用Python打开压缩的Dicom (MONOCHROME2)文件

Question

我试图打开一个Dicom文件，它是一个压缩版本(JPEG 2000图像压缩)。

• I使用不同的免费软件工具和Python库(pydicom、VTK、OpenCV)来打开它，但它们在pydicom中没有成功的
• ，decompress()采用数据集的传输语法，但光度法decompress()似乎不能处理压缩版本，但是在Windows上没有安装GDCM的“一键”解决方案！H 213/code>f 214

我希望对此有任何建议。

字典标签：

(0008, 0016) SOP Class UID                       UI: 
(0008, 0018) SOP Instance UID                    UI: 1.2.276.0.75.2.2.42.114374073191699.20160725100733359.3844234830
(0008, 0020) Study Date                          DA: ''
(0008, 0021) Series Date                         DA: ''
(0008, 0022) Acquisition Date                    DA: ''
(0008, 002a) Acquisition DateTime                DT: ''
(0008, 0030) Study Time                          TM: '100304'
(0008, 0031) Series Time                         TM: '100733'
(0008, 0032) Acquisition Time                    TM: '100733'
(0008, 0050) Accession Number                    SH: ''
(0008, 0060) Modality                            CS: ''
(0008, 0070) Manufacturer                        LO: ''
(0008, 0080) Institution Name                    LO: ''
(0008, 1010) Station Name                        SH: ''
(0008, 1030) Study Description                   LO: ''
(0008, 103e) Series Description                  LO: 'Model Acquistion'
(0008, 1070) Operators' Name                     PN: ''
(0008, 1072)  Operator Identification Sequence   1 item(s) ---- 
   (0008, 0080) Institution Name                    LO: ''
   ---------
(0008, 1090) Manufacturer's Model Name           LO: '4000'
(0010, 0010) Patient's Name                      PN: ''
(0010, 0020) Patient ID                          LO: ''
(0010, 0021) Issuer of Patient ID                LO: ''
(0010, 0030) Patient's Birth Date                DA: ''
(0010, 0040) Patient's Sex                       CS: ''
(0010, 4000) Patient Comments                    LT: ''
(0018, 0088) Spacing Between Slices              DS: "0.0"
(0018, 1000) Device Serial Number                LO: '11307'
(0018, 1020) Software Versions                   LO: '6.5.0.772'
(0018, 1030) Protocol Name                       LO: ''
(0020, 000d) Study Instance UID                  UI: 1.2.276.0.75.2.2.42.114374073191699.20160725100304296.3844877810
(0020, 000e) Series Instance UID                 UI: 1.2.276.0.75.2.2.42.114374073191699.20160725100733328.3844960960
(0020, 0010) Study ID                            SH: '2016072510030428'
(0020, 0011) Series Number                       IS: "-2147483648"
(0020, 0012) Acquisition Number                  IS: "0"
(0020, 0013) Instance Number                     IS: "1"
(0020, 0052) Frame of Reference UID              UI: 1.2.276.0.75.2.2.42.114374073191699.20160725100733328.3844960960
(0020, 0060) Laterality                          CS: 'OS'
(0020, 0200) Synchronization Frame of Reference  UI: 1.2.276.0.75.2.2.42.114374073191699.20140417175345187.1980128920
(0020, 4000) Image Comments                      LT: ''
(0028, 0002) Samples per Pixel                   US: 1
(0028, 0004) Photometric Interpretation          CS: 'MONOCHROME2'
(0028, 0008) Number of Frames                    IS: "2"
(0028, 0010) Rows                                US: 1024
(0028, 0011) Columns                             US: 1024
(0028, 0030) Pixel Spacing                       DS: '0.005865103,0.001955034'
(0028, 0100) Bits Allocated                      US: 8
(0028, 0101) Bits Stored                         US: 8
(0028, 0102) High Bit                            US: 7
(0028, 0103) Pixel Representation                US: 1
(0028, 1050) Window Center                       DS: "29.0"
(0028, 1051) Window Width                        DS: "210.0"
(0028, 2110) Lossy Image Compression             CS: '01'
(0028, 2112) Lossy Image Compression Ratio       DS: "10.0"
(0032, 1060) Requested Procedure Description     LO: ''
(0040, 0008)  Scheduled Protocol Code Sequence   1 item(s) ---- 
   (0008, 0100) Code Value                          SH: 'SD-E1'
   (0008, 0102) Coding Scheme Designator            SH: '99CZM'
   (0008, 0103) Coding Scheme Version               SH: '1.0'
   (0008, 0104) Code Meaning                        LO: 'ALL SCANS'
   (0008, 010d) Context Group Extension Creator UID UI: CZM
   (0061, 0111) Private tag data                    UL: 1
   (0061, 0113) Private tag data                    LO: '1'
   (0061, 0115) Private tag data                    LO: ''
   (0061, 0117) Private tag data                    LO: 'SD-E1.xml'
   (0061, 0119) Private tag data                    LO: 'False'
   (0061, 011b) Private tag data                    LO: ''
   (0061, 011d) Private tag data                    LO: 'True'
   ---------
(0040, 0244) Performed Procedure Step Start Date DA: ''
(0040, 0245) Performed Procedure Step Start Time TM: '100733'
(0040, 0260)  Performed Protocol Code Sequence   1 item(s) ---- 
   (0008, 0100) Code Value                          SH: 'SD-S2'
   (0008, 0102) Coding Scheme Designator            SH: ''
   (0008, 0103) Coding Scheme Version               SH: '1.0'
   (0008, 0104) Code Meaning                        LO: 'Macular Cube 512x128'
   (0008, 010d) Context Group Extension Creator UID UI: CZM
   (0061, 0111) Private tag data                    UL: 2
   (0061, 0113) Private tag data                    LO: '1'
   (0061, 0115) Private tag data                    LO: ''
   (0061, 0117) Private tag data                    LO: 'SD-S2.xml'
   (0061, 0119) Private tag data                    LO: 'False'
   (0061, 011b) Private tag data                    LO: 'No Hires in center.No parameters can be modified.'
   (0061, 011d) Private tag data                    LO: 'False'
   ---------
(0040, 1001) Requested Procedure ID              SH: ''
(0057, 0001) Private Creator                     UI: 1.2.276.0.75.2.2.42.7
(0057, 1003) Private tag data                    UL: 1
(0057, 1015) Private tag data                    LO: 'CZMI'
(0057, 1021) Private tag data                    LO: ''
(0057, 1023) Private tag data                    LO: '116525681374'
(0059, 1000) Private tag data                    LO: 'DATAFILES/E039/3RT8Q85TM1Y7VT7X31WNLNBV99GA43BOJ27IOLS4X2ZU.EX.DCM'
(0059, 1005) Private tag data                    SL: 0
(0059, 3500) Private tag data                    SL: 1
(0063, 1000) Private tag data                    FL: 0.0
(0063, 1005) Private tag data                    FL: 6.0
(0063, 1010) Private tag data                    FL: 2.0
(0063, 1015) Private tag data                    FL: -64.0
(0063, 1020) Private tag data                    UL: 141
(0063, 1025) Private tag data                    FL: 0.0
(0063, 1026) Private tag data                    FL: 0.0
(0063, 1030) Private tag data                    FL: 1.0
(0063, 1032) Private tag data                    FL: 1.0
(0063, 1035) Private tag data                    SL: 113
(0063, 1047) Private tag data                    FL: 297.0
(0063, 1048) Private tag data                    FL: 872.0
(0063, 1049) Private tag data                    FL: 1222.0
(0071, 1070) Private tag data                    FL: -292.0
(0071, 1095) Private tag data                    FL: 0.0
(0071, 1100) Private tag data                    FL: 0.0
(0071, 1105) Private tag data                    SL: 0
(0073, 1085) Private tag data                    FL: 1.0
(0073, 1090) Private tag data                    SL: 0
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(0073, 1100) Private tag data                    SL: 0
(0073, 1105) Private tag data                    FL: 0.0
(0073, 1110) Private tag data                    FL: 0.0
(0073, 1125) Private tag data                    SL: Array of 128 elements
(0073, 1135) Private tag data                    FL: 0.6000000238418579
(0073, 1200) Private tag data                    SL: Array of 128 elements
(0075, 1015)  Private tag data   0 item(s) ---- 
(0075, 1020) Private tag data                    SL: 0
(0075, 1021) Private tag data                    SL: 0
(0075, 1035) Private tag data                    FL: 3.5299999713897705
(0075, 1065) Private tag data                    FL: 0.0
(0075, 1070) Private tag data                    FL: 0.0
(0075, 1075) Private tag data                    FL: 0.0
(0075, 1080) Private tag data                    FL: 0.0
(0075, 1085) Private tag data                    SL: 0
(0075, 1210) Private tag data                    UL: 0
(0075, 1215) Private tag data                    FL: -inf
(0075, 1220) Private tag data                    FL: -inf
(7fe0, 0010) Pixel Data                          OB: Array of 211106 elements ```

Answer 1

我已经决定了如何解读这些混淆的CZM DICOM数据集。从本质上讲，CZM转换了JPEG 2000数据的三个区域，然后每7字节就用0x5A覆盖这些数据，这非常糟糕。

下面的函数应该扭转这种情况，产生一个正常的JPEG 2000数据流，然后可以写入文件或用枕头打开：

import math


def unscramble_czm(frame: bytes) -> bytearray:
    """Return an unscrambled image frame.

    Parameters
    ----------
    frame : bytes
        The scrambled CZM JPEG 2000 data frame as found in the DICOM dataset.

    Returns
    -------
    bytearray
        The unscrambled JPEG 2000 data.
    """
    # Fix the 0x5A XORing
    frame = bytearray(frame)
    for ii in range(0, len(frame), 7):
        frame[ii] = frame[ii] ^ 0x5A

    # Offset to the start of the JP2 header - empirically determined
    jp2_offset = math.floor(len(frame) / 5 * 3)

    # Double check that our empirically determined jp2_offset is correct
    offset = frame.find(b"\x00\x00\x00\x0C")
    if offset == -1:
        raise ValueError("No JP2 header found in the scrambled pixel data")

    try:
        assert jp2_offset == offset
    except AssertionError:
        raise ValueError(
            f"JP2 header found at offset {offset} rather than the expected "
            f"{jp2_offset}"
        )

    d = bytearray()
    d.extend(frame[jp2_offset:jp2_offset + 253])
    d.extend(frame[993:1016])
    d.extend(frame[276:763])
    d.extend(frame[23:276])
    d.extend(frame[1016:jp2_offset])
    d.extend(frame[:23])
    d.extend(frame[763:993])
    d.extend(frame[jp2_offset + 253:])

    assert len(d) == len(frame)

    return d