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Cannot open mysterious DICOM file using Python

I am trying to open a DICOM file which is accompanied by a .jpeg . This pair of files is the result of exporting an image from a display device, which, I believe, is a proprietary DICOM or something else. However, I can read information and file tags, except to view the actual image data.

I use PyDicom and do the following:

import pydicom
myfile = pydicom.read_file("thedicomfile.dcm")
myfile.pixel_array # results in error
AttributeError: 'Dataset' object has no attribute 'TransferSyntaxUID'
# so I do 
myfile.file_meta.TransferSyntaxUID = pydicom.uid.ImplicitVRLittleEndian
# then 
myfile.pixel_array

lAttributeError: the number of pixel data 19404 does not match the expected data 76800

I do not know what to do or how to use the information from the .jpg file that accompanies my DICOM.

(The data itself, as well as a random change in the time of birth, so no privacy issues)

Hex dump of file 1:
file name: 1_DThumbN.jpg
mime type: 

0000-0010:  49 49 2a 00-08 00 00 00-18 00 fe 00-04 00 01 00  II*..... ........
0000-0020:  00 00 00 00-00 00 00 01-04 00 01 00-00 00 80 00  ........ ........
0000-0030:  00 00 01 01-04 00 01 00-00 00 80 00-00 00 02 01  ........ ........
0000-0040:  03 00 03 00-00 00 2e 01-00 00 03 01-03 00 01 00  ........ ........
0000-0050:  00 00 07 00-00 00 06 01-03 00 01 00-00 00 06 00  ........ ........
0000-0060:  00 00 12 01-03 00 01 00-00 00 01 00-00 00 15 01  ........ ........
0000-0070:  03 00 01 00-00 00 03 00-00 00 1a 01-05 00 01 00  ........ ........
0000-0080:  00 00 64 01-00 00 1b 01-05 00 01 00-00 00 6c 01  ..d..... ......l.
0000-0090:  00 00 1c 01-03 00 01 00-00 00 01 00-00 00 28 01  ........ ......(.
0000-00a0:  03 00 01 00-00 00 02 00-00 00 29 01-03 00 02 00  ........ ..).....
0000-00b0:  00 00 00 00-00 00 42 01-03 00 01 00-00 00 80 00  ......B. ........
0000-00c0:  00 00 43 01-03 00 01 00-00 00 80 00-00 00 44 01  ..C..... ......D.
0000-00d0:  04 00 01 00-00 00 f4 03-00 00 45 01-04 00 01 00  ........ ..E.....
0000-00e0:  00 00 e2 08-00 00 00 02-03 00 01 00-00 00 01 00  ........ ........
0000-00f0:  00 00 01 02-04 00 01 00-00 00 74 01-00 00 02 02  ........ ..t.....
0000-0100:  04 00 01 00-00 00 62 0b-00 00 03 02-03 00 01 00  ......b. ........
0000-0110:  00 00 00 00-00 00 12 02-03 00 02 00-00 00 02 00  ........ ........
0000-0120:  01 00 13 02-03 00 01 00-00 00 02 00-00 00 14 02  ........ ........
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0000-0140:  08 00 08 00-00 00 00 00-01 00 00 00-ff 00 00 00  ........ ........
0000-0150:  01 00 00 00-80 00 00 00-01 00 00 00-ff 00 00 00  ........ ........
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0000-0b70:  76 70 53 76-c7 71 b4 12-33 bc 12 7f-2f 4e 29 ee  vpSv.q.. 3.../N).
0000-0b80:  12 8a 48 64-ae 49 f9 db-23 00 29 c0-e5 46 79 ff  ..Hd.I.. #.)..Fy.
0000-0b90:  00 eb 53 32-37 12 47 cb-9e 09 c1 e7-8c e3 b1 a2  ..S27.G. ........
0000-0ba0:  ed 2b 30 4b-b0 34 87 cc-04 7c a7 a3-64 7e 7c 7e  .+0K.4.. .|..d~|~
0000-0bb0:  95 16 48 6c-f4 22 a6 4c-b8 a1 28 a9-28 51 8a 4f  ..Hl.".L ..(.(Q.O
0000-0bc0:  5a 60 14 bd-f9 fd 68 40-1e d4 aa c5-73 dc 11 82  Z`....h@ ....s...
0000-0bd0:  33 40 85 62-0e 30 a3 3d-f1 4d c1 e9-9f 7e b4 d8  3@.b.0.= .M...~..
0000-0be0:  20 c7 19 1f-fe aa 77 f0-7d 3a f3 d4-71 40 07 98  ......w. }:..q@..
0000-0bf0:  4f df 25 f9-cf 27 8a 6f-eb 49 bb 82-56 03 d4 8e  O.%..'.o .I..V...
0000-0c00:  3d 29 28 18-b8 ff 00 3e-b4 94 80 5c-7b 8a 4a 60  =)(....> ...\{.J`
0000-0c10:  14 76 a4 01-45 30 17 8c-7b d2 b1 04-e7 9e 7a e4  .v..E0.. {.....z.
0000-0c20:  e6 81 0d ef-4b 9e 28 18-0e 0f 34 94-00 b8 e3 34  ....K.(. ..4....4
0000-0c30:  94 00 0e 28-a0 02 8a 40-14 50 02 8a-4a 00 3f 1a  ...(...@ .P..J.?.
0000-0c40:  5e dd 29 80-94 b4 80 07-1c d2 53 00-fa d1 40 0a  ^.)..... ..S...@.
0000-0c50:  7d a9 29 00-51 40 05 14-00 52 8a 60-25 29 c0 c7  }.).Q@.. .R.`%)..
0000-0c60:  1f 5a 40 25-2e 78 c5 00-19 ce 79 a4-a0 05 cf 5e  .Z@%.x.. ..y....^
0000-0c70:  07 3f a5 25-00 1d 7a 51-40 05 14 00-a4 92 72 4e  .?.%..zQ @.....rN
0000-0c80:  4d 25 00 14-1a 00 28 ed-40 05 29 39-3e b4 c0 01  M%....(. @.)9>...
0000-0c90:  20 10 0f 5e-0d 04 e4 01-e8 3d 29 00-94 50 01 fc  ...^.... .=)..P..
0000-0ca0:  a8 a0 02 8a-00 29 73 f4-e2 80 12 8a-00 28 a0 02  .....)s. .....(..
0000-0cb0:  8a 00 28 a0-02 8a 00 28-a0 03 ad 14-00 51 40 05  ..(....( .....Q@.
0000-0cc0:  14 00 51 40-05 14 00 51-40 05 14 00-02 41 c8 e0  ..Q@...Q @....A..
0000-0cd0:  d1 40 05 14-00 52 8f ad-30 12 97 9e-87 23 06 80  .@...R.. 0....#..
0000-0cd6:  0c 7a 73 49-48 0f                                .zsIH.

Hex dump of file 2:
file name: 1_Video.dcm
mime type: 

0000-0010:  cc 4b 00 00-00 00 00 00-00 00 00 00-00 00 00 00  .K...... ........
0000-0020:  00 00 00 00-00 00 00 00-00 00 00 00-00 00 00 00  ........ ........
0000-0030:  00 00 00 00-00 00 00 00-00 00 00 00-00 00 00 00  ........ ........
0000-0040:  00 00 00 00-00 00 00 00-00 00 00 00-00 00 00 00  ........ ........
0000-0050:  00 00 00 00-00 00 00 00-00 00 00 00-00 00 00 00  ........ ........
0000-0060:  00 00 00 00-00 00 00 00-00 00 00 00-00 00 00 00  ........ ........
0000-0070:  00 00 00 00-00 00 00 00-00 00 00 00-00 00 00 00  ........ ........
0000-0080:  00 00 00 00-00 00 00 00-00 00 00 00-00 00 00 00  ........ ........
0000-0090:  44 49 43 4d-08 00 18 00-55 49 34 00-31 35 46 44  DICM.... UI4.15FD
0000-00a0:  41 36 34 2d-37 37 34 36-2d 34 36 43-46 2d 39 38  A64-7746 -46CF-98
0000-00b0:  44 42 2d 30-30 33 43 45-30 35 31 42-39 46 33 2e  DB-003CE 051B9F3.
0000-00c0:  35 31 33 31-2e 31 36 37-35 34 2e 36-31 39 35 36  5131.167 54.61956
0000-00d0:  08 00 20 00-44 41 08 00-32 30 30 37-30 39 31 38  ....DA.. 20070918
0000-00e0:  08 00 21 00-44 41 08 00-32 30 30 37-30 39 31 38  ..!.DA.. 20070918
0000-00f0:  08 00 31 00-54 4d 06 00-31 36 33 36-34 30 08 00  ..1.TM.. 163640..
0000-0100:  32 00 54 4d-06 00 31 36-33 36 34 31-08 00 60 00  2.TM..16 3641..`.
0000-0110:  43 53 04 00-4f 43 54 20-08 00 70 00-4c 4f 12 00  CS..OCT. ..p.LO..
0000-0120:  43 61 72 6c-20 5a 65 69-73 73 20 4d-65 64 69 74  Carl.Zei ss.Medit
0000-0130:  65 63 08 00-10 10 53 48-04 00 4f 43-54 33 08 00  ec....SH ..OCT3..
0000-0140:  90 10 4c 4f-04 00 33 30-30 30 10 00-10 00 50 4e  ..LO..30 00....PN
0000-0150:  06 00 63 33-5e 32 30 34-10 00 20 00-4c 4f 08 00  ..c3^204 ....LO..
0000-0160:  31 33 36 35-33 37 37 20-10 00 30 00-44 41 08 00  1365377. ..0.DA..
0000-0170:  31 39 34 35-30 31 31 32-10 00 40 00-43 53 02 00  19450112 ..@.CS..
0000-0180:  4d 20 10 00-54 21 53 48-02 00 5c 20-10 00 60 21  M...T!SH ..\...`!
0000-0190:  53 48 06 00-57 68 69 74-65 20 10 00-00 40 4c 54  SH..Whit e....@LT
0000-01a0:  00 00 18 00-00 10 4c 4f-0a 00 33 30-30 30 2d 36  ......LO ..3000-6
0000-01b0:  37 30 37 20-18 00 20 10-4c 4f 0c 00-34 2e 30 2e  707..... LO..4.0.
0000-01c0:  37 20 28 30-31 33 32 29-20 00 0d 00-55 49 28 00  7.(0132) ....UI(.
0000-01d0:  31 35 46 44-41 36 34 2d-37 37 34 36-2d 34 36 43  15FDA64- 7746-46C
0000-01e0:  46 2d 39 38-44 42 2d 30-30 33 43 45-30 35 31 42  F-98DB-0 03CE051B
0000-01f0:  39 46 33 2e-35 31 33 31-20 00 0e 00-55 49 2e 00  9F3.5131 ....UI..
+4
1

, DICOM. , . (, 15FDA64-7746-46CF-98DB-003CE051B9F3.5131.16754.61956), UID (- ), . . , .

. dcmdump, ExplicitVRLittleEndian , ( ):

# Dicom-File-Format

# Dicom-Meta-Information-Header
# Used TransferSyntax: Unknown Transfer Syntax

# Dicom-Data-Set
# Used TransferSyntax: Little Endian Explicit
(0008,0018) UI [15FDA64-7746-46CF-98DB-003CE051B9F3.5131.16754.61956] #  52, 1 SOPInstanceUID

[...]

(0008,0060) CS [OCT]                                    #   4, 1 Modality

[...]

(0028,0002) US 1                                        #   2, 1 SamplesPerPixel
(0028,0004) CS [MONOCHROME2]                            #  12, 1 PhotometricInterpretation
(0028,0010) US 240                                      #   2, 1 Rows
(0028,0011) US 320                                      #   2, 1 Columns
(0028,0034) IS [1\1]                                    #   4, 2 PixelAspectRatio
(0028,0100) US 8                                        #   2, 1 BitsAllocated
(0028,0101) US 8                                        #   2, 1 BitsStored
(0028,0102) US 7                                        #   2, 1 HighBit
(0028,0103) US 0                                        #   2, 1 PixelRepresentation

[...]

(7fe0,0010) OW 0000\0c00\506a\2020\0a0d\0a87\0000\1800\7466\7079\706a\2078\0000... # 19404, 1 PixelData

. , PixelData 19404 , 320x240x1 76800 . pydicom , . , . DICOM :

with open('PixelData.bin', mode='wb') as f:
    f.write(myfile.PixelData)

file:

$ file PixelData.bin
PixelData.bin: JPEG 2000 Part 2 (JPX)

PixelData JPEG 2000. PIL , pydicom. PIL :

from PIL import Image
import io

image = Image.open(io.BytesIO(myfile.PixelData))
pixels = np.array(image.getdata()).reshape((myfile.Columns, myfile.Rows))

:

  • DICOM , ;
  • ( , , VR), .
  • DICOM , . , , , PIL, .
+6

Source: https://habr.com/ru/post/1695066/

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