fix: guard division by zero in DICOMReader._get_affine for single-slice volumes (Fixes #8925)

[rtmalikian]

Fixes #8925

Problem

In DICOMReader._get_affine, when processing single-slice 3D DICOM segmentation volumes (where n == 1), the code computes:

k1, k2, k3 = (t1n - sx) / (n - 1), (t2n - sy) / (n - 1), (t3n - sz) / (n - 1)

Since n - 1 = 0, this raises a ZeroDivisionError. The issue occurs in the segmentation code path (_get_seg_data, line 898) where lastImagePositionPatient is always set from the frame metadata regardless of the number of frames. For a single-frame segmentation, the first and last positions are identical, producing 0 / 0.

Solution

Added an n > 1 guard before computing the z-axis direction vector from lastImagePositionPatient. For single-slice volumes, the z-axis column of the affine remains as the identity [0, 0, 1, 0] from np.eye(4), which is a correct default — there is no meaningful z-direction for a single slice.

Verification

import numpy as np

# Single-slice scenario (n=1) — previously caused ZeroDivisionError
n = 1
sx, sy, sz = 0.0, 0.0, 0.0
t1n, t2n, t3n = 0.0, 0.0, 0.0

affine = np.eye(4)
if n > 1:
    affine[0, 2] = (t1n - sx) / (n - 1)
    affine[1, 2] = (t2n - sy) / (n - 1)
    affine[2, 2] = (t3n - sz) / (n - 1)

print(f'z-axis column: {affine[:, 2]}')  # [0, 0, 1, 0] — identity ✓

# Normal multi-slice case (n=10) — still works correctly
n = 10
t1n, t2n, t3n = 0.0, 0.0, 45.0
affine2 = np.eye(4)
if n > 1:
    affine2[0, 2] = (t1n - sx) / (n - 1)
    affine2[1, 2] = (t2n - sy) / (n - 1)
    affine2[2, 2] = (t3n - sz) / (n - 1)

print(f'z-axis column: {affine2[:, 2]}')  # [0, 0, 5.0, 0] — correct direction ✓

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About the Author: Raphael Malikian — Clinical AI Solutions Architect. I specialise in building and fixing AI/ML systems for healthcare, including vector databases, RAG pipelines, and clinical NLP. If you need help with your project or think I can add value to your organisation, feel free to reach out — I'd love to connect.

📧 rtmalikian@gmail.com
🔗 GitHub: https://github.com/rtmalikian
🔗 LinkedIn: http://www.linkedin.com/in/raphael-t-malikian-mbbs-bsc-hons-71075436a

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Disclosure: This code was developed with assistance from mimo-2.5-pro (Xiaomi) via Hermes Agent (Nous Research). All changes were reviewed, tested against the actual codebase, and verified for correctness.

Changelog

Date	Change	Author
2026-06-18	Initial fix: guard division by zero for single-slice DICOM volumes	rtmalikian
2026-06-18	Added DCO sign-off to commit	rtmalikian
2026-06-18	Updated PR documentation with changelog	rtmalikian

Files Changed

• monai/data/image_reader.py — Added n > 1 guard before computing affine offsets for multi-slice volumes in DICOMReader._get_affine()

Verification

• ✅ Single-slice 3D DICOM volumes no longer trigger ZeroDivisionError
• ✅ Multi-slice volumes continue to compute affine correctly
• ✅ DCO sign-off present on all commits

[coderabbitai]

📝 Walkthrough

Walkthrough

In PydicomReader._get_affine, the three affine z-axis component assignments (affine[0,2], affine[1,2], affine[2,2]) derived from lastImagePositionPatient are now wrapped in an if n > 1: guard, preventing division by zero when only a single image (n == 1) is processed.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~2 minutes

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title clearly identifies the specific fix (division by zero guard) and the affected component (DICOMReader._get_affine) with the issue reference.
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Description check	✅ Passed	Pull request provides comprehensive description with problem statement, solution, verification code, and changelog.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

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