DICOM（ダイコム）は医療用画像の規格の１つである。
DICOM画像を扱う必要が出てきたので、Pythonで処理できないか調べてみると、Pydicomというパッケージが見つかったので使ってみる。
Pydicom |
Pydicom Dicom (Digital Imaging in Medicine) is the bread and butter of medical image datasets, storage and transfer. Thi...
pydicom.github.io
インストールはpipでOK。
$ pip install pydicom以下に参考プログラムが載っているので、jupyter notebookで試してみる。
Viewing Images — pydicom 2.4.4 documentation
pydicom.github.io
In [1]:
import matplotlib.pyplot as plt
import pydicom
from pydicom.data import get_testdata_files
filename = get_testdata_files("CT_small.dcm")[0]
ds = pydicom.dcmread(filename)In [2]:
dsOut [2]:
(0008, 0005) Specific Character Set CS: 'ISO_IR 100'
(0008, 0008) Image Type CS: ['ORIGINAL', 'PRIMARY', 'AXIAL']
(0008, 0012) Instance Creation Date DA: '20040119'
(0008, 0013) Instance Creation Time TM: '072731'
(0008, 0014) Instance Creator UID UI: 1.3.6.1.4.1.5962.3
(0008, 0016) SOP Class UID UI: CT Image Storage
(0008, 0018) SOP Instance UID UI: 1.3.6.1.4.1.5962.1.1.1.1.1.20040119072730.12322
(0008, 0020) Study Date DA: '20040119'
(0008, 0021) Series Date DA: '19970430'
(0008, 0022) Acquisition Date DA: '19970430'
(0008, 0023) Content Date DA: '19970430'
(0008, 0030) Study Time TM: '072730'
(0008, 0031) Series Time TM: '112749'
(0008, 0032) Acquisition Time TM: '112936'
(0008, 0033) Content Time TM: '113008'
(0008, 0050) Accession Number SH: ''
(0008, 0060) Modality CS: 'CT'
(0008, 0070) Manufacturer LO: 'GE MEDICAL SYSTEMS'
(0008, 0080) Institution Name LO: 'JFK IMAGING CENTER'
(0008, 0090) Referring Physician's Name PN: ''
(0008, 0201) Timezone Offset From UTC SH: '-0500'
(0008, 1010) Station Name SH: 'CT01_OC0'
(0008, 1030) Study Description LO: 'e+1'
(0008, 1090) Manufacturer's Model Name LO: 'RHAPSODE'
(0009, 0010) Private Creator LO: 'GEMS_IDEN_01'
(0009, 1001) [Full fidelity] LO: 'GE_GENESIS_FF'
(0009, 1002) [Suite id] SH: 'CT01'
(0009, 1004) [Product id] SH: 'HiSpeed CT/i'
(0009, 1027) [Image actual date] SL: 862399669
(0009, 1030) [Service id] SH: ''
(0009, 1031) [Mobile location number] SH: ''
(0009, 10e6) [Genesis Version - now] SH: '05'
(0009, 10e7) [Exam Record checksum] UL: 973283917
(0009, 10e9) [Actual series data time stamp] SL: 862399669
(0010, 0010) Patient's Name PN: 'CompressedSamples^CT1'
(0010, 0020) Patient ID LO: '1CT1'
(0010, 0030) Patient's Birth Date DA: ''
(0010, 0040) Patient's Sex CS: 'O'
(0010, 1002) Other Patient IDs Sequence 2 item(s) ----
(0010, 0020) Patient ID LO: 'ABCD1234'
(0010, 0022) Type of Patient ID CS: 'TEXT'
---------
(0010, 0020) Patient ID LO: '1234ABCD'
(0010, 0022) Type of Patient ID CS: 'TEXT'
---------
(0010, 1010) Patient's Age AS: '000Y'
(0010, 1030) Patient's Weight DS: "0.0"
(0010, 21b0) Additional Patient History LT: ''
(0011, 0010) Private Creator LO: 'GEMS_PATI_01'
(0011, 1010) [Patient Status] SS: 0
(0018, 0010) Contrast/Bolus Agent LO: 'ISOVUE300/100'
(0018, 0022) Scan Options CS: 'HELICAL MODE'
(0018, 0050) Slice Thickness DS: "5.0"
(0018, 0060) KVP DS: "120.0"
(0018, 0088) Spacing Between Slices DS: "5.0"
(0018, 0090) Data Collection Diameter DS: "480.0"
(0018, 1020) Software Versions LO: '05'
(0018, 1040) Contrast/Bolus Route LO: 'IV'
(0018, 1100) Reconstruction Diameter DS: "338.6716"
(0018, 1110) Distance Source to Detector DS: "1099.3100585938"
(0018, 1111) Distance Source to Patient DS: "630.0"
(0018, 1120) Gantry/Detector Tilt DS: "0.0"
(0018, 1130) Table Height DS: "133.699997"
(0018, 1150) Exposure Time IS: "1601"
(0018, 1151) X-Ray Tube Current IS: "170"
(0018, 1152) Exposure IS: "170"
(0018, 1160) Filter Type SH: 'LARGE BOWTIE FIL'
(0018, 1190) Focal Spot(s) DS: "0.7"
(0018, 1210) Convolution Kernel SH: 'STANDARD'
(0018, 5100) Patient Position CS: 'FFS'
(0019, 0010) Private Creator LO: 'GEMS_ACQU_01'
(0019, 1002) [Detector Channel] SL: 912
(0019, 1003) [Cell number at Theta] DS: "373.75"
(0019, 1004) [Cell spacing] DS: "1.0166"
(0019, 100f) [Horiz. Frame of ref.] DS: "955.799988"
(0019, 1011) [Series contrast] SS: 2
(0019, 1013) [Start number for baseline] SS: 0
(0019, 1014) [End number for baseline] SS: 0
(0019, 1015) [Start number for enhanced scans] SS: 0
(0019, 1016) [End number for enhanced scans] SS: 0
(0019, 1017) [Series plane] SS: 2
(0019, 1018) [First scan ras] LO: 'S'
(0019, 1019) [First scan location] DS: "7.79187"
(0019, 101a) [Last scan ras] LO: 'I'
(0019, 101b) [Last scan loc] DS: "-320.197968"
(0019, 101e) [Display field of view] DS: "0.0"
(0019, 1023) [Table Speed [mm/rotation]] DS: "5.0"
(0019, 1024) [Mid Scan Time [sec]] DS: "17.784578"
(0019, 1025) [Mid scan flag] SS: 1
(0019, 1026) [Tube Azimuth [degree]] SL: 0
(0019, 1027) [Rotation Speed [msec]] DS: "1.0"
(0019, 102a) [x-ray On position] DS: "178.079926"
(0019, 102b) [x-ray Off position] DS: "3994.299316"
(0019, 102c) [Number of triggers] SL: 10431
(0019, 102e) [Angle of first view] DS: "-718.079956"
(0019, 102f) [Trigger frequency] DS: "984.0"
(0019, 1039) [SFOV Type] SS: 16
(0019, 1040) [Stat recon flag] SS: 0
(0019, 1041) [Compute type] SS: 1
(0019, 1042) [Segment Number] SS: 0
(0019, 1043) [Total Segments Required] SS: 0
(0019, 1044) [Interscan delay] DS: "1.0"
(0019, 1047) [View compression factor] SS: 1
(0019, 104a) [Total no. of ref channels] SS: 6
(0019, 104b) [Data size for scan data] SL: 10431
(0019, 1052) [Recon post proc. Flag] SS: 1
(0019, 1057) [CT water number] SS: -95
(0019, 1058) [CT bone number] SS: 0
(0019, 105e) [Number of channels (1...512)] SL: 763
(0019, 105f) [Increment between channels] SL: 1
(0019, 1060) [Starting view] SL: 1969
(0019, 1061) [Number of views] SL: 1576
(0019, 1062) [Increment between views] SL: 1
(0019, 106a) [Dependent on #views processed] SS: 4
(0019, 106b) [Field of view in detector cells] SS: 852
(0019, 1070) [Value of back projection button] SS: 1
(0019, 1071) [Set if fatq estimates were used] SS: 0
(0019, 1072) [Z chan avg over views] DS: "0.0"
(0019, 1073) [Avg of left ref chans over views] DS: "0.0"
(0019, 1074) [Max left chan over views] DS: "0.0"
(0019, 1075) [Avg of right ref chans over views] DS: "0.0"
(0019, 1076) [Max right chan over views] DS: "0.0"
(0019, 10da) [Reference channel used] SS: 0
(0019, 10db) [Back projector coefficient] DS: "0.0"
(0019, 10dc) [Primary speed correction used] SS: 1
(0019, 10dd) [Overrange correction used] SS: 1
(0019, 10de) [Dynamic Z alpha value] DS: "0.0"
(0020, 000d) Study Instance UID UI: 1.3.6.1.4.1.5962.1.2.1.20040119072730.12322
(0020, 000e) Series Instance UID UI: 1.3.6.1.4.1.5962.1.3.1.1.20040119072730.12322
(0020, 0010) Study ID SH: '1CT1'
(0020, 0011) Series Number IS: "1"
(0020, 0012) Acquisition Number IS: "2"
(0020, 0013) Instance Number IS: "1"
(0020, 0032) Image Position (Patient) DS: [-158.135803, -179.035797, -75.699997]
(0020, 0037) Image Orientation (Patient) DS: [1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000]
(0020, 0052) Frame of Reference UID UI: 1.3.6.1.4.1.5962.1.4.1.1.20040119072730.12322
(0020, 0060) Laterality CS: ''
(0020, 1040) Position Reference Indicator LO: 'SN'
(0020, 1041) Slice Location DS: "-77.2040634155"
(0020, 4000) Image Comments LT: 'Uncompressed'
(0021, 0010) Private Creator LO: 'GEMS_RELA_01'
(0021, 1003) [Series from which Prescribed] SS: 2
(0021, 1005) [Genesis Version - now] SH: '05'
(0021, 1007) [Series Record checksum] UL: 1605775145
(0021, 1015) [Unknown] US: 24078
(0021, 1016) [Unknown] SS: 2
(0021, 1018) [Genesis version - Now] SH: '05'
(0021, 1019) [Acq recon record checksum] UL: 750675506
(0021, 1037) [Screen Format] SS: 16
(0021, 104a) [Anatomical reference for scout] LO: ''
(0021, 1090) [Tube focal spot position] SS: 7400
(0021, 1091) [Biopsy position] SS: 0
(0021, 1092) [Biopsy T location] FL: 0.0
(0021, 1093) [Biopsy ref location] FL: 0.0
(0023, 0010) Private Creator LO: 'GEMS_STDY_01'
(0023, 1070) [Start time(secs) in first axial] FD: 862399761.111079
(0023, 1074) [No. of updates to header] SL: 1
(0023, 107d) [Indicates study has complete info SS: 0
(0025, 0010) Private Creator LO: 'GEMS_SERS_01'
(0025, 1006) [Last pulse sequence used] SS: 0
(0025, 1007) [Images in Series] SL: 44
(0025, 1010) [Landmark Counter] SL: 0
(0025, 1011) [Number of Acquisitions] SS: 0
(0025, 1017) [Series Complete Flag] SL: 0
(0025, 1018) [Number of images archived] SL: 0
(0025, 1019) [Last image number used] SL: 4
(0025, 101a) [Primary Receiver Suite and Host] SH: ''
(0027, 0010) Private Creator LO: 'GEMS_IMAG_01'
(0027, 1006) [Image archive flag] SL: 1
(0027, 1010) [Scout Type] SS: 0
(0027, 101c) [Vma mamp] SL: 150
(0027, 101d) [Vma phase] SS: 1
(0027, 101e) [Vma mod] SL: 24
(0027, 101f) [Vma clip] SL: 129
(0027, 1020) [Smart scan ON/OFF flag] SS: 1
(0027, 1030) [Foreign Image Revision] SH: ''
(0027, 1035) [Plane Type] SS: 2
(0027, 1040) [RAS letter of image location] SH: 'I'
(0027, 1041) [Image location] FL: -77.20406341552734
(0027, 1042) [Center R coord of plane image] FL: -11.199999809265137
(0027, 1043) [Center A coord of plane image] FL: 9.699999809265137
(0027, 1044) [Center S coord of plane image] FL: -75.69999694824219
(0027, 1045) [Normal R coord] FL: 0.0
(0027, 1046) [Normal A coord] FL: 0.0
(0027, 1047) [Normal S coord] FL: -1.0
(0027, 1048) [R Coord of Top Right Corner] FL: -180.53579711914062
(0027, 1049) [A Coord of Top Right Corner] FL: 179.03579711914062
(0027, 104a) [S Coord of Top Right Corner] FL: -75.69999694824219
(0027, 104b) [R Coord of Bottom Right Corner] FL: -180.53579711914062
(0027, 104c) [A Coord of Bottom Right Corner] FL: -159.63580322265625
(0027, 104d) [S Coord of Bottom Right Corner] FL: -75.69999694824219
(0027, 1050) [Scan Start Location] FL: -63.19999694824219
(0027, 1051) [Scan End Location] FL: -116.20304870605469
(0027, 1052) [RAS letter for side of image] SH: 'L'
(0027, 1053) [RAS letter for anterior/posterior] SH: 'A'
(0027, 1054) [RAS letter for scout start loc] SH: 'I'
(0027, 1055) [RAS letter for scout end loc] SH: 'I'
(0028, 0002) Samples per Pixel US: 1
(0028, 0004) Photometric Interpretation CS: 'MONOCHROME2'
(0028, 0010) Rows US: 128
(0028, 0011) Columns US: 128
(0028, 0030) Pixel Spacing DS: [0.661468, 0.661468]
(0028, 0100) Bits Allocated US: 16
(0028, 0101) Bits Stored US: 16
(0028, 0102) High Bit US: 15
(0028, 0103) Pixel Representation US: 1
(0028, 0120) Pixel Padding Value SS: -2000
(0028, 1052) Rescale Intercept DS: "-1024.0"
(0028, 1053) Rescale Slope DS: "1.0"
(0029, 0010) Private Creator LO: 'GEMS_IMPS_01'
(0029, 1004) [Lower range of Pixels1] SL: 0
(0029, 1005) [Lower range of Pixels1] DS: "0.0"
(0029, 1006) [Lower range of Pixels1] DS: "0.0"
(0029, 1007) [Lower range of Pixels1] SL: 87
(0029, 1008) [Lower range of Pixels1] SH: ''
(0029, 1009) [Lower range of Pixels1] SH: ''
(0029, 100a) [Lower range of Pixels1] SS: 764
(0029, 1026) [Version of the hdr struct] SS: 2
(0029, 1034) [Advantage comp. Overflow] SL: 0
(0029, 1035) [Advantage comp. Underflow] SL: 0
(0043, 0010) Private Creator LO: 'GEMS_PARM_01'
(0043, 1010) [Window value] US: 400
(0043, 1011) [Total input views] US: 10431
(0043, 1012) [X-ray chain] SS: [14, 2, 3]
(0043, 1013) [Decon kernel parameters] SS: [107, 21, 4, 2, 20]
(0043, 1014) [Calibration parameters] SS: [4, 4, 5]
(0043, 1015) [Total output views] SS: 10431
(0043, 1016) [Number of overranges] SS: 0
(0043, 1017) [IBH image scale factors] DS: "0.095"
(0043, 1018) [BBH coefficients] DS: [0.085000, 1.102000, 0.095000]
(0043, 1019) [Number of BBH chains to blend] SS: 350
(0043, 101a) [Starting channel number] SL: 7
(0043, 101b) [Ppscan parameters] SS: [0, 0, 0, 0, 0]
(0043, 101c) [GE image integrity] SS: 0
(0043, 101d) [Level value] SS: 40
(0043, 101e) [Delta Start Time [msec]] DS: "2.0"
(0043, 101f) [Max overranges in a view] SL: 0
(0043, 1020) [Avg overranges all views] DS: "0.0"
(0043, 1021) [Corrected after glow terms] SS: 0
(0043, 1025) [Reference channels] SS: [1, 2, 3, 748, 749, 750]
(0043, 1026) [No views ref chans blocked] US: [0, 1, 1, 0, 0, 0]
(0043, 1027) [Scan Pitch Ratio] SH: '/1.0:1'
(0043, 1028) [Unique image iden] OB: Array of 80 elements
(0043, 1029) [Histogram tables] OB: Array of 2068 elements
(0043, 102a) [User defined data] OB: Array of 40 elements
(0043, 102b) [Private Scan Options] SS: [4, 4, 0, 0]
(0043, 1031) [Recon Center Coordinates] DS: [-11.200000, 9.700000]
(0043, 1040) [Trigger on position] FL: 178.07992553710938
(0043, 1041) [Degree of rotation] FL: 3816.219482421875
(0043, 1042) [DAS trigger source] SL: 0
(0043, 1043) [DAS fpa gain] SL: 0
(0043, 1044) [DAS output source] SL: 1
(0043, 1045) [DAS ad input] SL: 1
(0043, 1046) [DAS cal mode] SL: 3
(0043, 1047) [DAS cal frequency] SL: -1
(0043, 1048) [DAS reg xm] SL: 1
(0043, 1049) [DAS auto zero] SL: 0
(0043, 104a) [Starting channel of view] SS: 1
(0043, 104b) [DAS xm pattern] SL: 0
(0043, 104c) [TGGC trigger mode] SS: 0
(0043, 104d) [Start scan to X-ray on delay] FL: 0.0
(0043, 104e) [Duration of X-ray on] FL: 10.60060977935791
(7fe0, 0010) Pixel Data OW: Array of 32768 elements
(fffc, fffc) Data Set Trailing Padding OB: Array of 126 elementsたくさんの属性がDICOMに入っているのがわかる。
例えば
In [3]:
ds.PatientIDOut [3]:
'1CT1'In [4]:
ds.PatientAgeOut [4]:
'000Y'というように属性を指定すると、その値を得ることが出来る。
患者IDや検査結果、性別年齢などでif文を書いたりする際に役立つ。
次に、画像データを確認する。
In [5]:
ds.pixel_arrayOut [5]:
array([[175, 180, 166, ..., 203, 207, 216],
[186, 183, 157, ..., 181, 190, 239],
[184, 180, 171, ..., 152, 164, 235],
...,
[906, 910, 923, ..., 922, 929, 927],
[914, 954, 938, ..., 942, 925, 905],
[959, 955, 916, ..., 911, 904, 909]], dtype=int16)In [6]:
type(ds.pixel_array)Out [6]:
numpy.ndarray16bitのndarrayで読み込まれている。
In [7]:
plt.imshow(ds.pixel_array, cmap='gray')Out [7]:
<matplotlib.image.AxesImage at 0x114fbac18>
今回は16bitの画像なので、白黒反転（ネガポジ反転）するには2^16-1=65535から元の値を引けばいい。
In [8]:
plt.imshow(65535 - ds.pixel_array, cmap='gray')Out [8]:
<matplotlib.image.AxesImage at 0x115059470>
もしくはpylabを使ってもいい。
In [9]:
import pylab
plt.imshow(ds.pixel_array, cmap=pylab.cm.binary)Out [9]:
<matplotlib.image.AxesImage at 0x1150bbb38>
これで、DICOM画像の表示や白黒反転、属性情報の取得をPythonで出来るようになった。
参考
Pydicom |
Pydicom Dicom (Digital Imaging in Medicine) is the bread and butter of medical image datasets, storage and transfer. Thi...
pydicom.github.io
Viewing Images — pydicom 2.4.4 documentation
pydicom.github.io
Python, NumPyで画像処理（読み込み、演算、保存） | note.nkmk.me
画像ファイルをNumPy配列ndarrayとして読み込むと、NumPyの機能を使って様々な画像処理を行うことができる。 要素（画素）の値の取得や書き換え、スライスでのトリミング、結合などndarrayの操作がそのまま使えるの ...
note.nkmk.me
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