Question

我有很多图像（pydicom文件）。我想一分为二。从1张图片中，我想要2张图片：左部分和右部分。

输入：1000x1000 输出：500x1000（宽x高）。

当前，我只能读取文件。

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

第一部分，我想将一半放在一个文件夹中，另一半放在第二个文件夹中。这就是我所拥有的： enter image description here 这就是我要的： enter image description here

我使用Mask-RCNN来解决对象本地化问题。我希望裁剪图像尺寸（pydicom文件）的50％。

EDIT1：

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，但无法显示。

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()后，像素数据将在ds.pixel_array可用。您可以只切片所需的数据，并将其保存在任何合适的库中。在此示例中，我将使用matplotlib，因为我还将使用它来验证切片是否正确。显然，根据您的需求进行调整，您需要做的一件事就是生成正确的路径/文件名进行保存。玩得开心！（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 = 'generate\the\path\and\filename\for\the\left\image.bmp'
    path_to_right_image = 'generate\the\path\and\filename\for\the\right\image.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，如果不更新适当的数据，它们可能不是有效的DICOM。例如，从技术上说，不允许SOP实例UID与原始DICOM文件中的SID或其他任何SOP实例UID相同。这到底有多重要，取决于您。

使用下面的脚本，您可以定义命名的切片，并将在提供的路径中找到的所有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)

如何使用python将pydicom文件（图像）分成两半？

1 个答案: