在Python中获取DICOM结构轮廓作为数组 [英] Getting DICOM structure contours as array in Python
问题描述
因此，如果我有图像(CT，MRI等)甚至是放射治疗的剂量，我可以通过以下方式将剂量或图像值提取到阵列中:
So if I have an image (CT, MRI, etc.) or even a dose from radiation therapy I can pull out the dose or image values into an array through:
import dicom
ds = dicom.read_file("dicom_file.dcm")
print ds.pixel_array
这非常简单，使我能够根据需要操纵图像/剂量.但是，通常您还拥有一个结构文件，其中包含不同的轮廓结构，然后您可以在图像查看器中看到类似的东西.再次，非常简单.
This is pretty straightforward, and gives me the ability to manipulate images/doses as I want. However, often you also have a structure file that includes different contoured structures that you can then see in an image viewer or something like that. Again, pretty straightforward.
我的问题是，我也希望这些单独的结构也可以作为数组.如果我运行相同的代码，我只会得到TypeError: No pixel data found in this dataset.
My problem is that I would also like these individual structures as an array as well. And if I run the same code I just get TypeError: No pixel data found in this dataset.
我猜想结构DICOM文件的制作方式与剂量/图像DICOM文件的制作方式不同.
I'm guessing that structure DICOM files are not "made" the same way as dose/images DICOM files.
那么有没有我无法找到的解决方案?我还查看了dicompyler_core程序包，但是从我看到的结果来看，没有任何方法可以仅仅"将不同的结构分解为数组.
So is there a solution to this that I haven't been able to find ? I have also looked at the dicompyler_core package, but from what I could see there wasn't any way to "just" get out the different structures into arrays.
推荐答案
以下是一个交互式会话，它使用pydicom随附的rtstruct.dcm文件说明了数据布局:
Here is an interactive session illustrating the data layout using the rtstruct.dcm file included with pydicom:
>>> import dicom
>>> ds = dicom.read_file("rtstruct.dcm", force=True)
>>> ds.dir("contour")
['ROIContourSequence']
>>> ctrs = ds.ROIContourSequence
>>> ctrs[0]
(3006, 002a) ROI Display Color IS: ['220', '160', '120']
(3006, 0040) Contour Sequence 3 item(s) ----
(3006, 0042) Contour Geometric Type CS: 'CLOSED_PLANAR'
(3006, 0046) Number of Contour Points IS: '5'
(3006, 0048) Contour Number IS: '1'
(3006, 0050) Contour Data DS: ['-200.0', '150.0', '-20
0.0', '-200.0', '-150.0', '-200.0', '200.0', '-150.0', '-200.0', '200.0', '150.0
', '-200.0', '-200.0', '150.0', '-200.0']
---------
(3006, 0042) Contour Geometric Type CS: 'CLOSED_PLANAR'
(3006, 0046) Number of Contour Points IS: '6'
(3006, 0048) Contour Number IS: '2'
(3006, 0050) Contour Data DS: ['200.0', '-0.0', '-190.
0', '200.0', '-150.0', '-190.0', '-200.0', '-150.0', '-190.0', '-200.0', '150.0'
, '-190.0', '200.0', '150.0', '-190.0', '200.0', '-0.0', '-190.0']
---------
(3006, 0042) Contour Geometric Type CS: 'CLOSED_PLANAR'
(3006, 0046) Number of Contour Points IS: '6'
(3006, 0048) Contour Number IS: '3'
(3006, 0050) Contour Data DS: ['200.0', '-0.0', '-180.
0', '200.0', '-150.0', '-180.0', '-200.0', '-150.0', '-180.0', '-200.0', '150.0'
, '-180.0', '200.0', '150.0', '-180.0', '200.0', '-0.0', '-180.0']
---------
(3006, 0084) Referenced ROI Number IS: '1'
数据(在这种情况下，通常如此)存储为每个平面的一组坐标.要获取一个轮廓，一个平面的数据，您可以使用
The data is stored (in this case, as is usual) as a set of coordinates for each plane. To get the data for one contour, for one plane, you could use
>>> ctrs[0].ContourSequence[0].ContourData
['-200.0', '150.0', '-200.0', '-200.0', '-150.0', '-200.0', '200.0', '-150.0', '
-200.0', '200.0', '150.0', '-200.0', '-200.0', '150.0', '-200.0']
这些是(x，y，z)坐标一个接一个的三胞胎.
These are triplets of (x, y, z) coordinates one after the other.
您可以在StructureSetROISequence序列中找到有关每个轮廓(名称等)的更多信息，以获取由参考的ROI编号"给出的索引.
You can find out more information about each contour (name, etc) in the StructureSetROISequence sequence, for the index given by Referenced ROI Number.
通过遍历ContourSequence中特定轮廓的每个数据集并将它们附加到一个数组中，您可以获得所有这些的完整数组.
You could get a complete array for all of these by looping through each dataset in the ContourSequence for that particular contour and appending them together into one array.
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