Question

我正在尝试从标准尺寸（512 x 512或256 x 256）的numpy阵列创建一个新的dicom图像。看起来这应该是直截了当的，我已经调整了http://code.google.com/p/pydicom/source/browse/source/dicom/examples/write_new.py的代码，它似乎执行相同的过程，但是当我保存文件时，我无法在RadiAnt或MicroDicom中查看它。

import dicom, dicom.UID
from dicom.dataset import Dataset, FileDataset

def write_dicom(pixel_array,filename):

    file_meta = Dataset()
    ds = FileDataset(filename, {},file_meta = file_meta,preamble="\0"*128)
    ds.PixelData = pixel_array.tostring()
    ds.save_as(filename)
    return

if __name__ == "__main__":
    import numpy as np
    pixel_array = np.tile(np.arange(256).reshape(16,16), (16,16)) * 4
    write_dicom(pixel_array,'pretty.dcm')

Answer 1

这是我需要编写的代码的功能版本。它将从给定的2D像素阵列写入16位灰度DICOM图像。根据DICOM标准，UID对于每个图像和系列应该是唯一的，这段代码不担心，因为我不知道UID实际上做了什么。如果其他人这样做，我会很乐意将其添加进去。

import dicom, dicom.UID
from dicom.dataset import Dataset, FileDataset
import numpy as np
import datetime, time

def write_dicom(pixel_array,filename):
    """
    INPUTS:
    pixel_array: 2D numpy ndarray.  If pixel_array is larger than 2D, errors.
    filename: string name for the output file.
    """

    ## This code block was taken from the output of a MATLAB secondary
    ## capture.  I do not know what the long dotted UIDs mean, but
    ## this code works.
    file_meta = Dataset()
    file_meta.MediaStorageSOPClassUID = 'Secondary Capture Image Storage'
    file_meta.MediaStorageSOPInstanceUID = '1.3.6.1.4.1.9590.100.1.1.111165684411017669021768385720736873780'
    file_meta.ImplementationClassUID = '1.3.6.1.4.1.9590.100.1.0.100.4.0'
    ds = FileDataset(filename, {},file_meta = file_meta,preamble="\0"*128)
    ds.Modality = 'WSD'
    ds.ContentDate = str(datetime.date.today()).replace('-','')
    ds.ContentTime = str(time.time()) #milliseconds since the epoch
    ds.StudyInstanceUID =  '1.3.6.1.4.1.9590.100.1.1.124313977412360175234271287472804872093'
    ds.SeriesInstanceUID = '1.3.6.1.4.1.9590.100.1.1.369231118011061003403421859172643143649'
    ds.SOPInstanceUID =    '1.3.6.1.4.1.9590.100.1.1.111165684411017669021768385720736873780'
    ds.SOPClassUID = 'Secondary Capture Image Storage'
    ds.SecondaryCaptureDeviceManufctur = 'Python 2.7.3'

    ## These are the necessary imaging components of the FileDataset object.
    ds.SamplesPerPixel = 1
    ds.PhotometricInterpretation = "MONOCHROME2"
    ds.PixelRepresentation = 0
    ds.HighBit = 15
    ds.BitsStored = 16
    ds.BitsAllocated = 16
    ds.SmallestImagePixelValue = '\\x00\\x00'
    ds.LargestImagePixelValue = '\\xff\\xff'
    ds.Columns = pixel_array.shape[0]
    ds.Rows = pixel_array.shape[1]
    if pixel_array.dtype != np.uint16:
        pixel_array = pixel_array.astype(np.uint16)
    ds.PixelData = pixel_array.tostring()

    ds.save_as(filename)
    return



if __name__ == "__main__":
#    pixel_array = np.arange(256*256).reshape(256,256)
#    pixel_array = np.tile(np.arange(256).reshape(16,16),(16,16))
    x = np.arange(16).reshape(16,1)
    pixel_array = (x + x.T) * 32
    pixel_array = np.tile(pixel_array,(16,16))
    write_dicom(pixel_array,'pretty.dcm')

Answer 2

以上示例有效，但会导致许多工具抱怨DICOM，甚至根本不能使用itk / SimpleITK作为堆栈来读取它们。我发现从numpy制作DICOM的最好方法是使用SimpleITK工具并逐片生成DICOM。一个基本示例（https://github.com/zivy/SimpleITK/blob/8e94451e4c0e90bcc6a1ffdd7bc3d56c81f58d80/Examples/DicomSeriesReadModifyWrite/DicomSeriesReadModifySeriesWrite.py）显示了如何加载堆栈，执行转换然后重新保存文件，但这可以通过使用

轻松修改

import SimpleITK as sitk
filtered_image = sitk.GetImageFromArray(my_numpy_array)

最终输出图像中的标签数量非常大，因此手动创建所有这些标签非常繁琐。另外，SimpleITK支持8,16,32位图像以及RGB，因此比在pydicom中制作它们要容易得多。

(0008, 0008) Image Type                          CS: ['DERIVED', 'SECONDARY']
(0008, 0016) SOP Class UID                       UI: Secondary Capture Image Storage
(0008, 0018) SOP Instance UID                    UI: 1.2.826.0.1.3680043.2.1125.1.35596048796922805578234000521866725
(0008, 0020) Study Date                          DA: '20170803'
(0008, 0021) Series Date                         DA: '20170803'
(0008, 0023) Content Date                        DA: 0
(0008, 0030) Study Time                          TM: '080429.171808'
(0008, 0031) Series Time                         TM: '080429'
(0008, 0033) Content Time                        TM: 0
(0008, 0050) Accession Number                    SH: ''
(0008, 0060) Modality                            CS: 'OT'
(0008, 0064) Conversion Type                     CS: 'WSD'
(0008, 0090) Referring Physician's Name          PN: ''
(0010, 0010) Patient's Name                      PN: ''
(0010, 0020) Patient ID                          LO: ''
(0010, 0030) Patient's Birth Date                DA: ''
(0010, 0040) Patient's Sex                       CS: ''
(0018, 2010) Nominal Scanned Pixel Spacing       DS: ['1', '3']
(0020, 000d) Study Instance UID                  UI: 1.2.826.0.1.3680043.2.1125.1.33389357207068897066210100430826006
(0020, 000e) Series Instance UID                 UI: 1.2.826.0.1.3680043.2.1125.1.51488923827429438625199681257282809
(0020, 0010) Study ID                            SH: ''
(0020, 0011) Series Number                       IS: ''
(0020, 0013) Instance Number                     IS: ''
(0020, 0020) Patient Orientation                 CS: ''
(0020, 0052) Frame of Reference UID              UI: 1.2.826.0.1.3680043.2.1125.1.35696880630664441938326682384062489
(0028, 0002) Samples per Pixel                   US: 1
(0028, 0004) Photometric Interpretation          CS: 'MONOCHROME2'
(0028, 0010) Rows                                US: 40
(0028, 0011) Columns                             US: 50
(0028, 0100) Bits Allocated                      US: 32
(0028, 0101) Bits Stored                         US: 32
(0028, 0102) High Bit                            US: 31
(0028, 0103) Pixel Representation                US: 1
(0028, 1052) Rescale Intercept                   DS: "0"
(0028, 1053) Rescale Slope                       DS: "1"
(0028, 1054) Rescale Type                        LO: 'US'
(7fe0, 0010) Pixel Data                          OW: Array of 8000 bytes

Answer 3

Corvin的2020年更新几乎对我有用。该meta仍未写入文件，因此在读取它时引发了以下异常：

pydicom.errors.InvalidDicomError：文件缺少DICOM文件元信息标头或标头中缺少'DICM'前缀。

为了解决此问题并将元数据写入dicom文件，我需要在enforce_standard=True调用中添加the save_as()：

ds.save_as(filename=out_filename, enforce_standard=True)

Answer 4

DICOM是一种非常复杂的格式。有许多方言，兼容性是运气的问题。你也可以试试nibabel，也许它的方言对RadiAnt或MicroDicom更有吸引力。

一般情况下，我建议尽可能使用Nifti格式。它的标准更加简洁，不兼容性很少。 nibabel也支持这一点。

从numpy数组创建pydicom文件

4 个答案: