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Add basic Parser.Next based benchmark
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@suyashkumar
suyashkumar authored and Suyash Kumar committed Sep 30, 2023
1 parent 8f1f151 commit e7dfaa4
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Showing 2 changed files with 52 additions and 18 deletions.
11 changes: 6 additions & 5 deletions parse.go
View file
Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,7 @@ func parseInternal(in io.Reader, bytesToRead int64, frameChan chan *frame.Frame,
}

for !p.reader.rawReader.IsLimitExhausted() {
_, err := p.Next()
elem, err := p.Next()
if err != nil {
if errors.Is(err, io.EOF) {
// exiting on EOF
Expand All @@ -83,6 +83,7 @@ func parseInternal(in io.Reader, bytesToRead int64, frameChan chan *frame.Frame,
// exit on error
return p.dataset, err
}
p.dataset.Elements = append(p.dataset.Elements, elem)
}

// Close the frameChannel if needed
Expand Down Expand Up @@ -130,8 +131,9 @@ func NewParser(in io.Reader, bytesToRead int64, frameChannel chan *frame.Frame,
optSet := toParseOptSet(opts...)
p := Parser{
reader: &reader{
rawReader: dicomio.NewReader(bufio.NewReader(in), binary.LittleEndian, bytesToRead),
opts: optSet,
rawReader: dicomio.NewReader(bufio.NewReader(in), binary.LittleEndian, bytesToRead),
opts: optSet,
datasetCtx: &Dataset{},
},
frameChannel: frameChannel,
}
Expand Down Expand Up @@ -182,7 +184,7 @@ func (p *Parser) Next() (*Element, error) {
}
return nil, ErrorEndOfDICOM
}
elem, err := p.reader.readElement(&p.dataset, p.frameChannel)
elem, err := p.reader.ReadElement(p.frameChannel)
if err != nil {
// TODO: tolerate some kinds of errors and continue parsing
return nil, err
Expand All @@ -201,7 +203,6 @@ func (p *Parser) Next() (*Element, error) {
p.reader.rawReader.SetCodingSystem(cs)
}

p.dataset.Elements = append(p.dataset.Elements, elem)
return elem, nil

}
Expand Down
59 changes: 46 additions & 13 deletions read.go
View file
Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,11 @@ var (
type reader struct {
rawReader dicomio.Reader
opts parseOptSet
// datasetCtx is the top-level context Dataset holding only elements that
// may be needed to parse future elements (e.g. like tag.Rows). See
// datasetContextElementPassList for elements that will be automatically
// included in this context.
datasetCtx *Dataset
}

func (r *reader) readTag() (*tag.Tag, error) {
Expand Down Expand Up @@ -162,7 +167,7 @@ func (r *reader) readHeader() ([]*Element, error) {

// Must read metadata as LittleEndian explicit VR
// Read the length of the metadata elements: (0002,0000) MetaElementGroupLength
maybeMetaLen, err := r.readElement(nil, nil)
maybeMetaLen, err := r.readElementInternal(nil, nil)
if err != nil {
return nil, err
}
Expand All @@ -187,7 +192,7 @@ func (r *reader) readHeader() ([]*Element, error) {
}
defer r.rawReader.PopLimit()
for !r.rawReader.IsLimitExhausted() {
elem, err := r.readElement(nil, nil)
elem, err := r.readElementInternal(nil, nil)
if err != nil {
// TODO: see if we can skip over malformed elements somehow
return nil, err
Expand All @@ -214,7 +219,7 @@ func (r *reader) readHeader() ([]*Element, error) {
if group != 0x0002 {
break
}
elem, err := r.readElement(nil, nil)
elem, err := r.readElementInternal(nil, nil)
if err != nil {
// TODO: see if we can skip over malformed elements somehow
return nil, err
Expand Down Expand Up @@ -506,7 +511,7 @@ func (r *reader) readSequence(t tag.Tag, vr string, vl uint32, d *Dataset) (Valu
seqElements := &Dataset{}
if vl == tag.VLUndefinedLength {
for {
subElement, err := r.readElement(seqElements, nil)
subElement, err := r.readElementInternal(seqElements, nil)
if err != nil {
// Stop reading due to error
log.Println("error reading subitem, ", err)
Expand All @@ -533,7 +538,7 @@ func (r *reader) readSequence(t tag.Tag, vr string, vl uint32, d *Dataset) (Valu
return nil, err
}
for !r.rawReader.IsLimitExhausted() {
subElement, err := r.readElement(seqElements, nil)
subElement, err := r.readElementInternal(seqElements, nil)
if err != nil {
// TODO: option to ignore errors parsing subelements?
return nil, err
Expand All @@ -559,7 +564,7 @@ func (r *reader) readSequenceItem(t tag.Tag, vr string, vl uint32, d *Dataset) (

if vl == tag.VLUndefinedLength {
for {
subElem, err := r.readElement(&seqElements, nil)
subElem, err := r.readElementInternal(&seqElements, nil)
if err != nil {
return nil, err
}
Expand All @@ -577,7 +582,7 @@ func (r *reader) readSequenceItem(t tag.Tag, vr string, vl uint32, d *Dataset) (
}

for !r.rawReader.IsLimitExhausted() {
subElem, err := r.readElement(&seqElements, nil)
subElem, err := r.readElementInternal(&seqElements, nil)
if err != nil {
return nil, err
}
Expand Down Expand Up @@ -733,17 +738,24 @@ func (r *reader) readInt(t tag.Tag, vr string, vl uint32) (Value, error) {
return retVal, err
}

// readElement reads the next element. If the next element is a sequence element,
// ReadElement reads the next element. This is the top level function that should
// be called to read elements. If the next element is a sequence element,
// it may result in reading a collection of Elements.
func (r *reader) ReadElement(fc chan<- *frame.Frame) (*Element, error) {
return r.readElementInternal(r.datasetCtx, fc)
}

// readElementInternal reads the next element. If the next element is a sequence element,
// it may result in a collection of Elements. It takes a pointer to the Dataset of
// elements read so far, since previously read elements may be needed to parse
// certain Elements (like native PixelData). If the Dataset is nil, it is
// treated as an empty Dataset.
func (r *reader) readElement(d *Dataset, fc chan<- *frame.Frame) (*Element, error) {
func (r *reader) readElementInternal(datasetCtx *Dataset, fc chan<- *frame.Frame) (*Element, error) {
t, err := r.readTag()
if err != nil {
return nil, err
}
debug.Logf("readElement: tag: %s", t.String())
debug.Logf("readElementInternal: tag: %s", t.String())

readImplicit := r.rawReader.IsImplicit()
if *t == tag.Item {
Expand All @@ -755,20 +767,24 @@ func (r *reader) readElement(d *Dataset, fc chan<- *frame.Frame) (*Element, erro
if err != nil {
return nil, err
}
debug.Logf("readElement: vr: %s", vr)
debug.Logf("readElementInternal: vr: %s", vr)

vl, err := r.readVL(readImplicit, *t, vr)
if err != nil {
return nil, err
}
debug.Logf("readElement: vl: %d", vl)
debug.Logf("readElementInternal: vl: %datasetCtx", vl)

val, err := r.readValue(*t, vr, vl, readImplicit, d, fc)
val, err := r.readValue(*t, vr, vl, readImplicit, datasetCtx, fc)
if err != nil {
log.Println("error reading value ", err)
return nil, err
}

elem := &Element{Tag: *t, ValueRepresentation: tag.GetVRKind(*t, vr), RawValueRepresentation: vr, ValueLength: vl, Value: val}
addToContextIfNeeded(datasetCtx, elem)
return elem, nil

return &Element{Tag: *t, ValueRepresentation: tag.GetVRKind(*t, vr), RawValueRepresentation: vr, ValueLength: vl, Value: val}, nil

}
Expand Down Expand Up @@ -829,3 +845,20 @@ func (r *reader) readRawItem(shouldSkip bool) ([]byte, bool, error) {
func (r *reader) moreToRead() bool {
return !r.rawReader.IsLimitExhausted()
}

// datasetContextElementPassList holds the set of DICOM Element Tags that should
// be included in the context Dataset. These are elements that may be needed to
// read downstream elements in the future.
var datasetContextElementPassList = tag.Tags{
&tag.Rows,
&tag.Columns,
&tag.NumberOfFrames,
&tag.BitsAllocated,
&tag.SamplesPerPixel,
}

func addToContextIfNeeded(datasetCtx *Dataset, e *Element) {
if datasetContextElementPassList.Contains(&e.Tag) {
datasetCtx.Elements = append(datasetCtx.Elements, e)
}
}

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