Single workflow

[arkiev]

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.

[wiz-788c0877ba]

Wiz Scan Summary

Scanner	Findings
Vulnerabilities	-
Sensitive Data	-
Secrets	-
IaC Misconfigurations	-
SAST Findings	3
Software Management Findings	-
Total	3

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[codecov-commenter]

Codecov Report

❌ Patch coverage is 4.87122% with 1699 lines in your changes missing coverage. Please review.
✅ Project coverage is 29.51%. Comparing base (3216caf) to head (25b5f91).

Files with missing lines	Patch %	Lines
phantomkit/dwi_processing.py	0.00%	852 Missing ⚠️
phantomkit/phantom_processor.py	0.00%	424 Missing ⚠️
phantomkit/pipeline.py	0.00%	272 Missing ⚠️
phantomkit/plotting/vial_intensity.py	39.31%	61 Missing and 10 partials ⚠️
phantomkit/cli.py	19.11%	55 Missing ⚠️
phantomkit/plotting/visualization.py	4.16%	23 Missing ⚠️
phantomkit/plotting/maps_te.py	89.47%	2 Missing ⚠️

❌ Your patch status has failed because the patch coverage (4.87%) is below the target coverage (80.00%). You can increase the patch coverage or adjust the target coverage.

Additional details and impacted files

@@             Coverage Diff             @@
##             main       #5       +/-   ##
===========================================
- Coverage   68.73%   29.51%   -39.22%     
===========================================
  Files          12       15        +3     
  Lines        1206     2937     +1731     
  Branches      110      404      +294     
===========================================
+ Hits          829      867       +38     
- Misses        350     2034     +1684     
- Partials       27       36        +9     

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