Select input bold node

[Gab-D-G]

Summary by CodeRabbit

• Bug Fixes

  • Fixed power spectral density calculation to use updated time-series data, resulting in improved frequency resolution and accuracy of spectral analysis results.

• Refactor

  • Optimized internal preprocessing workflow configuration for improved maintainability.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 1aa619d9-69c6-4ae6-ac74-f5a0cd3baf94

📥 Commits

Reviewing files that changed from the base of the PR and between a8b3c39 and 8afa7b4.

📒 Files selected for processing (4)

• rabies/analysis_pkg/diagnosis_pkg/diagnosis_functions.py
• rabies/confound_correction_pkg/main_wf.py
• rabies/preprocess_pkg/bold_main_wf.py
• rabies/preprocess_pkg/main_wf.py

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📝 Walkthrough

Walkthrough

This PR refactors BOLD input selection across preprocessing workflows by standardizing field names to bold_file, consolidating dual selection nodes into a single select_input_bold_node, and updating all downstream references. A separate bug fix corrects PSD sample count calculation in diagnosis.

Changes

BOLD Input Selection and Field Naming Refactoring

Layer / File(s)	Summary
Standardize BOLD field naming in bold_main_wf rabies/preprocess_pkg/bold_main_wf.py	The BOLD input field is renamed from bold to bold_file across the workflow: inputnode interface, despiking connections, inho-correction source, motion estimation wiring, mask resampling, and native/common-space transform references. A docstring formatting adjustment is also included.
Consolidate BOLD selection in main_wf rabies/preprocess_pkg/main_wf.py	Separate format_bold_node and input_bold_node are replaced with a single select_input_bold_node using match_iterables. The unused pathlib import is removed, input_bold is removed from outputnode, and all downstream nodes (bold_main_wf, bold_inho_cor_diagnosis, inho_cor_bold_main_wf, QC/datasink nodes) are rewired to reference the consolidated node.
Update confound correction workflow references rabies/confound_correction_pkg/main_wf.py	The preprocessing workflow mapping is updated to reference the new main_wf.select_input_bold node path instead of the removed main_wf.input_bold when matching BOLD split outputs.
Fix PSD sample count calculation in diagnosis rabies/analysis_pkg/diagnosis_pkg/diagnosis_functions.py	The plot_freqs function now calculates sample count N from the censoring-filled timeseries_ instead of the original timeseries, ensuring correct nperseg selection for Welch PSD computation.

Estimated Code Review Effort

🎯 2 (Simple) | ⏱️ ~12 minutes

Poem

🐰 A rabbit hops through workflows new,
Bold files get their names made true,
Selection nodes consolidated,
PSD bugs eliminated,
Clean pipelines in every view! 🎯

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 50.00% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title 'Select input bold node' clearly and specifically describes the main refactoring change across the PR: replacing separate formatting nodes with a single select_input_bold_node for BOLD input handling in the preprocessing workflow.
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.

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✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch select_input_bold_node

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