[hjmjohnson]

DCMTKSeriesFileNames now throws when slice positions repeat, matching GDCMSeriesFileNames, and gains FailOnAmbiguousOrdering and DidUseAmbiguousOrdering. GDCM's DidUseAmbiguousOrdering no longer resets when a later series orders cleanly.

A series with repeated positions (multi-volume DWI, for example) has no geometric order and is not one 3D volume. DCMTK sorted it by position anyway and silently returned a position-major interleave, which mis-paired gradients in BRAINSTools DWIConvert.

Related: #6463, #6464, #6466, #6468

Behavior

• GetFileNames() and GetInputFileNames() throw for a series whose positions along the slice normal repeat (tolerance 1e-3 mm). GetSeriesUIDs() still enumerates without throwing.
• With FailOnAmbiguousOrdering off, the series comes back in InstanceNumber order when every slice has one and they are unique, else in file name order. This is the GDCM fallback, and also the DCMTK order in ITK 5.4.
• DidUseAmbiguousOrdering is true when any series returned since the last directory parse was ambiguous. GDCM assigned it per series, so ordering a later, well-ordered series cleared it; it is now OR-ed and cleared only on a new parse.
• Series without orientation or position keep the existing InstanceNumber, then file name, fallback and do not throw.

Local testing

Linux, GCC 13.3, Release. A minimal build with ITKIODCMTK, IOTransformDCMTK, and ITKIOGDCM: all 36 DCMTKSeriesFileNames*, GDCMSeriesFileNamesContract*, and GDCMSeriesDirection* GTests pass.

New tests:

• DCMTKSeriesFileNamesParity.RepeatedPositionsThrowByDefault
• DCMTKSeriesFileNamesParity.RepeatedPositionsFallBackWhenAllowed
• DCMTKSeriesFileNamesParity.AmbiguityFlagIsSticky
• DCMTKSeriesFileNamesParity.MissingInstanceNumberFallsBackToFileNames
• GDCMSeriesFileNamesContract.AmbiguityFlagIsSticky (fails on the unfixed GDCM code, passes with the fix)

Downstream: BRAINSTools DWIConvert, built against this branch, passes all 52 of its tests (GE, Siemens, Philips, and Hitachi DWI series, several with repeated positions).

pre-commit run --all-files passes.

AI assistance

Claude Code researched how dcm2niix, dicm2nii, MRtrix3, and GDCM order DWI series, wrote the change and tests, and ran the builds above. I directed the design (throw by default, sticky flag) and reviewed the change.

🤖 Generated with Claude Code

[greptile-apps]

Confidence Score: 5/5

[Medium impact] The PR appears safe to merge; no actionable new issues remain.

Summary

DCMTKSeriesFileNames now rejects repeated slice positions by default and offers an explicit fallback.

• DCMTK series requests reject repeated slice positions unless callers opt into a fallback.
• GDCM keeps its ambiguity flag set across later series requests.

_{Reviews (2) · Last reviewed commit: "BUG: Keep GDCMSeriesFileNames DidUseAmbi..." · Reviewed by Greptile}

[hjmjohnson]

@greptileai review