Unable to read dicom file with Python3 and pydicom

Question

I trying to read dicom file with python3 and pydicom library. For some dicom data, I can't get data correctly and get error messages when I tried to print the result of pydicom.dcmread.

However, I have tried to use python2 and it worked well. I checked out the meta information and compared it with other dicom files which can be processed, I didn't find any difference between them.

import pydiom

ds = pydicom.dcmread("xxxxx.dicom")
print(ds)

Traceback (most recent call last):
  File "generate_train_data.py", line 387, in <module>
    tf.app.run()
  File "/usr/local/lib/python3.5/dist-packages/tensorflow/python/platform/app.py", line 125, in run
    _sys.exit(main(argv))
  File "generate_train_data.py", line 371, in main
    create_ann()
  File "generate_train_data.py", line 368, in create_ann
    ds_ann_dir, case_name, merge_channel=False)
  File "generate_train_data.py", line 290, in process_dcm_set
    all_dcms, dcm_truth_infos = convert_dicoms(dcm_list, zs)
  File "generate_train_data.py", line 179, in convert_dicoms
    instance_num, pixel_spacing, img_np = extract_info(dcm_path)
  File "generate_train_data.py", line 147, in extract_info
    print(ds)
UnicodeEncodeError: 'ascii' codec can't encode characters in position 2277-2279: ordinal not in range(128)

Anyone has come across the same problem?

Answer 1

I believe the cause of the problem is that Python (for me it only happened in Python 3 running on Centos 7.6 Linux printing to a terminal window on MacOS) is not able to figure out how to print a string that contains a non-ascii character because of the setting of the locale. You can use the locale command to see the results. Mine started out with everything set to "C". I set the LANG environment variable to en_US.UTF-8. With that setting it worked for me. In csh this is done using

setenv LANG en_US.UTF-8

In bash use:

export LANG=en_US.UTF-8

My problem resulted from having 'µ' in the Series Description element. The file was an attenuation map from a SPECT reconstruction on a Siemens scanner. I used the following Python code to help figure out the problem.

#! /usr/bin/env python3
import pydicom as dicom
from sys import exit, argv

def myprint(ds, indent=0):
    """Go through all items in the dataset and print them with custom format
    Modelled after Dataset._pretty_str()
    """
    dont_print = ['Pixel Data', 'File Meta Information Version']

    indent_string = "   " * indent
    next_indent_string = "   " * (indent + 1)

    for data_element in ds:
        if data_element.VR == "SQ":   # a sequence
            print(indent_string, data_element.name)
            for sequence_item in data_element.value:
                myprint(sequence_item, indent + 1)
                print(next_indent_string + "---------")
        else:
            if data_element.name in dont_print:
                print("""<item not printed -- in the "don't print" list>""")
            else:
                repr_value = repr(data_element.value)
                if len(repr_value) > 50:
                    repr_value = repr_value[:50] + "..."
                try:
                    print("{0:s} {1:s} = {2:s}".format(indent_string,
                                                   data_element.name,
                                                   repr_value))

                except:
                    print(data_element.name,'****Error printing value')

for f in argv[1:]:
    ds = dicom.dcmread(f)
    myprint(ds, indent=1)

This is based on the myprint function from]1

The code tries to print out all the data items. It catches exceptions and prints "****Error printing value" when there is an error.

Answer 2

Can you give an example for such a dicom file? When running the pydicom example with python 3.7 it's working perfectly:

import matplotlib.pyplot as plt
import pydicom
from pydicom.data import get_testdata_files
filename = get_testdata_files("CT_small.dcm")[0]
ds = pydicom.dcmread(filename)
plt.imshow(ds.pixel_array, cmap=plt.cm.bone)

It's also working with the sample dicom files from the Medical Image Samples.