Optimize readNativeFrame performance using chunked IO and direct casting

read.go

@@ -546,36 +546,52 @@ func readNativeFrame[I constraints.Integer](bitsAllocated, rows, cols, bytesToRe
 	}
 
 	bo := rawReader.ByteOrder()
-	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)
+	if bitsAllocated < 8 || bitsAllocated%8 != 0 {
+		return frame.Frame{}, bytesToRead, fmt.Errorf("readNativeFrame unsupported bitsAllocated=%d : %w", bitsAllocated, ErrorUnsupportedBitsAllocated)
+	}
+
+	bytesPerSample := bitsAllocated / 8
+
+	// Use a 4KB chunk buffer to minimize io.ReadFull calls
+	chunkSize := 4096
+	// ensure chunkSize is a multiple of bytesPerSample
+	chunkSize = (chunkSize / bytesPerSample) * bytesPerSample
+	chunkBuf := make([]byte, chunkSize)
+
+	totalSamples := pixelsPerFrame * samplesPerPixel
+	samplesRead := 0
+
+	for samplesRead < totalSamples {
+		samplesLeft := totalSamples - samplesRead
+		bytesToReadChunk := samplesLeft * bytesPerSample
+		if bytesToReadChunk > chunkSize {
+			bytesToReadChunk = chunkSize
+		}
+
+		_, err := io.ReadFull(rawReader, chunkBuf[:bytesToReadChunk])
+		if err != nil {
+			return frame.Frame{}, bytesToRead,
+				fmt.Errorf("could not read uint%d from input: %w", bitsAllocated, err)
+		}
+
+		samplesInChunk := bytesToReadChunk / bytesPerSample
+		switch bitsAllocated {
+		case 8:
+			for i := 0; i < samplesInChunk; i++ {
+				nativeFrame.RawData[samplesRead+i] = I(chunkBuf[i])
 			}
-			switch bitsAllocated {
-			case 8:
-				v, ok := any(pixelBuf[0]).(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
-			case 16:
-				v, ok := any(bo.Uint16(pixelBuf)).(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
-			case 32:
-				v, ok := any(bo.Uint32(pixelBuf)).(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
-			default:
-				return frame.Frame{}, bytesToRead, fmt.Errorf("readNativeFrame unsupported bitsAllocated=%d : %w", bitsAllocated, ErrorUnsupportedBitsAllocated)
+		case 16:
+			for i := 0; i < samplesInChunk; i++ {
+				nativeFrame.RawData[samplesRead+i] = I(bo.Uint16(chunkBuf[i*2 : i*2+2]))
 			}
+		case 32:
+			for i := 0; i < samplesInChunk; i++ {
+				nativeFrame.RawData[samplesRead+i] = I(bo.Uint32(chunkBuf[i*4 : i*4+4]))
+			}
+		default:
+			return frame.Frame{}, bytesToRead, fmt.Errorf("readNativeFrame unsupported bitsAllocated=%d : %w", bitsAllocated, ErrorUnsupportedBitsAllocated)
 		}
+		samplesRead += samplesInChunk
 	}
 	return currentFrame, bytesToRead, nil
 }

read_test.go

@@ -1032,8 +1032,15 @@ func BenchmarkReadNativeFrames(b *testing.B) {
 			dataset, rawReader := buildReadNativeFramesInput(c.Rows, c.Cols, c.NumFrames, c.SamplesPerPixel, b)
 			r := &reader{rawReader: rawReader}
 			b.ResetTimer()
+			// BitsAllocated is hardcoded to 16, meaning 2 bytes per sample.
+			bytesAllocated := 2
+			vl := uint32(c.Rows * c.Cols * c.NumFrames * c.SamplesPerPixel * bytesAllocated)
+
 			for i := 0; i < b.N; i++ {
-				_, _, _ = r.readNativeFrames(dataset, nil, uint32(c.Rows*c.Cols*c.NumFrames))
+				_, _, err := r.readNativeFrames(dataset, nil, vl)
+				if err != nil {
+					b.Fatalf("readNativeFrames error: %v", err)
+				}
 			}
 		})
 	}
@@ -1064,7 +1071,8 @@ func buildReadNativeFramesInput(rows, cols, numFrames, samplesPerPixel int, b *t
 		}
 	}
 
-	return &dataset, dicomio.NewReader(bufio.NewReader(&dcmdata), binary.LittleEndian, int64(dcmdata.Len()))
+	rawReader := dicomio.NewReader(bufio.NewReader(&dcmdata), binary.LittleEndian, int64(2*numFrames*rows*cols*samplesPerPixel))
+	return &dataset, rawReader
 }
 
 func buildTagData(t *testing.T, tg tag.Tag) []byte {