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Support parsing NativePixelData when it appears multiple times in a DICOM #79

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merged 3 commits into from
Jun 8, 2020
Merged

Support parsing NativePixelData when it appears multiple times in a DICOM #79

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2834c48
Read native pixel metadata from current sequence, if any
suyashkumar May 22, 2020
77289c6
Cleanup
suyashkumar May 22, 2020
4d46e0d
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suyashkumar Jun 8, 2020
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34 changes: 25 additions & 9 deletions parse.go
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,10 @@ type parser struct {
parsedElements *element.DataSet
op ParseOptions
frameChannel chan *frame.Frame
file *os.File // may be populated if coming from file
file *os.File // may be populated if this parser is coming from a file
// currentSequenceDataset is populated with Elements read so far in a SQ DICOM sequence (or is nil if not currently
// reading a sequence).
currentSequenceDataset *element.DataSet
}

// NewParser initializes and returns a new Parser
Expand Down Expand Up @@ -161,11 +164,15 @@ func (p *parser) Parse(options ParseOptions) (*element.DataSet, error) {
}

}
if p.frameChannel != nil {
close(p.frameChannel)
}
return p.parsedElements, p.decoder.Error()
}

func (p *parser) ParseNext(options ParseOptions) *element.Element {
tag := readTag(p.decoder)

if tag == dicomtag.PixelData && options.DropPixelData {
return element.EndOfData
}
Expand Down Expand Up @@ -252,9 +259,7 @@ func (p *parser) ParseNext(options ParseOptions) *element.Element {
p.frameChannel <- &f // write frame to channel
}
}
if p.frameChannel != nil {
close(p.frameChannel)
}

data = append(data, image)
} else {
// Assume we're reading NativeData data since we have a defined value length as per Part 5 Sec A.4 of DICOM spec.
Expand All @@ -264,7 +269,13 @@ func (p *parser) ParseNext(options ParseOptions) *element.Element {
return nil // TODO(suyash) investigate error handling in this library
}

image, _, err := readNativeFrames(p.decoder, p.parsedElements, p.frameChannel)
datasetToUse := p.parsedElements

if p.currentSequenceDataset != nil && len(p.currentSequenceDataset.Elements) > 0 {
datasetToUse = p.currentSequenceDataset
}

image, _, err := readNativeFrames(p.decoder, datasetToUse, p.frameChannel)

if err != nil {
p.decoder.SetError(err)
Expand All @@ -278,6 +289,10 @@ func (p *parser) ParseNext(options ParseOptions) *element.Element {
// Note: when reading subitems inside sequence or item, we ignore
// DropPixelData and other shortcircuiting options. If we honored them, we'decoder
// be unable to read the rest of the file.

// TODO: refactor to avoid temporarily storing two copies
oldDataset := p.currentSequenceDataset
p.currentSequenceDataset = &element.DataSet{}
if vl == element.VLUndefinedLength {
// Format:
// Sequence := ItemSet* SequenceDelimitationItem
Expand Down Expand Up @@ -314,9 +329,12 @@ func (p *parser) ParseNext(options ParseOptions) *element.Element {
break
}
data = append(data, item)
p.currentSequenceDataset.Elements = append(p.currentSequenceDataset.Elements, item)
}
p.decoder.PopLimit()
}
// Restore oldDataset if any:
p.currentSequenceDataset = oldDataset
} else if tag == dicomtag.Item { // Item (component of SQ)
if vl == element.VLUndefinedLength {
// Format: Item Any* ItemDelimitationItem
Expand All @@ -330,6 +348,7 @@ func (p *parser) ParseNext(options ParseOptions) *element.Element {
break
}
data = append(data, subelem)
p.currentSequenceDataset.Elements = append(p.currentSequenceDataset.Elements, subelem)
}
} else {
// Sequence of arbitary elements, for the total of "vl" bytes.
Expand All @@ -341,6 +360,7 @@ func (p *parser) ParseNext(options ParseOptions) *element.Element {
break
}
data = append(data, subelem)
p.currentSequenceDataset.Elements = append(p.currentSequenceDataset.Elements, subelem)
}
p.decoder.PopLimit()
}
Expand Down Expand Up @@ -588,10 +608,6 @@ func readNativeFrames(d *dicomio.Decoder, parsedData *element.DataSet, frameChan
}
}

if frameChan != nil {
close(frameChan) // close frameChan if it exists
}

bytesRead = (bitsAllocated / 8) * samplesPerPixel * pixelsPerFrame * nFrames

return &image, bytesRead, nil
Expand Down