DICOM Text SR Writer Updates

[bluna301]

When preparing MAP pipelines for clinical integration, the DICOM SRs produced by the default DICOMTextSRWriterOperator were validated using libraries such as dciodvfy and dicom-validator. The following validation logs are produced:

Warning - Bad FileMetaInformationVersion Attribute - wrong VR, length or not 0x00,0x01

BasicTextSR

Error - Missing attribute Type 2 Required Element=<ReferencedPerformedProcedureStepSequence> Module=<SRDocumentSeries>
Error - Missing attribute Type 1 Required Element=<CompletionFlag> Module=<SRDocumentGeneral>
Error - Missing attribute Type 2 Required Element=<PerformedProcedureCodeSequence> Module=<SRDocumentGeneral>
Warning - Attribute is not present in standard DICOM IOD - (0x0008,0x002a) DT Acquisition DateTime
Warning - Attribute is not present in standard DICOM IOD - (0x0018,0x0015) CS Body Part Examined
Warning - Attribute is not present in standard DICOM IOD - (0x0018,0x1002) UI Device UID
Warning - Attribute is not present in standard DICOM IOD - (0x0040,0x1001) SH Requested Procedure ID
Warning - Dicom dataset contains attributes not present in standard DICOM IOD - this is a Standard Extended SOP Class

The non-standard attributes that throw warnings are defined in write_common_modules within dicom_utils.py; these are recognized in the source code as extensions of the DICOM IOD. This PR resolves the remaining warnings and errors.

---

The FileMetaInformation tags on the DICOM SR are written as follows (MicroDICOM viewer):

This is manually set in write_common_modules:

# File meta info data set
file_meta = Dataset()
file_meta.FileMetaInformationGroupLength = 198
file_meta.FileMetaInformationVersion = bytes("01", "utf-8")  # '\x00\x01'

However, this seems to encode the character 0 and 1 to their UTF-8 byte values of 0x30 and 0x31, respectively, which results in a value of b"\x30\x31" --> 30\31. This was updated to write the literal bytes 00 01 i.e. b"\x00\x01"; FileMetaInformationGroupLength setting was also removed, as this will be handled automatically during DICOM writing.

---

CompletionFlag indicates the degree of completeness of the DICOM SR. Considering the DICOM SR is complete in the context of the AI model (i.e. it is a finalized AI output from the model), this tag value was set to COMPLETE.

ReferencedPerformedProcedureStepSequence uniquely identifies the Performed Procedure Step SOP Instance for which the series is created. However, we are not tracking the Modality Performed Procedure Step (MPPS) via MAPs/MONAI Deploy; while this tag is Type 3 (Optional) for most modalities, it is not copied by write_common_modules. As such, this tag value was written as an empty Sequence.

PerformedProcedureCodeSequence conveys the codes of the performed procedures pertaining to this SOP Instance. However, we are not tracking the Modality Performed Procedure Step (MPPS) via MAPs/MONAI Deploy and this tag is not present for most imaging modalities. As such, this tag value was written as an empty Sequence.

---

Miscellaneous Updates:

• seg_purpose_of_reference_code.CodeMeaning = '"Processing Algorithm' typo corrected
• setuptools<81.0.0 pin; pkg_resources is deprecated above this version
• Formatting in test files

Summary by CodeRabbit

• Bug Fixes

  • Corrected metadata string formatting in DICOM segmentation output for proper data integrity
  • Added required metadata fields to DICOM structured report documents to improve compliance with medical imaging standards

• Chores

  • Updated dependency version constraints for improved environment compatibility
  • Reformatted test files for consistency

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: dfce3df0-b6d2-43bd-9bae-2af871ee0eba

📥 Commits

Reviewing files that changed from the base of the PR and between a3a64b2 and 07b50eb.

📒 Files selected for processing (1)

• requirements-min.txt

Walkthrough

The PR includes minor bug fixes to DICOM metadata handling, particularly correcting malformed string values and adding SR-specific metadata requirements. Dependencies are constrained, test fixtures are reformatted, and copyright years are updated. No public API signatures are altered.

Changes

Cohort / File(s)	Summary
DICOM Operators & Utilities monai/deploy/operators/dicom_seg_writer_operator.py, monai/deploy/operators/dicom_text_sr_writer_operator.py, monai/deploy/operators/dicom_utils.py	Corrections to CodeMeaning string quotation in DICOM segmentation writer, addition of SR-specific metadata (CompletionFlag, VerificationsFlag, empty sequences), FileMetaInformationVersion byte literal update, and copyright year increments. No control flow changes.
Dependency Constraints requirements-min.txt	Added upper bound constraint to setuptools version (<81.0.0) with deprecation comment for pkg_resources.
Test Fixtures & Formatting tests/fixtures/runner_fixtures.py, tools/pipeline-generator/tests/test_cli.py	Reformatted multiline JSON and YAML string literals by consolidating closing markers; no semantic changes.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~12 minutes

Poem

🐰 A hop through the code, a quote here, a byte there,
Metadata mended with utmost care,
SR sequences nestled, dependencies tight,
Tests format anew—everything just right! ✨

🚥 Pre-merge checks | ✅ 1 | ❌ 2

❌ Failed checks (1 warning, 1 inconclusive)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 55.56% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.
Title check	❓ Inconclusive	The PR title 'DICOM Text SR Writer Updates' is vague and generic, referring broadly to updates without specifying the actual nature or scope of changes.	Consider a more specific title that highlights the key fix, such as 'Fix DICOM Text SR Writer validation issues' or 'Add required DICOM SR elements and fix metadata encoding'.

✅ Passed checks (1 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.

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[sonarqubecloud]

Quality Gate passed

Issues
1 New issue
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

[coderabbitai]

🧹 Nitpick comments (1)

requirements-min.txt (1)

3-3: Consider tracking pkg_resources migration to importlib as separate technical debt work.

The codebase uses pkg_resources.working_set in monai/deploy/utils/importutil.py (4 functions: is_dist_editable(), dist_module_path(), is_module_installed(), dist_requires()). While the setuptools <81.0.0 pin correctly addresses the immediate deprecation issue, migrating to importlib.metadata would eliminate this version constraint and is a worthwhile long-term improvement. However, this refactoring is best tracked as separate work since it requires code changes beyond the scope of the requirements file.

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In `@requirements-min.txt` at line 3, Create a technical-debt task to migrate uses
of pkg_resources to importlib.metadata for the functions is_dist_editable(),
dist_module_path(), is_module_installed(), and dist_requires() in
monai/deploy/utils/importutil.py; the task should list the exact functions to
change, describe replacing pkg_resources.working_set calls with
importlib.metadata (or importlib_metadata for older Python), include tests to
preserve current behavior (editable/install detection and requirement parsing),
and note that once migration is complete the setuptools>=59.5.0,<81.0.0 pin in
requirements-min.txt can be revisited or removed.

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Nitpick comments:
In `@requirements-min.txt`:
- Line 3: Create a technical-debt task to migrate uses of pkg_resources to
importlib.metadata for the functions is_dist_editable(), dist_module_path(),
is_module_installed(), and dist_requires() in monai/deploy/utils/importutil.py;
the task should list the exact functions to change, describe replacing
pkg_resources.working_set calls with importlib.metadata (or importlib_metadata
for older Python), include tests to preserve current behavior (editable/install
detection and requirement parsing), and note that once migration is complete the
setuptools>=59.5.0,<81.0.0 pin in requirements-min.txt can be revisited or
removed.

[chezhia]

All minor changes, if we are enabling enhanced SR support in this PR, please make a not in the relevant docs too, so people are aware we support it.

[sonarqubecloud]

Quality Gate passed

Issues
1 New issue
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

[bluna301]

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