Skip patient/Series processing if corrupted DICOM cannot be read by pydicom's dcmread()

[denbonte]

Steve,

As we discussed, I think it could be beneficial to have the possibility to skip the processing of a patient/specific Series if one of the DICOM files in the Series/folder is corrupted or, in general, if it cannot be read by pydicom's dcmread()†.

† as I reported at the end of the issue, this is already done in some cases - so I'm sorry if the title is a bit misleading but I didn't know how to name this properly!

For the sake of completeness, I'm pasting here the example I already shared privately:

Considering file XXXXXXXXXXXXXXXXXXXXXXXXX.dcm
ERROR, UNEXPECTED EXCEPTION
'bytes' object has no attribute 'name'
Traceback (most recent call last):
  File "dicomsort.py", line 493, in <module>
    if not sorter.renameFiles():
  File "dicomsort.py", line 214, in renameFiles
    if self.renameFile(file):
  File "dicomsort.py", line 232, in renameFile
    ds = dicom.read_file(file,stop_before_pixels=True)
  File "/home/dennis/.local/lib/python3.6/site-packages/pydicom/filereader.py", line 1034, in dcmread
    specific_tags=specific_tags,
  File "/home/dennis/.local/lib/python3.6/site-packages/pydicom/filereader.py", line 874, in read_partial
    if class_uid and class_uid.name == "Media Storage Directory Storage":
AttributeError: 'bytes' object has no attribute 'name'

If it can help in any way, apparently another .dcm file in the dataset was not readable - and was put under the folder UnknownPatientID/UnknownStudyInstanceUID/UnknownSeriesInstanceUID.

When I tried to open that single .dcm file, pydicom wasn't happy again and raised an exception (unfortunately, I removed the file without thinking this through, but it was something almost identical to this problem here - except the tags were different).

That exception was somehow handled correctly by DICOMSort (even if the file was not readable - I guess the exception raised was probably different and correctly caught).

[pieper]

Let's go ahead and add an extra except clause for AttributeError to this block:

dicomsort/dicomsort.py

Lines 231 to 240 in c9cf5ad

	try:
	ds = dicom.read_file(file,stop_before_pixels=True)
	except (IOError, os.error) as why:
	print( "dicom.read_file() IO error on file %s, exception %s" % (file,str(why)) )
	return False
	except InvalidDicomError:
	return False
	except KeyError:
	# needed for issue with pydicom 0.9.9 and some dicomdir files
	return False

[pieper]

Plus let's add a catch-all except at as a fallback. Probably we should be printing the errors for the other cases, probably with some logging level controls.