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

145
April 10, 2022, at 11:30 AM

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 <g.lemaitre58@gmail.com>
# 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")
Answer 1

The code looks OK. But, you are not overwriting original file.

You load the file with:

filename = get_testdata_files('MR_small.dcm')[0]
ds = pydicom.dcmread(filename)

where original file name is "MR_small.dcm".

Then you save the file with:

ds.save_as("after.dcm")

where destination file name is different. That means, original file is still unchanged.

You should either load "after.dcm" in your DICOM viewer to test

OR

You should overwrite the file (pydicom.filewriter.dcmwrite) while saving it.

Not a part of your problem, but if you are creating copy of original image with change in pixel data, it is recommended that you also modify instance specific information in dataset like InstanceNumber (0020,0013), SOPInstanceUID (0008,0018) etc.

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