Support parsing NativePixelData when it appears multiple times in a D…

…ICOM (#79)

This fixes #77 and appears to work on provided DICOMs. This is a relatively quick fix, that does seem to get the job done. There are some minor improvements that can be made in future PRs, but it will be best to get these changes in to unblock future work.

This also appears to fix #82, and fix #65 (we are able to parse those images without errors).

For most of the provided images, the issue was that an icon image sequence could appear in the DICOMs in addition to the primary PixelData. When reading that particular image sequence, a different set of metadata tags need to be used (instead of the global ones, which apply only to the core PixelData).

There may be additional work to fully and correctly parsing icon image sets (most of the icons seem to be unpopulated in the sample images), but this change will at least prevent the parser from failing on DICOMs like this.

parse.go

@@ -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
@@ -163,11 +166,15 @@ 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
 	}
@@ -254,9 +261,7 @@ 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.
@@ -266,7 +271,13 @@ 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)
@@ -280,6 +291,10 @@ 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
@@ -316,9 +331,12 @@ 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
@@ -332,6 +350,7 @@ 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.
@@ -343,6 +362,7 @@ func (p *parser) ParseNext(options ParseOptions) *element.Element {
 					break
 				}
 				data = append(data, subelem)
+				p.currentSequenceDataset.Elements = append(p.currentSequenceDataset.Elements, subelem)
 			}
 			p.decoder.PopLimit()
 		}
@@ -590,10 +610,6 @@ 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