Comments (10)
jacksonofalltrades
commented on August 17, 2024
Correction: I had not seen how to install the jpeg plugin, am trying that now. Will close if that fixes!
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jacksonofalltrades
commented on August 17, 2024
Closing, that fixed it. Thank you.
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jacksonofalltrades
commented on August 17, 2024
Actually, although I do get a pixel array without errors, now, when I try to write the image it still has mostly green in it. Please advise?
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jacksonofalltrades
commented on August 17, 2024
Output attached.
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jacksonofalltrades
commented on August 17, 2024
Ok more info: I tried forcing this to be interpeted by PIL as RGB and then I can write this out to look correct. My code was assuming however that this should be written out as "YCbCr" since the Photometric Interpretation is YBR_FULL_422. Should I be checking other DICOM attributes to determine whether or not to use "YCbCr"?
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jacksonofalltrades
commented on August 17, 2024
Correct image attached forcing RGB image mode when writing out.
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scaramallion
commented on August 17, 2024
pydicom returns the Pixel Data as-is, so if the Photometric Interpretation is YBR_FULL_422 then you get back a YCbCr image, if it's RGB you get back an RGB image. To convert to RGB you can use the pydicom.pixel_data_handlers.util.convert_color_space() function.
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scaramallion
commented on August 17, 2024
Ah, I misunderstood. It should be displayed as YCbCr but its coming back as RGB.
Let me take a look
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scaramallion
commented on August 17, 2024
OK, looking at the data inside the JPG file, the SOF0 marker has three components with the component IDs: 'R', 'G', and 'B'. This is pretty standard when data has been encoded in the RGB colourspace rather than YCbCr, particularly images from Adobe like this one. I think in this case the Photometric Interpretation should be 'RGB'.
A quick googling shows this page has a bit more info.
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scaramallion
commented on August 17, 2024
For reference, heres the JPEG info:
=================== SOI marker at offset 0 ====================
------------- APP14 marker at offset 2, length 16 -------------
Adobe v100:
64 00 00 00 00 00
------------- DQT marker at offset 18, length 69 --------------
Table destination ID: 0
Table precision: 0 (8-bit)
Quantization table:
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
------------- SOF0 marker at offset 87, length 19 -------------
Baseline sequential DCT
Sample size (px): 800 x 600
Sample precision (bits): 8
Number of component images: 3
Component ID: R
Horizontal sampling factor: 1
Vertical sampling factor: 1
Quantization table destination: 0
Component ID: G
Horizontal sampling factor: 1
Vertical sampling factor: 1
Quantization table destination: 0
Component ID: B
Horizontal sampling factor: 1
Vertical sampling factor: 1
Quantization table destination: 0
------------- DHT marker at offset 106, length 33 -------------
Lossless/DC Huffman, table ID: 0
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
01 00 01 04 03 01 01 01 00 00 00 00 00 00 00 00 : # codes
00 : L = 1
06 : L = 3
04 05 07 08 : L = 4
02 03 09 : L = 5
0a : L = 6
01 : L = 7
0b : L = 8
------------ DHT marker at offset 139, length 112 -------------
AC Huffman, table ID: 0
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
00 01 03 03 03 02 03 04 04 08 0a 08 03 00 00 27 : # codes
01 : L = 2
02 03 04 : L = 3
05 06 11 : L = 4
00 07 12 : L = 5
08 21 : L = 6
13 14 31 : L = 7
09 15 22 41 : L = 8
32 51 52 61 : L = 9
16 23 54 91 92 a1 a2 d1 : L = 10
17 18 33 42 62 97 a3 d3 d6 e1 : L = 11
0a 24 57 71 93 98 d2 d7 : L = 12
43 53 81 : L = 13
19 25 56 72 34 55 82 b2 c1 f0 26 27 58 59 73 75 : L = 16
83 63 66 b1 35 36 39 44 64 c2 c3 c4 1a 28 37 38 : L = 16
74 76 88 b4 b6 b7 b8 : L = 16
------------- SOS marker at offset 251, length 14 -------------
Number of image components: 3
Component: R, DC table: 0, AC table: 0
Component: G, DC table: 0, AC table: 0
Component: B, DC table: 0, AC table: 0
Spectral selectors start-end: 0-63
Successive approximation bit high-low: 0-0
................... ENC marker at offset 263...................
399085 bytes of entropy-coded data
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Related Issues (20)
- Change pixel data decoding interface to pass group 0028 elements
- Add documentation that defines the plugin interface
- v1.3.0 Release HOT 3
- Pixel handler with support for JPEG2000 HOT 5
- Add version awareness to plugins
- [DCM] Convert output J2K data to match Pixel Representation when required
- using pylibjpeg with executable creator libraries HOT 7
- failure in pixel_data_handlers\pylibjpeg_handler HOT 2
- JPEG encoding HOT 6
- RuntimeError: Unable to convert the Pixel Data as the 'pylibjpeg-libjpeg' plugin is not installed HOT 19
- Conda install support? HOT 5
- `RuntimeError: Unable to convert the Pixel Data as the 'pylibjpeg-libjpeg' plugin is not installed` when running the executable generated with PyInstaller (but not with the script.py) HOT 2
- Dependency on pylibjpeg-rle
- Circular import error HOT 3
- Unable to convert the Pixel Data as the 'pylibjpeg-libjpeg' plugin is not installed
- RuntimeError: Unable to convert the Pixel Data as the 'pylibjpeg-libjpeg' plugin is not installed when running the executable generated with PyInstaller (but not with the script.py)
- Libjpeg-turbo HOT 8
- Use importlib rather than pkg_resources
- DICOM compressed image ( JPEG Extended (Process 2 and 4)) problems HOT 7
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