RuntimeError: Unable to convert the Pixel Data as the 'pylibjpeg-libjpeg' plugin is not installed #58
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triage
Cause of issue still being determined
Comments
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You are aware that the message relates to the |
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Yeah, I installed the two of them. |
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Could you post the complete traceback that you're getting along with: import platform, sys, pydicom
print(
platform.platform(),
"\nPython", sys.version,
"\npydicom", pydicom.__version__
)
try:
import pylibjpeg
from pylibjpeg.utils import get_decoders
print(pylibjpeg.__version__, get_decoders())
except ImportError:
print("pylibjpeg not found")
try:
import libjpeg
print(libjpeg.__version__)
except ImportError:
print("libjpeg not found") |
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This is the terminal output: Linux-5.0.0-37-generic-x86_64-with-Ubuntu-18.04-bionic |
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Hmm, weird. libjpeg is available to Python but not to pylibjpeg. Could you try the following on this file: from libjpeg import decode
with open("A1.JPG", "rb") as f:
arr = decode(f.read())
print(arr)Oh, also could you upgrade to v1.1.0 of the pylibjpeg-libjpeg plugin too? I think I refactored how the plugins work in pylibjpeg between v1.0 and v1.1, which might be the cause. |
from libjpeg import decode
with open("A1.JPG", "rb") as f:
arr = decode(f.read())
print(arr)For this, it worked without any problem because it was a jpeg image, then I tried to upgrade the pylibjpeg it was already upgraded and I run the program again, always the same problem Here is the program that I am trying to run, (the error is in the line pixel_array. import pydicom
import pylibjpeg
im = pydicom.dcmread('dcm_image_for_test.dcm')
arr = im.pixel_array`The error: |
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Right, like I said, because the version of the -libjpeg plugin is v1.0.0 then it won't be available to pylibjpeg. Could you post the output of the following: |
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This is the output: Then I installed the version 1.1 of pylibjpeg and it was successfully installed, but when I run the program again, I obtained another problem now: Knowing that I am always using this program: The problem began from the line 3. |
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You didn't post the -v output for pip so I don't really understand why the newest version wasn't installed. Could you try (for Python 3.6) and post the full output please: Note the |
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Here is the output: |
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I don't know what to tell you The following works fine for me on Ubuntu 18.04.1, Python 3.6.7 (note this with the newest releases): Python 3.6.7 (default, Oct 22 2018, 11:32:17)
[GCC 8.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from pylibjpeg.utils import get_decoders
>>> get_decoders()
{'libjpeg': <function decode at 0x7f0835bf1488>, 'openjpeg': <function decode at 0x7f0835bf1b70>}
>>>This also works fine: >>> import libjpeg
>>> libjpeg.__version__
'1.1.0' |
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Actually that was the whole output: |
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Could you upgrade pip and try again? Are you running on some weird architecture or something? Hmm, no its x86_64 from what you posted earlier. |
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I upgraded pip and I run it again, here is the output (I think that the version 1.1 has been successfully installed) Than I run the program to open a dicom image, so I have got this error: |
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Upgrade pylibjpeg as well: Also, with pydicom v2.1+ you don't need to |
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Now it is working perfectly, thank you for your great answers! |
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No problem! |
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Can someone take a look at my Kaggle that's seeing the same issue and give me some tips: https://www.kaggle.com/jonathoncwik/pylibjpeg-libjpeg-plugin-install-error |
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I'm not familiar with Kaggle, but in the output I don't see any errors related to |
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Hi all,
I am trying to work with dicom images, at first I had a problem saying 'gdcm' so I knew that the problem was about the compressed pixels in the image then after installing all the packages I have now this problem, knowing that I installed the pylibjpeg.
Can you help me with this issue please.
Thank you
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