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… scatter, updated checkpoints, didn't crash
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…API change (plugin → worker) and Click's automatic underscore-to-hyphen conversion in option names (--metric_dir → --metric-dir).
Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## main #5 +/- ##
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- Coverage 68.73% 24.92% -43.82%
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Files 12 19 +7
Lines 1206 3796 +2590
Branches 110 546 +436
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+ Hits 829 946 +117
- Misses 350 2809 +2459
- Partials 27 41 +14 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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…HECK TEMPLATE T1!
…an.csv and vial LUT
phantomkit plot compare-plots accepts multiple phantomkit HTML output files (ADC, T1 mapping, T2 mapping), reads their embedded JSON, and produces a single self-contained HTML scatter plot with: - one uniquely coloured dataset per input file (filled circles) - reference values as red open circles (auto-loaded from template_data/) - toggle buttons to show/hide individual sessions - checkboxes to select which sessions contribute to the group mean - group mean displayed as adaptive-colour filled squares Phantom and template_data/ are auto-detected from embedded data and the installed package; --phantom / --template-dir override if needed. Session labels default to filename stems, falling back to meaningful ancestor directory names when all stems are the same (e.g. all "ADC.html"). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…om detection maps_ir and maps_te now accept a `phantom` kwarg and include it in the embedded JSON so compare-plots can auto-load the correct reference file. phantom_processor.py and visualization.py pass phantom_name through. compare-plots phantom auto-detection now falls back to scanning all available phantom subdirectories and selecting the one whose reference vials best overlap with the measured vials — handles HTML files generated before the phantom field was added, and multi-phantom installations. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Label derivation now finds the first path component that differs between input files by walking inward from the right and identifying the common suffix — surfaces the subject/session directory (e.g. P000009_testing) rather than a shared scan-type directory (native_contrasts_staging). Font sizes increased (axis titles 13→15px, ticks 12→14px, controls 11–12→14px); marker radii increased (session circles 6→9, reference open circles 8→11, group mean squares 8→11); chart height 440→500px. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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The primary contribution of this fork is the addition of a complete DWI preprocessing and QC pipeline integrated as a first-class stage alongside the existing native contrast workflow. This includes automatic DICOM series classification, phase-encoding correction mode selection (rpe_none, rpe_pair, rpe_all, rpe_split), FSL-based DWI preprocessing via dwifslpreproc, tensor fitting to produce ADC and FA maps, and rigid-body T1-to-DWI coregistration using FLIRT — all orchestrated through a new pipeline.py entry point that runs all three stages from a single command. Several refinements were also made to the existing codebase: the ANTs registration check threshold was updated, vial masks are now transformed with nearest-neighbour interpolation to preserve binary values, and the ADC scatter plot was redesigned with open-circle reference markers plotted over the measured values for clearer visual comparison against SPIRIT reference data.