如何使用python将pydicom文件(图像)分成两半

Question

我有很多图像(pydicom文件(。我想分成两半。从 1 张图片中，我想要 2 张图片：部分左侧和部分右侧。

输入： 1000x1000输出：500x1000(宽 x 高(。

目前，我只能读取文件。

ds = pydicom.read_file(image_fps[0]) # read dicom image from filepath 

第一部分，我想把一半放在一个文件夹中，另一半放在第二个文件夹中。这是我所拥有的：在此处输入图像描述这就是我想要的：在此处输入图像描述

我使用Mask-RCNN来对象定位问题。我想裁剪图像大小的 50%(pydicom 文件(。

编辑1：

import SimpleITK as sitk
    filtered_image = sitk.GetImageFromArray(left_part)
    sitk.WriteImage(filtered_image, '/home/wojtek/Mask/nnna.dcm', True)

我有 dicom 文件，但我无法显示它。

this transfer syntax JPEG 2000 Image Compression (Lossless Only), can not be read because Pillow lacks the jpeg 2000 decoder plugin

Answer 1

执行pydicom.dcm_read()像素数据后，可在 ds.pixel_array .您可以对所需的数据进行切片，然后使用任何合适的库保存。在这个例子中，我将使用 matplotlib，因为我也用它来验证我的切片是否正确。根据您的需求进行调整 显然，您需要做的一件事是生成正确的路径/文件名以进行保存。玩得愉快！(此脚本假定文件路径在 paths 变量中可用(

import pydicom
import matplotlib
# for testing if the slice is correct
from matplotlib import pyplot as plt
for path in paths:
    # read the dicom file
    ds = pydicom.dcmread(path)
    # find the shape of your pixel data
    shape = ds.pixel_array.shape
    # get the half of the x dimension. For the y dimension use shape[0]
    half_x = int(shape[1] / 2)
    # slice the halves
    # [first_axis, second_axis] so [:,:half_x] means slice all from first axis, slice 0 to half_x from second axis
    left_part  = ds.pixel_array[:, :half_x]
    right_part = ds.pixel_array[:,half_x:]
    # to check whether the slices are correct, matplotlib can be convenient
    # plt.imshow(left_part); do not do this in the loop
    # save the files, see the documentation for matplotlib if you want a different format
    # bmp, png are surely supported
    path_to_left_image = 'generatethepathandfilenamefortheleftimage.bmp'
    path_to_right_image = 'generatethepathandfilenamefortherightimage.bmp'
    matplotlib.image.imsave(path_to_left_image, left_part)
    matplotlib.image.imsave(path_to_right_image, right_part)

如果要保存 DICOM 文件，请记住，如果不更新相应的数据，它们可能不是有效的 DICOM。例如，SOP 实例 UID 在技术上不允许与原始 DICOM 文件或任何其他 SOP 实例 UID 中的相同。这有多重要，取决于你。

使用如下所示的脚本，您可以定义命名切片，并将其在提供的路径中找到的任何 dicom 图像文件拆分为适当的切片。

import os
import pydicom
import numpy as np
def save_partials(parts, path_to_directory):
    """
    parts: list of tuples, each tuple specifying a name and a list of four slice offsets
    path_to_directory: path to directory containing dicom files
    any file with a .dcm extension will have its image data split into the specified slices and saved accordingly. 
    original file will not be modified
    """
    dir_content = [os.path.join(path_to_directory, item) for item in os.listdir(path_to_directory)]
    files = [i for i in dir_content if os.path.isfile(os.path.join(path_to_directory, i))]
    for file in files:
        root, extension = os.path.splitext(file)
        if extension.lower() != '.dcm':
            # not a .dcm file, continue with next iteration of loop
            continue
        for part in parts:
            ds = pydicom.read_file(file)
            if not isinstance(ds.pixel_array, np.ndarray):
                # no image data available
                continue
            part_name = part[0] 
            p = part[1] # slice list
            ds.PixelData = ds.pixel_array[p[0]:p[1], p[2]:p[3]].tobytes()
            ds.Rows = p[1] - p[0]
            ds.Columns = p[3] - p[2]
            ##
            ## Here you can modify any tags using ds.KeyWord
            ##
            new_file_name = "{r}-{pn}{ext}".format(r=root, pn=part_name, ext=extension)
            ds.save_as(new_file_name)
            print('saved {}'.format(new_file_name))

dir_path = '/home/wojtek/Mask'
parts = [('left', [0,512,0,256]),
         ('right', [0,512,256,512])]
save_partials(parts, dir_path)