使用Pydicom从DICOMDIR文件中提取数据

Question

我无法像往常一样在DICOM文件中读取，原因是错误：

AttributeError: 'DicomDir' object has no attribute 'DirectoryRecordSequence'

我试过：

• pydicom.fileset.FileSet
• 在dcmread中使用特定的标记
• pydicom.filereader.read_dicomdir
• pydicom.filereader.read_partial
• 在dcmread中使用force=True

pydicom.filereader.read_file_meta_info是唯一没有返回错误和产生结果的东西；

(0002, 0000) File Meta Information Group Length  UL: 172
(0002, 0001) File Meta Information Version       OB: b'\x00\x01'
(0002, 0002) Media Storage SOP Class UID         UI: Media Storage Directory Storage
(0002, 0003) Media Storage SOP Instance UID      UI: 2.25.330614241706723499239981063503184149269
(0002, 0010) Transfer Syntax UID                 UI: Explicit VR Little Endian
(0002, 0012) Implementation Class UID            UI: 1.3.6.1.4.1.30071.8
(0002, 0013) Implementation Version Name         SH: 'fo-dicom 4.0.7'

此外，图像应该是一个常规的DICOM文件，而不是DICOMDIR。我可以在ImageJ中打开文件并查看头部信息，这样我就知道数据是可恢复的。有没有办法让我用Python阅读这个文件，或者强迫它忽略查找DirectoryRecordSequence？

编辑:使用FileSet的代码和堆栈跟踪：

from pydicom.fileset import FileSet
fs = FileSet("unprocessed.dcm")

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-4-2b6ba2e435fe> in <module>
      1 from pydicom.fileset import FileSet
----> 2 fs = FileSet("unprocessed.dcm")

c:\****\appdata\local\programs\python\python38-32\lib\site-packages\pydicom\fileset.py in __init__(self, ds)
    998         # Check the DICOMDIR dataset and create the record tree
    999         if ds:
-> 1000             self.load(ds)
   1001         else:
   1002             # New File-set

c:\****\appdata\local\programs\python\python38-32\lib\site-packages\pydicom\fileset.py in load(self, ds_or_path, include_orphans, raise_orphans)
   1641             ds = ds_or_path
   1642         else:
-> 1643             ds = dcmread(ds_or_path)
   1644 
   1645         sop_class = ds.file_meta.get("MediaStorageSOPClassUID", None)

c:\****\appdata\local\programs\python\python38-32\lib\site-packages\pydicom\filereader.py in dcmread(fp, defer_size, stop_before_pixels, force, specific_tags)
   1027         stop_when = _at_pixel_data
   1028     try:
-> 1029         dataset = read_partial(
   1030             fp,
   1031             stop_when,

c:\****\appdata\local\programs\python\python38-32\lib\site-packages\pydicom\filereader.py in read_partial(fileobj, stop_when, defer_size, force, specific_tags)
    879             DeprecationWarning
    880         )
--> 881         ds = DicomDir(
    882             fileobj,
    883             dataset,

c:\****\appdata\local\programs\python\python38-32\lib\site-packages\pydicom\dicomdir.py in __init__(self, filename_or_obj, dataset, preamble, file_meta, is_implicit_VR, is_little_endian)
     94 
     95         self.patient_records: List[Dataset] = []
---> 96         self.parse_records()
     97 
     98     def parse_records(self) -> None:

c:\****\appdata\local\programs\python\python38-32\lib\site-packages\pydicom\dicomdir.py in parse_records(self)
    125 
    126         # Build the mapping from file offsets to records
--> 127         records = self.DirectoryRecordSequence
    128         if not records:
    129             return

c:\****\appdata\local\programs\python\python38-32\lib\site-packages\pydicom\dataset.py in __getattr__(self, name)
    834             return {}
    835         # Try the base class attribute getter (fix for issue 332)
--> 836         return object.__getattribute__(self, name)
    837 
    838     @property

AttributeError: 'DicomDir' object has no attribute 'DirectoryRecordSequence'

​

Answer 1

pydicom正确读取数据集，但由于它标识为，因此它将由不推荐的DicomDir类处理，即使直接传递给FileSet类也是如此。由于dataset不是有效的媒体存储目录实例，因此会失败，从而产生所见的异常。

您应该能够通过在读取期间更改文件元信息的(0002,0002)媒体存储SOP类UID来修复这个问题：

from pydicom import dcmread
from pydicom import config

def fix_sop_class(elem, **kwargs):
    if elem.tag == 0x00020002:
        # DigitalXRayImageStorageForProcessing
        elem = elem._replace(value=b"1.2.840.10008.5.1.4.1.1.1.1.1")

    return elem

config.data_element_callback = fix_sop_class

ds = dcmread('path/to/file')

通过更改SOP类UID，将跳过该处理并返回数据集。