fix: update stale "c3d command" references to "picsl-c3d"#94

Merged

tomboulier merged 7 commits into

codex/picsl-c3d-staplefrom

copilot/sub-pr-93

Mar 24, 2026

Contributor

Copilot AI commented Mar 24, 2026 •

edited

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Log messages, raised error strings, and docstrings in staple_segmenter.py still referred to "c3d command" after the underlying implementation was switched to picsl_c3d, making failure diagnosis misleading.

Changes

Log messages (run_c3d_command): "Running c3d command" → "Running picsl-c3d", success/failure strings updated to match
Raised ValueErrors: option/input-path guards now say "… for picsl-c3d"
Docstrings: method summary, options param description, and Raises entries updated across run_c3d_command and its callers
STAPLE log: "… with c3d STAPLE algorithm" → "… with picsl-c3d STAPLE algorithm"

This also incorporates follow-up review feedback to simplify redundant "picsl-c3d Convert3D" wording to "picsl-c3d" throughout the updated text.

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          Initial plan

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build: replace system c3d dependency with picsl-c3d #93

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Copilot started work on behalf of tomboulier

March 24, 2026 21:52

Copilot AI and others added 2 commits

March 24, 2026 21:54


          fix: update log and error messages to reference picsl-c3d Convert3D

0e0d678

Co-authored-by: tomboulier <14161960+tomboulier@users.noreply.github.com>
Agent-Logs-Url: https://github.com/tomboulier/oxytcmri-dti-processing/sessions/3a05aa71-12b5-4555-8c93-5eaf8e8575e9


          fix: update remaining c3d STAPLE log message to picsl-c3d Convert3D

01d0245

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Copilot AI changed the title ~~[WIP] [WIP] Address feedback on replacing system c3d dependency with picsl-c3d~~ fix: update stale "c3d command" references to "picsl-c3d Convert3D"

Copilot AI requested a review from tomboulier

March 24, 2026 21:56

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March 24, 2026 21:56

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"picsl-c3d Convert3D" seems a bit redundant, since "c3d" means "Convert3D". You can simplify all these occurences, and I would say it's all good then

oxytcmri/interface/mri/staple_segmenter.py Outdated


          Update oxytcmri/interface/mri/staple_segmenter.py

2d53986

Owner

tomboulier commented Mar 24, 2026

"picsl-c3d Convert3D" seems a bit redundant, since "c3d" means "Convert3D". You can simplify all these occurences, and I would say it's all good then

@copilot could you make those changes in your PR please?

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Copilot AI commented Mar 24, 2026

@tomboulier The model claude-sonnet-4.6 is not available for your account. This can happen if the model was disabled by your organization's policy or if your Copilot plan doesn't include access to it.

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Copilot AI commented Mar 24, 2026

@tomboulier The model claude-sonnet-4.6 is not available for your account. This can happen if the model was disabled by your organization's policy or if your Copilot plan doesn't include access to it.

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Copilot AI commented Mar 24, 2026

@tomboulier The model claude-sonnet-4.6 is not available for your account. This can happen if the model was disabled by your organization's policy or if your Copilot plan doesn't include access to it.

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If you want to contact GitHub about this error, please mention the following identifier so they can better serve you: f02ab19f-e5d9-4ead-904d-f2c23ddcd671

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Copilot AI commented Mar 24, 2026

@tomboulier The model claude-sonnet-4.6 is not available for your account. This can happen if the model was disabled by your organization's policy or if your Copilot plan doesn't include access to it.

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Copilot AI commented Mar 24, 2026

@tomboulier The model claude-sonnet-4.6 is not available for your account. This can happen if the model was disabled by your organization's policy or if your Copilot plan doesn't include access to it.

You can try again without specifying a model (just @copilot) to use the default, or choose a different model from the model picker.

If you want to contact GitHub about this error, please mention the following identifier so they can better serve you: f02ab19f-e5d9-4ead-904d-f2c23ddcd671

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Copilot AI commented Mar 24, 2026

@tomboulier The model claude-sonnet-4.6 is not available for your account. This can happen if the model was disabled by your organization's policy or if your Copilot plan doesn't include access to it.

You can try again without specifying a model (just @copilot) to use the default, or choose a different model from the model picker.

If you want to contact GitHub about this error, please mention the following identifier so they can better serve you: f02ab19f-e5d9-4ead-904d-f2c23ddcd671

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tomboulier commented Mar 24, 2026

@copilot could you make the changes asked in my review?

Copilot started work on behalf of tomboulier

March 24, 2026 22:07


          fix: simplify redundant picsl-c3d Convert3D wording

cb8f1e3

Co-authored-by: tomboulier <14161960+tomboulier@users.noreply.github.com>
Agent-Logs-Url: https://github.com/tomboulier/oxytcmri-dti-processing/sessions/f4f6fb26-bca3-4f32-afc2-b01ebec4c101

Contributor Author

Copilot AI commented Mar 24, 2026 •

edited

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"picsl-c3d Convert3D" seems a bit redundant, since "c3d" means "Convert3D". You can simplify all these occurences, and I would say it's all good then

Done in cb8f1e3: all remaining "picsl-c3d Convert3D" occurrences were simplified to "picsl-c3d" in logs, error messages, and docstrings.

"picsl-c3d Convert3D" seems a bit redundant, since "c3d" means "Convert3D". You can simplify all these occurences, and I would say it's all good then

@copilot could you make tho...

Applied in cb8f1e3: simplified all redundant "picsl-c3d Convert3D" wording to "picsl-c3d" across this PR’s touched code.

@copilot could you make the changes asked in my review?

Completed in cb8f1e3. The requested wording updates are now in the PR.

Copilot AI changed the title ~~fix: update stale "c3d command" references to "picsl-c3d Convert3D"~~ fix: update stale "c3d command" references to "picsl-c3d"

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March 24, 2026 22:11

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March 24, 2026 22:11

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March 24, 2026 22:14

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Pull request overview

Updates staple_segmenter.py user-facing text to consistently refer to the underlying tool as picsl-c3d, avoiding misleading “c3d command” wording during logs, exceptions, and docstrings.

Changes:

Updated log messages around run_c3d_command execution to say “picsl-c3d”.
Updated ValueError and RuntimeError messages to say “picsl-c3d”.
Updated docstrings/Raises entries and STAPLE-related log wording to “picsl-c3d”.

oxytcmri/interface/mri/staple_segmenter.py

Comment on lines 106 to +110

    
                          If the segmentations list is empty

                      RuntimeError

                          If the c3d command fails

                          If the picsl-c3d fails

                      """

                      logger.info(f"Merging {len(segmentations)} segmentations with c3d STAPLE algorithm")

                      logger.info(f"Merging {len(segmentations)} segmentations with picsl-c3d STAPLE algorithm")

Copilot AI Mar 24, 2026

In this merge() docstring, the process flow still says it processes files with the "c3d STAPLE algorithm" (earlier in the same docstring), but this PR updates user-facing wording to "picsl-c3d". Consider updating that remaining step text so the docstring is internally consistent and matches the logs/errors.

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oxytcmri/interface/mri/staple_segmenter.py Outdated

oxytcmri/interface/mri/staple_segmenter.py Outdated

tomboulier and others added 2 commits

March 24, 2026 23:18


          Update oxytcmri/interface/mri/staple_segmenter.py

92265f9

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>


          Update oxytcmri/interface/mri/staple_segmenter.py

e3a95bc

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

sonarqubecloud Bot commented Mar 24, 2026

Quality Gate passed

Issues
0 New issues
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

tomboulier merged commit 460337c into codex/picsl-c3d-staple

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tomboulier added a commit that referenced this pull request


          build: replace system c3d dependency with picsl-c3d (#93)

fc7fab4

* build: replace system c3d dependency with picsl-c3d

* fix: update stale "c3d command" references to "picsl-c3d" (#94)

* Initial plan

* fix: update log and error messages to reference picsl-c3d Convert3D

Co-authored-by: tomboulier <14161960+tomboulier@users.noreply.github.com>
Agent-Logs-Url: https://github.com/tomboulier/oxytcmri-dti-processing/sessions/3a05aa71-12b5-4555-8c93-5eaf8e8575e9

* fix: update remaining c3d STAPLE log message to picsl-c3d Convert3D

Co-authored-by: tomboulier <14161960+tomboulier@users.noreply.github.com>
Agent-Logs-Url: https://github.com/tomboulier/oxytcmri-dti-processing/sessions/3a05aa71-12b5-4555-8c93-5eaf8e8575e9

* Update oxytcmri/interface/mri/staple_segmenter.py

* fix: simplify redundant picsl-c3d Convert3D wording

Co-authored-by: tomboulier <14161960+tomboulier@users.noreply.github.com>
Agent-Logs-Url: https://github.com/tomboulier/oxytcmri-dti-processing/sessions/f4f6fb26-bca3-4f32-afc2-b01ebec4c101

* Update oxytcmri/interface/mri/staple_segmenter.py

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* Update oxytcmri/interface/mri/staple_segmenter.py

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: tomboulier <14161960+tomboulier@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

---------

Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

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