如何使用PYDICOM创建JPEG压缩的DICOM数据集？ [英] How to create JPEG compressed DICOM dataset using pydicom?

问题描述

我正在尝试使用pydicom创建JPEG压缩的DICOM图像。here可以找到一个很好的关于彩色DICOM图像的素材，但它主要是理论和C++。在下面的代码示例中，我在output-raw.dcm(未压缩)中创建了一个淡蓝色省略号，如下所示：

import io
from PIL import Image, ImageDraw
from pydicom.dataset import Dataset
from pydicom.uid import generate_uid, JPEGExtended
from pydicom._storage_sopclass_uids import SecondaryCaptureImageStorage

WIDTH = 100
HEIGHT = 100


def ensure_even(stream):
    # Very important for some viewers
    if len(stream) % 2:
        return stream + b"x00"
    return stream


def bob_ross_magic():
    image = Image.new("RGB", (WIDTH, HEIGHT), color="red")
    draw = ImageDraw.Draw(image)
    draw.rectangle([10, 10, 90, 90], fill="black")
    draw.ellipse([30, 20, 70, 80], fill="cyan")
    draw.text((11, 11), "Hello", fill=(255, 255, 0))
    return image


ds = Dataset()
ds.is_little_endian = True
ds.is_implicit_VR = True
ds.SOPClassUID = SecondaryCaptureImageStorage
ds.SOPInstanceUID = generate_uid()
ds.fix_meta_info()
ds.Modality = "OT"
ds.SamplesPerPixel = 3
ds.BitsAllocated = 8
ds.BitsStored = 8
ds.HighBit = 7
ds.PixelRepresentation = 0
ds.PhotometricInterpretation = "RGB"
ds.Rows = HEIGHT
ds.Columns = WIDTH

image = bob_ross_magic()
ds.PixelData = ensure_even(image.tobytes())

image.save("output.png")
ds.save_as("output-raw.dcm", write_like_original=False)  # File is OK

#
# Create compressed image
#
output = io.BytesIO()
image.save(output, format="JPEG")

ds.PixelData = ensure_even(output.getvalue())
ds.PhotometricInterpretation = "YBR_FULL_422"
ds.file_meta.TransferSyntaxUID = JPEGExtended

ds.save_as("output-jpeg.dcm", write_like_original=False)  # File is corrupt

最后，我尝试创建压缩的DICOM：我尝试用PIL设置各种传输语法和压缩，但没有成功。我认为生成的DICOM文件已损坏。如果我要将原始DICOM文件转换为使用gdcm-Tools压缩的JPEG：

$ gdcmconv -J output-raw.dcm output-jpeg.dcm

通过对这个转换文件执行dcmdump，我们可以看到一个有趣的结构，我不知道如何使用pydicom重现它：

$ dcmdump output-jpeg.dcm

# Dicom-File-Format

# Dicom-Meta-Information-Header
# Used TransferSyntax: Little Endian Explicit
(0002,0000) UL 240                                      #   4, 1 FileMetaInformationGroupLength
(0002,0001) OB 001                                    #   2, 1 FileMetaInformationVersion
(0002,0002) UI =SecondaryCaptureImageStorage            #  26, 1 MediaStorageSOPClassUID
(0002,0003) UI [1.2.826.0.1.3680043.8.498.57577581978474188964358168197934098358] #  64, 1 MediaStorageSOPInstanceUID
(0002,0010) UI =JPEGLossless:Non-hierarchical-1stOrderPrediction #  22, 1 TransferSyntaxUID
(0002,0012) UI [1.2.826.0.1.3680043.2.1143.107.104.103.115.2.8.4] #  48, 1 ImplementationClassUID
(0002,0013) SH [GDCM 2.8.4]                             #  10, 1 ImplementationVersionName
(0002,0016) AE [gdcmconv]                               #   8, 1 SourceApplicationEntityTitle

# Dicom-Data-Set
# Used TransferSyntax: JPEG Lossless, Non-hierarchical, 1st Order Prediction
...
... ### How to do the magic below?
...
(7fe0,0010) OB (PixelSequence #=2)                      # u/l, 1 PixelData
  (fffe,e000) pi (no value available)                     #   0, 1 Item
  (fffe,e000) pi ffd8ffee0e41646f626506400000ffc3011... # 4492, 1 Item
(fffe,e0dd) na (SequenceDelimitationItem)               #   0, 0 SequenceDelimitationItem

我试着使用了pydicom的encaps module，但我想它主要是用来读数据的，不是用来写的。还有没有人知道如何处理这个问题，如何创建/编码这些PixelSequence？我希望在不运行外部工具的情况下在纯Python中创建JPEG压缩的DICOM。

推荐答案

DICOM要求像素数据为encapsulated(特别参见表)。获得压缩的图像数据后，您可以使用encaps.encapsulate()方法创建适合像素数据：

的bytes

from pydicom.encaps import encapsulate

# encapsulate() requires a list of bytes, one item per frame
ds.PixelData = encapsulate([ensure_even(output.getvalue())])
# Need to set this flag to indicate the Pixel Data is compressed
ds['PixelData'].is_undefined_length = True  # Only needed for < v1.4
ds.PhotometricInterpretation = "YBR_FULL_422"
ds.file_meta.TransferSyntaxUID = JPEGExtended

ds.save_as("output-jpeg.dcm", write_like_original=False)

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