How to get/make copy of pixel data?

[Paul Helmuth]

All,

I apologize for the simple question - but I'm somewhat new to C# and not thoroughly familiar with the Fellow Oak library.

What I would like to do, is to copy pixel data from a DicomFile object to an appropriate array.

So, for instance for OW data, copy to an array of unsigned short.

I can open the file and get to the Pixel Data Element...

DicomFile DICOM_file = Dicom.DicomFile.Open(DICOM_file_path);

var OWpixelDataEle = DICOM_file.Dataset.Get<DicomOtherWord>(DicomTag.PixelData);

...how do I reference the actual pixel data buffer to copy to a unsigned short array?

Thanks in advance,

-Paul

[Chris Hafey]

Something like this:

var dicomFile = DicomFile.Open(@"C:\image.dcm");

var dicomImage = new DicomImage(dicomFile.Dataset);

var pixelData = PixelDataFactory.Create(dicomImage.PixelData);

if(pixelData is GrayscalePixelDataU16) {

  var pixels = pixelData.Data;

  // access pixel data here

}

[Paul Helmuth]

Chris - thanks!

I'll have a look at "PixelDataFactory" and play with that code frag.

-Paul

[Matias]

I do it this way:

public List<ushort> Pixels16bits;

DicomDataset ds = Dicom.Imaging.Codec.DicomCodecExtensions.ChangeTransferSyntax(dicomImage.Dataset, DicomTransferSyntax.ExplicitVRLittleEndian);

bytes_image = Dicom.Imaging.DicomPixelData.Create(ds).GetFrame(0).Data;

int count = bytes_image.Length / 2;

ushort[] words = new ushort[count];

            for (int j = 0, p = 0; j < count; ++j, p += 2)

            {

                words[j] = BitConverter.ToUInt16(bytes_image, p);

            }

Pixels16bits = words.ToList();

[Matias]

Chris, your code doesn't work for some reason:

See, "Data" is not a member of PixelData

was there a typo?

Thanks,

[Chris Hafey]

Yes, I forgot to cast pixelData to GrayscalePixelDataU16 (use 'as' to do this)

[Paul Helmuth]

Thanks Matias and Chris for posting.

After looking things over - I believe this is the most direct way to do what I want...

[from original post]

DicomFile DICOM_file = Dicom.DicomFile.Open(DICOM_file_path);

var OWpixelDataEle = DICOM_file.Dataset.Get<DicomOtherWord>(DicomTag.PixelData);

[then add this...]

IByteBuffer IBBuff_pixelBuff = OWpixelDataEle.Buffer;

var vp = IBBuff_pixelBuff.Data;

Buffer.BlockCopy(vp, 0, rawShortBuff, 0, rawShortBuffSize*sizeof(short));  // copy the data from the IByteBuffer to the rawShortBuff array.

This seems to do exactly what I want - specifically, create an appropriately typed array containing all of the pixel data from an image.

Perhaps the library has a more elegant way to do this?

Is there anything fundamentally wrong with approach?

[making the assumption that the VR of the pixel data is known and the "endian-ness" of the target machine] 

Kind Regards,

-Paul

[Matias]

I tried Chris approach by doing this and it worked for me:

var PixelData = PixelDataFactory.Create(mydicomimage.PixelData,0) as GrayscalePixelDataS16;
short[] pixels = PixelData.Data;

So I think yes, assuming you know which type of image you're dealing with I think your code or Chris code will work.
You can always verify which type of image is the one you're dealing with prior to obtaining the Pixel Data with an if statement or case statement such as Chris put in his code in the initial answer of this pos

[Paul Helmuth]

Matias and Chris - thanks again for the posts!

[Mahesh Dubey]

Hello;

      

            DicomFile file = DicomFile.Open("dicomFile.dcm");
            DicomPixelData pxd = DicomPixelData.Create(file.Dataset);
            IByteBuffer buffer = pxd.GetFrame(0);
            ushort[] pixels = Dicom.IO.ByteConverter.ToArray<ushort>(buffer);

Mahesh

[Paul Helmuth]

Mahesh,

In your example, would buffer point to a buffer with all of the pixel data, or would it be a buffer with just frame 0?

I understand that frame 0 would be the first in the pixel data, just not sure if GetFrame creates a separate single frame buffer, or if it's pointing to the first byte of frame (n).

In my case, I want all of the pixel data.

Thanks for posting this alternative (showing Dicom.IO.ByteConverter).

-Paul

[Mahesh Dubey]

Hello;

         Frame 0 is the first frame pointing to all pixels in that frame not a single pixel, if you are dealing with single frame images then you don't have to worry about this number just put the 0 But if you are dealing with the multiframe images then this number is the index  (frame number minus one i.e for first frame 0, second frame 1 etc) of the frame for which you want the pixels. This is a generic method which work for all images irrespective of their pixel data type or VR.

Mahesh   

[Mahesh Dubey]

Hello;

          If any of the above solutions suggested to you solve your problem please mark it as a answer So that other will get benefit of it .

Mahesh

[Paul Helmuth]

Mahesh,

I believe you misunderstood my question 

Here is the question again...

        In your example, would buffer point to a buffer with all of the pixel data, or would it be a buffer with just frame 0?

Here is your response...

Frame 0 is the first frame pointing to all pixels in that frame not a single pixel, if you are dealing with single frame images then you don't have to worry about this number just put the 0 But if you are dealing with the multiframe images then this number is the index  (frame number minus one i.e for first frame 0, second frame 1 etc) of the frame for which you want the pixels. This is a generic method which work for all images irrespective of their pixel data type or VR.

Here is the rest of the qualifying info from that post...

I understand that frame 0 would be the first in the pixel data, just not sure if GetFrame creates a separate single frame buffer, or if it's pointing to the first byte of frame (n).

In my case, I want all of the pixel data.

When I said that I wanted all of the pixel data, I meant all - as in all frames (not all pixels in a single frame).

My apologies if I wasn't clear on that point.

Thanks again for posting.

-Paul

[Mahesh Dubey]

Hello;

         Oops !!!  I misunderstood your question. Frame 0 points only to the first frame.
 From the above code you get only the pixels from one frame. Best way is to get the data from all the frame, is to run a loop and concatenate the output (you can use above code) considering the padding.

OR 

     For non fragmented pixel data.

            //This code only works if pixel data is not fragmented

            IByteBuffer buffer = null;
            var dataset = dicomFile.Dataset;
            var pixelData = dataset.Get<DicomItem>(DicomTag.PixelData);
            if (pixelData is DicomOtherByte)
            {
                buffer = (pixelData as DicomOtherByte).Buffer;
            }
            else if (pixelData is DicomOtherWord)
            {
                buffer = (pixelData as DicomOtherWord).Buffer;
            }
            else // pixel data is fragmented.
            {
                buffer = null; 
            }
            if (buffer != null)
            {

                ushort[] pixels = Dicom.IO.ByteConverter.ToArray<ushort>(buffer);
            }

Mahesh

[Paul Helmuth]

Mahesh,

No worries (about misunderstanding the original question).

Your last code post is a very nice example.

I'll have to take a look at the Dicom.IO.ByteConverter to see what details are built in to that.