Reading CT Scan dicom file

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i am trying to read CT scan Dicom file using pydicom python library but i just can't get rid of this below error even when i install gdcm and pylibjpeg

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

Here is my code

!pip install pylibjpeg pylibjpeg-libjpeg pylibjpeg-openjpeg
!pip install python-gdcm

import gdcm
import pylibjpeg

import numpy as np
import pydicom
from pydicom.pixel_data_handlers.util import apply_voi_lut

import matplotlib.pyplot as plt
%matplotlib inline


def read_xray(path, voi_lut = True, fix_monochrome = True):
    dicom = pydicom.read_file(path)
    
    # VOI LUT (if available by DICOM device) is used to transform raw DICOM data to "human-friendly" view
    if voi_lut:
        data = apply_voi_lut(dicom.pixel_array, dicom)
    else:
        data = dicom.pixel_array
               
    # depending on this value, X-ray may look inverted - fix that:
    if fix_monochrome and dicom.PhotometricInterpretation == "MONOCHROME1":
        data = np.amax(data) - data
        
    data = data - np.min(data)
    data = data / np.max(data)
    data = (data * 255).astype(np.uint8)
        
    return data

img = read_xray('/content/ActiveTB/2018/09/17/1.2.392.200036.9116.2.6.1.44063.1797735841.1537157438.869027/1.2.392.200036.9116.2.6.1.44063.1797735841.1537157440.863887/1.2.392.200036.9116.2.6.1.44063.1797735841.1537154539.142332.dcm')
plt.figure(figsize = (12,12))
plt.imshow(img)

Here is the image link on which i am trying to run this code

https://drive.google.com/file/d/1-xuryA5VlglaumU2HHV7-p6Yhgd6AaCC/view?usp=sharing
pydicom python
2 Answers

Try running the following:

!pip install pylibjpeg
!pip install gdcm
user_144725710

In a similar problem as yours, we could see that the problem persists at the Pixel Data level. You need to install one or more optional libraries, so that you can handle the various compressions.

First, you should do:

$ pip uninstall pycocotools
$ pip install pycocotools --no-binary :all: --no-build-isolation

From here, you should do as follows:

$ pip install pylibjpeg pylibjpeg-libjpeg pydicom

Then, your code should look like this:

from pydicom import dcmread
import pylibjpeg
import gdcm

import numpy as np
import pydicom
from pydicom.pixel_data_handlers.util import apply_voi_lut

import matplotlib.pyplot as plt
%matplotlib inline


def read_xray(path, voi_lut = True, fix_monochrome = True):
    dicom = dcmread(path)
    
    # VOI LUT (if available by DICOM device) is used to transform raw DICOM data to "human-friendly" view
    if voi_lut:
        data = apply_voi_lut(dicom.pixel_array, dicom)
    else:
        data = dicom.pixel_array
               
    # depending on this value, X-ray may look inverted - fix that:
    if fix_monochrome and dicom.PhotometricInterpretation == "MONOCHROME1":
        data = np.amax(data) - data
        
    data = data - np.min(data)
    data = data / np.max(data)
    data = (data * 255).astype(np.uint8)
        
    return data

img = read_xray('/content/ActiveTB/2018/09/17/1.2.392.200036.9116.2.6.1.44063.1797735841.1537157438.869027/1.2.392.200036.9116.2.6.1.44063.1797735841.1537157440.863887/1.2.392.200036.9116.2.6.1.44063.1797735841.1537154539.142332.dcm')
plt.figure(figsize = (12,12))
plt.imshow(img)
user_23719870
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