读取CT扫描dicom文件

Question

我正在尝试使用pydicom python库读取CT扫描Dicom文件，但即使安装gdcm和pylibjpeg，我也无法摆脱下面的错误

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

以下是我的代码

!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)

下面是我尝试运行此代码的图像链接

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

Answer 1

尝试运行以下命令：

!pip install pylibjpeg
!pip install gdcm

Answer 2

在像您这样的similar problem中，我们可以看到问题仍然存在于像素数据级别。您需要install one or more optional libraries，以便您可以处理各种压缩。

首先，你应该这样做：

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

从这里开始，您应该执行以下操作：

$ pip install pylibjpeg pylibjpeg-libjpeg pydicom

然后，您的代码应该如下所示：

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)