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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:左侧和右侧。

输入:1000x1000 输出:500x1000(宽 x 高)。

目前,我只能读取一个文件。

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: 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 来解决对象定位问题。我想裁剪 50% 的图像大小(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

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1 回答 1

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一旦你执行pydicom.dcm_read()了你的像素数据就可以在ds.pixel_array. 您可以将所需的数据切片并使用任何合适的库保存。在这个例子中,我将使用 matplotlib,因为我也使用它来验证我的切片是否正确。显然,根据您的需要进行调整,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,如果您不更新适当的数据,它们可能不是有效的 DICOM。例如,SOP Instance UID 在技术上不允许与原始 DICOM 文件或任何其他 SOP Instance UID 相同。这有多重要,取决于你。

使用如下脚本,您可以定义命名切片并将它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)
于 2019-03-23T10:16:58.760 回答