{ "id": 341187, "title": "Problem reading dicom files", "url": "/competitions/rsna-2022-cervical-spine-fracture-detection/discussion/341187", "author_name": "Bartek Sadlej", "post_date": "2022-08-01T17:24:12.439000", "votes": 3, "comment_count": 4, "views": 0, "content": "

I came across a problem while reading dicom images.
\nI use this code from https://www.kaggle.com/code/raddar/convert-dicom-to-np-array-the-correct-way

\n

`def read_xray(path, voi_lut = True, fix_monochrome = True):
\n dicom = pydicom.dcmread(path)

\n
# VOI LUT (if available by DICOM device) is used to transform raw DICOM data to \"human-friendly\" view\nif voi_lut:\n    data = apply_voi_lut(dicom.pixel_array, dicom)\nelse:\n    data = dicom.pixel_array\n\n# depending on this value, X-ray may look inverted - fix that:\nif fix_monochrome and dicom.PhotometricInterpretation == \"MONOCHROME1\":\n    data = np.amax(data) - data\n\ndata = data - np.min(data)\ndata = data / np.max(data)\ndata = (data * 255).astype(np.uint8)\n\nreturn data`\n
\n

and I get this error

\n

The following handlers are available to decode the pixel data however they are missing required dependencies: GDCM (req. GDCM), pylibjpeg (req. )

\n

I tried many solutions found in google and could not solve it.
\nFor example
\n!pip install -U gdcm\n !pip install -U pylibjpeg[all]
\nTried to install gdcm, pylibjpeg[all].
\nSome of them throw different errors but also related to those libraries.
\nThanks for help.

", "messages": [ { "id": 1880603, "postDate": "2022-08-01T21:10:37.683Z", "content": "

Add this dataset to your notebook: https://www.kaggle.com/datasets/ipythonx/for-pydicom

\n

Add this to your notebook (before importing pydicom): !pip install -qU ../input/for-pydicom/python_gdcm-3.0.14-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl ../input/for-pydicom/pylibjpeg-1.4.0-py3-none-any.whl --find-links frozen_packages --no-index

\n

It will be necessary to do it this way because your notebook cannot be connected to the internet when you make a submission, so these libraries need to be installed from a Kaggle Dataset.

", "rawMarkdown": "Add this dataset to your notebook: https://www.kaggle.com/datasets/ipythonx/for-pydicom\n\nAdd this to your notebook (before importing pydicom): `!pip install -qU ../input/for-pydicom/python_gdcm-3.0.14-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl ../input/for-pydicom/pylibjpeg-1.4.0-py3-none-any.whl --find-links frozen_packages --no-index`\n\nIt will be necessary to do it this way because your notebook cannot be connected to the internet when you make a submission, so these libraries need to be installed from a Kaggle Dataset.", "votes": 6, "replies": [ { "id": 1881047, "postDate": "2022-08-02T07:59:23.700Z", "content": "

Thanks a lot! It solved my problem.

", "rawMarkdown": "Thanks a lot! It solved my problem.", "votes": 1 }, { "id": 1895186, "postDate": "2022-08-12T02:30:56.143Z", "content": "

I tried this but still get the error:
\nThe following handlers are available to decode the pixel data however they are missing required dependencies: pylibjpeg (req. ), GDCM (req. )
\nI did not import the modules, as that was not needed when running locally.

", "rawMarkdown": "I tried this but still get the error:\n```The following handlers are available to decode the pixel data however they are missing required dependencies: pylibjpeg (req. ), GDCM (req. )```\nI did not import the modules, as that was not needed when running locally. ", "votes": 1 } ] }, { "id": 1880396, "postDate": "2022-08-01T17:24:12.440Z", "content": "

I came across a problem while reading dicom images.
\nI use this code from https://www.kaggle.com/code/raddar/convert-dicom-to-np-array-the-correct-way

\n

`def read_xray(path, voi_lut = True, fix_monochrome = True):
\n dicom = pydicom.dcmread(path)

\n
# VOI LUT (if available by DICOM device) is used to transform raw DICOM data to \"human-friendly\" view\nif voi_lut:\n    data = apply_voi_lut(dicom.pixel_array, dicom)\nelse:\n    data = dicom.pixel_array\n\n# depending on this value, X-ray may look inverted - fix that:\nif fix_monochrome and dicom.PhotometricInterpretation == \"MONOCHROME1\":\n    data = np.amax(data) - data\n\ndata = data - np.min(data)\ndata = data / np.max(data)\ndata = (data * 255).astype(np.uint8)\n\nreturn data`\n
\n

and I get this error

\n

The following handlers are available to decode the pixel data however they are missing required dependencies: GDCM (req. GDCM), pylibjpeg (req. )

\n

I tried many solutions found in google and could not solve it.
\nFor example
\n!pip install -U gdcm\n !pip install -U pylibjpeg[all]
\nTried to install gdcm, pylibjpeg[all].
\nSome of them throw different errors but also related to those libraries.
\nThanks for help.

", "rawMarkdown": "I came across a problem while reading dicom images.\nI use this code from https://www.kaggle.com/code/raddar/convert-dicom-to-np-array-the-correct-way\n\n`def read_xray(path, voi_lut = True, fix_monochrome = True):\n dicom = pydicom.dcmread(path)\n \n # VOI LUT (if available by DICOM device) is used to transform raw DICOM data to \"human-friendly\" view\n if voi_lut:\n data = apply_voi_lut(dicom.pixel_array, dicom)\n else:\n data = dicom.pixel_array\n \n # depending on this value, X-ray may look inverted - fix that:\n if fix_monochrome and dicom.PhotometricInterpretation == \"MONOCHROME1\":\n data = np.amax(data) - data\n \n data = data - np.min(data)\n data = data / np.max(data)\n data = (data * 255).astype(np.uint8)\n \n return data`\n\nand I get this error\n\n`The following handlers are available to decode the pixel data however they are missing required dependencies: GDCM (req. GDCM), pylibjpeg (req. )`\n\nI tried many solutions found in google and could not solve it.\nFor example\n` !pip install -U gdcm\n !pip install -U pylibjpeg[all]`\nTried to install gdcm, pylibjpeg[all].\nSome of them throw different errors but also related to those libraries.\nThanks for help.", "votes": 3 }, { "id": 1885567, "postDate": "2022-08-05T09:00:20.610Z", "content": "

I sugesst you can use SimpleITK, for some dic files maybe you will get GDCM read error, so I choose SimpleITK. If you also get this error, I post the SimpleITK code in this notebook data pre-processing for RSNA. I hope it can help you.

", "rawMarkdown": "I sugesst you can use *SimpleITK*, for some dic files maybe you will get *GDCM read error*, so I choose *SimpleITK*. If you also get this error, I post the SimpleITK code in this notebook [data pre-processing for RSNA](https://www.kaggle.com/code/handsomeevy/data-pre-processing-for-rsna). I hope it can help you." } ], "comments": [ { "id": 1880603, "author_name": "Branden Murray", "author_url": "", "post_date": "2022-08-01T21:10:37.683000", "content": "

Add this dataset to your notebook: https://www.kaggle.com/datasets/ipythonx/for-pydicom

\n

Add this to your notebook (before importing pydicom): !pip install -qU ../input/for-pydicom/python_gdcm-3.0.14-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl ../input/for-pydicom/pylibjpeg-1.4.0-py3-none-any.whl --find-links frozen_packages --no-index

\n

It will be necessary to do it this way because your notebook cannot be connected to the internet when you make a submission, so these libraries need to be installed from a Kaggle Dataset.

", "votes": 6, "replies": [ { "id": 1881047, "author_name": "Bartek Sadlej", "author_url": "", "post_date": "2022-08-02T07:59:23.700000", "content": "

Thanks a lot! It solved my problem.

", "votes": 1, "replies": [] }, { "id": 1895186, "author_name": "SolverWorld", "author_url": "", "post_date": "2022-08-12T02:30:56.143000", "content": "

I tried this but still get the error:
\nThe following handlers are available to decode the pixel data however they are missing required dependencies: pylibjpeg (req. ), GDCM (req. )
\nI did not import the modules, as that was not needed when running locally.

", "votes": 1, "replies": [] } ] }, { "id": 1885567, "author_name": "柯慕灵", "author_url": "", "post_date": "2022-08-05T09:00:20.610000", "content": "

I sugesst you can use SimpleITK, for some dic files maybe you will get GDCM read error, so I choose SimpleITK. If you also get this error, I post the SimpleITK code in this notebook data pre-processing for RSNA. I hope it can help you.

", "votes": 0, "replies": [] } ], "raw_markdown_by_id": { "1880603": "Add this dataset to your notebook: https://www.kaggle.com/datasets/ipythonx/for-pydicom\n\nAdd this to your notebook (before importing pydicom): `!pip install -qU ../input/for-pydicom/python_gdcm-3.0.14-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl ../input/for-pydicom/pylibjpeg-1.4.0-py3-none-any.whl --find-links frozen_packages --no-index`\n\nIt will be necessary to do it this way because your notebook cannot be connected to the internet when you make a submission, so these libraries need to be installed from a Kaggle Dataset.", "1880396": "I came across a problem while reading dicom images.\nI use this code from https://www.kaggle.com/code/raddar/convert-dicom-to-np-array-the-correct-way\n\n`def read_xray(path, voi_lut = True, fix_monochrome = True):\n dicom = pydicom.dcmread(path)\n \n # VOI LUT (if available by DICOM device) is used to transform raw DICOM data to \"human-friendly\" view\n if voi_lut:\n data = apply_voi_lut(dicom.pixel_array, dicom)\n else:\n data = dicom.pixel_array\n \n # depending on this value, X-ray may look inverted - fix that:\n if fix_monochrome and dicom.PhotometricInterpretation == \"MONOCHROME1\":\n data = np.amax(data) - data\n \n data = data - np.min(data)\n data = data / np.max(data)\n data = (data * 255).astype(np.uint8)\n \n return data`\n\nand I get this error\n\n`The following handlers are available to decode the pixel data however they are missing required dependencies: GDCM (req. GDCM), pylibjpeg (req. )`\n\nI tried many solutions found in google and could not solve it.\nFor example\n` !pip install -U gdcm\n !pip install -U pylibjpeg[all]`\nTried to install gdcm, pylibjpeg[all].\nSome of them throw different errors but also related to those libraries.\nThanks for help.", "1885567": "I sugesst you can use *SimpleITK*, for some dic files maybe you will get *GDCM read error*, so I choose *SimpleITK*. If you also get this error, I post the SimpleITK code in this notebook [data pre-processing for RSNA](https://www.kaggle.com/code/handsomeevy/data-pre-processing-for-rsna). I hope it can help you." } }