[WIP] Generated pydicom/sr codes now append '__' to Python keyword names

[seandoyle]

Describe the changes

generated_concept_dicts.py was modified to add '__' to names which were also keywords in Python. New versions of the dictionary codes in python/sr/* were generated by
python ./source/generate_cids/generate_concept_dicts.py

>>>from pydicom.sr.codedict import codes
>>> codes.cid3716.None__
Code(value='260413007', scheme_designator='SCT', meaning='None', scheme_version=None)

This handles issue 1273.

Tasks

• Unit Test test_cid3716 added in test_codedict.py
• Closes 1273
• Unclear where documentation of original SyntaxError would be most helpful.
• Unit tests failing for codes which were not changed in this PR - see test_cid3111. Perhaps code libraries have changed?

[pep8speaks]

Hello @seandoyle! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file pydicom/sr/_cid_dict.py:

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Comment last updated at 2021-06-04 00:15:33 UTC

[seandoyle]

I'm unclear what I should do about the failing unit tests because they appear to be caused by changes outside of the scope of this PR. The PEP8 issues are on generated code - also a little outside the scope here. Open to suggestions.

[mrbean-bremen]

because they appear to be caused by changes outside of the scope of this PR

The test fails because the code for "Tc99mTetrofosmin" has changed - I actually don't understand it. There are a lot of changes (I guess you used a different version of the standard), but I was under the impression that these codes are fixed. Maybe @hackermd can have a look at this.

[seandoyle]

We're still working on this. CP 1850 has the details - there was a large number of coding changes from SNOMED-RT to SNOMED-CT. We'll respond with more details and a proposal.

[hackermd]

We learned that not only code meanings, but also code values may be subject to change. DICOM defers to the individual coding schemes on how codes are maintained. SNOMED sometimes retires codes (not sure what the procedures are).

We have too things that complicate comparison of codes:

1. There generally are SCT and SRT codes representing the same concept.
2. There may be two SCT or SRT codes representing the same concept, where one of them is active and the other is retired.

We already account for 1. in pydicom.sr._snomed_dict based on Part 16 Annex O SNOMED Concept ID to SNOMED ID Mapping. We only expose SCT codes in pydicom.sr.codedict, but consider the corresponding SRT codes internally for determining equality.

It seems we also need to account for 2. and should create an additional mapping for Part 16 Annex J SNOMED Retired Codes. I would argue that we should only expose active codes in pydicom.sr.codedict. However, we will need to be smart about updating the library using generated_concept_dicts.py and may have to maintain retired codes for backwards compatibility.

[hackermd]

I would suggest the following algorithm for updating:

1. Update concepts map in pydicom.sr._concepts_dict, including codes from Table J-1 using SCT codes as keys
2. Parse Table O-1 and extract SCT codes
3. Look up concept in concepts map using SCT code as key. Use meaning specified in the looked up value to construct attribute name for codes.SCT (to avoid backwards incompatible changes in case the meaning should have changed)

@mrbean-bremen what do you think?

[mrbean-bremen]

@hackermd - I will have a look tomorrow evening (didn't get to it today), though this is something that @darcymason and @scaramallion will probably want to check, too.

[scaramallion]

SR is outside my area of expertise, I'm happy to defer to those with more experience

[hackermd]

cc'ing @dclunie who pointed out Table J-1 and helped clarify questions regarding retired codes

[darcymason]

though this is something that @darcymason and @scaramallion will probably want to check, too.

SR is really outside my area of expertise too - I wrote some of the source code in pydicom, but I don't have knowledge really of the SR codes and their meanings/retirements etc. But having read through @hackermd's proposals and looking at the tables linked, I agree with the principles, which it sounds like are the same as previously - basically convert to latest definitions, be flexible on reading in codes, but more strict on assigning codes to try to keep to non-retired ones, and in any case try to be explicit rather than silently accepting ambiguous situations.

3. Look up concept in concepts map using SCT code as key. Use meaning specified in the looked up value to construct attribute name for codes.SCT

This sounds a bit tricky, but again, in principle seems like the safest way.

[mrbean-bremen]

Sorry, didn't get to this yesterday. I agree with @darcymason - as far as I can see, this all makes sense. And I also have to admit that I'm no expert by far for SR - I have been using it a long time ago and haven't been following it's development since then.

[hackermd]

3. Look up concept in concepts map using SCT code as key. Use meaning specified in the looked up value to construct attribute name for codes.SCT

This sounds a bit tricky, but again, in principle seems like the safest way.

Yes, that's going to be a bit tricky, but I think it's necessary. We should guarantee that the attributes of pydicom.sr.codedict.codes (generated keyword for for code meaning) remain the same when updating the library even if the codes in the standard may have changed.

[darcymason]

Just checking in on this PR -- we have upcoming release - can we get this in for the release?

[seandoyle]

I'm sorry - wasn't sure of of some of the steps and let this slip. I'll take a look tonight. If we follow @hackermd's recommendation then we should also change the unit tests to match the latest values. Don't know how many of these there will be. What is the timeframe for the upcoming release?

[darcymason]

What is the timeframe for the upcoming release?

We don't have fixed dates, but had planned May some time back ... I'm late getting around to it anyway. I'd be fine with around 2 weeks, at least for a release candidate.

[darcymason]

@seandoyle, I've just rediscovered this PR - my apologies that this slipped through the cracks. I somehow missed back then that you had submitted new commits.

Would there be any changes needed now before it could be pulled in?

[seandoyle]

It's been a while - but I need to review it. The problem as I remember it was that incorporating the changes as is might break backward compatibility because some of the code values had changed.

• The simplest thing would be to just have the code values be changed. This is consistent with the most recent version of the standard. But older files and older code might have difficulties.
• We could leave the older codes as-is and generate the new ones with one more level of indirection for different versions of the code.
• Accept @hackermd 's suggestion from Jan 7. I'm not entirely sure I understand step 3 - Use meaning specified in the looked up value to construct attribute name for codes.SCT - but it's been a while since I looked at this.

I would vote for following @hackermd's approach but I may ask some questions as I go along.

[hackermd]

There are two things that could pose problems for backwards compatibility:

1. A change of Code Meaning. This appears to happen relatively frequently. It is important to consider in this context that SNOMED-CT codes often have several synonyms, which can be used interchangeably.
2. A change of Code Value. This should be a relatively rare event, but it does occur and is at the discretion of the source standard (e.g., SNOMED-CT).

To ensure a dictionary entry in pydicom doesn't change if the Code Meaning changes in the standard, I suggest creating a "reverse" lookup table from the value (Code Value) to the corresponding dictionary keyword (derived from the "previous" Code Meaning). When we then regenerate the dictionary from the standard documents, we can find and reuse the existing keyword for a given value.