v1.0.1: test lanes, identity primitives, method seeds, and MCP docs

+exploreFNIRS/processMethods.m

@@ -15,7 +15,7 @@ function processMethods(rawMethodStr,oxyMethodStr)
 %   oxyMethodStr - Name of the oxy processing method
 %
 % Example:
-%   exploreFNIRS.processMethods('x5_TDDR', 'takizawa_easy');
+%   exploreFNIRS.processMethods('OD_TDDR', 'takizawa_easy');
 %   exploreFNIRS.processMethods([], 'None');  % oxy-only reprocessing
 %
 % See also: processFNIRS2, pf2.methods.raw.list, pf2.methods.oxy.list,

+pf2/+methods/+raw/describeMethod.m

@@ -35,7 +35,7 @@
 %   pf2.methods.raw.describeMethod('x2_lpf_smar');
 %
 %   % Get method details as variables for programmatic use
-%   [desc, funcs] = pf2.methods.raw.describeMethod('x5_TDDR');
+%   [desc, funcs] = pf2.methods.raw.describeMethod('OD_TDDR');
 %   fprintf('Method has %d processing functions\n', length(funcs));
 %
 %   % Describe method by index

+pf2/+methods/+raw/setMethod.m

@@ -30,7 +30,7 @@ function setMethod(raw_method, ctx)
 %
 %   % Typical workflow
 %   pf2.methods.raw.list();              % View available methods
-%   pf2.methods.raw.setMethod('x5_TDDR'); % Select TDDR method
+%   pf2.methods.raw.setMethod('OD_TDDR'); % Select TDDR method
 %   data = processFNIRS2(rawData);       % Process with selected method
 %
 % See also: pf2.methods.raw.list, pf2.methods.raw.describeMethod,

+pf2/+methods/+seeds/+oxy/BPF.m

@@ -0,0 +1,30 @@
+function p = BPF()
+% BPF Factory for the "BPF" oxy method (0.01-0.1 Hz Butterworth band-pass)
+%
+% Builds the shipped "BPF" oxy (Stage 3) processing method as an OxyPipeline: a
+% single Butterworth band-pass filter (0.01-0.1 Hz) applied to hemoglobin
+% signals, isolating the typical task-hemodynamic band while removing slow drift
+% and high-frequency noise. Used by pf2_initialize and pf2.methods.resetDefaults
+% to (re-)seed the default oxy methods. Returns a pipeline object you can save()
+% to register or run() directly.
+%
+% Syntax:
+%   p = pf2.methods.seeds.oxy.BPF()
+%
+% Inputs:
+%   None
+%
+% Outputs:
+%   p - pf2_base.OxyPipeline named 'BPF', ready for save() or run()
+%
+% Example:
+%   p = pf2.methods.seeds.oxy.BPF();
+%   p.save();
+%
+% See also: pf2.methods.seeds.oxy.LPF, pf2.methods.seeds.oxy.HPF,
+%           pf2.methods.resetDefaults, pf2_base.OxyPipeline
+
+p = pf2_base.OxyPipeline('BPF', ...
+    'Description', 'Butterworth band-pass filter (0.01-0.1 Hz) on hemoglobin signals');
+p = p.add('pf2_bpf_butter', 'lowF', 0.01, 'highF', 0.1);
+end

+pf2/+methods/+seeds/+oxy/HPF.m

@@ -0,0 +1,29 @@
+function p = HPF()
+% HPF Factory for the "HPF" oxy method (0.01 Hz high-pass filter)
+%
+% Builds the shipped "HPF" oxy (Stage 3) processing method as an OxyPipeline: a
+% single 0.01 Hz high-pass filter applied to hemoglobin signals to remove slow
+% drift. Used by pf2_initialize and pf2.methods.resetDefaults to (re-)seed the
+% default oxy methods. Returns a pipeline object you can save() to register or
+% run() directly.
+%
+% Syntax:
+%   p = pf2.methods.seeds.oxy.HPF()
+%
+% Inputs:
+%   None
+%
+% Outputs:
+%   p - pf2_base.OxyPipeline named 'HPF', ready for save() or run()
+%
+% Example:
+%   p = pf2.methods.seeds.oxy.HPF();
+%   p.save();
+%
+% See also: pf2.methods.seeds.oxy.LPF, pf2.methods.seeds.oxy.BPF,
+%           pf2.methods.resetDefaults, pf2_base.OxyPipeline
+
+p = pf2_base.OxyPipeline('HPF', ...
+    'Description', 'High-pass filter at 0.01 Hz on hemoglobin signals (drift removal)');
+p = p.add('pf2_hpf', 'freq_cut', 0.01);
+end

+pf2/+methods/+seeds/+oxy/takizawa_easy.m

@@ -0,0 +1,44 @@
+function p = takizawa_easy()
+% TAKIZAWA_EASY Factory for the "takizawa_easy" oxy method (lenient rejection)
+%
+% Builds the shipped "takizawa_easy" oxy (Stage 3) processing method as an
+% OxyPipeline: automatic channel rejection using the Takizawa criteria with the
+% lenient (non-strict) rule combination. Rejected channels are marked in the
+% data's fchMask rather than having their hemoglobin values transformed. Used by
+% pf2_initialize and pf2.methods.resetDefaults to (re-)seed the default oxy
+% methods. Returns a pipeline object you can save() to register or run()
+% directly.
+%
+% The strict/lenient switch is the pf2_TakizawaRejection strictCriteria flag:
+% lenient (strictCriteria = 0) combines the rejection rules with AND, so a
+% channel is dropped only when it fails every rule; the strict variant
+% (takizawa_hard) uses OR.
+%
+% Syntax:
+%   p = pf2.methods.seeds.oxy.takizawa_easy()
+%
+% Inputs:
+%   None
+%
+% Outputs:
+%   p - pf2_base.OxyPipeline named 'takizawa_easy', ready for save() or run()
+%
+% Example:
+%   % Build and register the takizawa_easy oxy method
+%   p = pf2.methods.seeds.oxy.takizawa_easy();
+%   p.save();
+%
+% References:
+%   Takizawa, R., Kasai, K., Kawakubo, Y., Marumo, K., Kawasaki, S.,
+%   Yamasue, H., & Fukuda, M. (2008). Reduced frontopolar activation during
+%   verbal fluency task in schizophrenia: A multi-channel near-infrared
+%   spectroscopy study. Schizophrenia Research, 99(1-3), 250-262.
+%   DOI: 10.1016/j.schres.2007.10.025
+%
+% See also: pf2.methods.seeds.oxy.takizawa_hard, pf2.methods.seeds.oxy.LPF,
+%           pf2.methods.resetDefaults, pf2_TakizawaRejection, pf2_base.OxyPipeline
+
+p = pf2_base.OxyPipeline('takizawa_easy', ...
+    'Description', 'Takizawa automatic channel rejection, lenient criteria (Takizawa et al. 2008)');
+p = p.add('pf2_TakizawaRejection', 'strictCriteria', 0);
+end

+pf2/+methods/+seeds/+oxy/takizawa_hard.m

@@ -0,0 +1,44 @@
+function p = takizawa_hard()
+% TAKIZAWA_HARD Factory for the "takizawa_hard" oxy method (strict rejection)
+%
+% Builds the shipped "takizawa_hard" oxy (Stage 3) processing method as an
+% OxyPipeline: automatic channel rejection using the Takizawa criteria with the
+% strict rule combination. Rejected channels are marked in the data's fchMask
+% rather than having their hemoglobin values transformed. Used by
+% pf2_initialize and pf2.methods.resetDefaults to (re-)seed the default oxy
+% methods. Returns a pipeline object you can save() to register or run()
+% directly.
+%
+% The strict/lenient switch is the pf2_TakizawaRejection strictCriteria flag:
+% strict (strictCriteria = 1) combines the rejection rules with OR, so a channel
+% is dropped when it fails any rule; the lenient variant (takizawa_easy) uses
+% AND.
+%
+% Syntax:
+%   p = pf2.methods.seeds.oxy.takizawa_hard()
+%
+% Inputs:
+%   None
+%
+% Outputs:
+%   p - pf2_base.OxyPipeline named 'takizawa_hard', ready for save() or run()
+%
+% Example:
+%   % Build and register the takizawa_hard oxy method
+%   p = pf2.methods.seeds.oxy.takizawa_hard();
+%   p.save();
+%
+% References:
+%   Takizawa, R., Kasai, K., Kawakubo, Y., Marumo, K., Kawasaki, S.,
+%   Yamasue, H., & Fukuda, M. (2008). Reduced frontopolar activation during
+%   verbal fluency task in schizophrenia: A multi-channel near-infrared
+%   spectroscopy study. Schizophrenia Research, 99(1-3), 250-262.
+%   DOI: 10.1016/j.schres.2007.10.025
+%
+% See also: pf2.methods.seeds.oxy.takizawa_easy, pf2.methods.seeds.oxy.LPF,
+%           pf2.methods.resetDefaults, pf2_TakizawaRejection, pf2_base.OxyPipeline
+
+p = pf2_base.OxyPipeline('takizawa_hard', ...
+    'Description', 'Takizawa automatic channel rejection, strict criteria (Takizawa et al. 2008)');
+p = p.add('pf2_TakizawaRejection', 'strictCriteria', 1);
+end

+pf2/+methods/+seeds/+raw/OD_SMAR.m

@@ -0,0 +1,31 @@
+function p = OD_SMAR()
+% OD_SMAR Factory for the "OD_SMAR" raw method (SMAR motion correction)
+%
+% Builds the shipped "OD_SMAR" raw (Stage 1) processing method as a RawPipeline:
+% log transform to optical density, then Sliding-window Motion Artifact
+% Rejection (SMAR), which rejects samples whose windowed coefficient of
+% variation falls outside acceptable bounds. Used by pf2_initialize and
+% pf2.methods.resetDefaults to (re-)seed the default raw methods. Returns a
+% pipeline object you can save() to register or run() directly.
+%
+% Syntax:
+%   p = pf2.methods.seeds.raw.OD_SMAR()
+%
+% Inputs:
+%   None
+%
+% Outputs:
+%   p - pf2_base.RawPipeline named 'OD_SMAR', ready for save() or run()
+%
+% Example:
+%   p = pf2.methods.seeds.raw.OD_SMAR();
+%   p.save();
+%
+% See also: pf2.methods.seeds.raw.OD_TDDR, pf2.methods.resetDefaults,
+%           pf2_base.RawPipeline, pf2_SMAR
+
+p = pf2_base.RawPipeline('OD_SMAR', ...
+    'Description', 'Log transform then SMAR (sliding-window motion artifact rejection)');
+p = p.add('pf2_Intensity2OD');
+p = p.add('pf2_SMAR');
+end

+pf2/+methods/+seeds/+raw/OD_TDDR.m

@@ -26,7 +26,7 @@
 %   p = pf2.methods.seeds.raw.OD_TDDR();
 %   p.save();
 %
-% See also: pf2.methods.seeds.raw.OD_TDDR_lpf, pf2.methods.resetDefaults,
+% See also: pf2.methods.seeds.raw.OD_SMAR, pf2.methods.resetDefaults,
 %           pf2_base.RawPipeline, pf2_MotionCorrectTDDR
 
 p = pf2_base.RawPipeline('OD_TDDR', ...

+pf2/+methods/Editor.m

@@ -862,7 +862,7 @@ function onSeedDefaults(app)
             sel = uiconfirm(app.UIFigure, ...
                 sprintf(['Install repo seed methods for the %s stage? ' ...
                         'This will overwrite any existing methods with the ' ...
-                        'same names (OD_TDDR, OD_TDDR_lpf for raw; ' ...
+                        'same names (OD_TDDR, OD_SMAR for raw; ' ...
                         'LPF, LPF_ROI for oxy). Other user methods are kept.'], ...
                         app.Stage), ...
                 'Install seed methods', ...

+pf2/+process/processRaw.m

@@ -56,7 +56,7 @@
 %
 %   % Compare different raw methods before committing to oxy processing
 %   result1 = pf2.process.processRaw(data, 'x2_lpf_smar');
-%   result2 = pf2.process.processRaw(data, 'x5_TDDR');
+%   result2 = pf2.process.processRaw(data, 'OD_TDDR');
 %
 % Notes:
 %   - This function sets 'SkipOxy' to true internally

+pf2/ProcessingContext.m

@@ -19,7 +19,7 @@
     %   ctx = pf2.ProcessingContext(Name, Value, ...)
     %
     % Inputs (Name-Value pairs; all optional):
-    %   'RawMethod'    - Name of a raw-stage method (e.g. 'x5_TDDR')
+    %   'RawMethod'    - Name of a raw-stage method (e.g. 'OD_TDDR')
     %   'OxyMethod'    - Name of an oxy-stage method (e.g. 'takizawa_easy')
     %   'DPFmode'      - 'None' | 'Fixed' | 'Calc'
     %   'FixedDPF'     - Fixed DPF value (used when DPFmode is 'Fixed')
@@ -36,18 +36,12 @@
     %
     % Examples:
     %   % Configure once, in one call, without touching globals
-    %   ctx = pf2.ProcessingContext('RawMethod','x5_TDDR', ...
+    %   ctx = pf2.ProcessingContext('RawMethod','OD_TDDR', ...
     %       'DPFmode','Calc', 'SubjectAge',25, 'blLength',10);
     %   out = processFNIRS2(data, 'Context', ctx);
     %   % ...or let the context be the receiver:
     %   out = ctx.process(data);
     %
-    %   % Save an analysis "recipe" and reload it in a fresh session
-    %   recipe = ctx.toStruct();
-    %   save('study_protocol.mat', '-struct', 'recipe');
-    %   s   = load('study_protocol.mat');
-    %   ctx = pf2.ProcessingContext.fromRecipe(s);     % fully usable again
-    %
     %   % Parallel, one independent context per worker (note copy(), not '='):
     %   parfor i = 1:numel(allData)
     %       c = ctx.copy();
@@ -156,23 +150,4 @@ function applySetting(obj, key, val)
         end
     end
 
-    methods (Static)
-        function obj = fromRecipe(s)
-            % FROMRECIPE Rebuild a usable context from a saved settings struct
-            %
-            % Delegates deserialization to the inherited (base) fromStruct --
-            % the single source of truth for which fields round-trip, and which
-            % also reloads the method libraries -- then returns the settings as
-            % a public pf2.ProcessingContext.
-            %
-            % Syntax:
-            %   ctx = pf2.ProcessingContext.fromRecipe(s)
-
-            base = pf2_base.ProcessingContext.fromStruct(s);
-            obj = pf2.ProcessingContext();
-            for p = properties(base)'
-                obj.(p{1}) = base.(p{1});
-            end
-        end
-    end
 end

+pf2_base/+identity/Contents.m

@@ -0,0 +1,24 @@
+% PF2_BASE.IDENTITY  Internal deterministic semantic-identity primitives.
+%
+% These functions support the future Recipe/RunSpec executor. They are not a
+% user-facing authoring API; public clients should eventually construct typed
+% artifacts and let the canonical executor apply identity policy.
+%
+% Semantic identity:
+%   canonicalBytes - Canonically encode schema-neutral MATLAB values.
+%   hashProjection - Hash a canonical value in an explicit artifact domain.
+%
+% Input identity and fail-closed verification:
+%   importedContentFingerprint - Hash normalized computation-visible input.
+%   preflightImport - Verify source/imported identity before Layer-1.
+%   sha256File     - Stream and hash exact file bytes.
+%   sourceFingerprint - Hash a portable multi-file source manifest.
+%   verifyExpected - Enforce an expected digest without warning fallback.
+%
+% Phase-0 proof carrier (not the future human-facing Recipe JSON format):
+%   decodeJsonTransport - Decode a lossless tagged canonical-value carrier.
+%   encodeJsonTransport - Encode a lossless tagged canonical-value carrier.
+%
+% Implementation support:
+%   normalizeText  - Normalize valid text to Unicode NFC and UTF-8.
+%   sha256Bytes    - Compute a lowercase prefixed SHA-256 byte digest.