AdrianCurtin · Oct 14, 2026 · Oct 14, 2026 · Oct 15, 2026 · Oct 15, 2026 · Oct 15, 2026
diff --git a/+exploreFNIRS/+core/Experiment.m b/+exploreFNIRS/+core/Experiment.m
@@ -759,7 +759,7 @@
 
             % Build channel labels as cell array
             if ~isempty(channels)
-                chLabels = cellstr(num2str(channels(:)));
+                chLabels = pf2_base.channelLabels(channels);
             else
                 chLabels = {};
             end
@@ -800,7 +800,7 @@
 
             % Build channel labels as cell array
             if ~isempty(channels)
-                chLabels = cellstr(num2str(channels(:)));
+                chLabels = pf2_base.channelLabels(channels);
             else
                 chLabels = {};
             end

diff --git a/+exploreFNIRS/+export/mergeGbyTablesLong.m b/+exploreFNIRS/+export/mergeGbyTablesLong.m
@@ -17,7 +17,8 @@
 %   times          - Time points to include (default: [] = all)
 %   exportAux      - Include auxiliary data (default: false)
 %   exportROI      - Include ROI-averaged data (default: false)
-%   channelLabels  - Cell array of channel name strings (default: numbers)
+%   channelLabels  - Cell array of channel name strings (default: zero-padded
+%                    numbers from pf2_base.channelLabels)
 %
 % Outputs:
 %   mergedTables   - Combined table in long format with columns:
@@ -53,7 +54,7 @@
 end
 
 if(nargin<7)
-    channelLabels=cellstr(num2str(channelIndexes));
+    channelLabels=pf2_base.channelLabels(channelIndexes);
 else
     channelLabels=cellstr(channelLabels);
 end
@@ -117,7 +118,7 @@
     if(emptyChannelFlag&&exportFNIR)
         numCh=size(curBarGA.HbO.data,2);
         channelIndexes=1:numCh;
-        channelLabels=cellstr(num2str(channelIndexes(:)));
+        channelLabels=pf2_base.channelLabels(channelIndexes);
     elseif(exportFNIR)
        numCh=length(channelIndexes);
     else
@@ -190,7 +191,7 @@
         end
 
         if(exportAux&&isfield(curBarGA,'Aux'))
-             curAuxFields=fields(curBarGA.Aux);
+             curAuxFields=fieldnames(curBarGA.Aux);
              for aux=1:length(curAuxFields)
                 curAuxName=curAuxFields{aux};
                 curAux= curBarGA.Aux.(curAuxName);

diff --git a/+exploreFNIRS/+export/mergeGbyTablesWide.m b/+exploreFNIRS/+export/mergeGbyTablesWide.m
@@ -17,7 +17,8 @@
 %   times        - Time points to include (default: [] = all)
 %   exportAux    - Include auxiliary data (default: false)
 %   exportROI    - Include ROI-averaged data (default: false)
-%   optodeNames  - Cell array of optode/channel names (default: numbers)
+%   optodeNames  - Cell array of optode/channel names (default: zero-padded
+%                  numbers from pf2_base.channelLabels)
 %
 % Outputs:
 %   mergedTables - Combined table in wide format with columns:
@@ -53,7 +54,7 @@
 end
 
 if(nargin<7)
-    optodeNames=num2str(channels);
+    optodeNames=pf2_base.channelLabels(channels);
 else
     optodeNames=cellstr(optodeNames);
 end
@@ -106,7 +107,7 @@
     if(emptyChannelFlag&&exportFNIR)
         numCh=size(curBarGA.HbO.data,2);
         channels=1:numCh;
-        optodeNames=cellstr(num2str(channels(:)));
+        optodeNames=pf2_base.channelLabels(channels);
     elseif(exportFNIR)
        numCh=length(channels); 
     else
@@ -185,7 +186,7 @@
      if(exportAux&&isfield(curBarGA,'Aux'))
          %warning('To-do add AUX fields to export wide'); % trouble is syncing up timing between each
 
-         curAuxFields=fields(curBarGA.Aux);
+         curAuxFields=fieldnames(curBarGA.Aux);
          for aux=1:length(curAuxFields)
             curAuxName=curAuxFields{aux};
             curAux= curBarGA.Aux.(curAuxName);

diff --git a/+exploreFNIRS/+plot/temporal.m b/+exploreFNIRS/+plot/temporal.m
@@ -366,7 +366,7 @@
 
                                else
                                      dataTime=data2plot.(bioM).time;
-                                     varNames=fields(data2plot.(bioM));
+                                     varNames=fieldnames(data2plot.(bioM));
                                      timeIdx=ismember(varNames,'time');
                                      firstVar=find(~timeIdx);
                                      data2plot.(bioM)=data2plot.(bioM).(varNames{firstVar(1)});

diff --git a/+pf2/+data/+aux/accelFeatures.m b/+pf2/+data/+aux/accelFeatures.m
@@ -1,4 +1,4 @@
-function [feat, info] = accelFeatures(x, fs, opts)
+function [feat, info] = accelFeatures(x, fs, varargin)
 % ACCELFEATURES Derive motion features from a multi-axis accelerometer signal
 %
 % Computes summary motion features from accelerometer/IMU axes: the vector
@@ -36,11 +36,14 @@
 %
 % See also: pf2_base.auxSignalType, pf2.data.auxOnGrid
 
-arguments
-    x {mustBeNumeric}
-    fs {mustBeNumeric, mustBeScalarOrEmpty, mustBePositive}
-    opts.RemoveGravity (1,1) logical = true
-end
+% Inputs are parsed with pf2_base.args rather than an arguments block so
+% the function also runs under GNU Octave. Spec rows are {name, default,
+% size, class, validators}.
+x = pf2_base.args.check(x, '', '', {@mustBeNumeric}, 'Invalid argument at position 1.');
+fs = pf2_base.args.check(fs, '', '', {@mustBeNumeric, @mustBeScalarOrEmpty, @mustBePositive}, 'Invalid argument at position 2.');
+opts = pf2_base.args.parse('accelFeatures', varargin, {}, {
+    'RemoveGravity', (true), '1,1', 'logical', {}
+    });
 removeGravity = opts.RemoveGravity;
 
 if isrow(x)

diff --git a/+pf2/+data/+aux/addFeature.m b/+pf2/+data/+aux/addFeature.m
@@ -1,4 +1,4 @@
-function data = addFeature(data, name, values, opts)
+function data = addFeature(data, name, values, varargin)
 % ADDFEATURE Store a derived signal as a typed auxiliary feature
 %
 % Writes a derived feature (e.g. an HR series from heartRateFrom, RVT from
@@ -38,14 +38,17 @@
 % See also: pf2_base.normalizeAux, pf2.data.aux.heartRateFrom,
 %           pf2.data.aux.respFeatures, pf2.export.asSNIRF
 
-arguments
-    data {mustBeA(data, 'struct')}
-    name {mustBeText}
-    values {mustBeNumeric}
-    opts.Time {mustBeNumeric} = []
-    opts.Unit = ''
-    opts.VarNames = {}
-end
+% Inputs are parsed with pf2_base.args rather than an arguments block so
+% the function also runs under GNU Octave. Spec rows are {name, default,
+% size, class, validators}.
+data = pf2_base.args.check(data, '', '', {@(v) mustBeA(v, 'struct')}, 'Invalid argument at position 1.');
+name = pf2_base.args.check(name, '', '', {@mustBeText}, 'Invalid argument at position 2.');
+values = pf2_base.args.check(values, '', '', {@mustBeNumeric}, 'Invalid argument at position 3.');
+opts = pf2_base.args.parse('addFeature', varargin, {}, {
+    'Time',     ([]), '', '', {@mustBeNumeric}
+    'Unit',     (''), '', '', {}
+    'VarNames', ({}), '', '', {}
+    });
 name = matlab.lang.makeValidName(char(string(name)));
 
 t = opts.Time;

diff --git a/+pf2/+data/+aux/edaDecompose.m b/+pf2/+data/+aux/edaDecompose.m
@@ -1,4 +1,4 @@
-function [tonic, phasic, info] = edaDecompose(x, fs, opts)
+function [tonic, phasic, info] = edaDecompose(x, fs, varargin)
 % EDADECOMPOSE Split electrodermal activity into tonic and phasic components
 %
 % Decomposes a galvanic skin response / electrodermal activity (GSR/EDA)
@@ -40,11 +40,14 @@
 %
 % See also: pf2_base.auxSignalType, pf2.data.aux.heartRateFrom
 
-arguments
-    x {mustBeNumeric}
-    fs {mustBeNumeric, mustBeScalarOrEmpty, mustBePositive}
-    opts.TonicCutoff {mustBeNumeric, mustBeScalarOrEmpty, mustBePositive} = 0.05
-end
+% Inputs are parsed with pf2_base.args rather than an arguments block so
+% the function also runs under GNU Octave. Spec rows are {name, default,
+% size, class, validators}.
+x = pf2_base.args.check(x, '', '', {@mustBeNumeric}, 'Invalid argument at position 1.');
+fs = pf2_base.args.check(fs, '', '', {@mustBeNumeric, @mustBeScalarOrEmpty, @mustBePositive}, 'Invalid argument at position 2.');
+opts = pf2_base.args.parse('edaDecompose', varargin, {}, {
+    'TonicCutoff', (0.05), '', '', {@mustBeNumeric, @mustBeScalarOrEmpty, @mustBePositive}
+    });
 cutoff = opts.TonicCutoff;
 
 x = x(:);

diff --git a/+pf2/+data/+aux/eegBandPower.m b/+pf2/+data/+aux/eegBandPower.m
@@ -1,4 +1,4 @@
-function [bandPower, info] = eegBandPower(x, fs, opts)
+function [bandPower, info] = eegBandPower(x, fs, varargin)
 % EEGBANDPOWER Extract canonical EEG band-power feature series
 %
 % Converts a raw EEG waveform (one or more channels) into per-band power
@@ -46,12 +46,15 @@
 %
 % See also: pf2_base.auxSignalType, pf2.data.auxOnGrid
 
-arguments
-    x {mustBeNumeric}
-    fs {mustBeNumeric, mustBeScalarOrEmpty, mustBePositive}
-    opts.Bands = []
-    opts.SmoothWin {mustBeNumeric, mustBeScalarOrEmpty, mustBePositive} = 1
-end
+% Inputs are parsed with pf2_base.args rather than an arguments block so
+% the function also runs under GNU Octave. Spec rows are {name, default,
+% size, class, validators}.
+x = pf2_base.args.check(x, '', '', {@mustBeNumeric}, 'Invalid argument at position 1.');
+fs = pf2_base.args.check(fs, '', '', {@mustBeNumeric, @mustBeScalarOrEmpty, @mustBePositive}, 'Invalid argument at position 2.');
+opts = pf2_base.args.parse('eegBandPower', varargin, {}, {
+    'Bands',     ([]), '', '', {}
+    'SmoothWin', (1), '', '', {@mustBeNumeric, @mustBeScalarOrEmpty, @mustBePositive}
+    });
 bands = opts.Bands;
 smoothWin = opts.SmoothWin;
 

diff --git a/+pf2/+data/+aux/heartRateFrom.m b/+pf2/+data/+aux/heartRateFrom.m
@@ -1,4 +1,4 @@
-function [hr, info] = heartRateFrom(x, fs, opts)
+function [hr, info] = heartRateFrom(x, fs, varargin)
 % HEARTRATEFROM Derive a heart-rate (bpm) series from a PPG or EKG waveform
 %
 % Detects cardiac beats in a pulsatile waveform (photoplethysmography or
@@ -47,13 +47,16 @@
 %
 % See also: pf2_base.auxSignalType, pf2.data.auxOnGrid, pf2.data.aux.edaDecompose
 
-arguments
-    x {mustBeNumeric}
-    fs {mustBeNumeric, mustBeScalarOrEmpty, mustBePositive}
-    opts.Band {mustBeNumeric} = [0.5 5]
-    opts.MinBPM {mustBeNumeric, mustBeScalarOrEmpty, mustBePositive} = 30
-    opts.MaxBPM {mustBeNumeric, mustBeScalarOrEmpty, mustBePositive} = 220
-end
+% Inputs are parsed with pf2_base.args rather than an arguments block so
+% the function also runs under GNU Octave. Spec rows are {name, default,
+% size, class, validators}.
+x = pf2_base.args.check(x, '', '', {@mustBeNumeric}, 'Invalid argument at position 1.');
+fs = pf2_base.args.check(fs, '', '', {@mustBeNumeric, @mustBeScalarOrEmpty, @mustBePositive}, 'Invalid argument at position 2.');
+opts = pf2_base.args.parse('heartRateFrom', varargin, {}, {
+    'Band',   ([0.5 5]), '', '', {@mustBeNumeric}
+    'MinBPM', (30), '', '', {@mustBeNumeric, @mustBeScalarOrEmpty, @mustBePositive}
+    'MaxBPM', (220), '', '', {@mustBeNumeric, @mustBeScalarOrEmpty, @mustBePositive}
+    });
 band = opts.Band;
 maxBPM = opts.MaxBPM;
 

diff --git a/+pf2/+data/+aux/hrvFeatures.m b/+pf2/+data/+aux/hrvFeatures.m
@@ -1,4 +1,4 @@
-function [hrv, info] = hrvFeatures(x, fs, opts)
+function [hrv, info] = hrvFeatures(x, varargin)
 % HRVFEATURES Heart-rate variability metrics from a waveform or beat series
 %
 % Computes standard time- and frequency-domain HRV metrics, which serve as
@@ -55,16 +55,20 @@
 %
 % See also: pf2.data.aux.heartRateFrom, pf2_base.auxSignalType
 
-arguments
-    x {mustBeNumeric}
-    fs {mustBeNumeric} = []
-    opts.Input = 'waveform'
-    opts.IBIUnit = 'ms'
-    opts.Band {mustBeNumeric} = [0.5 5]
-    opts.LFBand {mustBeNumeric} = [0.04 0.15]
-    opts.HFBand {mustBeNumeric} = [0.15 0.40]
-    opts.ResampleFs {mustBeNumeric, mustBeScalarOrEmpty, mustBePositive} = 4
-end
+% Inputs are parsed with pf2_base.args rather than an arguments block so
+% the function also runs under GNU Octave. Spec rows are {name, default,
+% size, class, validators}.
+x = pf2_base.args.check(x, '', '', {@mustBeNumeric}, 'Invalid argument at position 1.');
+[fs, opts] = pf2_base.args.parse('hrvFeatures', varargin, {
+    'fs', ([]), '', '', {@mustBeNumeric}
+    }, {
+    'Input',      ('waveform'), '', '', {}
+    'IBIUnit',    ('ms'), '', '', {}
+    'Band',       ([0.5 5]), '', '', {@mustBeNumeric}
+    'LFBand',     ([0.04 0.15]), '', '', {@mustBeNumeric}
+    'HFBand',     ([0.15 0.40]), '', '', {@mustBeNumeric}
+    'ResampleFs', (4), '', '', {@mustBeNumeric, @mustBeScalarOrEmpty, @mustBePositive}
+    });
 inputType = lower(char(opts.Input));
 ibiUnit = lower(char(opts.IBIUnit));
 lfBand = opts.LFBand;

diff --git a/+pf2/+data/+aux/hrvSeries.m b/+pf2/+data/+aux/hrvSeries.m
@@ -1,4 +1,4 @@
-function [series, t] = hrvSeries(signal, fs, opts)
+function [series, t] = hrvSeries(signal, fs, varargin)
 % HRVSERIES Time-resolved HRV metrics via a sliding window over a waveform
 %
 % Computes standard HRV metrics in successive overlapping windows of a PPG
@@ -130,19 +130,22 @@
 %           pf2.data.aux.addFeature, pf2.data.auxOnGrid,
 %           pf2.data.slidingWindows
 
-arguments
-    signal {mustBeNumeric, mustBeNonempty}
-    fs {mustBeNumeric, mustBeScalarOrEmpty, mustBePositive}
-    opts.Window     {mustBeNumeric, mustBeScalarOrEmpty, mustBePositive} = 60
-    opts.Step       {mustBeNumeric, mustBeScalarOrEmpty, mustBePositive} = []
-    opts.Overlap    {mustBeNumeric, mustBeScalarOrEmpty} = []
-    opts.Metric     = 'all'
-    opts.MinBeats   {mustBeNumeric, mustBeScalarOrEmpty} = []
-    opts.Band       {mustBeNumeric} = [0.5 5]
-    opts.LFBand     {mustBeNumeric} = [0.04 0.15]
-    opts.HFBand     {mustBeNumeric} = [0.15 0.40]
-    opts.ResampleFs {mustBeNumeric, mustBeScalarOrEmpty, mustBePositive} = 4
-end
+% Inputs are parsed with pf2_base.args rather than an arguments block so
+% the function also runs under GNU Octave. Spec rows are {name, default,
+% size, class, validators}.
+signal = pf2_base.args.check(signal, '', '', {@mustBeNumeric, @mustBeNonempty}, 'Invalid argument at position 1.');
+fs = pf2_base.args.check(fs, '', '', {@mustBeNumeric, @mustBeScalarOrEmpty, @mustBePositive}, 'Invalid argument at position 2.');
+opts = pf2_base.args.parse('hrvSeries', varargin, {}, {
+    'Window',     (60), '', '', {@mustBeNumeric, @mustBeScalarOrEmpty, @mustBePositive}
+    'Step',       ([]), '', '', {@mustBeNumeric, @mustBeScalarOrEmpty, @mustBePositive}
+    'Overlap',    ([]), '', '', {@mustBeNumeric, @mustBeScalarOrEmpty}
+    'Metric',     ('all'), '', '', {}
+    'MinBeats',   ([]), '', '', {@mustBeNumeric, @mustBeScalarOrEmpty}
+    'Band',       ([0.5 5]), '', '', {@mustBeNumeric}
+    'LFBand',     ([0.04 0.15]), '', '', {@mustBeNumeric}
+    'HFBand',     ([0.15 0.40]), '', '', {@mustBeNumeric}
+    'ResampleFs', (4), '', '', {@mustBeNumeric, @mustBeScalarOrEmpty, @mustBePositive}
+    });
 
 winLen   = opts.Window;
 if isempty(opts.MinBeats)

diff --git a/+pf2/+data/+aux/respFeatures.m b/+pf2/+data/+aux/respFeatures.m
@@ -1,4 +1,4 @@
-function [feat, info] = respFeatures(x, fs, opts)
+function [feat, info] = respFeatures(x, fs, varargin)
 % RESPFEATURES Derive respiration rate and RVT from a respiration waveform
 %
 % Detects breaths in a respiration signal (belt / RIP / derived) and returns
@@ -53,13 +53,16 @@
 %
 % See also: pf2.data.aux.heartRateFrom, pf2_base.auxSignalType, pf2.data.auxOnGrid
 
-arguments
-    x {mustBeNumeric}
-    fs {mustBeNumeric, mustBeScalarOrEmpty, mustBePositive}
-    opts.Band {mustBeNumeric} = [0.1 0.5]
-    opts.MinRate {mustBeNumeric, mustBeScalarOrEmpty, mustBePositive} = 5
-    opts.MaxRate {mustBeNumeric, mustBeScalarOrEmpty, mustBePositive} = 60
-end
+% Inputs are parsed with pf2_base.args rather than an arguments block so
+% the function also runs under GNU Octave. Spec rows are {name, default,
+% size, class, validators}.
+x = pf2_base.args.check(x, '', '', {@mustBeNumeric}, 'Invalid argument at position 1.');
+fs = pf2_base.args.check(fs, '', '', {@mustBeNumeric, @mustBeScalarOrEmpty, @mustBePositive}, 'Invalid argument at position 2.');
+opts = pf2_base.args.parse('respFeatures', varargin, {}, {
+    'Band',    ([0.1 0.5]), '', '', {@mustBeNumeric}
+    'MinRate', (5), '', '', {@mustBeNumeric, @mustBeScalarOrEmpty, @mustBePositive}
+    'MaxRate', (60), '', '', {@mustBeNumeric, @mustBeScalarOrEmpty, @mustBePositive}
+    });
 band = opts.Band;
 maxRate = opts.MaxRate;
 

diff --git a/+pf2/+data/auxOnGrid.m b/+pf2/+data/auxOnGrid.m
@@ -1,4 +1,4 @@
-function [vals, info] = auxOnGrid(data, name, opts)
+function [vals, info] = auxOnGrid(data, name, varargin)
 % AUXONGRID Resample a named auxiliary signal onto a target time base
 %
 % Returns an auxiliary signal aligned to an arbitrary time grid (the fNIRS
@@ -50,16 +50,19 @@
 %
 % See also: pf2_base.normalizeAux, pf2_base.auxSignalType, pf2.data.resample
 
-arguments
-    data {mustBeA(data, 'struct')}
-    name {mustBeText}
-    opts.Time {mustBeNumeric} = []
-    opts.Channels = []
-    opts.Method = 'linear'
-    opts.Offset (1,1) {mustBeNumeric} = 0
-    opts.AntiAlias (1,1) logical = true
-    opts.MaxGap (1,1) {mustBeNumeric, mustBePositive} = Inf
-end
+% Inputs are parsed with pf2_base.args rather than an arguments block so
+% the function also runs under GNU Octave. Spec rows are {name, default,
+% size, class, validators}.
+data = pf2_base.args.check(data, '', '', {@(v) mustBeA(v, 'struct')}, 'Invalid argument at position 1.');
+name = pf2_base.args.check(name, '', '', {@mustBeText}, 'Invalid argument at position 2.');
+opts = pf2_base.args.parse('auxOnGrid', varargin, {}, {
+    'Time',      ([]), '', '', {@mustBeNumeric}
+    'Channels',  ([]), '', '', {}
+    'Method',    ('linear'), '', '', {}
+    'Offset',    (0), '1,1', '', {@mustBeNumeric}
+    'AntiAlias', (true), '1,1', 'logical', {}
+    'MaxGap',    (Inf), '1,1', '', {@mustBeNumeric, @mustBePositive}
+    });
 
 name = char(string(name));
 method = char(string(opts.Method));