How to replace pixel data in same DICOM file using pyDicom to read it again with any DICOM viewer?

I want to read some DICOM files, so I’m testing pydicom for my work, which I think is considerably useful.

Now I want to load existing DICOM files, replace the pixel data array with another pixel array (e.g. pre-processing or literally another DICOM pixel array) and most of all, I want to read it again with any DICOM viewer application.

For this test, I used the tutorial code below. This code loads a test data file. The size of image is 64*64. The code below does sub-sampling from the original data. After that, the size of image is 8*8, and the result is saved to after.dcm.

But when I read the file using a DICOM viewer app (I used ‘Dicompass’), the size of DICOM image is still 64*64. What is it that I’m missing?

I referred to the pydicom documentation (http://pydicom.readthedocs.io/en/stable/getting_started.html, https://pydicom.github.io/pydicom/stable/index.html) to solve my problem.

# authors : Guillaume Lemaitre <[email protected]>
# license : MIT

import pydicom
from pydicom.data import get_testdata_files

print(__doc__)

# FIXME: add a full-sized MR image in the testing data
filename = get_testdata_files('MR_small.dcm')[0]
ds = pydicom.dcmread(filename)

# get the pixel information into a numpy array
data = ds.pixel_array
print(data)

print('The image has {} x {} voxels'.format(data.shape[0],
                                        data.shape[1]))
data_downsampling = data[::8, ::8]
print('The downsampled image has {} x {} voxels'.format(
    data_downsampling.shape[0], data_downsampling.shape[1]))

# copy the data back to the original data set
ds.PixelData = data_downsampling.tostring()
# update the information regarding the shape of the data array
ds.Rows, ds.Columns = data_downsampling.shape

# print the image information given in the dataset
print('The information of the data set after downsampling: n')
print(ds)
print(ds.pixel_array)
print(len(ds.PixelData))
ds.save_as("after.dcm")