Native multi-frame dicom parsing, multi-value native pixel parsing #7

suyashkumar · 2018-07-02T20:36:27Z

This change:

Implements multi-frame parsing of native (non-encapsulated) pixel data in DICOMs (closes Implement multi-frame parsing for Native pixel data formats #2)
Implements parsing of multi-value native pixel data in DICOMs (closes Sometimes bytes read is less than the value length for some Native Pixel dicoms #8)
Updates the dicomutil utility program to parse and write JPG images of native pixel data as well

suyashkumar · 2018-07-06T04:00:50Z

dicomutil/dicomutil.go

+ defer wg.Done()
+ i := image.NewGray16(image.Rect(0, 0, 512, 512)) //TODO(suyash): dont assume 512 x 512
+ for j := 0; j < len(frame); j++ {
+ i.SetGray16(j%512, j/512, color.Gray16{Y: uint16(frame[j][0])}) // for now, assume we're not overflowing uint16, assume gray image


Right now the utility tool only supports outputting gray images. Color output will be added in future diffs

suyashkumar · 2018-07-06T04:01:52Z

element.go

+
+ pixelsPerFrame := int(rows.MustGetUInt16()) * int(cols.MustGetUInt16())
+
+ dicomlog.Vprintf(1, "Image size: %d x %d", rows.MustGetUInt16(), cols.MustGetUInt16())


logging lib will be switched out in future diff

suyashkumar · 2018-07-06T04:16:08Z

element.go

@@ -441,7 +454,7 @@ var endOfDataElement = &Element{Tag: dicomtag.Tag{Group: 0x7fff, Element: 0x7fff
 // element is a pixel data, or it sees an element defined by options.StopAtTag.
 //
 // - On successful parsing, it returns non-nil and non-endOfDataElement value.
-func ReadElement(d *dicomio.Decoder, options ReadOptions) *Element {
+func ReadElement(d *dicomio.Decoder, parsedData *DataSet, options ReadOptions) *Element {


Parsing some attributes, namely PixelData requires information encoded in previously parsed attributes (for example: rows, cols, bits per sample, etc). For exploration purposes, this information was injected into ReadElement so that it can be used to parse PixelData into a relatively meaningful form (more than just bytes), but it may also be useful to keep ReadElement independent of previous elements and do a special second parsing pass on the PixelData element to put it into a well parsed form...decision will be made after additional consideration and taking stock of this library and any refactors that may be needed

though I find it very appealing for ReadElement's API to not rely on previous data (though one can always pass in nil here if not parsing PixelData elements), that change may have to accompany other refactors that should probably happen in future diffs. #11

switch order of parsedData *DataSet, options ReadOptions so that parsedData=nil can be the last argument if/when called with nil

suyashkumar · 2018-07-06T04:19:36Z

writer.go

@@ -148,14 +150,35 @@ func WriteElement(e *dicomio.Encoder, elem *Element) {
 if elem.UndefinedLength {
 encodeElementHeader(e, elem.Tag, vr, undefinedLength)
 writeBasicOffsetTable(e, image.Offsets)
- for _, image := range image.Frames {
+ for _, image := range image.EncapsulatedFrames {
 writeRawItem(e, image)
 }
 encodeElementHeader(e, dicomtag.SequenceDelimitationItem, "" /*not used*/, 0)
 } else {


Changes were made to prevent the writing tests from failing. These take into account the new internal representation of PixelInfo

suyashkumar · 2018-07-06T04:34:09Z

element.go

+ dicomlog.Vprintf(1, "Pixels Per Frame: %d", pixelsPerFrame)
+ dicomlog.Vprintf(1, "Number of frames %d", nFrames)
+
+ // Parse the pixels:


consider breaking this out into a more abstract function that takes a io.Reader and nFrames, pixelsPerFrame, etc and returns a [][][]int parsed pixel data.

May also be good to add a pixeldata package or an image package that has utility functions and type definitions for specifically parsing pixel data / images. This element.go is getting a bit large, and likely should live in a package (perhaps a parse package?)

larger refactors should probably happen in a separate dedicated diff though

suyashkumar · 2018-07-06T04:43:04Z

element.go

@@ -346,18 +348,29 @@ func readRawItem(d *dicomio.Decoder) ([]byte, bool) {

 // PixelDataInfo is the Element.Value payload for PixelData element.
 type PixelDataInfo struct {
- Offsets []uint32 // BasicOffsetTable
- Frames [][]byte // Parsed images


previously wasn't really "frames" because native frames would be parsed into a single frame as raw bytes.

suyashkumar added 6 commits June 28, 2018 21:45

Exploratory implementation of multi-frame native pixel parsing

b13b9bf

Parallel image generation

315ebd7

Add bytes read to native frame parser

0503fed

Update writer, comments

9777b1c

Update todo

d0f738d

Add additional todo

583285f

suyashkumar requested a review from Ouwen July 6, 2018 02:23

suyashkumar force-pushed the s/multi-frame-ct-explore branch from 9fa8a26 to 502231a Compare July 6, 2018 03:58

Implement parsing of images with multiple values per pixel

8cf48e4

suyashkumar force-pushed the s/multi-frame-ct-explore branch from 502231a to 8cf48e4 Compare July 6, 2018 03:59

suyashkumar commented Jul 6, 2018

View reviewed changes

suyashkumar mentioned this pull request Jul 6, 2018

Sometimes bytes read is less than the value length for some Native Pixel dicoms #8

Closed

suyashkumar commented Jul 6, 2018

View reviewed changes

suyashkumar added 2 commits July 6, 2018 00:54

Cleanup

bb1d094

Some cleanup

ce5846f

suyashkumar changed the title ~~[WIP] Native MultiFrame DICOM Parsing~~ [WIP] Native Multi Frame DICOM Parsing, color native pixel parsing Jul 6, 2018

suyashkumar changed the title ~~[WIP] Native Multi Frame DICOM Parsing, color native pixel parsing~~ Native Multi Frame DICOM Parsing, color native pixel parsing Jul 6, 2018

suyashkumar changed the title ~~Native Multi Frame DICOM Parsing, color native pixel parsing~~ Native multi-frame dicom parsing, multi-value native pixel parsing Jul 6, 2018

suyashkumar added 2 commits July 6, 2018 17:22

Cleanup

a39bac2

Update utility tool, cleanup

0743985

suyashkumar merged commit 0ff58da into master Jul 6, 2018

suyashkumar mentioned this pull request Jul 6, 2018

Explore making ReadElement independent of parsedData #11

Closed

suyashkumar self-assigned this Jul 6, 2018

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Native multi-frame dicom parsing, multi-value native pixel parsing #7

Native multi-frame dicom parsing, multi-value native pixel parsing #7

suyashkumar commented Jul 2, 2018 •

edited

Loading

suyashkumar Jul 6, 2018

suyashkumar Jul 6, 2018

suyashkumar Jul 6, 2018

suyashkumar Jul 6, 2018

suyashkumar Jul 6, 2018

suyashkumar Jul 6, 2018

suyashkumar Jul 6, 2018

suyashkumar Jul 6, 2018 •

edited

Loading

suyashkumar Jul 6, 2018


		pixelsPerFrame := int(rows.MustGetUInt16()) * int(cols.MustGetUInt16())

		dicomlog.Vprintf(1, "Image size: %d x %d", rows.MustGetUInt16(), cols.MustGetUInt16())

Native multi-frame dicom parsing, multi-value native pixel parsing #7

Native multi-frame dicom parsing, multi-value native pixel parsing #7

Conversation

suyashkumar commented Jul 2, 2018 • edited Loading

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

suyashkumar Jul 6, 2018 • edited Loading

Choose a reason for hiding this comment

Choose a reason for hiding this comment

suyashkumar commented Jul 2, 2018 •

edited

Loading

suyashkumar Jul 6, 2018 •

edited

Loading