[Rewrite] Native Pixel Data Parsing, handle value multiplicity. (#86)

This implements native pixel data parsing on the rewrite branch. This includes fixes done on the mainline branch to parse PixelData properly if it appears multiple times in a DICOM (PR #79). This also includes some fixes to better handle value multiplicity.

cmd/dicomtest/main.go

@@ -4,9 +4,10 @@ package main
 import (
 	"flag"
 	"fmt"
-	"io/ioutil"
+	"image/jpeg"
 	"log"
 	"os"
+	"strconv"
 
 	"github.com/suyashkumar/dicom"
 	"github.com/suyashkumar/dicom/pkg/tag"
@@ -44,21 +45,49 @@ func main() {
 			return
 		}
 
-		for _, elem := range ds.Elements {
+		for z, elem := range ds.Elements {
 			if elem.Tag != tag.PixelData {
 				log.Println(elem.Tag)
 				log.Println(elem.ValueLength)
 				log.Println(elem.Value)
-			} else {
-				imageInfo := elem.Value.GetValue().(dicom.PixelDataInfo)
-				for i, frame := range imageInfo.Frames {
-					err := ioutil.WriteFile(fmt.Sprintf("image_%d.jpg", i), frame.EncapsulatedData.Data,
-						0644)
-					if err != nil {
-						log.Println(err)
+				// TODO: remove image icon hack after implementing flat iterator
+				if elem.Tag == tag.IconImageSequence {
+					for _, item := range elem.Value.GetValue().([]*dicom.SequenceItemValue) {
+						for _, subElem := range item.GetValue().([]*dicom.Element) {
+							if subElem.Tag == tag.PixelData {
+								writePixelDataElement(subElem, strconv.Itoa(z))
+							}
+						}
 					}
 				}
+			} else {
+				writePixelDataElement(elem, strconv.Itoa(z))
 			}
+
+		}
+	}
+}
+
+func writePixelDataElement(e *dicom.Element, id string) {
+	imageInfo := e.Value.GetValue().(dicom.PixelDataInfo)
+	for idx, f := range imageInfo.Frames {
+		i, err := f.GetImage()
+		if err != nil {
+			log.Fatal("Error while getting image")
 		}
+
+		name := fmt.Sprintf("image_%d_%s.jpg", idx, id)
+		f, err := os.Create(name)
+		if err != nil {
+			fmt.Printf("Error while creating file: %s", err.Error())
+		}
+		err = jpeg.Encode(f, i, &jpeg.Options{Quality: 100})
+		if err != nil {
+			log.Println(err)
+		}
+		if err = f.Close(); err != nil {
+			log.Println("ERROR: unable to properly close file: ", f.Name())
+		}
+
 	}
 }

dataset.go

@@ -1,6 +1,24 @@
 package dicom
 
+import (
+	"errors"
+
+	"github.com/suyashkumar/dicom/pkg/tag"
+)
+
+var ErrorElementNotFound = errors.New("element not found")
+
 type Dataset struct {
 	Elements []*Element
-	Size     uint64
+}
+
+// FindElementByTag searches through the dataset and returns a pointer to the matching element.
+// It DOES NOT search within Sequences as well.
+func (d *Dataset) FindElementByTag(tag tag.Tag) (*Element, error) {
+	for _, e := range d.Elements {
+		if e.Tag == tag {
+			return e, nil
+		}
+	}
+	return nil, ErrorElementNotFound
 }

element.go

@@ -130,3 +130,15 @@ func (e *PixelDataValue) String() string {
 	// TODO: consider adding more sophisticated formatting
 	return ""
 }
+
+func MustGetInt(v Value) int {
+	return v.GetValue().([]int)[0]
+}
+
+func MustGetInts(v Value) []int {
+	return v.GetValue().([]int)
+}
+
+func MustGetString(v Value) string {
+	return v.GetValue().([]string)[0]
+}

parse.go

@@ -72,7 +72,7 @@ func (p *parser) readHeader() ([]*Element, error) {
 	}
 
 	// Read the length of the metadata elements: (0002,0000) MetaElementGroupLength
-	maybeMetaLen, err := readElement(p.reader)
+	maybeMetaLen, err := readElement(p.reader, nil)
 	if err != nil {
 		log.Println("read element err")
 		return nil, err
@@ -93,7 +93,7 @@ func (p *parser) readHeader() ([]*Element, error) {
 	}
 	defer p.reader.PopLimit()
 	for !p.reader.IsLimitExhausted() {
-		elem, err := readElement(p.reader)
+		elem, err := readElement(p.reader, nil)
 		if err != nil {
 			// TODO: see if we can skip over malformed elements somehow
 			log.Println("read element err")
@@ -109,7 +109,7 @@ func (p *parser) readHeader() ([]*Element, error) {
 func (p *parser) Parse() (Dataset, error) {
 	for !p.reader.IsLimitExhausted() {
 		// TODO: avoid silent looping
-		elem, err := readElement(p.reader)
+		elem, err := readElement(p.reader, &p.dataset)
 		if err != nil {
 			// TODO: tolerate some kinds of errors and continue parsing
 			return Dataset{}, err

pkg/dicomio/reader.go

@@ -15,6 +15,8 @@ var (
 // Reader provides common functionality for reading underlying DICOM data.
 type Reader interface {
 	io.Reader
+	// ReadUInt8 reads a uint16 from the underlying reader
+	ReadUInt8() (uint8, error)
 	// ReadUInt16 reads a uint16 from the underlying reader
 	ReadUInt16() (uint16, error)
 	// ReadUInt32 reads a uint32 from the underlying reader
@@ -80,6 +82,12 @@ func (r *reader) Read(p []byte) (int, error) {
 	return n, err
 }
 
+func (r *reader) ReadUInt8() (uint8, error) {
+	var out uint8
+	err := binary.Read(r, r.bo, &out)
+	return out, err
+}
+
 func (r *reader) ReadUInt16() (uint16, error) {
 	var out uint16
 	err := binary.Read(r, r.bo, &out)