v1.0.0: two-layer fNIRS toolbox - group analysis, DOT, aux signals, first-party DSP, and visualization - #7

Merged

AdrianCurtin merged 72 commits into

Jul 12, 2026

Commits on Jan 24, 2026

Refactor plotting helpers and add modular utilities
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7bb5097
Refactor plotting functions to use flexible argument parsing
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cbc2e25
Add unit tests for synthetic data processing
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7fbbdfe

Commits on Jan 30, 2026

Rename gui module to GUI for consistency
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bb2d606

Commits on Feb 6, 2026

Add Experiment API, connectivity tools, and tests
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cf7bc64

Commits on Feb 10, 2026

Fix white mode styling in report figures - use full package path
AdrianCurtin
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06842d2

Commits on Feb 12, 2026

Add connectivity analysis and plotting modules
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65edc2e
Add connectivity analysis and plotting modules
AdrianCurtin
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1af3fc6

Commits on Feb 13, 2026

Refactor HRF, AR-IRLS GPU support, add tests
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89f0513
Add GLM diagnostics and pipeline improvements
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d991423
Add GUI plotting helpers and baseline option
AdrianCurtin
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75e051e
Fix unpack output and pass flags to processing
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566954b
Add graph metrics, HB-ICA, and pf2 updates
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60ca283
Add literature references; refactor calcCBSI
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8bfb13e
Fix scanFiles init and canonicalize rootPath
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d1ccef2
Update quickSetup.m
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b085a03

Commits on Feb 19, 2026

Preserve select() order and add bar error color
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87e3261

Commits on Feb 20, 2026

Add FFT-based CWT and batch wcoherence
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2c3202b
Add neural efficiency plots; enable parfor
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d86d651
Add NE outputs and per-point neTable; fix INI writer
AdrianCurtin
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e375812

Commits on Apr 9, 2026

Add partialCorr and mutualInfo coupling methods
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eba421c
Fix resample, import, QC, INI, ROI signature
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bad1874
Add VLines option to plotTemporal
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45e6db6
Resolve probe layout using MNI/Pos2D, fallback grid
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d99c8d1
Add stable signal filters and qualify lpf call
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625e2fc
Refactor Takizawa QC into pf2.qc.takizawa
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d23b15a
Standardize pf2 warnings and add suppression API
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afca8ad

Commits on Apr 10, 2026

Add statWindow, fromConfig, and stats utilities
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72427e9
Add caching, hierarchicalAverageMulti, and tests
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8b59978
Refactor group preprocessing and parallel grand-avg
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39fabc5
Parallel resampling and metadata collection
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402fbb8
Optimize segment table builder; parallel import
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69e9fdc
Add per-segment pp cache, optimize resample & GUI
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178d1d3
Plotting tweaks: styles, vline visibility, and warnings
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dfb1d00
Fix warning state restore and query saving
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5ab6b4d
Use style for legend and add Colors option
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55e764f
Improve processing, resampling and optode handling
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2de7def
Dark-mode colors and improved timeline labels
AdrianCurtin
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5a4ba2d

Commits on Apr 11, 2026

Enhance plotting: escape TeX, TightLayout, VLines
AdrianCurtin
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fb2f5cf

Commits on Apr 13, 2026

Fix up grand average resampling and add padding support
AdrianCurtin
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4908ec1

Commits on Apr 17, 2026

Commits on May 1, 2026

Add stat projection wrappers & transparent overlay
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3cd7f51
INI: split only on first '=' and recover structs
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17c4d5e
Enhance ChannelCheck UI, QC, and multi-file support
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3ad4b93
Add methods editor, seeds, reset & tests
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0f81d35
Support fNIR3000 probe and RGB vline options
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57ebccb

Commits on May 2, 2026

Robust probe detection and add LD device cfg
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6b5930b

Commits on May 12, 2026

Remove redundant fclose calls
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bd07428
Update barchart_infogroup.m
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bd2a0dd

Commits on Jun 5, 2026

Headless QC/topo, Octave checks, pipeline tweaks
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48d6087
Add Filename option and duplicate-ID diagnostics
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d37659f
Block averaging, QC tweaks, and WaveLab fixes
AdrianCurtin
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7c1549c

Commits on Jun 17, 2026

Add marker dictionary subsystem and headless channel-check gating
AdrianCurtin
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444da37

Commits on Jun 18, 2026

Add support for artinis3
AdrianCurtin
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b9623fc
Fixes for addFunction and plotIntraROI
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bad957a

Commits on Jun 22, 2026

Commits on Jun 23, 2026

Commits on Jun 24, 2026

Add typed auxiliary signals, high-quality 3D rendering, and export refinements
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d5e3e9d

Commits on Jun 25, 2026

Add diffuse optical tomography, cross-brain PPI, and tidy-table import
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feda591
Adjust docs
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3426818
Add first-party signal-processing functions (butter, fir1, sgolay, windows)
AdrianCurtin
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c345006

Commits on Jun 28, 2026

Add parcelation projectsion and other fixes
AdrianCurtin
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728bb36

Commits on Jul 12, 2026

Add public ProcessingContext and arg validation
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c04b709
Improve plot theming and bar alignment
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1d30ed2