1.DICOM文件转array

DICOM文件读取

来源于 Convert dicom to np.array - the correct way

1. 读取

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

def read_xray(path, voi_lut=True, fix_monochrome=True):
    """读取DICOM格式数据转为np.array uint8格式"""
    dicom = pydicom.read_file(path) #读取数据

    #VOI LUT(DICOM 设备可用)将原始DICOM格式转为人类适应的格式voi_lut
    if voi_lut:
        data = apply_voi_lut(dicom.pixel_array, dicom)
    else:
        data = dicom.pixel_array #直接用dicom

    # "MONOCHROME1"：灰度值格式 fix_monochrome固定灰度值
    if fix_monochrome and dicom.PhotometricInterpretation == "MONOCHROME1":
        data = np.amax(data) - data #不要改成max避免decode错误

    #类似归一化后乘以255像素范围来转为黑白的图片
    data = data - np.min(data)
    data = data / np.max(data)
    data = (data * 255).astype(np.uint8)
    return data

读取看看数据

dicom_path = "abc.dcm"
data = read_xray(dicom_path)
data.shape
=================
(3093, 2850)

data
==================
array([[  5,   5,   4, ...,   0,   0,   0],
       [  4,   5,   5, ...,   0,   0,   0],
       [  5,   5,   5, ...,   0,   0,   0],
       ...,
       [ 55,  54,  53, ..., 121, 121, 119],
       [ 55,  55,  53, ..., 121, 122, 121],
       [ 54,  54,  54, ..., 121, 124, 123]], dtype=uint8)

也可用matplotlib展示

import matplotlib.pyplot as plt
plt.figure(figsize=(10, 6), dpi=150)
plt.title("dicom")
plt.imshow(data, 'gray')
plt.show()

2. resize到指定大小

def resize(array, size, keep_ratio=False, resample=Image.LANCZOS):
    """resize array到指定大小，采样格式为Image.LANCZOS
    resample有:Image.BICUBIC，Image.LANCZOS，
    Image.BILINEAR，Image.NEAREST四种采样方法
    """
    img = Image.fromarray(array)
    if keep_ratio:
        img.thumbnail((size, size), resample) #缩略图，只能缩小
    else:
        img = img.resize((size, size), resample)
    return img

resize_data = resize(data, 256)
plt.figure(figsize=(10, 6), dpi=150)
plt.title("resize dicom")
plt.imshow(resize_data, 'gray')
plt.show()