffer data to the I type (%T), where bitsAllocated=%v", *new(I), bitsAllocated)
}
nativeFrame.RawData[(pixel*samplesPerPixel)+value] = v
bufIdx++
case 16:
v, ok := any(bo.Uint16(pixelBuf)).(I)
v, ok := any(bo.Uint16(buf[bufIdx:])).(I)
if !ok {
return frame.Frame{}, bytesToRead, fmt.Errorf("internal error - readNativeFrame unexpectedly unable to type cast pixel buffer data to the I type (%T), where bitsAllocated=%v", *new(I), bitsAllocated)
}
nativeFrame.RawData[(pixel*samplesPerPixel)+value] = v
bufIdx += 2
case 32:
v, ok := any(bo.Uint32(pixelBuf)).(I)
v, ok := any(bo.Uint32(buf[bufIdx:])).(I)
if !ok {
return frame.Frame{}, bytesToRead, fmt.Errorf("internal error - readNativeFrame unexpectedly unable to type cast pixel buffer data to the I type (%T), where bitsAllocated=%v", *new(I), bitsAllocated)
}
nativeFrame.RawData[(pixel*samplesPerPixel)+value] = v
bufIdx += 4
default:
return frame.Frame{}, bytesToRead, fmt.Errorf("readNativeFrame unsupported bitsAllocated=%d : %w", bitsAllocated, ErrorUnsupportedBitsAllocated)
}
Expand Down